BIOLOGICAL CHARACTERIZATION OF A GLATIRAMER ACETATE RELATED

DRUG PRODUCT USING MAMMALIAN AND HUMAN CELLS

This application claims the priority of U.S. Provisional Application No. 62/162,308, filed May 15, 2015, U.S. Provisional Application No. 62/134,245, filed March 17, 2015, U.S. Provisional Application No. 62/078,369, filed November 11, 2014, U.S. Provisional Application No. 62/047,437, filed September 8, 2014, U.S. Provisional Application No. 62/025,953, filed July 17, 2014, U.S. Provisional Application No. 62/020,358, filed July 2, 2014, and U.S. Provisional Application No. 62/019,857, filed July 1, 2014, the contents of which are hereby incorporated by reference.

Throughout this application various publications are referenced by numerical identifiers in parentheses. Full citations of these references can be found following the Examples. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.

Multiple sclerosis (MS) is a chronic, debilitating autoimmune disease of the central nervous system (CNS) with either relapsing-remitting (R ) or progressive course leading to neurologic deterioration and disability. At time of initial diagnosis, RRMS is the most common form of the disease (1) which is characterized by unpredictable acute episodes of neurological dysfunction (relapses) , followed by variable recovery and periods of clinical stability. The vast majority of RRMS patients eventually develop secondary progressive (SP) disease with or without superimposed relapses. Around 15% of patients develop a sustained deterioration of their neurological function from the beginning; this form is called primary progressive (PP) MS. Patients who have experienced a single clinical event (Clinically Isolated Syndrome or "CIS") and who show lesion dissemination on subsequent magnetic resonance imaging (MRI) scans according to McDonald's criteria, are also considered as having relapsing MS. (2) With a prevalence that varies considerably around the world, MS is the most common cause of chronic neurological disability in young adults. (3, 4) Anderson et al. estimated that there were about 350,000 physician-diagnosed patients with MS in the United States in 1990 (approx. 140 per 100, 000 population) . ( 5 ) It is estimated that about 2.5 million individuals are affected worldwide . ( 6) In general, there has been a trend toward an increasing prevalence and incidence of MS worldwide, but the reasons for this trend are not fully understood. (5) Current therapeutic approaches consist of i) symptomatic treatment ii) treatment of acute relapses with corticosteroids and iii) treatment aimed to modify the course of the disease. Currently approved therapies target the inflammatory processes of the disease. Most of them are considered to act as immunomodulators but their mechanisms of action have not been completely elucidated. Immunosuppressants or cytotoxic agents are also used in some patients after failure of conventional therapies. Several medications have been approved and clinically ascertained as efficacious for the treatment of RR-MS; including BETASERON®, AVONEX® and REBIF®, which are derivatives of the cytokine interferon beta (IFNB) , whose mechanism of action in MS is generally attributed to its immunomodulatory effects, antagonizing pro-inflammatory reactions and inducing suppressor cells. (7) Other approved drugs for the treatment of MS include Mitoxantrone and Natalizumab.

Copaxone ^® (Teva Pharmaceutical Industries Ltd.) is a glatiramer acetate drug product approved for treatment of patients with relapsing-remitting multiple sclerosis (RRMS) and clinically isolated syndrome (CIS) (8) . Glatiramer acetate drug substance (GA) , the active substance of Copaxone ^® , is a complex mixture of polypeptides and is the first member of the glatiramoid class; i.e., a complex mixture of synthetic polypeptides of varying sizes assembled from four naturally occurring amino acids: L-glutamic acid, L-alanine, L-lysine, and L- tyrosine, in a defined molar ratio (9) .

GA elicits anti-inflammatory as well as neuroprotective effects in various animal models of chronic inflammatory and neurodegenerative diseases (10-14) and has been shown to be safe and effective in reducing relapses and delaying neurologic disability in MS patients following long-term treatment (15) . The mechanisms underlying GA therapeutic activity are not fully elucidated, but GA activity on immune cells has been well demonstrated. GA appears to act as an altered peptide ligand (APL) of encephalitogenic epitopes within myelin basic protein (MBP) (16) and demonstrates cross-reactivity with MBP at the humoral and cellular levels (17-23) . The unique antigenic sequences of the GA polypeptide mixture compete with myelin antigens for binding to MHC class II molecules on antigen presenting cells (APCs) and presentation to the T cell receptor (TCR) , resulting in the induction of anergy or deletion of autoreactive MBP-reactive T cells and proliferation of GA-reactive T cells. At initiation of Copaxone ^® treatment, GA-reactive CD4+ T- cell lines from MS patients secrete both pro-inflammatory T helper type 1 (Thl) and anti-inflammatory Th2 cytokines (21, 24), but continued exposure to Copaxone ^® induces a shift in GA-reactive T cells toward the Th2 phenotype (21, 23, 25-28) .

Copaxone ^® also increases the number and suppressive capacity of CD4+CD25+FOXP3+ regulatory T cells, which are functionally impaired in MS patients (29-31) . Furthermore, treatment leads to antigen- nonspecific modulation of APC function. Copaxone ^® treatment promotes development of anti-inflammatory type II monocytes characterized by an increase in interleukin (IL)-10 and transforming growth factor- beta (TGF-β) and decreased production of IL-12 and tumor necrosis factor (TNF) (32) .

SUMMARY OF THE INVENTION

The present invention provides a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) i) determining the level of expression of at least one gene selected from the group consisting of ABCF2, ABI2, ACP6, AFG3L2,

AL S1, A PC4, CALM3, CCDC64, CD84, CDC6, CHAF1A, CLU, C0X11, DLGAP1 , DTX4 , FAM 9B, FHL1 , FNTB, GYPC, HFE, IL10, LPHN1, NACA, OLAH, PATZ1, PDK1, POLI, REEP5, RPL5, RPS6KA2, SEC31A, SETBPl, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TPM1, TSHZl, TSPAN13, UBAP2, VAV3 , VDAC2, and ZFAND6 (hereinafter Gene Group 1); ii) determining the level of expression of at least one gene selected from the group consisting of BIRC3, CCL24, CCR1, CISH, CSF1R, CX3CR1, CXCL10, HSPD1, ICAM1, IL1B, IFNGR1, IL27, IL2RG, IL7R, IL1RN, MMP1, MMP9, MMP14, PGRMC1, PRDM1, CARD15, CCL2 , CCL5 , CD14, IL10, THBD, and NFKBIA (hereinafter Gene Group 2), wherein if IL1B, IL10, or MMP9 is the at least one gene selected in part (c) (ii) , then selecting at least a second different gene from the group other than IL1B, IL10, or MMP9; iii) determining the level of expression of at least one gene selected from the group consisting of C130RF31, C14ORF10, C10RF51, C10RF63, CBR4, CB36,

CD9, C0L6A1, DAB2 , GATA2, KIAA0907, LOC100506233, MCM6, MMPl, MS4A4A, MTSS1, PCMTD1, STK4 , STX7 , TAF15, TARP, TIA1, TMFl, TRGC2, TXNDC11, and ZCCHC7 (hereinafter Gene Group 3); iv) determining the level of expression of at least one gene selected from the group consisting of ANXA1, ARRB2, BEAN, BIN1, C10RF63,

CD44, CD9, CFP, C0L6A1, CRIP2, EPB41, Famll9a, FGR, FOX03B, HSD11B1, HSPD1P6, LOC387790, PEG1, YB, 0LIG1, PLD1, PPP4R2, PRDM1, RBM6, SNX27 , SOD2, STATH, TARP, TREM1, TRGC2, UBN2, and ZCCHC7 (hereinafter Gene Group 4); v) determining the level of expression of at least one gene selected from the group consisting of ADAM9, ADAMDEC1, AKR1C2, ANXA2, ANXA2P2, ARHGAP18, ARHGAP18, ARL6IP5, ARL6IP5 , ATP2C1, BID, BIRC3, BTG1, CARD15 , C10RF21, C130RF31, C50RF13, C50RF32, C9ORF130, CAST, CCL2 , CCL5, CD14, CD300A, CD36, CD40, CD55, CD9, CENTA2, CHST11, COL6A1,

CRYBB2, CXCL10, CYLD, DAB2 , EBI3, EBI2, ECOP, EGF, FABP4, FXYD2 , GHRL, GIMAP8 , GLIPR1, G0S2, HMGB2, HNRPLL, ICAM1, ICAM2 , IFIH1, IFNGR1, IL10, IL10RA, IL4I1, INADL, ISG20, ITGB5, KIAA1505, YNU, LACTB, LOC54103, LOC388344, LOC652751, LPAAT-THETA, LPXN, MAFB, MALT1, MFI2, MGC5618, MGLL, MITF, MLF1, MMP1, MMP9, MPEG1,

MTSS1, MXD1, NT5E, NFKBIE, NF BIA, NFE2L3, NFE2L3, OSBPL11, P2RX4, P2RY5, PLEKHOl, POPDC3, PLAUR, PRDM1 , PSCDBP, PTX3, RAB27B, RCSD1, RPL13, SGIP1, SLC39A8, SNORD68, SRPX2, SRA1, SLIC1, SLAMF8, SLIC1, SOD2, STATH, STEAP1, SYNJ2, SYNJ2, TATDN3, TGM5 , THBD, TNFAIP3 , TNFAIP6, TNFRSF9, TNFSF13B, TPSAB1, TPSB2,

TREM1, TXNL2, VPS33A, and VSNL1 (hereinafter Gene Group 5); vi) determining the level of expression of at least one gene selected from the group consisting of ACTN4, BTBD14A, C14ORF10, CISH, CLK1, CRLF3 , FAM62A, FBX045, GAPDHS, HDAC4, HIC2, HNRPD, HSPD1, LOC648342, MYB, NAPB, OXCT2, SERPINB2, SFRS14, SPFH1,

STT3B, WDFY1, ZNF250, and ZNF566 (hereinafter Gene Group 6) ; vii) determining the level of expression of at least one gene selected from the group consisting of A2 , ABCB1, ABCC3, ABHD2, ACPP, ADAMDEC1, ADFP, ADORA2B, ADO A3 , AHNAK, ALCAM, AN H, ANKRD57, ANXA2, ANXA2P2, APBB1IP, AQP1, ARHGAP18 , ARHGAP20,

ARHGEF3 , ARID5B, ARMC9, ATF5 , ATP1B1, ATP6V0D2, ATP9A, ATP10A, AYTL1 , BCL2A1, BCL6 , C3AR1 , C130RD31, C90RF88, C90RF89, C10RF21, C10RF21, C10ORF95, C130RF31, C210RF7, CARD12 , CARD15 , CCDC83, CCL5, CCL24, CCND1, CCR1, CD9, CD36, CD52, CD86, CD109, CD180, CD244, CD 5RAP2 , CDKN1A, CENTA2 , CKB, CKLF, CLEC7A, CNIH3,

COL6A1, COL22A1, CRIP2, CSF1R, CSPG4, CTSL, CTSLL3, CX3CR1, CXCR7, CYBB, CYP1B1, DAB2, DAPP1, DDIT4L, DIXDCl, DOCK4 , DOK2, DKFZP564O0823, DKFZP68601327 , EBI2, EMP1, EMR2 , ENPP2, EPAS1, EPS8, EPSTI1, EVL, FABP4, FADS3 , FAM26B, FGD2, FGD2, FGD4, FGL2, FN1, FTH1, GBP2, GBP3, GBP5, GCNT1, GDPD1 , GNDL, GNLY, GLIPR1,

GLIS3 , GPC1, GPR35, H2A/R, HAVCR2 , HMCN1, HIPK2, HIST2H2AA, HIVEP1, HMOX1, HSPB7 , ICAM1, ID2, ID2B, IFI30, IFI44, IFNGR1, IGFBP3, IL2RG, IL4I1, IL10RA, IL27RA, IL7R, IL10, INA, IRF7, ITGB5, ITGB7 , ΚΙΑΆ1505, KIAA1706, KMO, LBH, LFNG, LILRB1, LILRB2 , LMNA, LOC51334, LOC201895, LOC284262, LOC51334, LOC643424, LOC643834, LOC643847, LOC644242, LOC645238, LOC650429, LOC650446, LOC652543, LOC653610, LOC653754, LPAAT- THETA, LPXN, MAF, MAFB, MAML2, MAML3, MARCH1, MCOLN3, MDGA1 , ME1, MFI1, MFI2, MGC45491, MGLL, MITF, MMP1, MMP2, MMP9, MMP14, MMP19 , MTMR11, MTSS1, MTSU1, NGEF, NME7, NPTX1, NRCAM, NRP1, NRP2, NT5E, 0AS1, OLR1, P2RY5, P2RY14, PALLD, PAPSS2 , PAQR5 , PCDHGA1, PCDHGA2, PCDHGA3, PCDHGA4 , PCDHGA5 , PCDHGA6, PCDHGA7, PCDHGA8 , PCDHGA9, PCDHGA10, PCDHGA11, PCDHGA12 , PCDHGB1 , PCDHGB2, PCDHGB3, PCDHGB4 , PCDHGB5 , PCDHGB7, PCDHGC3, PCDHGC4, PCDHGC5, PDK4 , PDLIM7, PFKFB4 , PGA5 , PDLIM4, PHLDA1 , PLA2G4A, PLEKHA7, PLEKH01, POPDC3 , PRDM1, PRSS23, PSCDBP, PSD3 , PTAFR, PTGS1, PTPRO, PTRF, PTX3, RAB27B, RAB38, RAB7B, RAPH1, RASGRF1, RGL1 , RGS13 , RHBDF1, RIN2, S100A2, SART2, SERPINE2 , SERTAD1 , SETBP1, SGIP1, SH3TC1 , SKIL, SLA, SLAMF7, SLAMF8, SLC6AS, SLC7A11, SLC12A6, SLC37A2, SLC41A2, SLC38A6, SLC43A2, SNAI3 , ST3GAL5, STATH, STEAP1, SUCNR1, SYTL1, TBXAS1, TCF4 , TFAP2A, THBD, TLR4, TM7SF4, TMEM39A, TME 158, TNCRNA, TNFSF13B, TNFRSF21, TREM1, TRIM22, TRPA1, TRPM8, TRPS1, TUBB2A, UBXD5, UGCG, UPP1, VASH1, VEGF, VSNL1, and ZFP36L1 (hereinafter Gene Group 7) ; viii) determining the level of expression of at least one gene selected from the group consisting of ABCG1, ADAMTS1, ANKRD41 , ANXA3, APCDD1, BCL2 , BCL11A, BMP8B, C10RF71, C10RF76, C10RD121, C120RF24, C160RF73, C160RF74, C20ORD27, C20ORF103, C20ORF112, CACNA2D3, CAMTA1, CAV1, CCDC85B, CDCA7L, CEBPD, CKAP4, CNTN4, COL8A2, CSPG5 , CXCR4 , DCUN1D4, DEPDC6, DMRT2, DUSP2, DZIP1, EBF3, EGR4 , FAM117A, FKBP4, FL135848, FLOT2 , GFI1, GMDS, GPR18, HAL, HNF4G, HSPC049, IL17D, IRX3, KBTBD11, KCNQ4, KCTD15 , KIAA0146, KIAA0984, KIAA1026, KIAA1553, KLHL23, LGR4, LOC201164, LOC284454, LOC387763, LOC642083, LOC648232, MGC2408, MICALl, MID1IP1, MSRB3, MUC19, NAPSB, NR1D2, PCDH8, PDE4B, PDGFD, PER2, PHF15, P P2, PLK2 , OAF, OSBPL1A, OSR2, OXCT2 , PGM1, PMAIP1, PNMA6A, POU4F2, PSAT1, RAB33A, RASGRP2, RBM38, RET, RFTN1, SERPINB2, SERPINB10, SLAIN1, SLC1A3, SLC16A1, SLC19A1, SLC27A2, SLC29A1, SLC39A14, SLC04A1, SNF1LK, SOX12, SPFH1, SPRY1, STEAP3, SYDE2, SYNP02, TARP, TEAD4, TDRD7 , TMEM67, TPD52, TRGC2 , TRGV2 , TRGV9, TRIB3, TSPAN2 , TUBA1, VIT, WDR49, WNT3, WT1, and YES1 (hereinafter Gene Group 8) ; ix) determining the level of expression of at least one gene selected from the group consisting of AHRR, CCDC36, CYP1B1, DOC1, EPB41L3, GAS7 , GPR68 ,

NPTX1, PDCD6, and TIPARP (hereinafter Gene Group 9); x) determining the level of expression of at least one gene selected from the group consisting of ADRB2, COTL1, LOC285758, LOC644137, MALATl, PRG1, RNF43, SATl, THAP5, TIMP3, and TSC22D1 (hereinafter Gene Group 10); xi) determining the level of expression of at least one gene selected from the group consisting of AW011738, Bst2, Daxx, Gml6340, Hck, Herc6, Ifi202b, Ifi203, Ifi204, Ifi44, Ifi441, Ifit2, Inpp5b, LOC100044068, LOC100862473, Mxl, Oasll, Phflld, Oyhinl, Sdc3, Setdb2, Tor3a, Uspl8, and Zcchc2 (hereinafter Gene Group 11); xii) determining the level of expression of at least one gene selected from the group consisting of Ccdc711, D13ERTD608E, Fads2, Gm2a, Ifi2711, Ighm, Klkl, Scd2, Siglech, and Tspan2 (hereinafter Gene Group 12); xiii) determining the level of expression of at least one gene selected from the group consisting of Ahrr, AI607873, AtplOa, AW011738, Casp44, Cxcl3, Gm9706, Ifi202b, Ifit2, Ifitm6, 1118, Lcn2, LOC100044068, Ms4a6d, Mxl, Papd7, Rsad2, Slfn3, Slfn4, Tdrd7, Tiparp, and Zcchc2 (hereinafter Gene Group 13); xiv) determining the level of expression of at least one gene selected from the group consisting of Aldoc, Casp6, Ccdc711, Cox7al, Egln3, Faml62a, Gfil, Gpil, Grhpr, Ifi2711, Ighm, Kcnq5, Klhdc2, Pgkl, Pkm, Tpil, and Trappc6a (hereinafter Gene Group 14); xv) determining the level of expression of at least one gene selected from the group consisting of 1600014C10Rik, 2810474O19Rik, 6720475J19Rik,

Adam8, Adar, Agrn, Ahrr, AI607873, Amigo2, Ankfyl, Apobecl, Arf4, Asb2, Ascc3, AtplOa, Atp8b4, AW011738, B4galt5, BC147527, Bst2, Casp4, Chicl, Cmpk2, Csprs, Cxcl3, Cybb, Daxx, Ddit3, Ddx24, Ddx58, Ddx60, Dpp4, Eif2ak2, Emrl, Epstil, Evi2a, Fcgrl, Fcgr4, Ftsjd2, Gcntl, Gmll772, Gml4446, Gml5433, Gml6340,

Gm20559, Gm2666, Gm7609, Gm9706, Gpnmb, Gprl5, H2-T10, H2-T9, Hck, Helz2, Herc6, Hsh2d, Hspalb, Ifi202b, Ifi203, Ifi204, Ifi205, Ifi2712a, Ifi35, Ifi44, Ifi441, Ifihl, Ifitl, Ifit2, Ifit3, Ifitm3, 1118, I17r, Inpp5b, Insl6, Irf7, Isg20, Klrkl, Lgals3bp, Lgals9, LOC100041903, LOC100044068, LOC100503923, LOC100505160, LOC100862473, LOC664787, Lpar6, Ly6cl, Ly6c2, b21dl, itdl, Mlkl, Mmp8, nda, ndal, Ms4a4c, Ms4a6d, Mxl,

Naa20, Ncehl, Ncoa7, Ngp, Nlrc5, Nmrall, Nqol, Nt5c3, Oasla, Oas2, Oas3, Oasll, Oasl2, Ogfr, Papd7, ParplO, Parpll, Parpl2, Parpl4, Phflld, Pik3apl, Pla2g7, Plec, Pnptl, Ppmlk, Pydc4, Pyhinl, Ramp3, Rnf213, Rnf8, Rsad2, Rtp4, Samd91, Scin, Sdc3, Setdb2, Sgcb, Shisa5, Slco3al, , Slfnl, Slfn3, Slfn4, Slfn5,

Slfn8, Slfn9, St3gal6, Tcstv3, Tdrd7, Tiparp, Tmeml40, Tmeml84b, TnfsflO, Torlaip2, Tor3a, Trafdl, Trim25, Trim30a , Trim30d, Trim34a, Trim34b, Tspo, Uba7, Ubr4, Uspl8, ntlOa, Xafl, Xafl, Zc3havl, Zcchc2, Zfyve26, Znfxl, and Zufsp (hereinafter Gene Group 15); xvi) determining the level of expression of at least one gene selected from the group consisting of Ccdc711, D13ERTD608E, Fads2, Gm2a, Ifi2711, Ighm, Klkl, Scd2, Siglech, and Tspan2 (hereinafter Gene Group 16) ; xvii) determining the level of expression of at least one gene selected from the group consisting of CC12, CYBASC3, CYP1B1, FCAR, HBEGF, ID1, IL1B,

IL4I1, MSC, NQOl, PPP1R15A, PRDM1, SLC7A11, SRXN1, TIPARP, T EM138 , TXNRD1 , and VEGF (hereinafter Gene Group 17); xviii) determining the level of expression of at least one gene selected from the group consisting of BCL2, CACNA2D3, C130RF18, C20ORF103, C50RF13, CDCA7, DEPDC6, GATM, HAL, HSPA1A, HSPC049,

LOC645919, LRMP, OAF, POU4F2, RASGRP2, RET, SERPINB2, SERPINB8, SPFH1, and TDRD7 (hereinafter Gene Group 18); xix) determining the level of expression of at least one gene selected from the group consisting of ABCC1, ABHD12, ABHD5, ACPP, ACSL1, ADFP, ADORA2B, ADORA3, AHRR, AKNA, AKR1C1, AKR1C2, A R1C3, ALAS1,

ALOX5AP, ANKRD57, ANXA2, APBB1IP, APRIN, ARHGAP20, ARHGEF3, ARRB2, ARRDC4, ASB2, ATF5, ATG7, ATP6V0B, ATP6V0C, ATP9A, ATP9B, AXL, AYTL1, BCL2A1, BCL3, BCL6, BHLHB2, BTG1, BTG2, BTG3, C10ORF22, C10ORF54, C10ORF56, C120RF35, C130RF31, C140RF43, C150RF39, C170RF32, C190RF58, C10RF122, C10RF144, C10RF162,

C10RF21, C10RF38, C3AR1, C5ORF20, C60RF166, C90RF16, C90RF88, CALN1, CARD15 , CCL2, CCL5, CCND3, CCNL1, CCR1, CD109, CD244, CD300A, CD40, CD44, CD83, CD9, CDCA4, CDK5RAP2, CDKN1A, , CHSTll, CIDEC, CKB, CLEC5A, CLEC7A, CMTM3, CPEB2 , CPEB4, CSF1R, CSGLCA- T, CSGLCA-T, CSPG2 , CSPG2, CTSB, CTSH, CUTL1, CXCL1, CXCL2 , CXXC5, CYBASC3, CYBB, CYLD, CYLD, CYP1B1, DDB1, DGAT2, D FZP68601327, D0C1, DOK2, DUSP6, EBI2, ECGF1 , ECOP, EFHD2 ,

EIF1, ELL2, ELOVL1, EMP2, EMR2 , EPAS1, EPB41L3 , EPB41L3, EXT1, F3, FADS3 , FA 100B, FCAMR, FCAR, FGD3 , FGD , FGL2 , FLJ20489, FLJ20701, FLJ90013, FLRT2 , FPRL1, FTH1, FUCA1, GAS7 , GCNT1, GNA15, GPR35 , GPR68 , GSR, GSR, H2A, HBEGF, HERPUD1, HIPK2, HIST2H2AA, HIVEP1, HMOX1, HNRPLL, HPCAL1, ID1, ID2, IER5, IFI30,

IFNGR1, IFNGR2, IGFBP3, IL10RA, IL1B, IL1R1, IL1RN, IL1RN, IL21R, IL27RA, IL27RA, IL4I1, IL4R, IRF5, ITGB7, JDP2, JUN, JUNB, JUND, KCNN4, KIAA0247, KIAA0999, KIAA1505, KIAA1706, KIAA1913, KITLG, KLF13 , KLF4, KLF6, KLHL18, LACTB, LAT, LHX2 , LOC113179, LOC338758, LOC440934, LOC54103, LOC644242 , LOC648998

LOC650429, LOC650446, LOC651816, LOC653524, LOC653361, LOC653840, LOC653361, LOC653506, LOC653610, LOC653840, LOC653626, LPAAT-THETA, LPL, LPXN, LRG1, LRP10, MAFB, MAFF, ALT1, MAML2, MAP1LC3B, MARCKSL1, MBP, MCL1, ME1, METRNL, MGAT A, MGC13379, MGLL, MMP2, MMP9, MOBKL2A, SC, MST150, MTF1,

MTUS1, MYH10, NAB1, NCF1, NCF2, NCF4, NEU1, NFE2L3, NFKBl, NFKB2, NFKBIA, NFKBIE, NFXL1, NINJ1, NOTCHl, NOTCH2NL, NPTX1, NQOl, NRP1, NRP2, NT5E, NUAK1, P2RY5, P2RY6, PACSIN2, PDCD6, PDK4 , PDLIM , PECAM1, PEX19, PGD, PHLDA1, PHLDA2 , PIK3R5, PIR, PITPNA, PKM2, PLAU, PLAUR, PLEKHOl, PNKD, POPDC3, PPIF, PPP1R15A, PRD 1,

PRKCA, PSCD4, PSCDBP, PS D1, PTAFR, PTGS1, PTPN14, PTPRE, PTX3, QPRT, RAB13, RAB27B, RAB38 , RAB6IP1, RAI17, RAP2B, RAPGEF1 , RCN1, RELB, RGL1, RGS1, RGS2, RIN3, RIT1, RND3, RSNL2, RSP03, RUNX3, SAMSN1, SAP30, SASH1, SAT1, SDC4, SEMA4C, SERPINE2, SERTAD1, SFRS7, SGK, SH3GL1 , SH3TC1, SLAMF8, SLC15A3, SLC16A3,

SLC20A1, SLC23A2, SLC25A14, SLC25A19, SLC25A20, SLC2A1, SLC2A6, SLC37A2, SLC39A8, SLC43A2, SLC45A3, SLC4A2, SLC4A5, SLC6A6, SLC7A11, SLC7A11, SLIC1, SMOX, SNAI3 , SOD2, SPRY2, SPSB1, SQRDL, SQSTM1, SRXN1, SSH1, ST3GAL5, STAT1, STK40, TFAP2A, TFDPl, TFEB, TGIF, THBD, TIPARP, T EM138, TMTC1 , TNFAIP3, TNFAIP6, TNFAIP8L1,

TNFRSF10D, TNFRSF1B, TNFRSF21 , TNFSF13B, TNFSF7, TP53BP2, TRAF3, TRAF3IP2, TRIB1, TRIB3 , TRIM16, TRIM16L, TRPA1, TRPS1, TRPS1, TSHZ3 , TTLL4, TXN D1, UBE2S , UGCG, ULBP2, UPP1, URP2, VASH1, VEGF, VSNL1, YRDC, ZBTB24, ZCCHC10, ZFAND5, ZFP36L1, ZNF366, ZNF516, and ZNF697 (hereinafter Gene Group 19) ; xx) determining the level of expression of at least one gene selected from the group consisting of ABHD14B, ACTN1, ACY1L2, ADA, ADD2 , AFF1 ,

AIG1, AK2, AKAP1, ALS2CR13, AN RD45, ANKRD55, APPL, ARHGEF6, ATG16L2, ATP8B3 , ATP8B4, ATPBD1C, B3GNT7 , BCL11A, BCL2 , B P8B, BRE, BSPRY, BTBD14A, C130RF18, C130RF18, C14ORF106, C150RF41, C160RF73, C10RF121, C10RF63, C1QBP, CIS, C20ORF103, C20ORF112, C20ORF12, C30RF14, C50RF13, C60RF147, C70RF24, C9ORF103, CABC1,

CACNA2D3, CACYBP, CALCOC02, CAMSAP1L1, CAMSAPILI, CAT, CAV1, CDCA7 , CER L, CHST12, CHST5, CITED4, CLINT1, CLSTN2, CLTCL1, CNTN4, COL4A1, COL8A2, CUGBP2, CXORF21, DAB1, DENND4A, DEPDC6, DHRS9, DMRT2, DUT, EIF4A2, ESD, FLJ12078, FLJ20152, FLJ23861, FLJ36166, FOXP1, GATM, GGA2, GOLGA1, GOLGA8C, GOLGA8D, GOLGA8E,

GOLGA8F, GOLGA8G, GPD1L, GPR18, HADH, HAL, HDAC9, HGF, HIG2, HISPPD1, HNRPA3, HNRPH3, HOXB3, HSPA1A, HSPA4L, HSPB1, HSPC049, ID2, ID2B, IDH1, IDH1, IHPK2, IRX3, ITGA4, KBTBD11, KCNN2, KIAA0960, KLF10, LARS, LGR4 , LIMA1, LIX1L, LOC129285, LOC148203, LOC197322, LOC203274, LOC220594, LOC254559, LOC284702,

LOC285084, LOC285758, LOC340061, LOC340061, LOC388189, LOC474170, LOC643458, LOC645919, LOC646456, LOC90835 LONRF1, LRMP, LYST, MACF1, MDH1, METTL7B, ETTL8, MICALl, MLSTD1, MNDA, MRPL24, MS4A3, MS4A4A, S4A6A, MS4A7, MSRB3, MT1E, MT1H, MT1M, MTBP, MTHFD1 , MTL5 , MTR, MUC19, MU 1, MYADM, NAPSB, NAPSB, AT11 ,

NOC2L, NPAL3, OAF, OCRL, OMA1, OSBPL1A, OXCT2, PDCD4, PHACTR3, PHYH, PIGM, PI IL4, PNMA6A, POU4F2, PRKAB2, PRLR, PSAT1, PSAT1, PTGER3 , PTPLAD2, RABGAP1L, RAD17, RASGRP2, RBKS, RET, RNASEH2B, RNASET2, SELPLG, SERPINB10, SERPINB2, SERPINB8, SERPINI2, SKAP2, SLAIN1, SLC16A4, SLC22A15, SLC22A16, SLC40A1, SMARCA2 , SNAPC3,

SNX10, SPFH1, SPTBN1, ST3GAL3 , STAR , STRBP, SYNP02, TADA1L, TCFL5, TDRD7, THTPA, TIFA, TLE1, TMEM14A TOP2B, TPD52 , TPM1, TRAF3IP3, TSPAN2, TTC9C, UBE2B, UBP1, UHRF2, VLDLR, VPS35, WASF1, WDFY1, WDR49, WDR68, WHDC1L1, WHDC1L2, ZBTB33, ZBTB44, ZF, ZNF207, ZNF519, ZNF658, and ZNF92 (hereinafter Gene Group

20) ; xxi) determining the level of expression of at least one gene selected from the group consisting of CCL2, CCL5, CXCL10, IL1RN, and MMP9 (hereinafter Gene Group 21); xxii) determining the level of expression of at least one gene selected from the group consisting of CCL5, CXCL10, and MP9 (hereinafter Gene Group 22); xxiii) determining the level of expression of at least one gene selected from the group consisting of IL10 and CCL2

(hereinafter Gene Group 23) ; xxiv) determining the level of expression of at least one gene selected from the group consisting of IFNg, TNF, CCL3, CXCL8, and IL-10 (hereinafter Gene Group 24); xxv) determining the level of expression of at least one gene selected from the group consisting of MP9, CCL2,

CCL5, CXCL1, and ILIB (hereinafter Gene Group 25); xxvi) determining the level of expression of at least one gene selected from the group consisting of MMP9, CXCL10, CCL2, and CCL5 (hereinafter Gene Group 26) ; xxix) determining the level of expression of at least one gene selected from the group consisting of CCL3 , MMP9, CCL22, CCL24, CX3CL1, CCL20, CCL2 , TNF, IL8, CCL13, CCL5, IL1B, CCL8 , IL10, CXCL11, CXCL13, CXCL10, CCL7, CCL1, CXCL1, IFNg, CCL26, and MIF (hereinafter Gene Group 29) ; or xxx) determining the level of expression of at least one gene selected from the group consisting of CCL3, MMP9, CCL22,

CCL24, CX3CL1, CCL20, CCL2, TNF, IL8, CCL13, CCL5, IL1B, CCL8, IL10, CXCL11, CXCL13 , CXCL10, CCL7, CCL1, CXCL1, IFNg, CCL26, MIF, IL16, IL6, CCL25, IL2, CCL19, CXCL2 , CXCL9, and CXCL5 (hereinafter Gene Group 30) , thereby characterizing the glatiramer acetate related drug substance or drug product of step a) .

The present invention also provides a process for discriminating between glatiramer acetate related drug substances or drug products comprising the steps of: a) characterizing two or more glatiramer acetate related drug substances or drug products according to the process of the claimed invention to obtain characteristics of each of the glatiramer acetate related drug substances or drug products; and b) comparing the characteristics of the glatiramer acetate related drug substances or drug products obtained in step a) , thereby discriminating between glatiramer acetate related drug substances or drug products.

The present invention also provides a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of : a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) xxii) determining the protein level expression of at least one protein selected from the group consisting of RANTES, IP-10, and MMP-9 (hereinafter Protein Group A) ; xxiii) determining the protein level expression of at least one protein selected from the group consisting of IL10 and MCP-1 (hereinafter Protein Group B) ; xxiv) determining the protein level expression of at least one protein selected from the group consisting of IFNg, TNFa, MIP-la, IL-8, and IL-10 (hereinafter Protein Group C) ; xxv) determining the protein level expression of at least one protein selected from the group consisting of MMP-9, MCP-1, RANTES, Gro- a, and IL-lb (hereinafter Protein Group D) ; xxvi) determining the protein level expression of at least one protein selected from the group consisting of MMP-9, IP-10, MCP-1, and RANTES (hereinafter Protein Group E) ; xxvii) determining the protein level expression of at least one protein selected from the group consisting of MIP-la, MMP-9, MDC, CCL24, CX3CL1, MIP-3a, MCP-1, TNF-a, IL-8, MCP-4, RANTES, IL-lb, MCP-2, IL-10, I-TAC, CXCL13, IP-10, MCP-3, CCL1, CXCL1, INF-g, CCL26, and MIF (hereinafter Protein Group F) ; or xxviii) determining the protein level expression of at least one protein selected from the group consisting of MIP-la, MMP-9, MDC, CCL24, CX3CL1, MIP-3a, MCP-1, TNF-a, IL-8, MCP-4, RANTES, IL-lb, MCP-2, IL-10, I-TAC, CXCL13, IP-10, MCP-3, CCL1, CXCL1, INF-g, CCL26, MIF, IL-16, IL-6, TECK, IL-2, IP-3b, CXCL2, MIG, and CXCL5 (hereinafter Protein Group G) , thereby characterizing the glatiramer acetate related drug substance or drug product of step a) . The present invention also provides a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) i) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 1; ii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 2, wherein if IL1B, IL10, or MMP9 is the at least one gene selected in part (c) (ii) , then selecting at least a second different gene from the group other than IL1B, IL10, or MMP9; iii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 3; iv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 4; v) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 5; vi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 6; vii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 7; viii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 8; ix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 9; x) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 10; xi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 11; xii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 12; xiii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 13; xiv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 14; xv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 15; xvi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 16; xvii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 17; xviii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 18; xix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 19; xx) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 20; xxi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 21; xxii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 22; xxiii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 23; xxiv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 24; xxv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 25; xxvi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 26; xxix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 29; or xxx) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 30, thereby characterizing the glatiramer acetate related drug substance or drug product of step a) .

BRIEF DESCRIPTION OF THE DRAWINGS

Figure 1: Framework of studies conducted in mouse splenocytes and human THP-1 monocyte cell line.

Figure 2: Roadmap for human THP-1 monocyte cell line study. Figure 3: Levels of Copaxone ^® measured over time in cell culture medium from human THP-1 monocyte cell line. Copaxone ^® concentration in medium over time remains steady in the range of 44-52 g/mL over 24 hours.

FIGS. 4A-D: Differentially expressed genes in human THP-1 monocyte cell line (a) Increased expression of IL10 with GA treatment at 6 hours for the single IL10 probeset on the array (207433_at) (FDR adjusted p<3.1e-9); (b-d) Increased expression of IL1RN with GA treatment at 6 hours for multiple probesets (adjusted p values as shown) .

Figure 5: Pathways enriched in experimental systems in mouse splenocytes, human THP-1 monocyte cell line and PBMCs from MS patients among top genes modulated by Copaxone ^® at 6 hours (subject to FC and adjusted p value filters of 1.5 and le-5, respectively). The volcano plot show - log (adjusted p value) for the enrichment plotted versus the fold enrichment score from DAVID for each pathway. A selected subset of pathways are labeled.

Figure 6: Probeset for cytokine-cytokine receptor interaction pathway genes significantly modulated by Copaxone ^® at 6 hours in human THP-1 monocyte cell line (subject to FC and adjusted p value filters of 1.5 and le-5, respectively) . The volcano plot show - log (adjusted p value) for differential pexpression plotted versus the fold change from LIMMA for each probeset.

Figure 7: MMP9 is significantly upregulated by Probioglat stimulation in human THP-1 monocyte cell line compared to Copaxone ^® stimulation at 6 and 24 hours (FDR adjusted p values for each timepoint are 2.74e- 6, 0.098, and 0.004 for 6, 12, and 24 hours, respectively).

Figure 8: CD14 expression in human THP-1 monocyte cell line is significantly higher with Probioglat stimulation compared to Copaxone ^® stimulation at 6 hours.

Figure 9: Focus on the "response to LPS" pathway as differentially expressed by Probioglat versus Copaxone ^® at 6 hours in human THP-1 monocyte cell line.

Figure 10: Pathway-level analysis depicts enrichment among genes upregulated by Probioglat stimulation compared with Copaxone ^® at 6 hours in human THP-1 monocyte cell line (a) Pathways enriched among genes upregulated by Probioglat stimulation compared with GA at 6 hours. The volcano plot shows -log (adjusted p value) for the enrichment plotted versus the fold enrichment score from DAVID for each pathway; (b) Focus on response to LPS pathway, differentially expressed by Probioglat versus GA at 6 hours. The volcano plot shows -log (adjusted p value) for differential expression plotted versus the fold change from LIMMA for each probeset. A selected subset of pathways are labeled.

Figure 11: Each present probeset for ICAM1 is significantly upregulated by Probioglat stimulation compared to Copaxone ^® stimulation at 6 hours in human THP-1 monocyte cell line.

Figure 12: CISH is downregulated by Probioglat stimulation compared to Copaxone ^® stimulation at 6 hours in human human THP-1 monocyte cell line . Figure 13: Upregulation of IL10 with GA treatment in all three studies in mouse splenocytes, human THP-1 monocyte cell line and PBMCs from MS patients.

Figure 14: Overlap of genes significantly modulated by GA between studies in three model systems in mouse splenocytes, human THP-1 monocyte cell line and PBMCs from MS patients. FIGS. 15A-B: Higher levels of (a) CD14 and (b) CD40 (bottom) are induced by a Probioglat generic than by Copaxone ^® or other generics in human monocytes . Figure 16: Expression of IL1B in Copaxone ^® and multiple generics in mouse splenocytes .

Figure 17: Expression of CD44 in Copaxone ^® and Escadra generic in human monocytes .

Figure 18 : IL27 expression in Copaxone ^® and various generics in mouse splenocytes .

Figure 19: MP9 expression induced by Copaxone ^® , Probioglat, and other generics in human monocytes.

Figure 20: Significant gene expression difference are observed between Copaxone ^® and the purported generics Natco and Escadra in many genes, including several relevant to MS .

Figure 21: MMP14 expression is significantly elevated by TV-5010 relative to Copaxone ^® in mouse splenocytes.

Figure 22: The expression of PGRMC1 and IL1B shows significantly different expression following stimulation with proposed generics from different manufacturers in human THP-1 monocytes.

Figure 23: Pathway-level analysis depicts enrichment among genes upregulated by Copaxone ^® stimulation compared with mannitol control at 6 hours in human THP-1 monocyte cell line.

Figure 24: IL1RN is significantly upregulated by Copaxone ^® stimulation in human THP-1 monocyte cell line compared to mannitol control at 6 hours (FDR adjusted p value < 2.8e-10). Fig. 25a: Higher level of CYP1B1 is induced by Polimunol generic than by Copaxone ^® in human THP-1 monocyte cell line at 6 hours (FDR adjusted p values < 1.5e-10). Fig. 25b: Higher level of GPR68 is induced by Polimunol generic than by Copaxone ^® in human THP-1 monocyte cell line at 6 hours (FDR adjusted p values < 1.5e-5).

Figure 26: Lower level of ADRB2 is induced by Polimunol generic than by Copaxone ^® in human THP-1 monocyte cell line at 6 hours (FDR adjusted p value < 0.009) .

FIGS. 27A-E: Copaxone ^® treatment in mouse splenocytes upregulated (a- b) anti-inflammatory cytokines and (c-d) markers of regulatory T cells, and (e) downregulated pro-inflammatory cytokines.

Figure 28: Pathways enriched among probesets modulated by Copaxone ^® relative to medium in splenocytes from mice immunized with Copaxone ^® . Figure 29: IL18 expression is reduced to a greater extent by Copaxone ^® than Polimunol, regardless of which substance is utilized for the immunization in mouse splenocytes.

Figure 30: Pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® (in Copaxone ^® -immunized mice) .

Figure 31: Pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® (in Polimunol-immunized mice) . Fig. 32a: IL-18 signaling pathway (from Dinarello, Front Immunol, 2013; Figure 1) .

Fig. 32b: Mice definicient for IL-18 are resistant to EAE (from Shi, J. Immuno, 2000; Figure la) . Figure 33: Type I interferon signaling pathway (from Trinchieri et al, Journal of Experimental Medicine, 2010; Figure 1)

FIGS. 34A-C: Anti-inflammatory gene IL1RN is signfiicantly upregulated by Copaxone ^® in human THP-1 monocyte cell line.

Figure 35: Pathways enriched among top probesets modulated by Copaxone ^® relative to mannitol control in human THP-1 monocyte cell line .

Figure 36: Genes in the cytokine-cytokine receptor interaction pathway modulated by Copaxone ^® relative to mannitol control (each point represents a probeset, labeled with its gene annotation) in human THP- 1 monocyte cell line.

Figure 37: CYP1B1 is significantly upregulated by Polimunol relative to Copaxone ^® .

Figure 38: Pathways significantly enriched among top probesets differentially expressed between Polimunol and Copaxone ^® .

Figure 39: Genes in the cytokine-cytokine receptor interaction pathway, which is significantly enriched among top probesets differentially expressed between Polimunol and Copaxone ^® (each point represents a probeset, labeled with its gene annotation) .

Fig. 40a: Volcano plot showing probesets driving the enrichment of the response to lipopolysaccharide pathway among probesets upregulated by Polimunol relative to Copaxone ^® . The dashed line indicates significance level of adjusted p value < 0.05.

Fig. 40b: Volcano plot showing probesets driving the enrichment of the response to lipopolysaccharide pathway among probesets upregulated by Probioglat relative to Copaxone® in prior study (FDA-2014-P-0933- 0001 available at www. regulations . gov/# ! documentDetail; D=FDA-2014-P- 0933-0001, and also described herein) . The dashed line indicates significance level of adjusted p value < 0.05.

Figure 41: Expression levels of genes differing between Probioglat and GA (a) MMP9 is significantly upregulated following stimulation by Probioglat compared to GA at 6 and 24 hours (FDR-adjusted p values for the single MMP9 probeset on the chip, 203936_s_at, are 2.74e-6, 0.098, and 0.004 for the 6, 12, and 24 hour timepoints, respectively); (b) CD14 expression is significantly higher with stimulation by Probioglat compared to GA at 6 hours (the single CD14 probeset on the chip is shown, 201743_at) ; (c) Both present ICAM1 probesets are significantly upregulated following stimulation by Probioglat compared to GA at 6 hours (A: probeset 202637_s_at; B: probeset 202638_s_at) ; (d) CISH is downregulated following stimulation by Probioglat compared to GA at 6 hours (both present probesets are shown, A: probeset 223961_s_at; B: probeset 223377_x_at) .

Figure 42: Expression levels of genes differing between Probioglat and GA by qRT-PCR in primary human monocytes. CCL2 (p < 0.009), CCL5 (p < 0.029), CXCL10 (p < 0.020), MMP9 (p < 0.009), and IL1RN (p < 0.013) are expressed more highly under Probioglat stimulation relative to GA stimulation.

Figure 43: Principal Component Analysis (PCA; a multivariate approach) showed that the main effect in the first principal component remained due to treatment effects after batch correction (a) First principal component accounts for experimental factor (treatment time 6, 12, 24 hours) ; (b) PCA demonstrates batch effect correction required for scan date (legand as in (c) ) ; (c) After batch correction, PCA shows more uniform distribution of scan dates.

Figure 44: Box plots showing maximum and minimum expression values for Probioglat (red lines) and Copaxone (blue lines) . FIGS. 45A-B: Protein levels at 24 hours are consistent with upregulation of pro-inflammatory mRNA markers by Probioglat vesus Copaxone ^® treatment at 6h (a) CCL, CXCL10 and MMP-9 protein levels are higher with Probioglat versus Copaxone ^® at 24 hr, consistent with mRNA level observations by RT-PCR and microarray in THP-1 cells; (b) CCL2 and IL-10 protein levels are higher with Probioglat versus Copaxone ^® at 24 hr, consistent with mRNA level observations by microarray (not tested by RT-PCR in THP-1 cells.

Figure 46: Number of relapses reported to the Patient Support Program in Mexico. FIGS. 47A_E: Levels of Secreted Protein with Polimunol Versus GA Treatment: Levels of IFNg, TNFa, MlPla (CCL3) , IL-8 (CXCL8 ) , and IL- 10 were higher with Polimunol versus GA treatment.

FIGS. 48A-E: Levels of Secreted Protein with Polimunol Versus GA Treatment: Consistent with gene level data, levels of MMP-9, MCP-1 (CCL2), RANTES (CCL5), Gro-a (CXCL1) , and IL-lb were higher with Polimunol versus GA treatment.

FIGS. 49A-E: Levels of Secreted Protein with Probioglat Versus GA Treatment: Levels of IFNg, TNFa, MlPla (CCL3) , IL-8 (CXCL8), and IL- 10 were higher with Probioglat versus GA treatment.

FIGS. 50A-D: Levels of Secreted Protein with Probioglat Versus GA Treatment: Consistent with gene level data, levels of MMP-9, MCP-1 (CCL2), RANTES (CCL5), and IP-10 (CXCL10) were higher with Probioglat versus GA treatment.

W

23

DETAILED DESCRIPTION OF THE INVENTION

Embodiments of the Invention

The present invention provides a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) i) determining the level of expression of at least one gene selected from the group consisting of Gene Group 1; ii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 2, wherein if IL1B, IL10, or MMP9 is the at least one gene selected in part (c) (ii) , then selecting at least a second different gene from the group other than XL1B _/ IL10 _/ or P9; iii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 3; iv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 4; v) determining the level of expression of at least one gene selected from the group consisting of Gene Group 5; vi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 6; vii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 7; viii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 8; ix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 9; x) determining the level of expression of at least one gene selected from the group consisting of Gene Group 10; xi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 11; xii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 12; xiii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 13; xiv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 14; xv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 15; xvi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 16; xvii ) determining the level of expression of at least one gpne selected from the group consisting of Gene Group 17; xviii ) determining the level of expression of at least one gene selected from the group consisting of Gene Group 18; xix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 19; xx) determining the level of expression of at least one gene selected from the group consisting of Gene Group 20; xxi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 21; xxii ) determining the level of expression of at least one gene selected from the group consisting of Gene Group 22; xxiii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 23; xxiv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 24; XXV) determining the level of expression of at least one gene selected from the group consisting of Gene Group 25; xxvi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 26; xxix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 29; or xxx) determining the level of expression of at least one gene selected from the group consisting of Gene < Group 30,

thereby characterizing the glatiramer acetate related drug substance or drug product of step a) . In some embodiments of the present invention step (c) comprises i) determining the level of expression of at least one gene selected from the group consisting of Gene Group 1; ii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 3; or vi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 6.

In some embodiments of the present invention, all genes Gene Group 1, are selected for determining the level of expression.

In some embodiments of the present invention, all genes ABCF2, ABI2, ACP6, AFG3L2, ALMS1, ARPC4, CALM3 , CCDC64, CD84, CDC6, CHAF1A, CLU, COX11, DLGAP1, DTX4, FAM49B, FHL1 , FNTB, GYPC, HFE, LPHN1, OLAH, PATZ1, PDK1, POLI, REEP5, RPS6KA2, SEC31A, SETBP1, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TPM1, TSPAN13 , UBAP2, VAV3, VDAC2, and ZFAND6, are selected for determining the level of expression.

In some embodiments of the present invention, if the at least one gene selected in part(c) (i) is IL10, the process comprises the step of selecting at least a second different gene from the group of (c) (i) and (c) (ii) other than IL10.

In some embodiments of the present invention, if the at least one gene selected in part(c) (ii) is CARD15 , CCL2, CCL5, CD14, IL10, THBD, or NFKBIA, the process comprises the step of selecting at least a second different gene from the group of (c) (i) and (c) (ii) other than CARD15, CCL2, CCL5, CD14, IL10, THBD, or NFKBIA.

In one or more embodiments of the present invention, if two or more genes are selected in step (c) , then the second or additional gene selected is different from the other selected gene or genes

In one or more embodiments of the present invention, the level of expression is determined for all genes identified in Table 5 or Table 12 to be involved in one or more than one pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in at least one pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in two or more pathways. In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in three or more pathways.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in four or more pathways.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in five or more pathways.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 5 or Table 12 to be involved in six pathways .

In one or more embodiments of the present invention, the level of expression is determined for at least one gene which is involved in only one pathway set forth in Table 5 or Table 12. In one or more embodiments of the present invention, the level of expression is determined for at least two genes identified in Table 5 or Table 12 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least three genes identified in Table 5 or Table 12 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least four genes identified in Table 5 or Table 12 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least five genes identified in Table 5 or Table 12 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least six genes identified in Table 5 or Table 12 to be involved in the same pathway. In one or more embodiments of the present invention, the level of expression is determined for all genes identified in Table 6 to be involved in one or more than one pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in at least one pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in two or more pathways.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in three or more pathways .

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in four or more pathways . In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in five or more pathways .

In one or more embodiments of the present invention, the level of expression is determined for at least one gene identified in Table 6 to be involved in six or more pathways.

In one or more embodiments of the present invention, the level of expression is determined for at least one gene which is involved in only one pathway set forth in Table 6.

In one or more embodiments of the present invention, the level of expression is determined for at least two genes identified in Table 6 W

28 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least three genes identified in Table 6 to be involved in the same pathway. In one or more embodiments of the present invention, the level of expression is determined for at least four genes identified in Table 6 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least five genes identified in Table 6 to be involved in the same pathway.

In one or more embodiments of the present invention, the level of expression is determined for at least six genes identified in Table 6 to be involved in the same pathway.

In one or more embodiments of the present invention, contacting the mammalian cells in step (b) comprises i) administering to a mammal a predetermined amount of glatiramer acetate related drug substance or drug product of step (a) , or ii) incubating the cells with an amount of the glatiramer acetate related drug substance or drug product of step (a) , or a combination thereof; and wherein step (c) comprises i) determining the level of expression of at least one gene selected from the group consisting of Gene Group 1, thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) .

In one or more embodiments of the present invention, contacting the mammalian cells in step (b) comprises i) administering to a mammal a predetermined amount of glatiramer acetate related drug substance or drug product of step (a), and ii) obtaining cells from the mammal at one or more predetermined time points; and wherein step (c) comprises determining the level of expression of at least one gene selected from the group consisting of Gene Group 1, thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) .

In one or more embodiments, the mammal is human and the cells are peripheral mononuclear blood cells. In one or more embodiments, the predetermined time point is 0, 1, 2, or 3 months.

In one or more embodiments, contacting the mammalian cells in step (b) comprises incubating monocytic cell line cells with an amount of the glatiramer acetate related drug substance or drug product of step (a) ; and wherein step (c) comprises determining the level of expression of at least one gene selected from the group consisting of Gene Group 1; ii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 2; iii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 3; iv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 4; v) determining the level of expression of at least one gene selected from the group consisting of Gene Group 5; vi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 6; vii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 7; viii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 8; ix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 9; x) determining the level of expression of at least one gene selected from the group consisting of Gene Group 10; xvii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 17; xviii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 18; xix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 19; xx) determining the level of expression of at least one gene selected from the group consisting of Gene Group 20; xxi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 21; xxii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 22; xxiii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 23; xxiv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 24; xxv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 25; xxvi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 26; xxix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 29; or xxx) determining the level of expression of at least one gene selected from the group consisting of Gene Group 30, thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) .

In one or more embodiments, contacting the mammalian cells in step (b) comprises incubating monocytic cell line cells with an amount of the glatiramer acetate related drug substance or drug product of step (a) ; and wherein step (c) comprises i) determining the level of expression of at least one gene selected from the group consisting of Gene Group 2; ii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 3; iii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 4; iv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 5; v) determining the level of expression of at least one gene selected from the group consisting of Gene Group 6; vi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 7; or vii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 8; ix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 9; x) determining the level of expression of at least one gene selected from the group consisting of Gene Group 10; xvii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 17; xviii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 18; xix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 19; xx) determining the level of expression of at least one gene selected from the group consisting of Gene Group 20; xxi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 21; xxii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 22; xxiii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 23; xxiv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 24; xxv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 25; xxvi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 26; xxix) determining the level of expression of at least one gene selected from the group consisting of Gene Group 29; or xxx) determining the level of expression of at least one gene selected from the group consisting of Gene Group 30, thereby characterizing the glatiramer acetate related drug substance or drug product of step a) .

In one or more embodiments of the present invention, the mammalian cells are THP-1 cells.

In one or more embodiments of the present invention, contacting the mammalian cells in step (b) comprises i) immunizing a mammal with a predetermined amount of glatiramer acetate related drug substance or drug product, ii) preparing a culture of cells from the mammal of step i) at one or more predetermined time points after immunization, and iii) incubating cells from the culture of cells obtained from the mammal with an amount of the glatiramer acetate related drug substance or drug product of step (a) ; and wherein step (c) comprises i) determining the level of expression of at least one gene selected from the group consisting of Gene Group 1; xi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 11; xii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 12; xiii) determining the level of expression of at least one gene selected from the group consisting of Gene Group 13; xiv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 14; xv) determining the level of expression of at least one gene selected from the group consisting of Gene Group 15; or xvi) determining the level of expression of at least one gene selected from the group consisting of Gene Group 16, thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) . In one or more embodiments of the present invention, the glatiramer acetate related drug substance or drug product of step (iii) is the same glatiramer acetate related drug substance or drug product of step (i) . In one or more embodiments of the present invention, the glatiramer acetate related drug substance or drug product of step (iii) is a different glatiramer acetate related drug substance or drug product of step (i) .

In one or more embodiments of the present invention, the incubation is for about 24 hours, for about 12 hours, or for about 6 hours.

In one or more embodiments of the present invention, the predetermined time point after immunization is 3 days.

In one or more embodiments of the present invention, the contacting of step (b) is in a cell culture. In one or more embodiments of the present invention, the culture is a primary culture.

In one or more embodiments of the present invention, the contacting of step (b) is in a mammal.

In one or more embodiments of the present invention, the mammal is a rodent or human.

In one or more embodiments of the present invention, the glatiramer acetate related drug substance or drug product is other than glatiramer acetate drug substance or drug product.

In one or more embodiments of the present invention, the cell is of a type i) selected from the group of cell types consisting of FoxP3+ T cells, regulatory T cells, natural killer T cells, T helper 2 cells, CD8+ T cells, CD4+ T cells, B cells, macrophage cells, monocyte cells, eosinophils, dendritic cells, granulocytes, megakaryocytes, and myeloid progenitors; ii) selected from the group of cell types identified in Table 9; iii) selected from the group of cell types identified in Table 10; or iv) selected from the group of cell types identified in Table 11.

In one or more embodiments of the present invention, the process of characterizing two or more glatiramer acetate related drug substances or drug products further comprises obtaining characteristics of each of the glatiramer acetate related drug substances or drug products; and comparing the characteristics of the drug related substances or drug products, thereby discriminating between glatiramer acetate related drug substances or drug products . In one or more embodiments of the present invention, the mammal is a rodent or human.

In one or more embodiments of the present invention, the level of expression is determined in hematological cells.

In one or more embodiments of the present invention, the level of expression is determined in splenocytes .

In one or more embodiments of the present invention, the level of expression is determined in monocytes.

In one or more embodiments of the present invention, the monocytes are THP-1. In one or more embodiments of the present invention, the level of expression is determined in peripheral blood mononuclear cells.

In one or more embodiments of the present invention, the peripheral blood mononuclear cells are from a human.

In one or more embodiments of the present invention, the human has previously been treated with a glatiramer acetate related drug substance or drug product.

In one or more embodiments of the present invention, the human is a naive human.

In one or more embodiments of the present invention, the human is a glatiramoid naive human. In one or more embodiments of the present invention, the human is afflicted with RRMS.

In one or more embodiments of the present invention, the rodent is a mouse . In one or more embodiments of the present invention, the mouse is a female (SJL X BALB/C) Fl mouse.

In one or more embodiments of the present invention, the mouse is about 8 to 12 weeks old.

In one or more embodiments of the present invention, the primary culture is a culture of spleen cells.

In some embodiments of the present invention, the primary culture is a culture of lymph node cells.

In some embodiments of the present invention, the primary culture of spleen cells is prepared about 3 days after immunization. In one or more embodiments of the present invention, the glatiramer acetate related drug substance is a glatiramoid or the glatiramer acetate related drug product comprises a glatiramoid.

In one or more embodiments of the present invention, the glatiramer acetate related drug substance is a glatiramoid other than glatiramer acetate related drug substance, or the glatiramer acetate related drug product comprises a glatiramoid other than glatiramer acetate drug substance .

In one or more embodiments of the present invention, process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting a first group of mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; c) contacting a second group of mammalian cells of the same type with an amount of a reference standard; and d) determining a set of genes differentially expressed by the first group after the contacting of step (b) relative to genes expressed by the second group after the contacting of step (c) , thereby characterizing the glatiramer acetate related drug substance or drug product of step a) . In one or more embodiments of the present invention, the cells are THP-1 cells.

In one or more embodiments of the present invention, the reference standard is glatiramer acetate related drug substance or drug product.

In one or more embodiments of the present invention, the reference standard is mannitol

In one or more embodiments of the present invention, the reference standard is medium.

In one or more embodiments of the present invention, the determining step (d) comprises comparing the expression of genes expressed by the first group to the expression of genes expressed by the second group.

In one or more embodiments of the present invention, the determining step (d) comprises comparing the expression of genes by bother the first group of cells and by the second group of cells to expression of the genes by the same type of cells exposed to mannitol or medium.

In one or more embodiments of the present invention, process for discriminating between glatiramer acetate related drug substances or drug products comprising the step of characterizing two or more glatiramer acetate related drug substances or drug products to obtain characteristics of each of the glatiramer acetate related drug substances or drug products; and comparing the characteristics of the glatiramer acetate related drug substances or drug products, thereby discriminating between glatiramer acetate related drug substances or drug products .

In some embodiments of the present invention in a process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the improvement comprising including in the array of testing the steps of: a) characterizing the glatiramer acetate related drug substance according to the process of any one of the above characterization methods; and b) i) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; ii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; iii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; iv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; v) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; vi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6, is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; vii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; viii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 8 , is downregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; or ix) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 9 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; x) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 10 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xi) including the batch of the glatiramer acetate W

related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 11 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 12 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 13 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 14 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 15 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 16 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 17 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xviii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 18 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xix) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 19 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xx) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 20 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 21 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 22 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 23 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 24 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 25 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxvi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 26 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxix) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 29 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; or xxx) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 30 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions . In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of ABCF2, ABI2, ACP6, AFG3L2, ALMS1 , ARPC4, CALM3 , CCDC64, CD84, CDC6, CHAF1A, CLU, COX11, DLGAP1, DTX4, FAM49B, FHL1, FNTB, GYPC, HFE, LPHN1, OLAH, PATZ1, PDK1, POLI, REEP5 , RPS6KA2, SEC31A, SETBP1, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TPM1, TSPAN13, UBAP2 , VAV3 , VDAC2 , and ZFAND6 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions .

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions. In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises i) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of ABI2, ARPC4, CD84, CLU, HFE, and IL10 is upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; or ii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of ABCF2, ACP6, AFG3L2, CHAF1A, COX11, LPHN1, NACA, OLAH, POLI, SEC31A, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TSHZ1, TSPAN13, UBAP2, VDAC2, and TSHZ1 is downregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises, if, one or more genes selected from the group consisting of ABI2, ARPC4, HFE, and IL10 is upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions, then including the batch of the glatiramer acetate related drug substance in the production of the drug product.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises, if, one or more genes selected from the group consisting of ACP6, LPHN1, POLI, SEC31A, SYNCRIP, and TSHZ1 is downregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions, then including the batch of the glatiramer acetate related drug substance in the production of the drug product.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises i) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of CCL2, CCL5, M P1, MP9, CXCL10, CARD15 , CD14, ICAM1, BIRC3, THBD, NF BIA, IL10, PRDM1 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; ii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of CISH and HSPD1 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; iii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of CC124, CCR1, CSF1R, CX3CR1, IL27, IFNGR1, IL2RG, and IL7R is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate drug related substance under the same conditions; iv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of PGRMC1 is upregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; v) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of MMP14 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; vi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of IL1RN is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; or vii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of IL1B is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions .

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions .

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions. In one or more embodiments of the present invention, in the process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is downregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In some embodiments of the present invention in a process for releasing a drug product comprising a glatiramer acetate related drug substance, which process involves an array of testing, the improvement comprising including in the array of testing the steps of: a) characterizing the glatiramer acetate related drug product according to the process of any one of the above characterization methods; and b) i) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions; ii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; iii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; iv) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; v) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; vi) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6, is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; vii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; viii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is downregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions, ix) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 9 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; x) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 10 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; xi) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 11 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xii) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 12 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xiii) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group _^ 13 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xiv) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 14 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xv) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 15 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xvi) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 16 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xvii) releasing the batch of the glatxramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 17 is substantially identical to the level of expression by the same type of cells in the presence of the glatxramer acetate drug substance under the same conditions; xviii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 18 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xix) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 19 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xx) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 20 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxi) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 21 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 22 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 23 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiv) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 24 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxv) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 25 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxvi) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 26 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxix) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 29 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; or xxx) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 30 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions. In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of ABCF2, ABI2, ACP6, AFG3L2, ALMS1 , ARPC4, CALM3, CCDC64 , CD84, CDC6, CHAF1A, CLU, COX11, DLGAP1, DTX4 , FAM49B, FHL1, FNTB, GYPC, HFE, LPHN1 , OLAH, PATZ1, PDK1, POLI, REEP5, RPS6KA2, SEC31A, SETBP1, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TPM1, TSPA 13, UBAP2, VAV3, VDAC2 , and ZFAND6 is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions. In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions .

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is substantially identical to the level of W 201

52 expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5, is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises i) releasing the batch of the glatiramer acetate related drug product if the level of expression of one of more genes selected from the group consisting of ABI2, ARPC4, CD84, CLU, HFE, and IL10 is upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions; or ii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one of more genes selected from the group consisting of ABCF2, ACP6, AFG3L2, CHAF1A, COX11, LPHN1, NACA, OLAH, POLI, SEC31A, SNRPA1, SYNCRIP, TNFSF9, TOM 40, TSHZ1, TSPAN13, UBAP2, VDAC2, and TSHZ1 is downregulated relative to the level of expression by the same type of cells in the W

53 absence of the glatiramer acetate related drug product under the same conditions .

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug substance further comprises, if, one or more genes selected from the group consisting of ABI2, ARPC4, HFE, and IL10 is upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions, then releasing the batch of the glatiramer acetate related drug product.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises, if, one or more genes selected from the group consisting of ACP6, LPHN1, POLI, SEC31A, SYNCRIP, and TSHZ1 is downregulated relative to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions, then releasing the batch of the glatiramer acetate related drug product.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises i) releasing the batch of the glatiramer acetate related drug product if the level of expression of one of more genes selected from the group consisting of CCL2, CCL5 , MMP1, MMP9, CXCL10, CARD15 , CD14, ICAM1, BIRC3, THBD, NFKBIA, IL10, PRDM1 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; ii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one of more genes selected from the group consisting of CISH and HSPD1 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; iii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one of more genes selected from the group consisting of CC124, CCR1, CSF1R, CX3CR1, IL27, IFNGR1 , IL2RG, and IL7R is not substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate drug related substance under the same conditions; iv) releasing the batch of the glatiramer acetate related drug product if the level of expression of PGRMC1 is upregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; v) releasing the batch of the glatiramer acetate related drug product if the level of expression of MMP14 is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions; vi) releasing the batch of the glatiramer acetate related drug product if the level of expression of IL1RN is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; or vii) releasing the batch of the glatiramer acetate related drug product if the level of expression of IL1B is substantially identical to the level of expression by the same type of cells in the presence of glatiramer acetate drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5, is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6 is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is upregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In one or more embodiments of the present invention, in the process for releasing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the characterizing the glatiramer acetate related drug product further comprises releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is downregulated to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions.

In one or more embodiments of the present invention, a glatiramer acetate related drug product produced by a process of the present invention, wherein the glatiramer acetate related drug product is other than glatiramer acetate drug product.

In one or more embodiments of the present invention, a glatiramer acetate related drug product other than glatiramer acetate drug product which is capable of inducing a level of expression of ABCF2, ABI2, ACP6, AFG3L2, ALMS1 , ARPC4, CALM3, CCDC64, CD84, CDC6, CHAF1A, CLU, COX11, DLGAP1, DTX4, FAM49B, FHL1, FNTB, GYPC, HFE, LPHN1, OLAH, PATZ1, PDK1, POLI, REEP5, RPS6KA2, SEC31A, SETBP1, SNRPA1, SYNCRIP, TNFSF9, TOMM40, TPM1, TSPAN13, UBAP2, VAV3, VDAC2, and ZFAND6 that is not substantially identical to the level of expression of the genes induced in the same tpe of cells and under the same conditions in the absence of the glatiramer acetate related drug product. In one or more embodiments of the present invention, a glatiramer acetate related drug product, wherein the glatiramer acetate related drug product is capable of inducing a level of expression of Gene Group 1. In one or more embodiments of the present invention, the glatiramer acetate related drug product, which is capable of upregulating genes ABI2, ARPC4, HFE, and IL10 relative to the level of expression of the genes in the same type of cells and under the same conditions in the absence of the glatiramer acetate related drug product, and capable of downregulating genes ACP6, LPHN1, POLI, SEC31A, SYNCRIP, and TSHZ1 relative to the level of expression of the genes in the same type of cells and under the same conditions in the absence of the glatiramer acetate related drug product.

In one or more embodiments of the present invention, a glatiramer acetate related drug product other than glatiramer acetate drug product which is capable of inducing a level of expression of Gene Group 7 and Gene Group 8, that is not substantially identical to the level of expression of the genes induced in the same type of cells and under the same conditions in the absence of the glatiramer acetate related drug product.

In one or more embodiments of the present invention, 'the glatiramer acetate related drug product, which is capable of upregulating genes Gene Group 7, relative to the level of expression of the genes in the same type of cells and under the same conditions in the absence of the glatiramer acetate related drug product, and capable of downregulating genes Gene Group 8 relative to the level of expression of the genes in the same type of cells and under the same conditions in the absence of the glatiramer acetate related drug product

In some embodiments of the present invention, the process further comprises i) determining the one or more proteins produced by each of the one of more genes selected in step c) ; and ii) determining protein level expression for each protein in step i) .

In some embodiments of the present invention, the process further comprises i) determining the one or more proteins produced by each of the one of more genes selected in step b) ; and ii) determining protein level expression for each protein in step i) .

In some embodiments of the present invention, the process further comprises determining the set of proteins produced by each gene of the set of genes in step d) .

In some embodiments of the present invention, in a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) xxii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group A; xxiii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group B; xxiv) determining the protein level expression of at least one protein selected from the group consisting of Protein Group C; xxv) determining the protein level expression of at least one protein selected from the group consisting of Protein Group D; xxvi) determining the protein level expression of at least one protein selected from the group consisting of Protein Group E; xxvii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group F; or xxviii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group G, thereby characterizing the glatiramer acetate related drug substance or drug product of step a) .

In some embodiments of the present invention, in a process for characterizing a glatiramer acetate related drug substance or drug product comprising the steps of: a) obtaining a batch of the glatiramer acetate related drug substance or drug product; b) contacting mammalian cells with an amount of the glatiramer acetate related drug substance or drug product of step a) ; and c) i) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 1; ii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 2, wherein if IL1B, IL10, or MMP9 is the at least one gene selected in part (c) (ii) , then selecting at least a second different gene from the group other than IL1B, IL10, or MMP9; iii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 3; iv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 4; v) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 5; vi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 6; vii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 7; viii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 8; ix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 9; x) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene

Group 10; xi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 11; xii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 12; xiii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 13; xiv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 14; xv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 15; xvi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 16; xvii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 17; xviii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 18; xix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 19; xx) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 20; xxi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene

Group 21; xxii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 22; xxiii) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 23; xxiv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 24; xxv) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 25; xxvi) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 26; xxix) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 29; or xxx) determining the protein level expression of at least one protein produced by a gene selected from the group consisting of Gene Group 30, thereby characterizing the glatiramer acetate related drug substance or drug product of step a) .

In some embodiments of the present invention the process, wherein contacting the mammalian cells in step (b) comprises incubating monocytic cell line cells with an amount of the glatiramer acetate related drug substance or drug product of step (a) and wherein step (c) comprises xxii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group A; xxiii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group B; xxiv) determining the protein level expression of at least one protein selected from the group consisting of Protein Group C; xxv) determining the protein level expression of at least one protein selected from the group consisting of Protein Group D; xxvi) determining the protein level expression of at least one protein selected from the group consisting of Protein Group E; xxvii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group F; or xxviii) determining the protein level expression of at least one protein selected from the group consisting of Protein Group G, thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) .

In some embodiments of the present invention, the process wherein the mammalian cells are THP-1 cells.

In some embodiments of the present invention, the process, wherein the incubation is for about 24 hours. In some embodiments of the present invention, the process, wherein contacting the mammalian cells in step (b) comprises i) immunizing a mammal with a predetermined amount of glatiramer acetate related drug substance or drug product, ii) preparing a culture of cells from the mammal of step i) at one or more predetermined time points after immunization, and iii) incubating cells from the culture of cells obtained from the mammal with an amount of the glatiramer acetate related drug substance or drug product of step (a) , thereby characterizing the glatiramer acetate related drug substance or drug product of step (a) .

In some embodiments of the present invention, the process, wherein the glatiramer acetate related drug substance or drug product of step (iii) is the same glatiramer acetate related drug substance or drug product of step (i) .

In some embodiments of the present invention, the process, wherein the glatiramer acetate related drug substance or drug product of step (iii) is a different glatiramer acetate related drug substance or drug product of step (i) .

In some embodiments of the present invention, in a process for producing a drug product comprising a glatiramer acetate related drug substance which involves an array of testing, the improvement comprising including in the array of testing the steps of: a) characterizing the glatiramer acetate related drug substance according to the process of any one of the above characterization methods; and b) xxii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group A is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; xxiii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group B is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; xxiv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group C is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; xxv) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group D is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; xxvi) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group E is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; xxvii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group F is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions; or xxviii) including the batch of the glatiramer acetate related drug substance in the production of the drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group G is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance under the same conditions .

In some embodiments of the present invention, in a process for releasing a drug product comprising a glatiramer acetate related drug substance, which process involves an array of testing, the improvement comprising including in the array of testing the steps of: a) characterizing the glatiramer acetate related drug product according to the process of any one of the above characterization methods; and xxii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group A is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; xxiii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group B is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; xxiv) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group C is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; xxv) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group D is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; xxvi) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group E is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; xxvii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group F is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions; or xxviii) releasing the batch of the glatiramer acetate related drug product if the level of expression of one or more proteins selected from the group consisting of Protein Group G is substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug product under the same conditions .

In some embodiments of the present invention, in a process for discriminating between glatiramer acetate related drug substances or drug products comprising the steps of: a) characterizing one or more glatiramer acetate related drug substances or drug products according to the process of any one of the above characterization methods to obtain characteristics of each of the glatiramer acetate related drug substances or drug products; b) obtaining characteristics of a glatiramer acetate drug substance or drug product; and c) comparing the characteristics of the glatiramer acetate related drug substances or drug products obtained in steps a) and b) , thereby discriminating between glatiramer acetate related drug substances or drug products.

Additional Embodiments of the Invention

In a process for producing a drug product comprising a glatiramer acetate related drug substance, the improvement comprising the steps of: a) characterizing the glatiramer acetate related drug substance according to the process of any one of the above characterization methods; and b) i) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is substantially identical to the level of expression by the same type of cells in the absence

• of the glatiramer acetate related drug substance under the same conditions; ii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; iii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; iv) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; v) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; vi) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 6, is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; vii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is downregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; viii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is upregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions; ix) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 9 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; x) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 10 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xi) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 11 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 12 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiii) discarding the batch of the glatiramer acetate ' related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 13 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiv) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 14 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xv) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 15 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvi) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 16 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 17 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xviii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 18 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xix) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 19 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xx) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 20 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxi) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 21 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 22 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiii) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 23 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiv) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 24 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxv) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene

Group 25 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxvi) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 26 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxix) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 29 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; or xxx) discarding the batch of the glatiramer acetate related drug substance as unacceptable for inclusion in the drug product if the level of expression of one or more genes selected from the group consisting of Gene Group 30 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions. In a process for releasing a drug product comprising a glatiramer acetate related drug substance, the improvement comprising the steps of: a) characterizing the glatiramer acetate related drug product according to the process of any one of the above characterization methods; and b) i) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug product under the same conditions; ii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene

Group 2 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; iii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; iv) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; v) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 5, is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; vi) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 6 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; vii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 7, is downregulated or substantially identical to the level of expression by the same type of cells in the absence of glatiramer acetate drug product under the same conditions; viii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is upregulated or substantially identical to the level of expression by the same type of cells in the absence of glatiramer acetate drug product under the same conditions; ix) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene

Group 9 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; x) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 10 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug product under the same conditions; xi) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 11 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 12 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 13 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiv) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 14 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xv) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 15 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvi) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 16 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 17 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xviii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 18 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xix) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 19 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xx) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 20 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxi) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 21 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 22 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiii) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 23 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiv) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 24 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxv) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 25 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxvi) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 26 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxix) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 29 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; or xxx) discarding the batch of the glatiramer acetate related drug product as unacceptable for release if the level of expression of one or more genes selected from the group consisting of Gene Group 20 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions .

In one or more embodiments of the present invention, in a process for identifying suboptimal activity of a glatiramer acetate related drug substance or drug product comprising the steps of: a) administering a glatiramer acetate related drug substance or drug product to a mammal; b) characterizing the glatiramer acetate related drug substance or drug product according to the process of any one of the above characterization methods; and i) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 1 is substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance or drug product under the same conditions; ii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 2 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance or drug product under the same conditions; iii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 3 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance or drug product under the same conditions; iv) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 4 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance or drug product under the same conditions; v) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 5 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance or drug product under the same conditions; vi) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 6, is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate related drug substance or drug product under the same conditions; vii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

7, is downregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance or drug product under the same conditions; viii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 8, is upregulated or substantially identical to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance or drug product under the same conditions; ix) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 9 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance or drug product under the same conditions; x) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 10 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance or drug product under the same conditions; xi) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 11 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 12 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

13 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xiv) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

14 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xv) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

15 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvi) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

16 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xvii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

17 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xviii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

18 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xix) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

19 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xx) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

20 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxi) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

21 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

22 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiii) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 23 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxiv) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

24 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxv) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group 25 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxvi) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

26 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; xxix) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

29 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions; or xxx) identifying the glatiramer acetate related drug substance or drug product as causing a suboptimal activity if the level of expression of one or more genes selected from the group consisting of Gene Group

30 is not substantially identical to the level of expression by the same type of cells in the presence of the glatiramer acetate drug substance under the same conditions.

The Additional Embodiments described above can be readily applied and practiced with features of Embodiments of the Invention described in the section preceeding the Additional Embodiments .

For example, in a process for producing a drug product comprising a glatiramer acetate related drug substance, where the batch of the glatiramer acetate related drug substance is included in the drug product if the level of expression of one or more genes selected from one or more Gene Groups is substantially upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions, then conversely the batch of the glatiramer acetate related drug substance is discarded if the level of expression of one or more genes selected from one or more Gene Groups is not substantially upregulated relative to the level of expression by the same type of cells in the absence of the glatiramer acetate related drug substance under the same conditions as unacceptable for inclusion in the drug product.

Definitions

As used herein, a "naive human" is a human that has not been treated with any multiple sclerosis drug.

As used herein, a "glatiramoid naive human" is a human that has not been treated with any glatiramoid drug. A glatiramoid naive human could have been treated with another multiple sclerosis drug.

As used herein, "in the blood of" is represented by peripheral blood mononuclear cells (PBMCs) , lymphocytes, monocytes, macrophages, basophils, dendritic cells or other cells derived from a mammal's blood.

As used herein, a "reference standard" is a sample or value which serves as a point of comparison for another sample or value which differs from the reference standard with respect to one or more variables. With specific regard to a human, a "reference standard" is a value or range of values that characterizes a defined population in a defined state of health. For example, a reference standard can characterize a healthy human or a human afflicted with multiple sclerosis, and when the human is afflicted with multiple sclerosis the human can be naive or having received glatiramer acetate drug substance.

As used herein, the term "glatiramer acetate related drug substance" (GARDS) is intended to include include polypeptides with a predetermined sequence as well as mixtures of polypeptides assembled from the four amino acids glutamic acid (E) , alanine (A) , lysine (K) , and tyrosine (Y) from any three of the amino acids Y, E, A and K, i.e. YAK, YEK, YEA or EAK; or from three of the amino acids Y, E, A and K and a fourth amino acid. Examples of glatiramer acetate related polypeptides are disclosed in U.S. Patents 6,514,938 Al, 7,299,172 B2, 7,560,100 and 7,655,221 B2 and U.S. Patent Application Publication No. US 2009-0191173 Al, the disclosures of which are hereby incorporated by reference in their entireties . Glatiramer acetate related substances include glatiramoids . As used herein, a "glatiramer acetate related drug product" (GARDP) contains a glatiramer acetate related drug substance.

As used herein, a "glatiramer acetate related drug substance or drug product" is a glatiramer acetate related drug substance or a glatiramer acetate related drug product.

As used herein a "glatiramoid" is a complex mixture of synthetic proteins and polypeptides of varying sizes assembled from four naturally occurring amino acids: L-glutamic acid, L-alanine, L-lysine, and L-tyrosine, in a defined molar ratio. Examples of glatiramoids include glatiramer acetate drug substance (e.g. Copaxone ^® ) as well as glatiramoids other than Copaxone ^® , e.g. GA-Natco.

As used herein, a "glatiramer acetate drug substance" (GADS) is glatiramer acetate produced by Teva Pharmaceutical Industries, Ltd. and is the active ingredient in a glatiramer acetate drug product. As used herein, a "glatiramer acetate drug product" (GADP) contains a glatiramer acetate drug substance produced by Teva Pharmaceutical Industries, Ltd. which consists of the acetate salts of synthetic polypeptides, containing four naturally occurring amino acids: L- glutamic acid, L-alanine, L-tyrosine, and L-lysine with an average molar fraction of 0.141, 0.427, 0.095, and 0.338, respectively, and has an average molecular weight of 5,000 - 9,000 daltons . (8) Copaxone ^® is a glatiramer acetate drug product.

As used herein, a "glatiramer acetate drug substance or drug product" is a glatiramer acetate drug substance or a glatiramer acetate drug product.

As used herein a "glatiramer acetate reference standard" is or contains the drug substance found in a glatiramer acetate drug product .

As used herein "suboptimal activity" refers to a negative response or to a response which is less than the response to glatiramer acetate drug substance or glatiramer acetate drug product produced by Teva Pharmaceutical Industries, Ltd. As used herein, "release" of a drug product refers to making the product available to consumers .

As used herein, "about" with regard to a stated number encompasses a range of +10 percent to -10 percent of the stated value. By way of example, about 100 mg therefore includes the range 90-110 mg and therefore also includes 90, 91, 92, 93, 94, 95 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109 and 110 mg. Accordingly, about 100 mg includes, in an embodiment, 100 mg.

As used herein, "hematological cell" comprises neutrophils, erythrocytes, basophils, monocytes, eosinophils, platelets, lymphocytes, and splenocytes .

As used herein, an "array of testing" for a glatiramer acetate related drug substance or drug product includes, but is not limited to, any analytical method test such as in vitro tests or molecular weight tests, biological assays such as the ex vivo tests and clinical efficacy tests which characterize the GARDS or GARDP, or clinical trials . Examples of testing for a glatiramer acetate related drug substance or drug product are disclosed in U.S. Patent Application Publication Nos . US 2012-0309671 and US 2011-0230413, and in PCT International Application Publication Nos. WO 2000/018794, WO 2012/051106, WO 2013/055683, WO 2014/058976, the disclosures of which are hereby incorporated by reference in their entireties .

It is understood that where a parameter range is provided, all integers within that range, tenths thereof, and hundredths thereof, are also provided by the invention. For example, "0.2-5 mg" is a disclosure of 0.2 mg, 0.21 mg, 0.22 mg, 0.23 mg etc. up to 0.3 mg, 0.31 mg, 0.32 mg, 0.33 mg etc. up to 0.4 mg, 0.5 mg, 0.6 mg etc. up to 5.0 mg.

All combinations of the various elements described herein are within the scope of the invention. It is understood that where "at least one" or "one or more" is recited along with a list, then 1, 2, 3, 4... or all members of that list are disclosed in every combination. For example, in a group of 43 genes, "at least one" and "one or more" is a disclosure of one gene, two genes, three genes, etc., in any combination, up to the forty three genes .

As used herein, "characterization" or "characterizing" is understood to include obtaining information which was produced in the same location or country, or a different location or country from where any remaining steps of the method are performed.

As used herein, processes of producing a glatiramer acetate related drug substance or drug product are known in the art. Examples of such manufacturing processes are disclosed in U.S. Patent 5,800,808, and in PCT International Application Publication Nos. WO 2005/032553, WO 2005/032395, WO 1999/22402, the disclosures of which are hereby incorporated by reference in their entireties.

Each embodiment disclosed herein is contemplated as being applicable to each of the other disclosed embodiments. Thus, all combinations of the various elements described herein are within the scope of the invention .

This invention will be better understood by reference to the Experimental Details which follow, but those skilled in the art will readily appreciate that the specific experiments detailed are only illustrative of the invention as described more fully in the claims which follow thereafter.

Experimental Details Methods

The null hypothesis in traditional gene-expression studies, including Teva's studies with the glatiramoids , is that there are no significant gene expression differences induced between the treatments. As such, the expectation is that regardless of the biological system used for testing, genes would show no statistically significant, nor biologically meaningful differences among the various treatments. Only in cases where the treatments induce significant observable effects, genes differentially expressed between treatments will pass the stringent statistical tests, and false discovery rate (FDR) correction for multiple hypotheses (Benjamini and Hochberg, 1995) . These stringent requirements were imposed a priori across all tests to ensure robustness of results and minimizing of spurious findings. Such statistically significant differences, if biologically meaningful (i.e., related to the disease biology or any of the drug's known or putative targets and downstream pathways) , warrant further studies, as two drugs that have identical activities in biological systems should not induce statistically observable and biologically enriched differences when compared against each other.

These studies were not designed to establish a particular set of genes in a specific model system as a panel to evaluate sameness between differently manufactured glatiramoids. Instead, these were designed to assess the degree of similarity in the impact of two glatiramoids on relevant biological pathways. The application of robust methodology (high number of replicates, conditions and time-points, where relevant) was aimed to describe pathways changed by different treatments out of the entire milieu of genomic patterns. The results obtained across the tested experimental models revealed statistically significant differences between drugs, which were intended to be similar and to perform the same function, despite stringent statistical threshold requirements. This was noteworthy particularly in genes highly relevant to disease processes and drug response mechanisms. In addition, the differences observed revealed a complex interplay between immunological pathways, such that some differences were common to multiple systems, while many others were dependent on the specific model system (for example, some key genes modulated in T cells were not the same as in monocytes) . This is not surprising for a process that involves multifaceted interactions between many immune system components, and is also exemplified in experimental studies of Copaxone®' s mechanism of action. Thus, no single model system, characterization method, or set of genes tested was sufficient to comprehensively capture the differences between the drugs. These observations indicate a need for in-depth investigation of comparative gene expression profiles in several relevant pre-clinical systems as key indicators of similarity and/or sameness between generic candidates and the original drug within the context of Non-Biological Complex Drugs (NBCD) . Ideally, the concordance between high- resolution physicochemical measures (e.g. ion motility mass spectrometry, IMMS), gene expression profiling and clinical trials would allow a more definitive assessment of equivalence in terms of patient benefit and safety.

Mice

All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee.

Preparation of Mouse Spleen Cell Cultures

All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee.

Mouse Splenocytes : Gene Expression Analysis

In the first of the genomic studies, 8- to 12-week old female mice (N=8) of the (Balb/c x SJL) Fl variety (Harlan, Israel) were injected subcutaneously with glatiramer acetate (GA) in order to induce specific GA-reactive T cells as would be present in a Copaxone ^® treated patient . After 3 days, the mice were sacrificed and cells from their spleens (splenocytes) were isolated because such cells are representative of, and commonly utilized as a gold standard to study the immune system. The aqueous activator samples, mannitol (the non-active excipient in Copaxone ^® and all other marketed proposed generics) and medium were used as negative controls.

Given the robustness of the model established in our first mouse splenocyte study, we sought to expand the scope of the investigation using the exact same study design, but with an expanded set of treatments (Fig. 1) . In addition to comparing Copaxone ^® to a purported foreign generic version, we also sought to compare purported generics from various manufacturers to each other. Using the mouse splenocyte procedure described herein, we generated expression data in response to activation with proposed generic glatiramer acetate samples from Escadra (Argentina) , Probioglat (Mexico; Probiomed) , and Hangzhou (China: API). A total of 21 samples of Copaxone ^® from 21 different batches were used, along with 10 samples from 2 lots of Escadra, 12 samples from 4 batches of Natco, 4 samples from 1 batch of Probioglat, 5 samples of Hangzhou from 2 batches, 12 samples of GA-RS from 1 batch, and 8 samples of medium.

Mouse Splenocytes : RNA Isolation and Microarray Expression Profiling Extraction of total RNA from activated splenocytes was extracted using PerfectPure RNA Cultures CEKK kit 50 (5Prime GmbH, Hamburg, Germany) and following the manufacturer's instructions. RNA quality was assessed using the absorbance ratio at 260/280 ran and gel electrophoresis (Experion, Bio-Rad, Hercules, CA, USA) . Total RNA extracted from samples was hybridized to Illumina Mouse WG-6_V2 microarray chips containing more than 45,200 transcripts.

Samples were randomized on the chips to avoid batch effects. Illumina' s BeadStudio software was utilized for image processing, quantification of signal intensity per bead, and background signal correction. Multiple probes were analyzed for a given gene were averaged and batch correction was conducted using Partek. Further analysis was conducted individually within the context of known pathways, and batch correction was conducted using ComBat, as implemented in the SVA R package sva: Surrogate Variable Analysis. Available :

www . bioconductor . org/packages/release/bioc/html/sva . html ) . Briefly, ComBat is an empirical Bayesian approach utilizing location and scale metrics across several genes to adjust for batch effects in datasets, even datasets containing small sample sizes. Treatment labels were added as covariates to the batch correction in order to preserve relevant treatment effects. Principal Component Analysis (a multivariate approach) showed that the main effect in the first principal component remained due to treatment effects after batch correction.

Mouse Splenocytes: Gene Expression Analysis - Polimunol versus Copaxone ^® Gene Expression Studies

Mice

All experimental procedures conformed to accepted ethical standards for use of animals in research and were in accordance with Committee for the Care and Use of Experimental Animals guidelines and approved by the Teva Institutional Animal Care and Use Committee. For these experiments, 8- to 12-week-old female (Balb/c X SJL) Fl mice (Janvier, France) were purchased. Mice were kept at 21±3°C; the relative humidity was 30-70%, the light/dark cycle was 12/12 h. Animals were maintained on a standard rodent pellet diet and sterile filtered tap water available ad libitum.

Preparation of mouse spleen cell cultures

To stimulate induction of GA-reactive T cells, twelve mice were injected with 100 μΐι of a 2.5 mg/mL solution of GA reference standard (GA-RS) in phosphate-buffered saline (250 \ig GARS per mouse) . GA-RS (Teva) is a selected GA drug substance batch defined as the standard batch and used as a reference in quality control release tests of all Copaxone ^® batches. Another group of twelve mice were injected with 100 L of a 2.5 mg/mL solution of Polimunol in phosphate-buffered saline (250 g Polimunol per mouse) . Polimunol is a proposed generic manufactured a company other than Teva. Mice were housed for 3 days after immunization; mice were then sacrificed and their spleens were aseptically removed and placed on ice in RPMI 1640. A single cell suspension was prepared. After red blood cells lysis, splenocytes from the same immunization group were pulled and resuspended to a final concentration of 10 x 106 cells/mL in defined cell culture media (DCCM1) (Biological Industries, Beit Haemek, Israel) (96.7% v/v) enriched with L-glutamine 2 mM (1% v/v), MEM Non-Essential Amino Acids 2 mM (1% v/v), sodium pyruvate 1 mM (1% v/v), antibiotic/antimycotic solution (0.2% v/v) and 2-mercaptoethanol 50mM (0.1% v/v).

In vitro cell activation

Splenocytes were treated with activator samples diluted in medium (125 μΐι per well of 80 pg/mL solutions, final concentration in the well: 40 g/mL) of: i) 3 different batches of GA drug product manufactured by Teva ii) one batch of proposed generic (Polimunol) . Polimunol is a product marketed as generic GA and manufactured by a company other than Teva (i.e. Synthon) . The activator samples, mannitol (the nonactive excipient in Copaxone ^® ) , and medium were added to 96-well tissue culture plates (three wells per sample) . Splenocytes (125 pL 10 x 10 ^s SPL cell/mL suspension) were added to the activator solutions. Each activator sample was loaded in two different plates. One for the cells from mice immunized with GA and one for cells from mice immunized with proposed generic. Plates were incubated for 24 h at 37 °C. Cells were collected from the wells and were centrifuged at 300g for 5 minutes. Supernatants were aspirated and cell pellets were resuspended in RLT buffer (from RNeasy mini kit of Qiagen, Cat # 74106) for cell lysis. The cell lysates were centrifuged and supernatants were collected and frozen at -70°C. Samples were sent for further processing .

Analysis Methods

For additional detail on experimental methods used in mouse studies, please refer to publications [Bakshi et al; Towfic et al] . Note that in this study, mice were immunized with either Copaxone ^® or Polimunol, and subsequently splenocytes were isolated and treated ex vivo with Copaxone ^1® or Polimunol. RNA was extracted and expression profiled across the entire genome using the Affymetrix Mouse Genome 430 2 chip. Three lots of Copaxone ^® , and one lot of Polimunol were comparatively tested in six replicates each.

Outlier identification and normalization

Outlier samples were identified using the R package ArrayQCMetrics and excluded from further data processing steps. A sample was considered an outlier if it ^' failed more than half of the included tests either before or after RMA normalization. Data were RMA normalized using the Affy R package.

Batch correction

Correction for batch variation was performed using ComBat as described above (THP-1 methods) . Date of microarray experiment was used as batch, and the combination of treatment and immunization was used as covariate. Principal Component Analysis (a multivariate approach) showed that the main effect in the first principal component remained due to treatment effects after batch correction.

Differential expression analysis

Differentially expressed probesets were identified across conditions using linear models for microarray data (LIMMA; Smyth, G. K. (2004)), a standard R Bioconductor package. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3) . To compare GA and purported generic, comparisons were corrected to compare each treatment relative to mannitol control (e.g., [GA vs mannitol] was compared via LIMMA to [Polimunol vs mannitol]). Probesets were filtered by MAS5 calls of presence on the chip (to be considered present, a probeset was required to have on average a call of present or marginal across samples) . Probesets were mapped to genes using the annotation available for the Mouse 430 2 chip from Affymetrix. Unless otherwise noted, FDR adjusted p values reported for genes represent the lowest FDR adjusted p value for present probesets for that gene. Pathway enrichment analysis

Upregulated and downregulated probesets were analyzed separately for pathway enrichment, using DAVID (Huang et al, Nucleic Acids Res 2009) . Pathway enrichment results were visualized using volcano plots, plotting either -log adjusted p values or untransformed adjusted p values versus enrichment scores for the pathways. For comparisons between branded GA and Polimunol, upregulated or downregulated probesets with FDR-adjusted p values < 0.05 and fold changes (FC) with absolute value greater than 1.2 were used for pathway enrichment. For comparisons between branded GA and mannitol, upregulated or downregulated probesets with FDR-adjusted p values < 0.05 and FC with absolute value greater than 2 were used for pathway enrichment. DAVID runs were conducted in December 2014 and January 2015. Human Monocyte Cell Line: Gene Expression Analysis

THP-1 human monocytes (TIB-202) were purchased from ATCC®. Cells were maintained in recommended RPMI-1640 media containing FCS, L-Glutamine, Sodium Pyruvate, D-Glucose, HEPES, and 2-mercaptoethanol at 37 °C and 5% C02. Prior to treatment cells were passed and plated in a 6-well plate at a concentration of 1.0 x 10 ⁶ cells/mL. Cells were allowed to recover for four hours after passage (prior to treatment) . Using a predetermined non toxic concentration the cells were spiked with 50 g/mL of either Copaxone ^® , GA/RS, Escadra, Probioglat, and Natco, and 100μg/mL mannitol was spiked as a negative control (vehicle) . Each sample was analyzed in six replicates. Cells were treated for 6, 12, and 24 hours. Following treatment time cells were lysed using a Qiagen® based lysis kit. Prior to RNA isolation samples were randomized in order to avoid batch effect. Total RNA was isolated using Qiagen® RNeasy kit. RNA quality was assessed by determining the absorbance ratio 260/280nm as well as electrophoresis bioanalyzer with 260/280 ratio of 1.9-2.1 and RIN of above 9 were deemed acceptable. Gene expression was measured using Affymetrix® U133 plus 2.0 format. Sample processing was executed according to established manufacturer protocols. The scheme in (Fig. 2) illustrates the general experimental outline. W

92

Human Monocyte Cell Line: RNA Isolation and Microarray Expression

Profiling

RNA from THP-1 cells was extracted and expression profiled across the entire genome using the Affymetrix Human Genome U133 Plus 2.0 chip, interrogating a total of over 47,000 transcripts. Four batches of Copaxone ^® and one batch of Probioglat were comparatively tested in six biological replicates each. Key identified genes were independently evaluated for level of gene expression by quantitative Real-Time PCR of samples collected in the same experiments.

Methods for studies using MS patient data

Patient studies utilized a subset of MS patients treated with Copaxone ^® from FORTE clinical trial with time-series PBMC expression profiling. Timepoints of 0, 1, 2, 3 months were used. The study included 9 patients for a total of 36 samples.

Repeated-measures ANOVA

ANOVA was run taking into account multiple timepoints from each patient. Variability within patients across timepoints was taken into account in the p value calculation. qRT-PCR analysis

Key genes identified by differential expression analysis were assayed using qRT-PCR. RNA was utilized from each of 6 biological samples for each treatment (Copaxone ^® and Probioglat) and 15 technical replicates were performed for each sample (a total of 90 observations per transcript per treatment) . Since three Copaxone ^® batches and one Probioglat batch were available, a total of 360 observations from each transcript were evaluated. To evaluate the data, the 2 ^~AACt approximation was utilized with GAPDH as reference transcript and vehicle control (mannitol) as calibrator. A one-sided t-test with unequal variance was used to compare the RNA expression from the two treatments . Human Monocyte Cell Line: Gene Expression Analysis - Polimunol versus Copaxone ^® Gene Expression Studies

Experimental design

Cells from a human monocyte cell line (THP-1) were stimulated with either branded glatiramer acetate - Copaxone ^® , or the purported generic Polimunol, or vehicle control (mannitol) for 6 hours. RNA was extracted and expression profiled in a blinded fashion across the entire genome, using the Affymetrix Human Genome U133 Plus 2.0 chip, interrogating a total of over 47,000 transcripts. Three lots of Copaxone ^® (148, 164, 166) and one lot of Polimunol (XBN) were comparatively tested in six replicates each. This entire experiment was performed independently twice, using an identical study design, reagents and compounds by the same technicians on two separate days; resulting in twelve replicates total per condition.

A priori power analysis

Using the R statistical package ssize.fdr, power calculations were performed to determine the number of samples needed to detect differentially expressed genes with a fold-change between treatments of as low as 1.3 with 80% power. Based on the results of these power calculations, the experiment was designed to include six replicates of each condition. The order in which the samples were processed was randomized with respect to treatment and stimulation time in order to avoid creating confounding batch effects.

Outlier identification and normalization

Outlier samples were identified using the R package ArrayQCMetrics and excluded from further data processing .steps. A sample was considered an outlier if it failed more than half of the included tests either before or after R A normalization. Data were RMA normalized using the Affy R package.

Batch correction

Correction for batch variation was performed using ComBat (Johnson et al, Biostat, 2007) , as implemented in the SVA R package (Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD (2013) sva : Surrogate W

Variable Analysis. Available: www .bioconductor . org/packages/release/bioc/html/sva . html) . Briefly, ComBat is an empirical Bayesian approach utilizing location and scale metrics across several genes to adjust for batch effects in datasets, even datasets containing small sample sizes. Date of experiment was utilized as batch. Treatment labels were added as covariates to the batch correction in order to preserve relevant treatment effects. Principal Component Analysis (a multivariate approach) showed that the main effect in the first principal component remained due to treatment effects after batch correction.

Treatment labels were added as covariates to the batch correction to preserve relevant treatment effects . Principal Component Analysis showed the main effect in PCI remained due to treatment effects after batch correction (Figure 43) .

Differential expression analysis

Differentially expressed probesets were identified across conditions using linear models for microarray data (LIMMA; Smyth, G. . (2004) ) , a standard R Bioconductor package. Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3, No. 1, Article 3) . To compare Copaxone ^® and a purported generic, comparisons were corrected to compare each treatment relative to mannitol control (e.g., [GA vs mannitol] was compared via LIMMA to [purported generic vs mannitol] ) . For use in pathway analyses, probesets were filtered by MASS calls of presence on the chip for the relevant samples in the comparison (e.g., to be considered present, a probeset was required to have on average a call of present or marginal across samples) . An additional QC step was performed to remove probesets determined to be highly variable between multiple THP-1 datasets, as follows: a probeset was deemed highly variable if across three THP-1 studies to date, that probeset was observed to be upregulated, downregulated, and not modulated by Copaxone ^® across the three studies. This criterion resulted in filtering out 216 probesets. Probesets were mapped to genes using the annotation available for the U133 Plus 2.0 chip from Affymetrix. FDR adjusted p values reported for genes represent the lowest FDR adjusted p value for present probesets for that gene.

Pathway enrichment analysis

Upregulated and downregulated probesets were analyzed separately for pathway enrichment, using DAVID (Huang et al, Nucleic Acids Res 2009) . Pathway enrichment results were visualized using volcano plots, plotting -log p values versus enrichment scores. For comparisons between Copaxone ^® and Polimunol, upregulated or downregulated probesets with FDR-adjusted p values < 0.05 and fold changes (FC) with absolute value greater than 1.1 were used for pathway enrichment. For comparisons between Copaxone ^® and mannitol, upregulated or downregulated probesets with FDR-adjusted p values < 0.05 and FC with absolute value greater than 1.3 were used for pathway enrichment. DAVID runs were conducted December 5 and 10, 2014.

Protein Concentrations

THP-1 cells were activated with GA or Probioglat as described above. The supernatant (1.0 mL of cell culture media) was collected at the 24 hour timepoint (to account for the time duration required for translation relative to the 6 hour mRNA data reported herein) .

A Luminex assay was utilized to measure the concentrations of a panel of 45 chemokines and cytokines (in pg/ml) using Bio-Plex Human Chemokine (Bio Rad kit) and Luminex Performance Assay (R&D kit) . Three of the genes that were found to significantly differ between GA and Probioglat by qRT-PCR [CXCLIO, MMP9, and CCL5/RANTES) had corresponding proteins present in the Luminex panel. In addition, two other genes that were found to differ significantly between GA and Probioglat using the genome-wide microarray mRNA data were also present in the Luminex panel (CCL2, IL10) .

To calculate the fold change between the protein expression levels with Probioglat and with GA, the values for the four GA batches were averaged together and compared to the value for Probioglat (Probioglat expression level/ average GA expression level) . Primary Human Monocyte Study

50 mL of blood was obtained from a healthy donor, and CD14+ cells were separated from whole blood using magnetic beads (Miltenyi Biotech) . Purity was determined by FACS analysis using the following antibodies: CD14, CD15, CD16, CD45 (BD Biosciences) . Into each plate of the 6 well plate 0.5mL containing l.OxlO ⁶ cells was added. In addition 0.5mL of either Copaxone, Probioglat (100 g/mL) or mannitol (200 g/mL) was added, total volume in each well was lmL. Final concentration of Copaxone and Probioglat was 50pg/mL and mannitol final concentration was lOOpg/mL. Cells were incubated for 6 hours at 37 °C at 5% CO2 followed by centrifugation to pellet the cells. The cell pellets were then processed using a Qiagen RNeasy RNA purification protocol.

Expression levels of nine genes were measured using RT-PCR with GAPDH as reference transcript. Analyses reported compared Probioglat samples to GA samples as calibrator. Similar results were obtained when using mannitol as reference (i.e., the same set of genes were significantly upregulated in Probioglat relative to Copaxone) . Differences in expression levels were evaluated for significance using one-sided t- tests with unequal variance.

Example 1

Analysis of Time-sensitive Modulation of Genes by Copaxone ^® Treatment in THP-1 monocyte cell line

Three time points were tested to identify the time point reflecting the greatest impact of treatment in each model system. Examining the number of genes modulated by Copaxone ^® relative to the mannitol control, the 6 hour time point demonstrated the largest number of genes significantly modulated by Copaxone ^® (6,890 with an FDR-adjusted p < 0.05), over 2-fold more than at 12 hours (3,118 with FDR-adjusted p < 0.05) and nearly 4-fold more than at 24 hours (1,791 with FDR- adjusted p < 0.05) (Table 1). Subsequent analyses focused on the 6 hour time point, as the time point reflected the greatest impact of treatment in this model system. Table 1. Numbers of genes significantly modulated by GA treatment in THP-1 monocyte cell line at each timepoint

* FC - Fold Change; FDR - False Discovery Rate correction GA mechanism of action

To gain insight into GA' s MOA, the effect of GA treatment on THP-1 human monocytes was examined, since as discussed above, antigen- presenting cells in general, including monocytes in particular, have been shown to be involved in GA treatment effects (Weber et al . , Nat. Med. 2007; Kim et al, J. Immunol. Batim. Md. 2004; Burger et al., Proc. Natl. Acad. Sci. 2009; Smyth, Stat. Appl. Genet. Mol. Biol. 2004; Comi et al., Neurol. Bare. Spain 2002). In particular, the THP- 1 cell line has been used to examine GA effects (Rizvi et al., Int. J. Nanomedicine, 2006) . In addition, genes associated with monocytes in particular have previously been shown to be differentially expressed following treatment with a purported generic marketed by Natco in India, as compared with Copaxone (Huang et al . , Nucleic Acids Res. 2009) . mRNA expression levels were compared between GA and control (mannitol) tested with 6 sample replicates for each of 4 batches of GA and for mannitol, using LIMMA (Sim et al., Nat. Biotechnol . 2011) (Methods). Many genes were modulated significantly (FDR-adjusted p-value<0.05 ) at each timepoint by treatment with branded GA (Table 1; Table 2 lists top modulated probesets) . For example, at 6 hours of GA treatment, 2824 genes were significantly increased in expression (here termed upregulated) by FDR-adjusted p-value<0.05 (3511 genes by nominal p- value<0.05) and 4066 genes were significantly decreased in expression (here termed downregulated) by FDR-adjusted p-value<0.05 (4909 genes by nominal p-value<0.05 ) . Fewer genes were significantly modulated as treatment time increased, with approximately half as many modulated at 12 hours, and approximately one-quarter at 24 hours (Table 1) . We chose 6h for initial downstream analysis since this timepoint reflects the greatest impact of treatment. Levels of GA persisted in the cell culture medium in the range of 44-52 pg/mL over 24 hours (Figure 3) , indicates that this observation is unlikely to reflect a decrease in concentration of drug. Rather, this decrease in number of genes affected from early to later timepoints represents an attribute of the response of the cells to the drug.

GA impacts expression most pronouncedly at 6h (Table 2) . The use of this early timepoint may also be biologically relevant given that GA is thought to be rapidly degraded at the injection site, eventually without measurable blood levels (Vieira et al., J. Immunol. Baltim. Md 1950, 2003; Thamilarasan et al., J. Neuroinflammation 2013; Comi et al, Neurol 2002, Rizvi et al, Int J Nanomed 2006) . The differentially expressed genes included several anti-inflammatory genes. For instance, IL10, the gene encoding the anti-inflammatory cytokine IL-10, was increased in expression (upregulated) at the 6 hour timepoint (FDR adjusted p value 3.1e-9 fold change (FC) 1.52; Fig. 4a). Expression of IL1RN, encoding IL-lra, a protein that inhibits the activities of the pro-inflammatory cytokines IL-la and IL-lb, was increased (upregulated) at all three timepoints. Fig. 4b- d shows the 6h timepoint for all present probesets (FDR adjusted p values 6.7e-16, 1.7e-10, and 1.2e-9, and FC 1.43, 1.35, and 1.26, respectively) .

To determine whether the differentially-expressed genes related to one another in a coordinated fashion, top significantly up- and down- regulated genes were examined for pathway enrichment using DAVID as described in Methods (Figure 5; Table 5) . The top genes significantly upregulated by Copaxone ^® in the human THP-1 cell line at 6 hours of treatment were enriched significantly (by Benjamini corrected p value < 0.05) for 114 pathways (Table 5), including many immune-related pathways (Figure 5) . For example, the regulation of immune system process (GO : 0002682 ) and cytokine-cytokine receptor interaction (hsa04060) pathways were both significantly enriched among the top upregulated genes. The top upregulated genes identified as members of the cytokine-cytokine receptor interaction pathway (hsa04060) are shown in Figure 6. In addition, 9 pathways were significantly enriched among genes downregulated by GA (Table 5) .

Table 2. Human monocyte study : probesets significantly modulated by Copaxone ^® relative to mannitol at 6 hours, subject to fold-change and adjusted p value filters of 1.5 and le-5

Upregulated:

ID Gene raw.FC AveExpr P.Value adj.P.Vail

214054_at D0 2 1.67191836 12.2431311 8.80E-24 1.20E-20

228937 at C130RF31 2.42816683 9.90878354 9.66E-24 1.29E-20

211676 s at IFMGRl 1.64276331 12.0995889 1.08E-23 1.41E-20

230966_at IL4I1 3.68319718 10.6065738 1.1SE-23 150E-20

208816_x_at ANXA2P2 1.61606927 11.6007732 1 3E-23 1.66E-20

204912 at IL10RA 1,88097974 10.4596073 1.53E-23 1.83 E-20

220014_at LOC51334 3.95258058 6.49298277 1 4E-23 1.83 E-20

21S856_at TNFRSF21 1.97277863 11.9973199 2.06E-23 2.40E-20

34210 at CD52 1.74841624 11.3194919 2.57E-23 2.92E-20

211564 s at PDL1 4 2.13518707 9.68326105 2.72E-23 3.03 E-20

223502_s_at TNFSF13B 1.73530598 10.5512407 2.94E-23 3.21E-20

202727 s at [FNGR1 1.5463282 12.4669611 3.25E-23 3.48E-20

201243 s at ATP1B1 2.26738679 11.039008 4.33E-23 4.56E-20

209606 at PSCDBP 2.53767762 8.05776375 4.93E-23 5.08E-20

222670_s_at AF8 2.65652588 11.7521547 6.27E-23 6.35 E-20

223394 at SEHTAD1 1.65031524 9.76915308 6.91E-23 6.87E-20

214175 x at PDUM4 1.85137891 9.80931564 8.66E-23 8.45 E-20

223660 at ADORA3 1.89720977 9.3830598 9.01E-23 8.64E-20

203217 s at ST3GAL5 1.78903169 9.10901818 1-17E-22 1.11E-19

204257 at FADS3 1.78672893 9.74459459 1.23E-22 1.14E-19

223398 at C90RF89 134418891 11.0771528 1.25E-22 1.14E-19

211986_at AHNAK 1.64967948 12.0209047 1.63E-22 1.45 E-19

201278 at DAB2 136823308 9.36397364 1.64E-22 1.45E-19

229797 at COIN3 2.09980647 10.05113 2.01E-22 1.75 E-19

2Q2284_s_at CDKN1A 1.789083 11.1500265 2.69E-22 2.22 E-19

228579_at — 1.73158064 S.85Q26747 3.40E-22 2.78E-19

204653 at TFAP2A 1.98518712 8.32878609 5.70E-22 4.39E-19

201952 at ALCAM 132577304 12.9059918 6.14E-22 4.66E-19

202087_s_at CTSL 1.91284953 11.1924209 5.47E-22 4.84E-19

208978 at CRIP2 1.99640335 10.1060568 6.82E-22 5.04E-19

219434 at TREMl 1.77683605 11.1148543 6.95E-22 5.07E-19

235911_at MFI2 1.81455525 10.1578351 7.75E-22 5.57E-19

225173_at ARHGAP18 1.S5956949 10.0159515 7.35E-22 5.65 E-19

204661 at CD52 1.6752998 11.8608631 9.08E-22 6.2SE-19

202756 s at GPC1 1.88792383 8.93231998 9.08E-22 6.2SE-19

227240_at MGEF 1.97393626 9.35225393 9.96E-22 6.66E-19

220484 at MC0LN3 2.10889009 9.93061659 9.9SE-22 6.66E-19 14297 at CSPG4 1.98668454 8.74794884 9.99E-22 6.66E-19

203355 s at PSD3 1.68707305 9.97354098 1.13E-21 7.47E-19

21238S_at — L80977269 8.4443852 3L22E-21 7.91E-19

201242 s at ATP1B1 2.36020561 10.833866 1.62E-21 1.03 E-18

203760 s at SLA 1.76467647 10.2984296 1.71E-21 1.07 E-18

ID Gene raw FC AveExpr P.VaJue adj.P.Vai

204475_at MMP1 4.89045646 6.14908101 1.97E-21 1.21E-18

228964_at PRDM1 2.42316104 9.16116313 2.05E-21 1.24E-18

205566 at ABHD2 1.61609464 936280738 2.12E-21 1.27E-18

224990 at LOC201895 1.75486717 9.56572435 2.15E-21 1.28E-18

214830_at SLC3SA6 1.70065597 9.60777602 2.38E-21 1.38E-18

222876_s_at CENTA2 1.62337809 932111995 3.45E-21 1.92E-18

218501 at ARHGEF3 1.72054917 9.02047119 3.66E-21 2.02E-18

206134_at ADAMDEC1 1.90734854 8.46538539 3JB3E-21 2.10E-18

219385_at S A FS 2.3601545 8.87175449 4.64E-21 2.49E-18

212298 at NRP1 2.26706147 9.0154209 5.27E-21 2.77E-18

1556314_a_at — 1 4563197 9.96244884 5.97E-21 3.05E-18

204834_at FGL2 2.41220628 9.04212862 7.43E-21 3.63E-1S

227052 at — 1.7292497 9.65138189 8.49E-21 4.11E-18

223501 at — 1.77755998 10.4775991 938E-21 439E-18

238669_at PTGSl 1.79526928 9.00713066 1.52E-20 7.11E-18

203936_s_at MP9 1.83742157 934268719 2.01E-20 9.33E-18

205128 x at PTGSl 13Q682893 10.8982825 2.46E-20 1.12E-17

223019_at C90RF88 1.71440506 9.42451447 2.48E-20 1.12E-17

218223_s_at PLfKHOl 1.76062083 9.13759715 235E-20 1.14E-17

226545 at CD109 2.22747108 10.1210564 2.62E-20 1.17E-17

37145 at GNLY 2.52474166 7.62618078 2.77E-20 1.21E-17

211561_x_at PTAFR 1.65459655 9.40348625 3.20E-2Q 1.39E-17

223434_at GBP3 1.79281477 8.94069901 5.65E-20 2.39E-17

221011 s at LBH /// LOC653743 2.14546482 7.91354368 6.67E-20 2.79E-17

22747S_at LOC2S4262 2.55523487 8.16720299 737E-20 3.09E-17

205933 at SETBPl 2.06852059 8.31470678 9.65E-20 3.S8E-17

223126_s_at C10RF21 2.Q098249 9.34926366 l.QQE-19 3.99E-17

214255 at ATP10A 1.87404352 8.48741153 1.17E-19 4.64E-17

203888 at THBD 1.74251135 12.1003768 1.32E-19 5.18E-17

239761_at GC T1 1.60737016 9.89061934 1.78E-19 6.90E-17

205505 at GCNT1 1.63341734 9.51667582 1.80E-19 6.93E-17

203665 at HM0X1 2.77855009 12.0276078 1.83E-19 7.00E-17

228490 at ABHD2 1.7612845 9.44137483 1-92E-19 7.27E-17

213428_s_at COLSAl 1.6365876 9.11385826 2.21E-19 8.27E-17

202748 at GBP2 2.05214857 8.5030424 2.71E-19 l.OlE-16

63825 at ABHD2 1.60237791 9.12592031 333E-19 1.2SE-16

205542_at STEAP1 1.7513289 7.91561507 4.15E-19 1.49E-16

215813 s at PTGSl 131668643 10.9189252 4.31E-19 133E-16

205891 at ADORA2B 156662939 10.2505629 4.70E-19 1.66E-16

218613 at LOC653754 1.55398123 9.29556045 4.95E-19 1.73 E-l 6

205076_s_at T R11 3.59326395 11.2341764 5.05E-19 1.76E-16

212086 x at IMNA 1.50357006 12.1481348 5.14E-19 1.78E-16

ID Gene raw.FC AveExpr P.Value adj.P.Val

203104_at CSF1R 1.64383545 11.9446038 5.33E-19 1.83E-16

228368 at ARHGAP20 2.23117651 8.70S47261 5.37E-19 1.84E-16

227889 at AYTU 1.59282395 10.8879284 5.43E-19 1.84E-16

203797 at VSNL1 1.7523632 9.20419419 5.45E-19 1.84E-16

210145 at PLA2G4A 1.69920287 9.86166848 5.50E-19 1.84E-16

220307 at CD244 1.51030196 11.2887381 6.64E-19 2.20E-16

201280_s_at DAB2 1.6207775 8.250618 7.03E-19 2.30E-16

205898_at CX3CR1 1.5834422 12.3392251 7.53E-19 2.45E-16

212171_x_at VEGF 1.67886192 11.082533 8.08E-19 2.61E-16

205419 at EB12 1.87963971 10.3117587 8.24E-19 2.64E-16

242794 at A L3 1.71070972 8.2000023 S.71E-19 2.76E-16

1553141 at C130RF31 2.23957531 8.21534882 9.28E-19 2.90E-16

1556034_s_at MTMR11 1.54656669 10.734173 9.32E-19 2.90E-16

202436 s at CYP1B1 2.02551623 11.7446834 1.35E-18 4.08E-16

205718_at 1TGB7 1.61859456 10.0388412 1.64E-18 4.92E-16

222062_at 1L27RA 1.84145262 8.80213383 1.77E-18 5.26E-16

1565752_at FGD2 2.03973925 8.7032554 l.SOE-18 5.32E-16

203140_at BCL6 1.6321005 9.84693758 1.88E-18 5.54E-16

209568 s at RGL1 1.79068455 9.03375054 X04E-18 5.92E-16

212977 at CXCR7 1.95857569 9.06724SQ6 273E-18 7.74E-16

225809 at D FZP564O0823 2.61498482 6.81686881 3.21E-18 8.90E-16

223723 at MR2 1.33918768 7.73004392 3.45E-18 9.49E-16

204I41_at ^" FUBB2A 1.92837874 7.9645182 3.55E-18 9.72E-16

219358_s_at CENTA2 1.61743685 10.3689956 3.67E-18 9.97E-16

218280_x_at HIST2H2AA /// LOC653610 /// H2A/R 1.92645343 11.1017962 3.91E-18 1.G5E-15

200S84_at C B 1.62119168 10.3585418 3.91E-18 1.Q5E-15

213265_at PGA5 /// LOC643834 /// LOC643847 1.54256466 9.03735387 4.18E-18 1.12E-15

228499 at PF FB4 1.54265427 8.78361163 4.58E-18 1.22E-15

214581_x_at TNFRSF21 1.96726151 10.3862452 5.13E-18 1.35E-15

219256_s_at SH3TC1 1.81211933 8.14371592 5.59E-18 1.46E-15

227134 at SYTU 1.63431503 10.2085878 5.74E-18 1.50E-15

210512 s at VEGF 1.61269337 12.1528461 5.88E-18 1.52E-15

220066 at CARD15 1.63208119 8.81134661 6.12E-18 1.58E-15

207610 s at EM 2 1.96904599 7.45239164 6.31E-18 1.62E-15

225337 at ABHD2 1.52226303 10.585684 6.47E-18 1.65E-15

1553906 s at FGD2 1.56817402 11.6738144 8J5E-18 2.05E-15

210757_x_at DAB2 1.51596174 9.71603785 8.84E-18 2.22E-15

205306_x_at O 1.52538689 9.01246744 1.07E-17 2.64E-15

203980 at FABP4 2.44504844 7.91709543 1.14E-17 2.81E-15

205798 at 1L7R 2.15224639 6.90018766 1.20E-17 2.94E-15

235299_at — 2.92455443 6.38887226 1.23E-17 2.99E-15

201422 at IF130 1.53617841 1X1952 1.33E-17 3.23E-15

ID Gene raw.FC AveExpr P.Value adj.P.Val

201951_at A LCA 1.56151412 11.2835886 1.36E-17 3.29E-15

219412 at RAB38 1.69022517 7.7984244 1.40E-17 3.36E-1S

214290_s_at HIST2H2AA /// LOC653610 /// H2A/R 1.8793137 12.5116024 1.77E-17 4.19E-15

223Q92_at AN H 1.74621066 9.31182429 1.93E-17 4.53E-15

1552553_a_at CARD12 1.8300836 8.04038883 1.98E-17 4.61E-15

1565754 x at FGD2 2.05302245 &76658914 1.98E-17 4.61E-15

1562475 at 0KFZP686O1327 1.84932663 8.38987825 2.25E-17 5.18E-15

202435 s at CYPIBI 1.96043252 11.8853309 2.26E-17 5.18E-15

222877 at NRP2 2.43002847 6.1162318 2.37E-17 5.41E-15

201125_s_at iTGB5 1.55447321 9.61610321 2.48E-17 5.62E-15

204222_s_at GUPR1 1.64989211 10.4691144 3.30E-17 7.31E-15

1553142_at C130RF31 2.72312753 7.05894587 3.42E-17 7.51E-15

201279_s_at DAB2 1.51128632 9.36621678 3.53E-17 7.64E-15

203234 at UPP1 1.74387737 9.56780561 3.97E-17 832E-15

226136 at — 1.5023264 9.021618 4.37E-17 9.27E-15

206206 at CD180 1.61188665 9.82309399 6.95E-17 1.43E-14

212387 at — 1.62401877 7.80816226 1.05E-16 2.07E-14

204268 at S100A2 1.79310512 8.64238178 1.22E-16 2.38E-14

209122 at ADFP 1.6147S632 13.4092966 1.23E-16 2.41E-14

219994_at APBBliP 1.87740546 9.6208094 1.42E-16 2.74E-14

210095_s_at IGFBP3 2.98798358 8.63072598 1.43E-16 2.74E-14

227948 at FGD4 1.62553487 7.73111329 JL54E-16 2.92E-14

243483 at TRPM8 2.13837999 7.16652124 1.62E-16 3.04E-14

212062 at ATP9A 2.12S8S023 730745486 1.77E-16 3.29E-14

218502 s at TRPS1 1.61387671 8.89822927 1.95E-16 3.60E-14

213891 s at — 1.67207935 830917084 2.03E-16 3.68E-14

200878 at EPASl 1.51714595 9.20362299 2.04E-16 3.69E-14

201565_s_at ID2 1.52829092 12.7810873 2.26E-16 4.06E-14

212190_at SERPINE2 1.92452066 9.90116936 2.57E-16 4.60E-14

224480 s at LPAAT-THETA 1.96245654 8.74709429 2.64E-16 4.67E-14

220333 at PAQR5 3.58344803 7.84174393 2.70E-16 4.76E-14

218589 at P2RY5 1.65149795 9.3651465 3.Q0E-16 5.23E-14

225166 at ARHGAP18 1.75622288 733398136 3.29E-16 5.64E-14

226066 at MiTF 1.750697 7.87439597 3.35E-16 5.73E-14

221211_s_at C210RF7 2.0S949444 5.978895 3.41E-16 5.80E-14

225842_at PHLDA1 2.51724542 8.55236084 3.48E-16 5.89E-14

1554992_at RASGRF1 1.56735654 6.94135257 3.77E-16 6.35E-14

225097 at HIP 2 1.50753986 10.7130384 3.84E-16 6.45E-14

212464 s at FN1 1.70809888 9.26484812 4.53E-16 7.53E-14

240076 at — 1.5987436 8.40204375 4.66E-16 7.73E-14

203798_s_at VSNL1 1.91644457 7.87623259 4.84E-16 7.92E-14

204575 5 at MMP19 /// LOC652543 1.83367508 7.70439226 4.88E-16 7.96E-14

ID Gene raw.FC AveExpr P.Value adj-P.Val

204465_s_at INA 1.60147629 8.20221976 5.17E-16 8.36E-14

201566 x at 1D2/// ID2B 1.57371123 10.7833858 5.52E-16 8.87E-14

230360 at GLDN 1.98086959 6.74193069 6.80E-16 1.07E-13

222146 s at TCF4 1.54556332 7.51472351 8,25E-16 1.28E-13

224341_x_at TLR4 1.7396424 8.97197657 8.61E-16 1.32E-13

219637 at ARMC9 1.80286893 7.06720581 8.87E-16 1.35E-13

211138_s_at KMO 1.54711526 8.79132849 9.12E-16 1.38E-13

202437_s_at CYP1B1 1.80921395 12.1893518 9.54E-16 1.43E-13

235458_at HAVCR2 2.48536941 7.7122454 9.75E-16 1.46E-13

203922_s_at CYB8 1.58449815 10.3814577 1.07E-15 1.58E-13

212143 s at 1GFBP3 2.76854721 7.92968375 1.26E-15 1.82E-13

227716 at USXD5 1.51942114 9.002862 1.28E-15 1.83E-13

214211 at FTH1 1.55999567 12.4970466 1.33E-15 1.90E-13

229004 at — 1.51039984 9.12368109 1.55E-15 2.18E-13

202609_at EPS8 1.5924097 8.52061192 1.82E-15 2.52E-13

217757_at A2M 1.67532065 8.4520092 1.98E-15 2.73E-13

1552798_a_at TLR4 1.62695353 9.04302518 2.09E-15 2.88E-13

57715 at FA 26B 1.79873285 7.75582627 2.40E-15 3.27E-13

226282 at — 1.60485814 9.41013847 2.84E-15 3.80E-13

222S38 at SLAMF7 1.86121844 7.05728625 3.11E-15 4.13E-13

216442 x at FN1 1.69780521 10.1409361 3.73E-15 4.87E-13

201324 at EM PI 2.S2O50293 6.11305975 3.81E-15 4.94E-13

210264_at GPR35 1.59109619 9.60072153 3.91E-15 5.05E-13

222858_s_at DAPP1 1.6313133 10.6750257 4.54E-15 5.78E-13

209684 at RIM2 2.16288563 7.25953396 5.48E-15 6.84E-13

201069 at MMP2 1.51386957 8.69855532 6.09E-15 7.55E-13

204998 s at ATF5 1.63500149 10.6267979 ai4E-15 7.60E-13

202434 s at CYP1B1 2.2027314 9.83119314 6.94E-15 8.52E-13

205099_s_at CCR1 1.57264838 9.76018397 7.25E-15 8.85E-13

207233 s at MfTF 1.66865012 8.30250431 8.03E-15 9.72E-13

20S552_s_at OASl 1.79452532 7.29881386 a53E-15 1.02E-12

226550_at — 1.79237731 7.77105086 9.20E-15 1.09E-12

212096_s_at MTUS1 1.62315248 8.50418445 9.61E-15 1.13E-12

222651 s at TRPS1 1.5940306 10.0878238 9.64E-15 1.13E-12

211719_x_at FN1 1.74293625 10.1007312 9.80E-15 1.15E-12

227609 at EPSTll 1.73531372 7.62913716 1.06E-14 1.24E-12

15581Q5_a_at — 1.89855059 6.81046182 1.07E-14 1.25E-12

225207 at PD 4 2.24881528 8.76581849 1.08E-14 1.25E-12

237160_at CCDC83 2.26816884 5.8347316 1.15E-14 1.33E-12

211026_s_at GU. 1.80987658 8.99536888 1.33E-14 1.53E-12

229450 at — 2.07979683 630012377 L42E-14 1.62E-12

215602 at FGD2 2.01984347 7.85983935 1.54E-14 1.74E-12

ID Gene raw.FC AveExpr P.Value adj.P.Val

22870S_at RAB27B 1.75996236 8.57078526 1.63E-14 1.33E-12

210258 at GS13 2.4181722 5.066755O3 1.77E-14 1.97E-12

210895 S at CD86 1.74036933 7.80363779 1.88E-14 2.07E-12

223672 at SGIP1 1.58033388 8.69396513 1.96E-14 2.14E-12

210513 s at VEGF 1.62960752 9.66705476 2.08E-14 2.25E-12

212614 at ARI053 1.64330835 6.34592171 2.09E-14 2.26E-12

1553995_a_at NT5E 2.06345466 6.49987213 2.17E-14 2.32E-12

233540_s_at CD 5RAP2 1.77928193 10.6899414 2.34E-14 2.48E-12

204059_s_at E1 1.78078662 11.5066468 2.46E-14 2.58E-12

211527 x at VEGF 1.6S079685 9.90807927 2.48E-14 2.60E-12

214724 at DIXDCl L55892061 7.67060007 2.63E-14 2.74E-12

227556 at NME7 2.07486651 9.31851129 2.92E-14 3.02E-12

237442 at APBB11P 1.97657406 7.17373032 3.09E-14 3.18E-12

224218 s at TRPS1 1.52587932 8.16882094 3.38E-14 3.46E-12

225188_at RAPH1 1.90298066 6.31647013 3.68E-14 3.73E-12

244414_at A L2 2.39160043 8.05798482 3.70E-14 3.74E-12

209906_at C3AR1 1.62034968 8.32122922 3.73E-14 3.76E-12

210510 s at NRP1 1.56055098 7.3171434 3.77E-14 3.78E-12

226629 at SLC43A2 1.57641868 8-50211433 3.97E-14 3.94E-12

237030 at ACPP 1.53890938 8.05225501 4.15E-14 4.10E-12

213338 at TME 158 1.73773739 10.7585184 4.18E-14 4.13E-12

219926 at P0PDC3 2.12181972 6.63647483 5.99E-14 5.68E-12

200897_s_at PALLD 1.64882729 8.35346573 6.07E-14 5.74E-12

208436_s_at ! F7 1.55075885 8.74418094 6.34E-14 5.96E-12

228438 at T PA1 1.65933581 10.3950167 6.S1E-14 6.30E-12

227747 at — 1.55198677 7.93194342 6.84E-14 6.32E-12

1554867 a at LOC51334 1.86507425 7.40812044 6.90E-14 6.36E-12

1563445 x at CTSLL3 1.82851184 6.84405898 9.09E-14 8.12E-12

242903 at IFNGR1 1.767S462 7.97757472 9.49E-14 8.42E-12

229900 at CD109 1.54089288 8.62103824 1.05E-13 9.24E-12

210495_x_at FN1 1.61505134 10.0973935 1.Q7E-13 9.43E-12

218854_at SART2 1.54263807 8.36626559 3E-13 9.81E-12

224989 at — 1.78010467 7.75893731 1.17E-13 1.02E-11

238638 at SLC37A2 1.63842433 9.93438242 1.31E-13 1.13E-11

212382 at — 1.60505834 7.06996616 1.35E-13 1.15E-11

209047 at AOP1 2.44653569 7.84720827 1.38E-13 1.17E-11

236345 at TBXAS1 1.66860916 8.46774141 1.40E-13 1.18E-11

228873 at COL22A1 1.56093003 7.43196243 1.41E-13 1.19E-11

239519_at NRP1 2.19110297 5.55763801 1.43E-13 1.20E-11

220935_s_at CDK5RAP2 1.84541222 10.4100106 1.54E-13 1.28E-11

1560228_at SNAI3 1.91948596 7.S146015 1.56E-13 1.30E-11

218934 s at HSPB7 1.65040526 8.10534113 2.40E-13 1.90E-11

ID Gene ra .FC AveExpr P.Value adj.P.Val

210146_x_at ULBB2 U9982938 6.76423766 2.86E-13 2.22E-11

209348 s at MAF 1.56472875 8.72338323 3.17E-13 2.42E-11

1558569 at LOC645238 1.75050375 7.56283286 3.25E-13 2.47E-11

243856 at — 1.73115631 8.03640769 3.81E-13 2.86E-11

223798 at SLC41A2 1.94681117 634582797 3.90E-13 2.92E-11

215990 s at BCL6 1.50671943 8.04953142 4.81E-13 332E-11

202869 at QAS1 1.63942747 6.73520018 5.30E-13 3.86E-11

225631 at K1AA1706 1.53753899 7.78142994 536E-13 4.03E-11

20411S at I12RG 1.53970115 7.99806857 5.88E-13 4.22E-11

225189 s at RAPH1 1.85367315 6.14549622 6.27E-13 4.47E-11

PCDHGC3 /// PCDHGB4 /// PCDHGA8

/// PCDHGA12 /// PCDHGC5 ///

PCDHGC4/// PCDHGB7 /// PCDHGB6

/// PCDHG85 /// PCDHGB3 ///

211066_x_at PCDHGB2 /// PCDHGB1 /// 138678656 10.4111947 7.90E-13 5.53E-11

PCDHGA11 /// PCDHGA10 ///

PCDHGA9 // PCDHGA7 /// PCDHGA6

/// PCDHGA5 /// PCDHGA4 ///

PCDHGA3 /// PCDHGA2 /// PCDHGAl

221266 s at TM7SF4 1.83671444 6.22762311 8.02E-13 5.60E-11

1560485 at HIVEP1 1.6480621 6.99003908 8.06E-13 5.62E-11

204881 s at UGCG 1.5102382 931481557 8.38E-13 5.83E-11

235286 at CKLF 1.61741462 8.34288205 9.26E-13 6.36E-11

205003 at D0C 4 13112689 8.20388936 1.02E-12 6.92E-11

218686 s at RHBDF1 131723286 7.92482272 1.05E-12 7.08E-11

221565 s at FAM26B 139642371 7.91365407 1.09E-12 7.32E-11

206675_s_at S IL L61042514 7.42083013 1.16E-12 7.69E-11

242358 at — 2.20249712 6.04968315 1.24E-12 8.20E-11

241392_at TMEM39A 1.61384348 7.05009494 1.87E-12 1.19E-10

232333 at MAML2 1.68481156 8.01950459 2.06E-12 1.30E-1Q

228762_at LFNG 135190457 9.0403074 2.08E-12 1.31E-10

242907_at GBP2 2.14738965 6.03707956 2.72E-12 1.64E-10

203753 at TCF4 130293289 7.65442858 2.78E-12 1.68E-10

207542 s at AQP1 1.69421791 6.82177348 3.02E-12 1.81E-10

242157_at — 137383098 8.76647265 3-26E-12 1.94E-10

204058 at ME1 L.7342Q796 931508263 333E-12 2.08E-10

209921 at SLC7A11 1.94348494 9.29226579 3.63E-12 2.13E-10

211030 s at SLC6A6 131035569 737360907 3.78E-12 2.21E-10

209392 at ENPP2 1.82310668 5.23034508 4.76E-12 2.73E-10

243894 at SIX41A2 1.69547735 5.15085274 4.80E-12 2.75E-10

229937_x_at ULHB1 1.58545389 7.41501062 5.O0E-12 2.84E-10

21 857_at C10ORF95 1.60255368 7.13065345 5.02E-12 2.85E-10

230944 at MGC45491 135203348 7.47S87362 5.53E-12 3.14E-10

228057_at DDIT4L 1.68290143 9.61033195 6.99E-12 3.82E-1Q ID Gene raw.FC AveExpr P.Value adj.P.Val

204105_s_at NRCA 2.27634648 6.95288228 7.49E-12 4.07E-10

205581 at BCL2A1 1.64702983 9.50173198 8.19E-12 4.40E-10

242405 at AML2 1.86052011 7.15057318 1.10E-11 5.73E-10

217678 at SLC7A11 1.75913555 8.8692241 1.22E-11 6.25E-10

211962 s at ZFP36U 139912563 8.8232205 1.23E-11 6.27E-10

221060 s at TLR4 1.53812487 8.81340284 2.27E-11 1.08E-O9

200907 5 at PALLD 1.50739688 7.44132987 2.28E-11 1.08E-09

22S918 at SLC43A2 1.66364865 7_201S6Q79 2.29E-11 1.09E-O9

1555606 a at GDPD1 1.51121338 6.61034166 2.39E-11 1.13E-09

228450 at PLEKHA7 130941089 6.45253703 2.70E-U 1.26E-09

229221 at — 1.60263592 839003199 4.03E-11 1.79E-09

229635_at LOC643424 133074512 735215178 4.38E- 1.94E-09

1569149 at P0U 7 1.54849621 9.14969141 536E-11 2.41E-09

207433_at iUO 132400243 5.63708634 7.49E-U 3.14E-09

221815 at ABHD2 135904737 8.11542769 1.01E-10 4.08E-09

203060_s_at PAPSS2 1.5764103 7.75963014 1.25E-10 4.94E-09

232746 at CXCR7 2.0719893 634641126 1.43E-10 5.55E-09

1560960 at MDGA1 1.97885133 5-71541524 1.47E-10 5.70E-O9

234645 at MAM12 1.87005824 633786268 1.72E-10 6.50E-09

223596 at SLC12A6 130709112 732492551 1.75E-10 6.60E-09

87100 at ABHD2 131939681 7.38326685 1.79E-10 6.75E-09

213931 at 1D2 /// ID2B 2.71874933 9.84931953 1.87E-10 7.02E-09

216874 at DKFZP68601327 1.70886875 5.93467446 2.11E-10 7.76E-09

244375 at EVL 136523772 7.93537524 2.24E-10 8.16E-09

1569150 x at POU 7 134117409 9.37943359 2.24E-10 8.18E-09

214453 s at 1F144 1.79674041 6.65852583 2.78E-10 9.87E-09

2Q4999_s_at ATF5 L64452594 9.14215678 3.41E-10 1.18E-0a

PCDHGC3 /// PCDHGB4 /// PCDHGA8

/// PCDHGA12 /// PCDHGC5 ///

PCDHGC4 /// PCDHGB7 /// PCDHGB6

/// PCDHGB5 /// PCOHGB3 ///

215S36_s_at PCDHGB2 /// PCDHGBl /// 132441384 9.29079122 4.72E-10 1.60E-08

PCDHGA11 /// PCDHGA10 ///

PCDHGA9 /// PCDHGA7 /// PCDHGA6

/// PCDHGA5 /// PCDHGA4///

PCDHGA3 /// PCDHGA2 /// PCDHGAl

208161 s at ABCC3 1.61726316 8.40189868 5.05E-10 1.S9E-08

202827 s at MMP14 1.62314882 10.2030389 5.39E-10 1.78E-08

208712 at CCND1 13393933 7.40438263 6.16E-10 2.blE-0S

223939 at SUCNR1 1.57537424 8.40597144 7.17E-10 2.32E-08

205960 at PDK4 1.69465703 7.19094792 1.2SE-09 3.84E-08

214841 at CNIH3 136253317 6.14111085 1.40E-O9 4.15E-08

209993_at ABCB1 138407983 5.06880643 132E-09 4.48E-08 ID Gene raw.FC AveExpr P.Value adj.P.Val

1557938_s_at PTRF 1.50339198 6.8700736 1.62E-09 4.73E-08

232068_s_at TUR4 1.74396268 &76798691 1.84E-09 5.28E-08

242321 at — 1.6662739 652856887 2.12E-09 5.99E-08

219574 at ARCH1 1.64000788 5.55000344 3.S4E-09 9.43E-08

202638 s at ICAM1 158753294 6.72394157 3.76E-09 9.97E-08

219496 at AN D57 1.50970429 7.47583744 4.86E-09 1.26E-07

1555756 a at CLEC7A 1.65932872 7.0882743 5.25E-09 1.35E-07

241929_at CD36 1.82152709 SJ2014251 5.66E-09 1.44E-07

1556423 at VASH1 155220936 7.02874938 8.01E-O9 1.97E-07

229435 at GUS3 1.5824943 4.92660385 8.07E-09 1.98E-07

217997 at PHLDA1 2.01871208 7.37991533 8.18E-09 2.00E-07

235944_at HMCN1 151434592 7.331681 9.15E-09 2.21E-07

206637 at P2 Y14 1.69022854 4.58701985 9.57E-09 2.30E-O7

213293_s_at TRIM22 1.54165851 659931282 9.57E-09 2.30E-O7

238581_at GBP5 157383447 7.67594481 1.Q3E-08 2.46E-07

LOC644242 /// LQC650429 ///

1558404_at 1.85121181 531545142 1.46E-08 3.35E-07

LOC650446

230559 x at FGD4 151987215 5.45151267 1.69E-08 3.83E-07

1553151 at ATP6V0D2 152950999 6.78084809 1.69E-0S 3.84E-07

1554285 at HAVCR2 1.64907555 7.49492704 3.O0E-O8 5.38E-07

244579 at TRPSl 1.5354261 8.45494277 5.93E-08 1.16E-06

228640_at — 1.5809974 4.58101232 7 52E-08 1.43E-06

210004 at 0LR1 159400178 5.26939608 8.40E-08 158E-06

243556_at NGEF 150840974 a?3352627 1.18E-07 2.14E-06

210360 s at MTSS1 L7452905 6.18923946 1.40E-07 2.49E-06

217999_s_at PHLDA1 1.73310668 6.08679858 2.07E-O7 352E-06

227062_at T CRNA 1.56840333 10.0441571 2.1BE-07 3.69E-06

237904_at AD0 A3 152521897 6.15098521 2.49E-07 4.15E-06

1S63621 at KJAA1706 155572929 7.60284745 6.48E-07 9.74E-06

Downregutated:

ID Gene raw.FC AveBcpr P.Value adj.P.Vai

204521_at C120RF24 -13676281 10.1844282 3.88E-17 3.36E-15

20 301_at KBTBD11 -1.5574513 10.253905 4.37E-17 9.27E-15

227920 at KSAA1553 -1.6307063 8.01525239 5.17E-17 1.09E-14

218251 at MID1IP1 -1359714 9.78570246 5.29E-17 1.11E-14

212646 at RFTN1 -1.658315 837843565 5.38E-17 1.12E-14

222799 at HSPC049 -1.5489442 8.60085628 1.10E-16 2.17E-14

227103_s_at MGC2408 -1381709 8.7267591 1.30E-16 2.51E-14

206057_s_at WT1 -1311783 9.85618462 1.37E-16 2.66E-14

214369_s_at ASGRP2 -13808582 9.41805033 1.69E-16 3.15E-14

206589_at GF11 -13996464 11.7281473 L.99E-16 3.65E-14

225619_at SLAIN1 -2-2453889 7.41012008 2.01E-16 3.68E-14

212660_at PHF15 -1.69531 8.00752875 2.63E-16 4.66E-14

218971 s at HSPC049 -13087203 9.12721477 3.08E-16 5.33E-14

201690_s_at TPD52 -1.5492402 9.27038373 3.25E-16 5.59E-14

229638 at IRX3 -1.6570492 11.8844594 3.38E-16 5.76E-14

223062_s_at PSAT1 -1.556602 9.43823571 4.70E-16 7.77E-14

225510 at OAF -1.6632727 10.1142626 6.67E-16 1.05E-13

209485 s at OSBPUA -1.6049308 8.36910929 7.34E-16 1.15E-13

204432 at SOX12 -1.7584476 63781916 8.71E-16 1.33E-13

205758 s at SLC27A2 -1.6303006 7.59181394 8.98E-16 1.36E-13

211576 s at SLC19A1 -13339487 9.8247482 9.81E-16 1.46E-13

201688 s at TPD52 -1.6048433 8.65393713 9.93E-16 1.48E-13

50314 i at C20O F27 -1361172 9.67877203 1.14E-15 1.66E-13

1553436 at Μυα9 -1.64037 7.99717726 1.18E-15 1.71E-13

202800 at SLC1A3 -13176496 8.18097955 1.51E-15 2.13E-13

41037 at TEAD -1.6405647 631029525 1.70E-15 2.36E-13

216953_s_at wri -13276508 7.76890727 2.15E-15 2.95E-13

228055 at APSa -13385754 10.1648177 2.61E-15 3.52E-13

218424_s_at STEAP3 -1.7692882 7.83028032 2.78E-15 3.74E-13

212855 at DCUN1D4 -1.508562 7.88387861 2.92E-15 3.90E-13

202933_s_at YES1 -1.5437793 9.12374841 3.76E-15 4.89E-13

1553138_a_at AN RD41 -2.0146608 6.96935627 6.26E-15 7.73E-13

227242_s_at fBF3 -1.8363477 4.86769268 8.15E-15 9.84E-13

237265 at C160RF73 -13296704 9-74165113 9.6QE-15 1.13E-12

213478 at KIAA1026 -1.8330762 7.39399329 1.16E-14 1.34E-12

225081_s_at CDCA7L -1.5491727 10.2951966 1.46E-14 1.66E-12

211299 s at FLQT2 -1.6145204 9.10864173 1.5SE-14 1.79E-12

213568 at OSR2 -2.2462672 5.99962469 1.64E-14 1.83E-12

227662_at SY P02 -13973696 8.62811124 1.76E-14 1.96E-12

200998_s_at CKAP4 -1.6910951 9.77491302 2.08E-14 2.25E-12

209900 s at SIC16A1 -1.5885969 7.84437981 2.30E-14 2.43E-12

229084_at CNTN4 -1.6415136 7.72735571 2.30E-14 2.43E-12

238694 at — -13762461 7.26420148 3.38E-14 3.46E-12

1555788_a_at TH1B3 -1.5022329 9.92495817 3.64E-14 3.70E-12

221900 at COLSA2 -13627579 10.2358313 4.09E-14 4.05E-12

225016_at APCDD1 -1.6872345 6.47036912 4.21E-14 4.14E-12

10 Gene raw.FC Ave&cpr P.Val e adj.P.Val

225768_at NR1D2 -1.7351352 6.8044854 5.44E-14 5.24E-12

222095 s at C10SF76 -1.7301956 7.38672115 6.40E-14 6.00E-12

229103 at W T3 -1.7749895 535503782 7.97E-14 7.21E-12

205769 at SLC27A2 -1.7824201 7.67753108 133E-13 1.27E-11

201689 s at TPD52 -1.645479 8-12663653 1.59E-13 1.31E-11

201350 at FLOT2 -1.5079906 11.0344892 2.08E-13 1.68E-11

221648 s at C10RF121 -1.517313 8.36815023 2.55E-13 2.00E-11

208078 s at SNFILK -1397736 7.64505173 2.81E-13 2.18E-11

1562484 at FU35848 -1.9050209 6.65405977 3.15E-13 2.41E-11

1555370 a at CAMTA1 -1.7040191 6.36041757 3.26E-13 2.47E-11

218376 s at MICAU. -13055354 11.194367 3.44E-13 2.61E-U

204567_s_at ABCG1 -1.8330717 5.8226155 331E-13 2.66E-11

39966 at CSPG5 -1.5105172 7.68266153 4.12E-13 3.07E-11

218326_s_at LGR4 -1.696564 6.525917 5.28E-13 3.85E-11

212430 at B 38 -13884137 8.88476901 5.78E-13 4.17E-11

227236_at TSPAN2 -1.7695047 638434119 7.37E-13 5.19E-11

204794 at DUSP2 -1.5957268 8.45706393 7.96E-13 5.57E-11

230888 at HSPC049 -1377802 7.20584208 9.14E-13 6.29E-11

212097 at CAV1 -1.56.28831 739130877 9.63E-13 6.57E-H

209353 s at C1GRF76 -1.7131519 7.30778535 1.Q2E-12 6.92E-11

201801 s at SLC29A1 -1.5246973 8.73200853 1.05E-12 7.08E-11

210279 at GPR1S -13350315 8.98079125 1.29E-12 8.49E-11

52651 at COL8A2 -1377706 9.9516637 1.31E-12 8.57E-11

235758 at PNMA6A -13784572 7.86091427 1.34E-12 8.77E-11

222162 s at ADAMTS1 -1.8422S4 5.45805339 1.37E-12 8.95E-11

209369 at ANXA3 -1.7449323 534631362 1.41E-12 9.18E-11

219911_s_at SUC04A1 -13143987 8.17455361 1.50E-12 9.71E-11

1557919 a at LOC648232 -13028156 123466889 1.73E-12 1.11E-10

219497_s_at BCU1A -13825B53 9-14635109 1.85E-12 l.lSE-10

232271 at HNF4G -1.5978388 7.3715225 2.04E-12 1.29E-10

206653 at — -1.5611734 6.70426513 2.13E-12 1.33E-10

225782 at MSRB3 -13020089 8.17316381 2.54E-12 1.55E-10

223704 s at DMRT2 -1.6370445 6.61601092 5.67E-12 3.20E-10

1558613 at OAF -13776535 73183993 6.15E-12 3.44E-10

1555434 a at SLC39A14 -13483414 7J91388969 6.58E-12 3.65E-10

1556194 a at — -1.7264827 7.80933003 1.10E-U 5.73E-10

219304 s at PDGFD -1.5313053 8.14849618 1.10E-11 5.73E-10

200894 s at FKBP4 -1.6280907 8.06454238 1.28E-11 6.49E-10

210347 s at BCU1A -13419287 7.82101671 1.36E-U 6.85E-10

221249_s_at FAM117A -13920148 8.42643515 1.45E-11 7.21E-10

239410 at — -1321547 6.86497836 1.72E-11 8.46E-10

206039_at RAB33A -1.5487461 8.85562976 2.20E-11 1.05E-09

1554660 a at C10RF71 -13203911 7.61313106 2.54E- 1.19E-09

209776_s_at SLC19A1 -13451778 7.72495148 2.90E-11 1.34E-09

1560495 at — -1.5478409 7.28259363 3.01E-11 1.38E-09

!D Gene raw.FC AveExpr P.Value adj.P.Val

202234_s_at SLC16A1 -1.5891823 7.76240785 4.97E-11 2.16E-09

207768 at EGR4 -2-266679 5.08097601 7.18E-11 3.02E-09

207717 s at PKP2 -1.5155863 45970225 1.26E-10 4.97E-09

213912 at K1AA0984 -13617265 6.49154577 1.30E-10 5.13E-09

222S91 s at ftCtllA -15929549 8.42933212 2.00E-10 7.44E-09

213268 at CA TA1 -1.7460973 5.75010725 2.03E-10 7.52E-09

232007 at — -1.5199738 9.70608088 2.60E-10 9.33E-09

227099 s at LOC3S7763 -13087957 6.4279952 2.97E-10 1.05E-08

23261 at BCL2 -1.5221488 7.30276639 2.99E-10 1.05E-08

222668 at CTD15 -1.5400712 5.79509816 3.31E-1Q 1.15E-08

213610 s at KLHL23 -13730988 7.2326013 4.60E-10 156E-08

206935_at PCDH8 -1.6992238 5.66380311 6.65E-1Q 2.16E-08

203708 at PDE48 -1.5144333 7.44164625 8.10E-10 2.59E-08

1554298_a_at WD 49 -15642625 6.77053726 8.63E-1Q 2.73E-08

212558_at SPRY1 -1.6087624 5 5823849 1.41E-09 4.18E-08

242509_at C160RF74 -13318238 6.48465026 2.21E-09 6.20E-08

201939 at PI 2 -15317787 7.43694803 5.43E-09 1.39E-07

242245 at SYDE2 -13851454 4.93022084 5.57E-09 1.42E-07

204557 s at DZIP1 -13326546 5.01217049 5.85E-09 1.48E-07

204875 s at GMDS -1.7607496 633236847 9.81E-09 2.35E-07

204285 s at PMA1P1 -1.7424137 103563243 1.15E-08 2.73E-07

213006 at CEBPD -13902998 8.08295825 1.47E-08 3.38E-07

1554830_a_at STEAP3 -1.6156641 5.65856155 2.19E-08 4.84E-07

204286 s at PMAiPl -1.7353429 9.45448346 6.05E-0S 1.18E-Q6

228325 at 1AA0146 -L8819676 8.36526925 8.31E-0S 157E-06

1569377 at T EM67 -1.9524092 4.4888277 1.11E-07 2.04E-06

242892_at PER2 -2.1304461 637699912 L72E-G7 3.00E-06

1555847 a at LOC284454 -2.1798122 9.88866319 1.88E-07 3.24E-06

Discussion — Example 1

The significant gene-expression changes observed in the human THP-1 cell line due to treatment with branded GA included changes consistent with previous literature (as discussed below) , supporting the validity of the chosen model system and current study design for revealing relevant treatment effects. For example, expression of the anti-inflammatory gene IL10 was increased at the 6 hour timepoint, consistent with known GA mechanism with regard to monocytes (Kim et al. J. Immunol. Baltim. Md 1950, 2004; Weber et al . Nat. Med. 2007; Mahad et al. Brain J. Neurol. 2006) . GA is thought to induce an anti-inflammatory effect, mediated by secretion of IL-4, IL-10, and other anti inflammatory cytokines both in terms of T cells (Thl to Th2 shift) but also in terms of monocytes, resulting in a shift from monocyte production of IL-12 to anti-inflammatory IL-10. For example, monocytes from mice treated with GA secreted more IL-10 than monocytes from untreated mice (Weber, Nat Med 2007) , and monocytes isolated from MS patients treated with GA were shown to produce more IL-10 relative to untreated patients (Kim, J Immunol 2004) . In addition, dendritic cells exposed to GA during maturation increased their production of IL-10 (Mahad et al . Brain J. Neurol. 2006) .

Another anti-inflammatory gene, IL1RN (encodinglL-lra, a protein that inhibits the activities of IL-la and IL-lb) showed increased expression at all three timepoints . These observations are consistent with work showing that blood levels of soluble ILl-ra increase with GA treatment in patients with MS as well as EAE mice, and that soluble ILl-ra is upregulated by GA treatment in human monocytes either stimulated with LPS or activated by T cell contact (Burger et al, PNAS 2009) .

Branded GA significantly modulated many pathways (Table 5) . At 6h, pathways enriched significantly among upregulated genes included broad categories such as immune response and regulation of immune processes, and more specifically cytokine-cytokine receptor interactions. Other significantly enriched pathways included adhesion, and other pathways with broad relevance to the disease process and/or proposed action of GA. Several of these pathways were also significantly enriched among genes modulated by GA in monocytes from RRMS patients (Rosenberg, The Lancet 2005) .

Example 2

Differences in gene expression induced by Probioglat versus branded GA

To identify differences between branded GA and differently manufactured glatiramoids , differential gene expression analysis was performed to compare directly between profiles induced by branded GA and by the purported generic glatiramoid, Probioglat. The standard R LIMMA bioconductor package was utilized to measure differentially expressed probesets across the entire microarray. To compare GA and Probioglat, comparisons were corrected to compare each treatment relative to mannitol control (i.e., [GA vs mannitol] was compared via LIMMA to [Probioglat vs mannitol] ) . Probesets were filtered by calls of presence on the chip for the relevant samples in the comparison (to be considered present at a given timepoint, a probeset was required to have on average a call of present or marginal across the relevant samples at that timepoint) . Probesets were mapped to genes using the annotation available for the U133 Plus 2.0 chip from Affymetrix. FDR adjusted p values reported for genes represent the lowest FDR adjusted p value for present probesets for that gene.

Many significant differences were observed between GA and Probioiglat (Table 3) . As expected based on the more extensive response to GA at 6h, the most differences were observed at the 6h timepoint.

Table 3. Dynamic profiles of differentially expressed RNA after stimulation of THP-1 cells by Probioglat versus Copaxone ^®

Upregulated:

Total

modulated

(up- and

down- regulated):

Numbers of genes and pretests modulated by ftsbjoglgt relative to GA

(percent of probesets detected as significantly differentiated between treatments as percentage of the total 47,000 probesets included in the Affymetrix U133 Plus 2.0 chip)

See Table 4a for the full list of differentially-expressed probesets at 6h: 138 upregulated, 24 downregulated (126 upregulated, 22 downregulated after presence/absence filtering) . These differences included proinflammatory genes that were increased in expression by Probioglat relative to GA, including CCL5 , CCL2, MMP9, MMP1, CXCL10, CD14, ICAM1 and BIRC3 (all significant by FDR adjusted p value < 0.05) (Table 4a) . At the same time, differences were observed in levels of anti-inflammatory genes. Probioglat downregulated anti-inflammatory genes CISH and HSPD1 relative to GA, and upregulated IL10 and PRDMl relative to branded GA (all significant by FDR adjusted p value < 0.05).

Table 4a. Human monocyte study: pxobesets significantly modulated by Copaxone ^® relative to Probioglat

Comparing GA to ProlHogtat (mannrtol-corre ted):

Upnegulated:

6 hr

Gene IO raw.FC AveExpr t P. alue adj_P.val 8

MMP9 203936_5_at -1.2926295 9.63366142 -90041791 5.02E-11 2.74E-06 13.793663

CXCU.0 204533. .at -1.4567763 5.93611913 -6.8101441 4.11E-08 0.00056208 8.11662055

P DM1 228964. at -13131543 9.26923221 -6.9712916 2.48E-0B 0.00056208 3.55501455

LPX.N 216250. A_a* -1.1B74257 11315416 -6.8905168 3.19E-OB 0.00056208 8.33560319

FABP4 203980_at -13897081 8.03922119 -6.4609935 l_24E-07 0.00100306 7.15838496

— 240076. .at -1.2154985 8.47153306 -6.4502687 1.28E-07 0.00100306 7.12879005

COL6A1 213428. A_at -1.1799797 9.17734162 -6.5227006 1.02E-O7 O.0O1O03M 7.3284926

SLC39A8 209257. -1.1403956 10.4538343 -5.3855772 1.58E-07 aOOI07772 6.950O9387

MGC5618 221477. A.a» -1.1617675 103471179 -6.2424898 2.48E-07 0.00035843 6.55382496

SLC39AS 219869. s_at -1.14866 ΪΟ-1877186 -6.2694824 2-2SE-07 0.00135843 6.62S67956

— 226218. .a* -1.2937342 7.33564432 -6.1059571 3.S4E-07 000140732 6.17456221

STEAPl 205542. -a* -1.198521 7.98610593 -6.0852841 4.10E-C7 aO014O732 6.11705174

CHST11 219634. .at -1JS16S63 9.51077621 -6.0764318 4.21E-07 O.D0140732 6.09241933

CDS 201005. .at -1.1480015 10.9097322 -6.0774378 4.20E-07 0.00140732 6.09521866

TNF5F13B 223502. A.at -1.137231 10.6086468 -6.1814333 3.02E-07 a0014O732 5.38434731.

LACTB 226354. .at -1.1146026 10.6969136 -6.1724213 3.10E-C7 0.00140732 6.35931437

ARL61P5 200761. _ ^s _at -1.110*95 11.9357889 -6.0645684 4.38E-Q7 0.00140732 6.05940234

NFKBIE 203927. .at -1. 646409 10.0523732 -5.9997498 5.3SE-07 00157615 5.S7BS9643

SLICl 228869. .at -1.1244476 10.02770O9 -5.994027 5.48E-07 0.00157615 5.86295139

MMP1 204475. .at -13039262 6.32353561 -5.9312361 6.69E-07 0.00174156 5.68791385

SOD2 215223. -S_ t -1-2035944 9.66361398 -5.9462273 6 8E-07 0.00174156 5.72972041

NFKBIA 201502. _s_at -1.1701699 11.S415903 -5.9153553 7.04E-O7 0.0017486 5.64362855

ADAMDEC1 206134. .at -1.1861.199 8.53747931 -5.7927992 1.04E-O6 O.OO247065 5.30158178

MPEG1 226841. .at -1.141713 9.90354597 -5.7187643 1.32E-C6 0.00281664 5.09479213

ANXA2P2 208316. _x_at -1.1086O74 11.6486476 -5.7130844 1.34E-06 0.00281664 5.07892372

~ 244434. .at -1_28469ϋ9 6.48107186 -5.6742369 132E-06 O.0O2B41M 4.97038261

CCL2 216598. .s_at -1.2516796 11-2421198 -5.6653825 136E-06 0.00284109 4.94564092

I5G20 204698. .at -1.2176821 6.18754674 -5.677111 13QE-Q5 aOO284109 4.97841335

MT551 203037. A_'t -1-2132697 113042636 -5.6909681 L44E-06 0.00284109 5.0171321

IFNGR1 211676. _s_at -1.1076638 12-1480464 -5.6472459 1.65E-C6 0.0029127 4.89496045

— 230795. .at -1.170214* 9.26991641 -5.6333398 1.73 E-06 0.00294926 4.85610012

NFE2L3 236471. .at -1-3257415 5.26403664 -5.6026446 1.90E-O6 0100315306 4.77032024

CD36 209555. _s_at -1.1414722 9.39991418 -5.5482888 2.26E-06 0.00363742 4.61841752

CYtD 221903. _ t -1.12D7309 9.54523467 -5.5045621 2.60E-06 0.00406002 4.49622693

1CAM1 202638. _s_at -1.4084929 6.8285265 -5.4886851 2.73 E-05 0.00415135 4.45186392

KIAA15Q5 227265. .at -1.1673293 9.93164349 -5.4623712 2.97E-06 a00423964 4.37834442

BID 227143. _s_at -1.1112056 113740779 -5.471422 2.S9E-06 0.00423964 4.40363069

BID 211725. - ^s _at -1.10177241 11.8106494 -5.4568423 3.02E-06 0.00423964 4.36289801

IL10 207433. .a -1.2783883 5.71640286 -5.3801791 3.86E-06 0.00508408 4.14877517

ANXA2 201590. _x_at -1.1067663 13-1932317 -5.3762172 3.91E-06 0.00508408 4.13771284

TNFA&P6 206026. _s_at -1.2533604 5.46505459 -5.3471287 4.28E-06 0.00544542 4.0565035

COl* 201743. _at -1.1683628 9.56313815 -5.3162757 4.72E-06 0.00586803 3.97039297

ICAM1 202637. _s_at -1.253703 7.7078627 -5.2602772 5.64E-06 0.00674579 3.81417837

ANXA2 210427. _X_3t -1.1021711 13.160O5O2 -5.2581893 5.6BE-06 0.O0674579 3.80835622

SYNJ2 212828. .at -1.1079961 9.8266126 -5.2259269 6.29E-06 0.00731141 3.71841109

GUPR1 226142 at -1.1476518 3.96232728 -5.2116592 6.57E-06 a00744619 3.67864746 ECOP 238604_at 1.1291845 9.93048271 -5.2069623 6.67E-06 0.00744619 3.66555947

CD40 205l53_5_a- 1-1516665 8.96773222 -5.187B467 7. Q9E-06 O.00775153 3.61230284

IFIH1 219209_at 1-1839872 8.421660 -5.1481808 8. Q3E-06 0.0086134 3.50184783

11411 230966_at 1-2886142 10.7302425 -5.1035983 9.25E-06 0.0O953971 3.3777992 AF8 21B559_S_at 1.1661438 12- 5070822 -5.0783026 1.0OE-05 0.01013992 3.30746517

DAB2 201278_at 1.1002534 9.40858428 -5.0704754 1.03E-O5 0.01020405 3.28570957

P2RX4 20 oas_at 1.11462 10- 5804136 -5.05893O2 1-.06E-O5 0LO1O392&8 3.25362692

MUFl 2047S4_s_at 1-1629248 9.99075341 -5.03B2007 1.14E-05 0.D1089897 3.19604331

STATH 206835_at 1-2217631 10.6277925 -4.9970174 1- 29E-05 0LO1198544 3.08172746

G1 APB 235306_at 1-1769391 7.15724646 -4.9534429 1 SE-05 0-01329267 2.96090645

TATDN3 235069_at 1-1552651 9.09091742 -4.9541849 1.48E-05 0.01329267 2.96296263

SYT-J2 216180_S_a- 1-1540719 8.13588041 -4.929194 1.60E-OS 0.01372355 2.39373383

TREM1 219434_at -1-1280034 11- 1714599 -4.9272524 1.61E-C5 O.01372355 2.88835722 x&z 213503_X_at -1.1003875 13- 1627385 -4.8992037 1.76E-05 0.01434614 2.81072248

G0S2 213524_S_at -1-1355006 8.75639391 -4.864242 1.96E-05 0.01577044 2.71404776

[LlOJtA 204912_Bt -1-1199911 10-5172379 -4.8323374 2.17E-OS O.01717268 2.62592271

B1HC3 210538_S_at -1-257364 4.57445587 -4.8159991 2- 28E-05 0.01765329 2.58083111

NT5E 203939_at -1-2383789 8.45460557 -4.8143591 2-29E-0 0.01765329 2.57630644 ecus 1555759_a_i -1-0910656 13.6361191 -4.8032103 2- 37E-05 0.01802488 2.54555373

5RPX2 2Q5499_at -1.224512 6.16138512 -4.767627 2.65 E-05 0,01937153 2.4474847

ARL6IP5 20076D_S_at -1-U07109 11.7204466 -4.7591181 2.72E-05 0.01959427 2.42405329

EBI3 219424_at -1-1775996 7.06372735 -4.7474062 2.82E-OS 0.01976554 2.39181393

CD40 21534fi_at -1-1705995 8.77095715 -4.7439006 2.86E-05 0.O1976554 2.38216714

SRA1 224130_S_at -1.094757 10- SO27383 -4.7442703 2.85 E-05 0.01976554 2.38318441

— 2385Qi_at -1-2105582 5.44953239 -4.73925 2.90E-05 0.01977223 2.36937124

SUCi 229045_at -1-1547886 8.27398536 -4.7357646 2JS3E-05 0.01977223 2.35978293

C50RFI3 23841i_X_at -1.1683694 3.79974787 -4.7297145 2.98E-G5 0.01979262 2.34314234

CARD15 220066_at -1-1393689 8.86627619 -4.7275995 3.OOE-05 0.01979262 2.33732587

PUEKHOi 218223_S_at -1-1393641 9.19617144 -4.7232262 3.05E-O5 0.01982503 2.3253O094

NFE2L3 204702_S_at -1-1949945 6.27002251 -4.7O019OS 3- 27E-05 0.02069819 2.26199661

P2RY5 218589_at -1-1719902 9.42743243 -4.69B0902 3.29E-05 0.02069819 2.25622666

P5COBP 2Q9606_at -1.1833853 8.14103401 -4.6940285 3.34E-OS 0.02072301 2.24507189

PTX3 206157_at -1-1323376 11- 2731131 -4.6853648 3.S3E-05 0.0210494 2-2212847S

GHRL 223862_at -1-184681 7.10722772 -4.6529266 3.79E-05 0.02252098 2.1323O051

SGIPl 223672_at -1-1713796 8.75400755 -4.6556052 3.76E-05 0.02252098 2.13964377

RP1-13 til LO 214976_at -1-149-1626 6.91302234 -4.6576183 3.73E-05 0.02252098 2.14516306

C130RF31 1553141_at -1-2240082 8.3027252 -4.6445617 3.89E-05 0.02286455 2.10937474

— 228573_at -1-0954948 10- 1938031 -4.631833 4.05E-O5 0.02353205 2.07450537

— 213891_S_at -1 1513505 8-36985954 -4.6072376 4.37E-05 0-02435882 2.00718586

C9ORF130 227893_at -1-1466602 7.477 1908 -4.6095058 4.34E-05 0.02435882 2.01339098

VPS33A 204590_X_a. -1-1717826 7.44063872 -4.5964894 4.51E-05 0.0246793 1.97779156

LACTB 1552486_S_- -1-1146334 9.43978855 -4.5992016 4.48E-05 0.0246793 1.98520746

RAB273 22870B_at -1-2146134 8.64471961 -4.5896791 4.61E-05 0.O2495536 1.95917448

FX¾fD2 207434_S_at -1-2391134 6.S7935784 -4.5721048 4.87E-05 0.02609092 1.91116075

SOD2 2i684i_S_at -1-1587002 8.29547849 -4.5601654 5.05E-05 0.O2658149 1.87856531

INADL 214493_S_at -1-1876014 5.13104061 -4.5382854 5.40E-05 0-02787086 1.81888217

BSD 204493_at -1.0962323 11- 1430522 -4.5406927 536E-05 0.02787086 1.82544538

BTG1 240347_at -1.1577464 6.46143817 -4.5117153 5.S6E-05 0.02941834 1.74649575

CENTA2 219358_S_at -1-1328376 10.4221094 -4.5125118 5.85ΕΌ5 0.02941834 1.74866433

LOC54103 213142_X_at -1-1327449 10.7990817 -4.5010122 6.Q6E-05 0.02985684 1.71736561

— 232297_at -1-13964S3 8.4593218 -4.4977208 6.12E-05 0.02989176 1.7084108

THBD 203887_S_at -1.0860181 12.8670409 -4.4922535 6.23 E-05 0.02996581 1.6935397

KYMU 2106«3_5_at -1-1273404 10-5827862 -4.4730592 6.61E-05 0.03124079 1.64136616

TATDM3 228867_at -1.0979673 8.53193411 -4.4719767 6.63 E-05 0.03124079 1.6384252

ITG B5 201125_S_at -1-1305667 9.66682503 -4.4663279 6.74E-05 0.03151651 1.62308225

HNRPLL 225386_S_at -1 038481 10-9979975 -4.4607622 6.86E-05 0.03178871 1.60796956

CRVBB2 206777 S at -1-1273748 9.09050704 -4.4486878 7.12E-05 0.03248173 1.57520029 C05S 1555950_3_i -1.101176 11.0430169 -4.4455718 7.19E-05 0.03248173 1.56674717

MPEGl 226818_at -1.102944 9.97O50985 -4.4364675 7.39E-05 0.Q3312B76 1.54205788

POPOC 219926_at -1.2923154 6.73431127 -4.4296067 7.55E-05 0.03333429 1.52346112

PLAUR 214866_at -1JL197536 10.1465619 -4.4291541 7.56E-05 α 3333429 1.52223465 GLL 239914_at -1.1755243 5.02263Q39 -4.4192631 7.79Έ-05 0.03354952 1.49543825

EB1Z 205419_at -1.1647466 10.3787766 -4.4209004 7.75E-05 0.03354952 1.49987275

TP5AB1 /// T2Cf7741_X_at -1.154419 7.49088254 -4.4208416 7.76E-05 0.03354952 1.49971361

5 LAMF8 219386_5_at -1.1604525 10.11B7042 -4.4123213 7.96E-05 αθ33706Ο5 1.47664099

VSNL1 203797_at -1.1465556 9.26432896 -4.4080282 8.O7E-05 0.03370605 1.46501964

1CAM2 213620_S_at -1.129714 7.80787761 -4.4083036 8.Q6E-05 0.03370605 1.46576519 YNU 217388_S_at -1.1268071 11.2241113 -4.4076297 8.0SE-05 0.03370605 1.4639412

ARHGAP18 225166_at -1.1854012 7.40195979 -4.3979297 S.32E-05 0.03445978 1.43769541

MITF 22606S_at -1.1771138 7.94053593 -4.3803753 8.78E-05 0.03578326 1.39023722

MXD1 226275_at -1.1272655 8.58697195 -4.3782779 S.84E-05 0.03578326 1.3B457024

— 2413S9_at -1.1324551 7.7O820O4 -4.3740983 8.95 E-05 0.03597723 1.37327956

EGF 206254_at -1.2273072 5.23328013 -4.3445051 9.80E-OS Ο.039Ο9529 1.29342221 ALT1 210O17_at -1.1361187 7.85916694 -4.3417635 9.88 E-05 0.03913824 1.23603152

AK 1C2 211653_X_at -1-214586 9.21551731 -4.3261491 0.00010361 0.03933789 1.24396403

LPAAT-THETJ 224480_S_at -1.2033448 8.82402466 -4.3329062 0.00010149 α 3933789 1.26216342

MFIZ 235911_at -1.1173645 10-2132798 -4.3339031 0.00010118 0.03933789 1.26484915

ARHG P18 225171_at -1.1011604 10.76 3262 -4.329986 0.0001024 0.03933789 1.25429744

TXNL2 20908Ojc_at -1.0905642 11.1937357 -4.3267122 0. 0O1 343 0.Ο3933789 1.24548038

CD55 201926_s_at -1.0876428 11.0124454 -4.3312016 O.00O1O202 0.03933789 1.25757168

ADAM9 2D238i_at -1JL2SS776 10.068453 -4.2795249 0.00011941 0.04461757 1.11860933

OS8PU.1 218304_s_at -1.1200967 3.30361724 -4.268338 0.00012355 0.04461757 1.03859065

C5GRF32 224707_at -1.1088424 9.6C174121 -4.2676443 0.0OO123S1 0.04461757 1.08672987

CD3O0A 2Q9933_S_at -1.0919O93 11.068246 -4.2779818 0.O0O11998 0.04461757 1.11446708

ATP2C1 23727B_X_at -1.1252002 4.516837 -4.2604681 0.00C12654 0.04474124 1.06748681

TGM5 20791i_S_at -1.0985729 10-9973837 -4.255458 0.00O12848 0.04474124 1.054057S8

CAST 2Q890B_s_at -1.0958388 10.4613552 -4.2557149 0.OO012S38 0.04474124 1.05474617

TNFRSF9 207536_S_at -1-1669411 6.6480Q58 -4.2459826 0.O0O13222 α04518347 1.02857283

H G B2 24336B_at -1.16O2025 4.38716386 -4.2463169 0.00013209 0.04518347 1.02956814

TNFAIP3 2D2644_S_at -1.1253187 10.6490533 -4.2484635 0.O0O13123 0L0451B347 1.03531746

C1QRF21 223125_S_at -1.1101543 11.0653204 -4.2399019 0.00013469 0.04S73B95 1.01239127

— 212387 at -1.148179 7.86470579 -4.2245512 0.0001411 0.04762227 0.97132047

12 hr;

Gene ID ra .FC AveExpr t P.Value adj.P.Val B

PRD l 228964. .a* -13131187 7.67111264 -8.6246024 1.41E-10 7.72E-06 11.3048141

RC5D1 239328. Λ -1-2917804 9.91539671 -6.452108 U2E-07 0.OO333O7 6.31495199

BTG1 240347_ .at -1.256 137 6.63516956 -5.7047112 1.33E-06 0.02422499 4.46209908

FBX045 225099_ .a* 1.13350791 9.69247626 5.51958363 2.40E-06 0.03282196 3.99779146

ZNF566 240239. .at 1.2O9O240S 6.20206745 5.35216774 4.09E-06 0.04477351 3.57707114

2 hr:

Gene ID raw.FC AveExpr t P.Value adjJ>.VaI 8

MP9 203936. -1.2587837 8.76550602 -6.6308842 7.B9E-08 0.00431641 6.0372842 Do nregufated:

6 br.

Gene ID raw.FC AveExpr t P.value adjjs.val

LOC64B342 1569392_at 1-25828385 6.46339373 5.71764607 -L32E-06 0.00281664 5J09166798

BTBD14A 243431_at 1.31196093 8.69387594 5.37680876 3.90E-06 O.OO5O8408 4.13936456

5ERPINB2 204614_at U5751S53 10.7388922 5.14040426 B.23E-06 0.O0865761 3.48020227

MYB 20479B_at 1.09897729 13.1513017 5.00361266 1.27E-05 O.01194194 3.10002645

5ΤΓ3Β 23B303_at 1.2645975 6.00460112 4.9254338 1.62E-05 0.01372355 2.88332163

HSPOl 241716_at 1.30689927 6.02121553 4.9223221 1.64E-05 O.01372355 2.87470616

ACTN4 23205B_at 1.1922B742 8.60657642 4.91815B47 1.66E-05 0.01372355 2.S6317939

FAM62A 244234_at 1.14S4G119 7.29749849 4.7B192868 2.54E-05 0.01B99S88 2.48688527

HIC2 1559600_at 1.17980654 3.38342055 4.76703429 2.66E-05 0.01937153 2.4458524

OXCT2 235275_at 1.16642629 12.33OO201 4.71420617 3.13E-05 0.02014951 230050545

— 22B907_at 1.17599277 8.21884465 4.63L20071 4.30E-05 O.02435BB2 2.02O23432

GAPDH5 222280_at 1.1646993 7.71035699 4.60723903 4.37E-05 0.02435882 2-0071S978

5PFH1 202441_at 1.12657525 11.0883546 4.55979394 5.06E-O5 0.02658149 1.87755147 APB 1570441_at 1.20267749 5.92073389 4.52611168 5.61E-05 O.02B66712 1.7S570418

H RPO 213359_at 1.16888386 9.72519123 4.50340998 6.02E-05 0.02985634 1.72389004

CISH 223377 _at 1.09133621 9.01105134 4.49116936 S.25E-05 0.02996581 1.69059129

SFR514 64371_at 1.124Q0512 3.1362891 4.44643142 7.17E-OS 0.03248173 1.5690791

C140RF1Q 23918B_at 1.16314645 6.54891766 4.3B8S5767 3.56E-05 0.03519643 1.4123519

— 232903_at 1J2177B341 6.93O50721 4.29620676 0.0Q01135 0.04279881 1.16341547

HDAC4 232225_at 1.14445571 7.77327378 4.27489999 0.00012111 0.04461757 1.10619611

CLK1. 2146B3 _at 1.160507 9.2702S645 4.268656 0.00012343 0.04461757 1.08944366

CRLF3 235803_at 1.19940674 9.07113133 4.2670238 0.00012404 0.04461757 1.08506571

ZNF25Q 24173B_at 1.11589598 4.2390353 4.26401964 .00O12518 0.04473242 1.07700912

WDFYl 234157_at 3-20859908 6.39793409 4.25895039 O.0O012712 0.04474124 1.06341818

12 hn

Gene IO raw.FC AveExpr t P.value adjJP.Val a

FBX045 225099_at 1.13350791 9.69247626 5.51958363 2.40E-06 0.03282196 3.99779146

ZNF566 240239_at 1.20902406 6.20206745 5.35216774 4.09E-06 0.04477351 3.57707114

Table 4b. Probioglat expression values for key genes compared to the range set by observed expression values under Copaxone ^® treatment

Red text indicates that the expression value for this Probioglat treated sample is outside of the observed range of all Copaxone samples.

Discussion - Example 2

Pro-inflammatory Genes

Gene-level differentiation analysis identifies specific proinflammatory markers when comparing Probioglat to Copaxone ^® . Upon comparison of GA with Probioglat, significant gene-expression differences were seen (Table 3 ) . Only one batch of Probioglat was available to compare to the four batches of GA, prohibiting the possibility to study batch-to-batch variability. However, the range of variation defined by the four GA batches represents a range of variation that has been demonstrated to be safe and effective by Copaxone ^® ' s clinical trials. The fact that any single batch of Probioglat results in values outside of that range (as illustrated in Table 4b and Figure 44), coupled with lack of PK or PD markers to determine equivalence of the two glatiramoids , warrants further investigation . The consistent confirmatory results obtained by single-probeset, pathway and independent qRT-PC analysis are particularly robust, given the stringent statistical framework employed. It should be noted that fewer genes were significantly modulated by GA relative to Probioglat than by GA relative to mannitol, an observation expected given the intended mimicry of structure between the compounds. Indeed many genes were modulated in the same direction by both GA and Probioglat versus control, but to differing extents (the cases for many genes discussed below, except where noted) . It is striking that differences were observed between branded GA and the designed purported generic, Probioglat. Two drugs cannot be said to have identical effects if significant differences are manifest. Importantly, the significant differences in gene expression observed between Probioglat and Copaxone ^® were seen in genes tied to highly relevant disease pathoetiology and known GA mode of action (MOA) . Bioinformatic analysis of differentially expressed genes (by FDR corrected p value) following Probioglat versus Copaxone ^® stimulation of human monocytes at 6 hours identified a number of genes tied to important immune system functions, in particular inflammation: CCL5, CCL2, MMP9, MMP1, CXCL10, CD14, ICAM1 and BIRC3. Several of these genes have been reported in the literature as modulated by GA treatment in patients.

1. CCL5 (RANTES) is a key chemokine thought to attract inflammatory immune cells to the CNS, and was significantly upregulated in Probioglat treatment relative to Copaxone ^® treatment at 6 hours (FDR adjusted p value 0.018, FC 1.09 in gene expression analysis; p value 4e-5, FC 1.12 in qRT-PCR confirmation) . Indeed, an antibody blocking CCL5 was shown to reduce disease metrics including immune infiltration into the CNS in a viral MS model (Glass et al, Immunol Res, 2004; Chirstensen et al . Mult. Scler. J. 2013). Expression of the

CCL5 receptor, CCR5, on GA-reactive T cells from MS patients was shown to be downregulated by chronic (1 year) GA treatment (Allie et al, Arch Neurol 2005; Kouwenhoven et al. J. Neuroimmunol . 2002) . This gene was tested and confirmed to be upregulated with Probioglat treatment relative to GA treatment in primary human monocytes (p < 0.029, FC 1.53).

2. Expression of MMP9 (Matrix Metalloproteinase 9) was significantly higher with Probioglat versus GA stimulation at 6h (FDR-adjusted p-value 2.8e-6, FC 1.29 in gene-expression analysis, Figure 41a; p-value 0.02, FC 1.24 in qRT-PCR confirmation), and at 24h (FDR-adjusted p-value 0.004, FC 1.25). The MMP9 gene was also upregulated with Probioglat relative to GA treatment in primary human monocytes (p < 0.009, FC 1.4). This protein is reported to increase access of immune cells to the CNS by contributing to disruption of the blood brain barrier (BBB) (Rosenberg et al, The Lancet 2005), and high levels of MMP9 have been associated with Multiple Sclerosis (Christensen et al, Mult. Scler 2013; Milward et al., J. Neuroimmunol . 2008; nop et al, Neurology 2013; Parks et al, Nat. Rev. Immunol 2004) . MMP9 was upregulated with Probioglat relative to Copaxone ^® stimulation at 6 hours (FDR adjusted p value 2.8e-6 in gene expression analysis; p value 0.02 in qRT-PCR confirmation). Expression levels of MMP9 at both the mRNA and protein level were increased in immature dendritic cells from MS patients relative to healthy controls ( ouwenhoven et al, J Neuroimmunol 2002). Elevated MMP9 levels were reported in patients with gadolinium-enhancing lesions relative to patients without (Waubant et al, Dis Markers 2006; Antonelli et al, Autoimmun. Rev. 2014), and MMP9 has been proposed as a biomarker for both MS diagnosis and progression (Milward et al, J Neuroimmunol 2008; Peperzak et al, J. Immunol. Batim. Md 1950, 2013) . GA has been reported to inhibit MMP9 expression in healthy human peripheral blood mononuclear cells (PBMC) (Knop et al, Neurology 2013 (Meeting Abstract); Adrem and Ulevitch, Nature 2000) . Increased expression of MMP9 for Probioglat relative to Copaxone ^® at multiple timepoints (Fig. 7) .

The level of MMP1 , another matrix metalloproteinase gene, was increased after Probioglat stimulation compared to Copaxone ^® at 6 hours (FDR adjusted p value 0.002, FC 1.50 in gene expression analysis; p value 0.02, FC 1.25 in qRT-PCR confirmation) . Matrix metalloproteinases are known to cleave pro-inflammatory cytokines and chemokines to regulate inflammation (Parks et al, Nat Rev Immunol, 2004; Baumann et al, J. Exp. Med. 2010) . Levels of MMP1 mRNA, as well as secreted MMP1, were observed to be higher in immature dendritic cells from MS patients relative to healthy controls (Kouwenhoven et al, J Neuroimmunol 2002; Parks et al, Nat Rev Immunol, 2004) .

Expression of the chemokine CXCLIO was increased by Probioglat stimulation compared to Copaxone ^® at 6 hours (FDR adjusted p value 0.0006, FC 1.46 in gene expression analysis; p value 0.0029, FC 2.28 in qRT-PCR confirmation). This finding was confirmed by qRT-PCR in primary human monocytes, where CXCLIO was upregulated by Probioglat relative to Copaxone treatment with p value < 0.02 and fold change of 2.1. CXCLIO level in peripheral fluids was previously shown as associated with host immune response, particularly with regard to Th-1 cells (Antonelli et al, Autoimm. Rev., 2014; Natarajan et al, J. Nueroimmunol . 2013). CXCLIO is involved in recruiting CD8+ and Thl CD4+ effector T cells to sites of inflammation (Peperzak et al, J Immunol, 2013; Hedegaard et al, PLoS ONE 2011) . A study using monocytes from RRMS patients demonstrated CXCLIO to be increased by GA therapy within the first two months of treatment (Thamilarasan et al, J Neuroinflammation 2013; Rosenberg, The Lancet 2005) .

CD14 is a marker of monocyte activation known to enhance inflammatory responses. CD14 was upregulated in human monocytes stimulated by Probioglat versus Copaxone ^® at 6 hours (FDR adjusted p value 0.006, FC 1.17; qRT-PCR not tested; Figure 41b) . CD14 was not modulated by GA treatment versus mannitol control. This marker of monocyte activation enhances inflammatory responses (Mycko et al, Ann. Neurol. 1998). In complex with LPS binding protein (LBP) , CD14 interacts with LPS and helps to present it to toll-like receptor 4 (TLR4), activating downstream expression of inflammatory genes via NF-kB (Park et al, Exp Mol Med, 2013) . CD14 has also been shown to be a coreceptor for other TLRs, and was demonstrated to be required for induction of proinflammatory cytokines via TLR7 and TLR9 in mouse and human cells in vitro (Baumann et al, J Exp Med, 2010; Bullard et al, J. Immunol. 2007). Increased expression of CD14 for Probioglat was determined relative to Copaxone ^® (Figure 8) .

CARD 15 (N0D2), another gene upregulated by Probioglat versus Copaxone ^® at 6 hours (FDR adjusted p value 0.02, FC 1.14; qRT- PCR not tested) , is also a key player in the immune response to LPS, participating in activation of NF-kB. Activation of NOD2 by peptidoglycan has been shown to induce CNS demyelination in rats (Natarajan et al, 2013; Sellner et al, Clin. Exp. Immunol. 2013). In addition, a SNP in NOD2 was shown to affect the responses of Th2 and Thl7 cells to myelin basic protein (MBP) in MS (Hedegaard et al, 2011; Bertrand et al, Immunity 2009) .

BIRC3 expression was increased by Probioglat relative to Copaxone ^® at 6 hours (FDR adjusted p value 0.018, FC 1.26; qRT-PCR not tested) . This gene codes for an Inhibitor of Apoptosis Protein (IAP-1), which in addition to its role in cell survival plays a role in both innate immunity (Bertrand, 2009; Kearny et al, J. Biol. Chem. 2013) and inflammation (Labbe et al, 2011; Ashburner et al, Nat. Genet. 2000), and has been suggested to have an immunomodulatory effect in autoimmune demyelination (Hebb et al, 2008; Kanehisa et al, Nucleic Acis Res. 2000) . IAPs including IAP-1 are required for production of pro-inflammatory cytokines via several different pathways, including TLR4 activation (Tseng et al, 2010; Zanin-Zhorov et al, J. Clin. Invest. 2006) and NOD2 activation by TNFa (Kearney et al, JBC, 2012; Qin et al, Proc. Natl. Acad. Sci. 2012) .

CCL2 (MCP-1) is another pro-inflammatory cytokine that was also expressed significantly more highly with Probioglat treatment relative to Copaxone ^® at 6 hours (FDR adjusted p value 0.003, FC 1.25; qRT-PCR not tested). CCL2 expression was decreased by GA treatment relative to mannitol control, and decreased to a lesser extent by Probioglat relative to mannitol control. CCL2 is thought to recruit inflammatory cells into the CNS in EAE and in MS (Mahad et al, 2006; Waubant, Dis. Markers 2006) . This gene was also confirmed to be upregulated with Probioglat relative to GA treatment in primary human monocytes (p < 0.009, FC 1.24).

8. ICAMl expression was increased by Probioglat relative to Copaxone ^® at 6 hours (FDR adjusted p value 0.004, FC 1.41; qRT-PCR not tested; Figure 41c) . ICAM1 is an adhesion molecule that plays a key role in inflammatory processes by promoting leukocyte adhesion to the endothelium of the vascular wall, and is known to have an important role in inflammatory cell infiltration into the CNS in both EAE and MS (Mycko et al, Ann. Neurol. 1994; Labbe et al, Immunity 2011) . In mice null for ICAM1, T cells produced significantly less IFNy and showed much less infiltration into the spinal cord (Bullard et al, J Immunol, 2007; Hebb et al, Mult. Scler. Houndmills Basingstoke Engl. 2008). In PBMC from RRMS patients, ICAMl levels were higher versus healthy controls, and chronic treatment with GA affected surface ICAMl levels in multiple immune cell types (Sellner et al, Clin Exp Immunol

2013; Tseng et al, Nat. Immunol. 2010). Increased expression of ICAMl for Probioglat was determined compared to Copaxone ^® stimulation (Figure 11) . Anti-inflammatory Genes

As discussed herein, a number of pro-inflammatory genes and pathways were shown to be significantly upregulated by Probioglat as compared to Copaxone ^® . At the same time, several anti-inflammatory genes were downregulated by Probioglat stimulation in comparison with Copaxone ^® at 6 hours.

CISH, also known as SOCS (Suppressor of Cytokine Signaling), was expressed at lower level with Probioglat relative to Copaxone ^® at 6 hours (FDR adjusted p value 0.03, FC -1.09; Figure 41d) . A closely related protein, SOCS3, has been shown in myeloid cells to protect from EAE, the mouse model of MS, via deactivating neuroinflammatory responses (Qin et al, PNAS 2012; Bakshi et al, Expert Opin. THer. Targets 2013) . Both present probesets for this gene were affected in the same direction (Fig. 12). A SNP in SOCS1, another family member, has been identified as a risk factor for MS (Towfic et al, PLoS ONE 2014) .

2. HSPD1, also known as HSP-60 (heat shock 60kDa protein 1), was downregulated in Probioglat relative to Copaxone ^® at 6 hours (FDR adjusted p value 0.01, FC -1.31). Zanin-Zhorov et al (2006) showed that HSP60 as well as synthetic peptide derived from HSP60 act as co-stimulators of Tregs through the TLR2 pathway. Tregs are immune regulatory cells that inhibit lympho-proliferation and IFNG and TNF secretion by proinflammatory T cells. Zanin-Zhorov et al concluded that HSP60 can downregulate adaptive immune responses by upregulating

Tregs. Thus, downregulation of HSPD1 may result in less inhibition of immune response by Probioglat compared to Copaxone ^® . It should be noted, however, the anti-inflammatory cytokine IL10, known to be relevant to the GA mechanism of action, was also expressed at a higher level subsequent Probioglat relative to Copaxone ^® treatment at 6 hours (FDR adjusted p value 0.005, FC 1.28). The same observation holds for another gene at 6 and 12 hours, PRDM1 (Blimpl) (FDR adjusted p value 0.0006 and 7.7e-6, and FC 1.31 and 1.31 respectively) , that when deleted results in inflammatory pathology (Chiang et al, PNAS 2013; Johnson et al, Biostat. Oxf. Engl. 2007). Blimpl is a target of FOXP3 and is needed for production of IL10 by Tregs; its expression can also be induced by IL2 and proinflammatory cytokines in Tregs (Cretney et al, Nat Immunol. 2011; Leek et al, Surrogate Variabel Analysis 2013) . However, it is not clear what these observations would imply for APCs such as monocytes. It is possible that higher Blimpl could be an attempted protective response to a higher inflammatory milieu. A statidtically significant difference in such a mechanistically relevant gene - in either direction - between two therapeutics intended to be identical presents motivation for further study. Example 3

Pathway Enrichment: Analysis

Upregulated and downregulated genes were analyzed separately for pathway enrichment, using DAVID (Huang et al, Nucleic Acids Res 2009) . Pathway enrichment results were visualized using volcano plots, plotting -log p values versus enrichment scores . For GA MOA, to obtain top-gene lists of appropriate size (tens-hundreds) for use with DAVID, an absolute-value-fold-change cutoff of 1.5 and p-value cutoff of le- 5 were utilized to obtain gene lists for pathway enrichment at 6h. For comparisons between branded GA and Probioglat, upregulated or downregulated genes with FDR-adjusted p values < 0.05 were used for pathway enrichment . DAVID runs were conducted May 21, 2014. Please note that the GO databases are updated daily (as noted on the GO site : www. geneontology. org/GO. downloads . ontology . shtml) and therefore performing the same enrichments on the same genesets may yield slightly varying results depending on the run date, as illustrated by the differences in Table 6 (results from runs on differing dates using broader or more restrictive subsets of GO) . Thus, the pathway p values may change slightly between runs conducted at different times; the overall picture of enriched pathways, however, is expected to remain consistent. Three time points were tested to identify the fold change and p value filters were used to obtain top gene lists of appropriate size (i.e. tens to hundreds) for use with DAVID (Table 5) .

No pathways were enriched significantly among downregulated genes, however 106 pathways were enriched significantly (Benjamini corrected p value < 0.05) among genes upregulated by Probioglat relative to GA, including immune system process (GO : 0002376) , immune system process (GO : 0002376) and immune response (GO: 0006955) pathways (Benjamini- corrected p-values 1.5e-5 and 3.3e-4, respectively), and many other immune system related pathways, such as regulation of lymphocyte mediated immunity (GO: 0002706, Benj amini-corrected p-value 0.007) and B cell proliferation (GO:0042100 Benjamini-corrected p-value 0.049) (Fig. 10 and Table 6) . Multiple significantly enriched pathways were relevant to inflammation, including response to lipopolysaccharide (LPS) (GO: 0032496; Figure 9), regulation of inflammatory response (GO : 0050727 ) , regulation of tumor necrosis factor production (GO: 0032680) , and NOD-like receptor signaling (hsa04621) (Benjamini- corrected p-values of 8.7e-4, 0.015, 0.028, and 0.027, respectively) . No pathways were enriched significantly among genes downregulated by Probioglat versus GA.

Genes analyzed for pathway enrichment (Tables 5 and 6) , using DAVID (conducted May 21, 2014) . Performing the same enrichments on the same genesets may yield slightly varying results depending on the run date (GO databases are updated daily: www . geneontology.org/GO . downloads . ontology. shtml) .

Table 5 . Human monocyte study : pathways significantly enriched among genes significantly upregulated by Copaxone' ⁸ relative to mannitol at 6 hours .

Enriched among top upreguiated genes:

Table 6. Human monocyte study : pathways significantly enriched among genes

*?

"1

E

I 8

Pathways significantly enriched among genes upregulated by Prcbiogiat reiattve to GA (mannitol-corre ted comparison) at 6 hours, earlier run including Kegg and GO BP only:

Example 4

Validation of pro-inflammatory markers' upregulation by stimulation with Probioglat compared to Copaxone ⁸ (qRT-PCR analysis)

Key genes identified by differential expression analysis were assayed using qRT-PCR. RNA was utilized from each of 6 biological samples for each treatment (Copaxone ^® and Probioglat) and 15 technical replicates were performed for each sample (a total of 90 observations per transcript per treatment) . Since three Copaxone ^® batches and one Probioglat batch were available, a total of 360 observations from each transcript were evaluated. To evaluate the data, the 2 ^"ΔΔ " approximation was utilized with GAPDH as reference transcript and vehicle control (mannitol) as calibrator. A one-sided t-test with unequal variance was used to compare the RNA expression from the two treatments .

To validate the results from the microarrays comparing Probioglat with Copaxone ^® for key inflammation and MS-related genes, two chemokines (CCL5, FDR p-value < 0.02 and CXCL10, FDR p-value < 0.0006), two matrix metalloproteinases (MMP1, FDR p-value < 0.002 and M P9, FDR p- value < 2.8e-6) and a non-secreted cell surface marker (CD9, FDR p- value < 0.002 with FC 1.15) that is a component of myelin and a marker of myelinogenic progenitor cells (Allie et al., Arch. Neurol. 2005) were tested independently by robust qRT-PCR analysis. Three Copaxone ^® batches and one Probioglat batch were available for use, and a total of 360 observations from each transcript were evaluated. Statistical analysis utilized a one-sided t-test with unequal variance to compare the RNA expression from the two treatments. All the genes tested were significantly differentially expressed between Probioglat and Copaxone ^® as expected based on the microarray analysis (Table 7) . Table 7. Differential expression (p value and fold change) of key immunological genes following Probioglat stimulation compared with Copaxone ^®

Gene- CCL5 cm CXCL10 MMP1 MMP9

Method FC p value FC p value FC p value FC p value FC p value aEGB. 1.12 4.05E-05 1.11 0.0004 2.28 0.0029 1.25 0.0201 1.24 0.0168

FDR- adjusted 1.09 0.02 1.15 0.002 1.46 ^" 0.0006 1.5 0.002 1.29 2.S0E-06 Microarray

FC: fold change; ¾E£3B" quantitative RT-PCR FDR For the microarray data, since all on the microarray were tested, p values were adjusted using FDR for testing multiple hypotheses.

Table 7 shows p-values from single-tailed t-test with unequal variance (for qPCR results) and FDR-adjusted p-values from LIMMA comparison of microarray data between human monocytes treated with Copaxone ^® and Probioglat .

Discussion — Examples 3-4

The genes significantly upregulated (FDR adjusted p value < 0.05) in Probioglat relative to Copaxone ^® treatment at 6 hours were found to be enriched significantly (Benjamini corrected p value < 0.05) for 106 pathways annotated in the GO (Biological Process, Cellular Component, and Molecular Function) and Kegg databases (The Gene Ontology Consortium. Gene ontology: tool for the unification of biology, Nat. Genet., May 2000; Kanehisa et al, KEGG: Kyoto Encyclopedia of Genes and Genomes, NAR, 2000) (Figure 10; Table 6) . These include immune system process (GO: 0002376) , response to lipopolysaccharide (LPS ) (GO: 0032496) , and immune response (GO:0006955) pathways (Benjamini corrected p values 1.5e-5, 8.7e-4, and 3.3e-4, respectively). Several of these pathways are relevant to inflammation (e.g., regulation of inflammatory response (GO: 0050727) and regulation of tumor necrosis factor production (GO: 0032680) , Benjamini corrected p values of 0.015 and 0.028, respectively).

Branded GA significantly modulated many validated pathways. At 6 hours, pathways enriched significantly among upregulated genes included broad categories such as immune response and regulation of immune processes, and more specifically cytokine-cytokine receptor interactions. Other significantly enriched pathways included adhesion; extracellular region; plasma membrane; membrane; response to external stimulus; response to stress; response to wounding; defense response; inflammatory response; and immune system process, all pathways with broad relevance to the disease process and/or proposed action of GA. Several of these pathways (e.g., extracellular region; immune system process; defense response; regulation of leukocyte activation) were also seen significantly enriched among genes modulated by GA in monocytes obtained from RRMS patients within the first two months of treatment (Thamilarasan, J Neuroinflamination 2013) .

As another example, NOD-like receptor signaling (hsa04621, Benjamini corrected p value 0.027) regulates inflammatory and apoptotic responses. The response to LPS pathway (GO:0050727; Figure 9) includes the genes CD14, CCL5, THBD, CARD15, NFKBIA, and CCL2 , all upregulated in Probioglat treatment versus GA at 6 hours. This pathway was also significantly enriched among probesets upregulated by GA treatment at 6 hours, though with a lower enrichment score (14.8 vs 2.7) and higher p value (0.00087 vs 0.036) . The strong enrichment induced by Probioglat relative to GA of this prototypical pro-inflammatory pathway warrants further investigation with respect to safety.

Interestingly, about half of the pathways (58 out of 114) significantly enriched (Benjamini corrected p value < 0.05) among genes upregulated by GA treatment versus mannitol control at 6 hours were also significantly enriched among genes upregulated by Probioglat relative to GA treatment. An additional 48 pathways were significantly enriched among genes upregulated by Probioglat relative to GA (and not modulated by GA relative to mannitol control) . These include pathways relevant to inflammation, such as response to molecule of bacterial origin (GO : 0002237) , regulation of tumor necrosis factor production (GO: 0032680) and NOD-like receptor signaling pathway (hsa04621) , as well as other immune pathways including regulation of lymphocyte mediated immunity (GO: 0002706) and B cell proliferation (GO: 0042100) .

Example 5

Integrated Analysis Spanning Multiple Species and Cell Types

Analyses were conducted to elucidate the gene expression changes induced by Copaxone ^® in the following systems:

1) primed, ex vivo mouse splenocytes;

2) THP-1 human monocyte cell line; and

3) samples from MS patients.

Genes, pathways and immune cell types modulated by Copaxone ^® were investigated, in order to determine which aspects of Copaxone ^® ' s mechanism were observed across all systems utilized, and which were detectable only in certain systems, but not others.

Genome-wide expression profiles in cells from three different datasets in two different species (human, mouse) were studied. LIMMA was utilized to identify a genome-wide list of differentially expressed genes induced by GA in the primed and ex vivo stimulated mouse splenocytes, as well as in the THP-1 human monocyte cell line. Repeated-measures ANOVA was utilized to find a genome-wide list of genes modulated by GA in treated MS patients. Advanced enrichment algorithms were then applied to elucidate the pathways and cell types modulated by GA.

Upregulated expression of the IL-10 gene, a key indicator of the well- studied Th2-shift induced by GA, was consistently demonstrated in all 3 systems (mouse splenocytes, human monocytes and MS patient PBMCs) (Fig. 13) . GA induces an anti-inflammatory effect, mediated by secretion of IL-4, IL-10, and other anti-inflammatory cytokines. This effect involves both a shift in T cell populations (from proinflammatory Thl to anti-inflammatory Th2) and a shift from monocyte production of IL12 to anti-inflammatory IL10. For example, in vitro GA treatment increased the proportion of ILlO-producing Treg cells in blood from MS patients (Putheti, J Neuroimmunol 2003) . Dendritic cells exposed to GA during maturation increased their production of IL10 (Vieira et al, J Immunol 2003) , monocytes from mice treated with GA secreted more IL10 than monocytes from untreated mice (Weber et al, Nat Med 2007), and monocytes isolated from MS patients treated with GA were shown to upregulate IL10 relative to untreated patients (Kim et al, J Immunol 2004) .

The genes modulated by GA treatment in multiple studies were examined for enrichment in particular immunological cell types. 39 genes were modulated significantly by GA in all three studies (Fig. 14) . Table 8 shows the expression level of each gene as modulated by Copaxone ^® compared to baseline (human PBMC) , mannitol (human monocyte) or medium (mouse splenocytes) . Although some genes are significantly differentially expressed in the same direction across all compartments and systems, other genes are modulated differently across the different systems. This shows that Copaxone ^® may induce pathways or cell types differently depending on a given experimental setup and a well-designed genome-wide assay is required to ascertain mechanism and effect of Copaxone ^® . Starred genes did not meet effect size cutoff of 0.5 employed in human PBMC study for conducting enrichments.

Table . 8. Genes significantly modulated by Copaxone treatment in all three studies

Example 6

Cell Type Enrichment Analysis

In addition to the shared induced effects discussed above, each system and platform clearly captured different aspects of GA' s impact on the immune system. In mouse splenocytes, genes associated with F0XP3+ regulatory T cells (Tregs) , B cells, T cells in general, macrophages, and dendritic cells were significantly modulated upon ex vivo stimulation with GA after prior inoculation (Table 9) . In human monocyte (THP-1) cells, upregulated genes were associated with monocytes along with NK cells, dendritic cells, and granulocytes (Table 10) . In human PB Cs, genes associated with immune cell types were modulated early in treatment (by month 3 ) , including certain cell types affected in prior systems, but also distinct cell types, such as megakaryocytes and myeloid progenitors (Table 11) .

Table 9. Immunological cell type enrichment for genes modulated by GA treatment in mouse splenocytes

a) Upregulated (top 20 results)

b) Downregulated (top 20 results)

All immunological cell type terminology in Tables 5-7 as defined via Immgen (www.immgen.org/). GN.BM.rnk 1212.480897 1.11E-16 3.57E-15

GN.BI.rnk 1184.87043 6.66E-15 1.84E-13

GN.UrAc.PC.rnk 1145.080376 5.87E-14 1.37E-12

GN.Thio.PC.rnk 1197.163456 6.39E-14 1.37E-12

GN.Arth.SynF.rnk 1160.159783 2.72E-11 5.25E-10

DC.llhilang.103.llblo.SLN.rnk 1112.24759 5.07E-08 8.90E-07

DC.IIhilang.l03.11b..SLN.rnk 1151.229363 9.94E-08 1.60E-06

DC.8.4.11b..SLN.rnk 1116.686609 1.86E-07 2.77E-06

proB.CLP.BM.rnk 1181.133013 1.35E-06 1.86E-05

Mo.6C.il..BM.rnk 1094.697148 1.71E-06 2.20E-05

DC.103.11b..LuLN.rnk 1151.971571 2.47E-06 2.98E-05

SC.GMP.BM.rnk 1340.719659 1.56E-05 0.000164843

SC.MDP.BM.rnk 1206.224359 1.56E-05 0.000164843

Mo.6C.llint.BI.rnk 1106.765118 1.62E-05 0.000164843

Table 10 . Immunological cell type enrichment for genes upregulated by GA treatment in human monocytes .

Table 11 . Immunological cell type enrichment for genes modulated by GA treatment in human PBMC .

a) Upregulated, by cluster resulting from consensus k-means clustering on gene expression profiles

Cluster 0:

Dataset Name Score p.val adj. p.val Genes in list >= threshold

PTPN18,ILK _; RAB27B FHL1 _J EP0R FYN,MA EGA2.rnk 32.42631137 1.24E-12 4.70E-11 X _; PARVB,TUBB1,TPM1,VCL.,TPM4 Cluster 2:

Cluster 4:

Dataset Name Score p.val adj.p.val Genes in list >= threshold

PARD3,GNB5,C50RF4,LIMS1,

ACTN1,ITGB3,ITGA2B,GPX1,IGF2BP EGA2.rnk 64.4584783 4.41E-12 1.67E-10 3,CLU,LTBP1

HMGA2,LIMS1,ACTN1,ITGB3,

MEGAl.rnk 38.04817949 4.66E-09 8.86E-08 ITGA2B,GPX1,IGF2BP3,LTBP1

HMGA2 LIMS1,ACTN1,ITGB3,

ERY2.rnk 47.24788403 4.70E-06 5.96E-05 ΙΤ6Α2Β,Ι6Ρ2Β 3, υ ΤΒ 1

GMP.rnk 33.12681006 0.000142682 0.001355477 ACTN1,GPX1,IGF2BP3,LTBP1

HMGA2,UMS1,GPX1,IGF2BP3,

HSC3.rnk 45.40525942 0.000287455 0.002184658 HIST1H3D,LTBP1,INPP4B

CLCN3,C50RF4,ITGB3,GPX1,

ERY5.rnk 73.41821315 0.000980846 0.006212027 IGF2BP3,LTBP1

CMP.rnk 23.1944575 0.002214239 0.010517637 HMGA2JGF2BP3

RAB6B,CLCN3,C50RF4,GPX1,

ERY4.rnk 77.37714483 0.001966408 0.010517637 IGF2BP3,LTBP1

HMGA2,GPX1 _/ IGF2BP3,MALL,

ERYl.rnk 45.00063371 0.002587112 0.010923363 LTBP1

RAB6B,CLCN3,C50RF4,GPX1,

ERY3.rnk 90.0166825 0.009061135 0.031302103 IGF2BP3,LTBP1

ACTN1,ITGB3,GPX1,IGF2BP3,

GRAN2.rnk 35.17942767 0.008750011 0.031302103 LTBP1 b) Downregulated, by cluster resulting from consensus k-means clustering on gene expression profiles (as described in methods) Cluster 0:

Discussion — Examples 5-6

The diversity of the cell types enriched from the list of 1200 genes (B cells, T cells, monocyte progenitors, megakaryocytes) indicates the wide-ranging effects of Copaxone ^® on the immune system. Similar to what was observed in the splenocyte data, it is difficult to define a small panel of genes to use as quality-control measures against a given Copaxone ^® lot due to the wide-ranging effect of the drug. Using genome-wide gene-expression arrays, the gene expression from the human PBMC data, mouse splenocytes and human THP-1 monocyte cell line were compared and discovered that although there are genes that are consistently modulated by Copaxone ^® across all those experimental systems (e.g., IL10), some gene-expression signatures and cell types (e.g., B-cells) were seen only in one system (e.g., human PBMC data) but not as clearly in the other systems (e.g., monocytes and splenocyte data) . Looking at genome-wide gene expression signatures can yield a good characterization of the impact of Copaxone ^® on a single system (e.g., THP-1 monocytes) but well-powered experiments in multiple systems are necessary to characterize the biological impact of Copaxone ^® . The generic glatiramer acetate manufactured by Probioglat induced significantly higher expression of CD14 than Copaxone ^® did (adj. p = 0.0135; Fig. 15a) and also induced significantly higher expression of CD40 than Copaxone ^® did (adj. p = 0.0128, Fig. 15b).

One key element of Copaxone ^® ' s putative mechanism of action is the ability to shift the immune response from a Thl/Thl7 phenotype, typically associated with MS pathoetiology and severity, to a Th2 response type that may mitigate the harmful effects of MS. Across multiple studies, we observed concerning differences between Copaxone ^® and proposed generics was observed in their impact on key genes associated with maintaining the balance between Th2 and Thl/Thl7.

Interleukin-1 beta (IL1B) is a cytokine that stimulates a variety of immune system cells, and may contribute to the development of MS by promoting Thl7 cell development. Consistent with these observations, IL1B has also been found to be associated with late disability progression and neurodegeneration in MS. Glatiramer acetate, on the other hand, was reported to significantly reduce interleukin-lbeta levels under chronic inflammatory conditions in vitro in human monocytes (p = 0.028).

A variety of glatiramoids were significantly less effective than Copaxone ^® at downregulating IL1B: Copaxone ^® induced significantly lower IL1B expression than a Natco purported generic in our first mouse splenocyte study (adjusted p = 0.043 by ANOVA) . Copaxone ^® was also extremely effective in downregulating IL1B relative to medium

(adjusted p = 5.72 x 10-7), while the Hangzhou purported generic (API, China) did not significantly downregulate IL1B relative to medium

(adjusted p = 0.159) (Fig. 16). Other Thl7-associated genes also seem to be modulated less effectively by purported generics than by Copaxone ^® . In human monocytes, CD44 was upregulated to a greater extent by Escadra635 than by Copaxone ^® (adj . p = 0.04 by LI MA at 6 hrs; Fig. 17) . CD44 has an established role in Thl7 differentiation, specifically: "deletion of CD44 inhibited Thl/Thl7 differentiation while simultaneously enhancing Th2/regulatory T cell differentiation. Thl7 associated genes also vary from one batch of generics to another. In mouse splenocytes, IL27 was upregulated to significantly different extents by different batches of Escadra, namely Escadra635 and Escadra253 (Fig. 18). IL27 has been proposed to have therapeutic effects in MS, due to its ability to suppress Thl7 cells and stimulate neuroprotective factors.

In human monocytes, Probioglat induces significantly higher expression of MMP9 than Copaxone ^® does (Adj . p = 2.07 x 10-5 by LIMMA for Copaxone ^® vs. Probioglat at 6 hrs in human monocytes; Fig. 19). MMP9 is an established biomarker and potential predictor of disease activity in MS. This finding is particularly concerning given the fact that MMP9 facilitates T-cell migration into the CNS, playing a key role in the disruption of the blood-brain barrier (BBB) and thus in the pathogenesis of MS.

Example 7

Compositional differences of GARDPs and GARDSs

Due to its molecular diversity, characterizing even a single, large polypeptide (assuming it could be isolated) would present significant technological and scientific barriers making full characterization, as well as a demonstration of active ingredient sameness, impossible. Analysis of Additional Purported Generics Reveals Limitations of Focused Gene Panels

Certain methods have been publicly described in patent application filings by manufacturers seeking to develop purported generics (including International Publication Number WO2008/157697 by Momenta Pharmaceuticals, Inc.), suggesting that glatiramoids can be compared by analyzing a panel comprising only a small subset of proteins and/or the genes coding for those proteins. To evaluate the effectiveness of such comparisons, we applied the same methods used to study Probioglat and Copaxone in human monocytes to also study purported generics Escadra (Raffo, Argentina) and Glatimer (Natco, India) . Both purported generics modulated many genes to a significantly different extent than Copaxone. These differentially expressed genes included genes with relevance for multiple sclerosis. For instance, both Natco and Escadra differed significantly from Copaxone in expression of CD9, a component of myelin and a marker of myelinogenic progenitor cells (Sim et al, Nature Biotechnology, 2011). As another example, Escadra differed significantly from Copaxone in expression of CD44, the receptor for hyaluronan which accumulates in demyelinated lesions (Back et al, Nature Medicine, 2005) . Despite significant differences such as these between Copaxone and the purported generics in expression of biologically relevant genes, when we examined only the small subset of genes coding for proteins identified in the Momenta patent, there were no significant differences in expression (Fig. 20) . This demonstrates that methods focusing on only a small selected subset of genes may miss important differences between two glatiramoids .

Compositional differences can be observed between Copaxone^ and other generics

TV-5010 was developed by making slight changes to the manufacturing process for Copaxone ^® , in order to produce a higher average molecular mass (in the range of 13,500-18,500 Daltons) and investigate whether such a change in molecular mass would be clinically beneficial. Surprisingly, TV-5010 proved toxic in long-term animal studies, inducing fibrosis, nephropathy, increases in eosinophil counts, and severe injection site lesions, including subcutaneous necrosis, vascular necrosis, cavity formation, and inflammation; in some cases these lesions were associated with mortality in both rats and monkeys, possibly related to vascular damage, hemorrhage, thrombus formation, and septicemia. These toxicities were never seen in any of the development programs for Copaxone, and led to the termination of TV- 5010' s development. Some patients treated with TV-5010 showed injection site reactions and/or developed anti-drug antibodies, but the clinical studies were completed in time to prevent any of the chronic toxicities observed in long-term animal studies from potentially occurring in humans. Because Copaxone ^® and TV-5010 had many similarities, with the two key differences that (1) TV-5010 had a higher average molecular mass than Copaxone ^® , and (2) Copaxone ^® was safe while TV-5010 induced toxicity in long-term animal studies, we sought to determine if there were genes differentially expressed in response to the two medicines that could have predicted toxicity prior to the initiation of long-term animal studies. Having generated gene expression profiles for TV-5010-stimulated splenocytes using the same procedures described above, we applied LIMMA to create a ranked list of genes with significantly different expression levels in response to TV-5010 compared to Copaxone, with both analyzed relative to medium. Among the genes with fold changes greater than 1.5, the gene with the lowest (best) p-value was Matrix Metalloproteinase 14 (MMP14) . MP14 expression was significantly higher in response to TV- 5010 than in response to Copaxone ^® as determined by both ANOVA (adj p < 4.53 x 10-7) and LIMMA (adj P < 1.07 x 10-5) (Fig. 21).

The observed upregulation of MMP14 was striking because MMP14 has been associated with fibrosis and eosinophil-related disorders in the literature, the very same toxicities seen in animals following long- term treatment with TV-5010. MMP14 levels increase to over 250% of control correlating with the pattern of fibrosis manifestation in rats, and MMP14 activity is chronically elevated in a mouse model of dermal fibrosis. Moreover, in patients with the eosinophil-related disorder Eosinophilic Esophagitis (EoE) , MMP14 is expressed at a 5.3- fold higher level than in controls. In addition to MMP14, another gene, Signal Transducer and Activator of Transcription 3

(STAT3) , which has also been linked to fibrosis, also showed significantly elevated expression in response to TV-5010 relative to Copaxone ^® . Overall, our findings with TV-5010 lend further support to the utility of mouse splenocyte gene expression studies for predicting drug safety issues. Example 8

Clinical Iinplications of the Use of Purported Generics

Purported "generics" are not only different from Copaxone ^® in many ways, but also different from each other, causing differential effects in a variety of pathways modulating immunological processes that could have clinical and biological significance. The differences among "generics" highlight the importance of the manufacturing process for glatiramer acetate, and demonstrate that even slight changes in the manufacturing process can alter the biological properties of the resulting medicine (Fig. 22) .

As part of Teva' s ongoing commitment to better understand Copaxone®, Teva also has studied Copaxone®' s effect at the level of gene expression across the entire genome (unbiased, without prior hypothesis about the genes for which expression pattern may be altered and without choosing which genes to focus on or study) . Genes encode proteins which carry out an array of biological processes in the body, including processes that are essential to the immune system response manifested by exposure to Copaxone®. So-called gene "microarray technology" allows scientists to observe which genes are "turned on" (in scientific terms, "upregulated") , as well as which genes are "turned off" (in scientific terms, "downregulated") after exposure to various conditions, including stimulation by pharmaceutical products, via measuring the level of mRNA, which is the transitional phase between genes and proteins along the translation process. Teva's gene expression analysis of mouse splenocytes, as well as a human monocyte cell line (THP-1) , exposed to Copaxone®, reveals favorable, upregulation of anti-inflammatory genes. These studies provide support for the vast experimental evidence that Copaxone® exerts its well- established therapeutic benefits in part by modulating the immune system to turn on beneficial (i.e. anti-inflammatory and neuroprotective) genes and turn off harmful ones (i.e. pro-inflammatory) .

Several competitors have sought approval to market putative generic versions of the drug in foreign countries. Although many of those jurisdictions have required applicants to conduct clinical trials as a condition of approval—and none of those jurisdictions has approved a generic version of Copaxone®—others have not been as careful, and those countries since have allowed purported Copaxone generics to enter the market without proof of the equivalence of the putative generics to Copaxone®. In particular, the findings for Probioglat discussed below should be carefully addressed, given the serious clinical reports from Mexico following introduction of this purported generic to the market. The complaints expressed by MS patients treated with Probioglat in Mexico included adverse reactions (increased injection site reactions and post injection reactions) and increased occurrence of relapses, even in patients who had been stable for years under Copaxone treatment. These effects may be underlined by a biological imbalance between anti-inflammatory and pro-inflammatory processes, which may be discernible in gene expression differences such as those described herein. The pro-inflammatory signal identified in pre-clinical analyses and its potential association with boosting of the autoimmune mechanisms of disease following switching to Probioglat treatment should raise concerns for the potential health consequences of these differences .

The Teva Patient Support Program in Mexico has an extensive database. Given that patients can switch between branded and purported generic GA, all patients are kept within the database and are provided with patient support services. Interestingly, the database shows differences in patient reports between 2012, when patients in the program were receiving only Copaxone ^® , vs 2013, when patients were receiving both Copaxone ^® and Probioglat.

The number of relapses reported by patients in Teva' s Patient Support Program on a monthly basis during the years 2012 and 2013 i. It is again clear that when Copaxone ^® alone was in use (i.e. throughout 2012) the overall, as well as per-month number of relapses was lower than that reported when Probioglat was present in the market (i.e. throughout 2013) .

Discussion — Examples 7-8

Gene expression data presented herein for Copaxone ^® further demonstrates the highly complex mechanism of action of GA, given that many of the GA-induced functional pathways in these experiments coincide with known mechanisms of GA activity in MS patients . Furthermore, the data suggests that other glatiramoids are associated with a significantly altered gene expression profile and thus would probably not behave the same as Copaxone ^® . Most importantly, these biological differences could lead to a marked difference in safety or efficacy profile over the course of chronic treatment.

Probioglat, a purported generic of Copaxone®, has been in commercial use in Mexico since January 2013. The introduction of Probioglat has resulted in a spike of injection site reactions and post injection reactions, as well as occurrence of relapses, even in patients who had been stably in remission for years. Accordingly, several pharmacovigilance reports have been issued by HCPs, and patients expressed complaints in the local media and in Teva' s Patient Support Program.

The high occurrence of relapses and adverse events after the treatment switch to Probioglat may be due to an immunological imbalance favoring pro-inflammatory effects, instead of the well recorded beneficial effect that Copaxone induces, reducing pro-inflammation and boosting anti-inflammation .

Overall, similarities in the physicochemical properties of the glatiramer acetate mixture are observed between Copaxone and

Probioglat, as well as other purported generics, particularly when using common non-specific analytical methods. However, clear differences are observed between Copaxone and purported generics when applying high resolution methodologies targeted at characterizing functionally relevant elements, e.g. IMMS analyses concomitantly capturing composition, size and charge distribution; and gene expression analyses capturing pro-inflammation distinctly upregulated by purported generics but not Copaxone®. Gene expression studies thus help explain the biological impact of the physicochemical differences observed, providing insight into some of the factors that may underlie the observed reduction in efficacy and parallel increase in adverse events reported with purported generic glatiramer acetate, notably Probioglat in Mexico.

As part of Teva' s ongoing commitment to better understand Copaxone®, Teva studies its effect at the level of gene expression across the entire genome (unbiased, without prior hypothesis about the genes for which expression pattern may be altered and without choosing which genes to focus on or study) in a variety of immunologically relevant model systems, including mouse splenocytes, human monocytes, and peripheral blood mononucleated cells (PBMCs) from MS patients. The genome-wide approach is critical, because two glatiramoids can appear identical based on a small panel of genes, yet differ significantly in their impact on other genes that are potentially highly relevant to safety and/or efficacy. Using multiple model systems is equally critical, since acting as an antigen, Copaxone significantly impacts a variety of immunological cell types. The unbiased approach allows identification of genes and pathways with subtle, yet robust, differential expression patterns following stimulation by different glatiramoids in different experimental contexts. The functionality of identified genes and pathways is then described based on experimental data reported in the peer-reviewed literature. The research has also shown that various model systems capture different aspects of Copaxone's mechanism of action, such that no single cell type or system tested was sufficient to fully characterize the biological impact of this medicine.

Example 9

Differences in gene expression induced by Palimunol versus branded GA

To identify differences between Copaxone ^® and differently manufactured glatiramoids, differential gene expression analysis was performed in this study to compare directly between profiles induced by Copaxone ^® and by the purported generic Polimunol. Based on previous power calculations (using the R package ssize.fdr), to detect differentially-expressed genes with a fold- change between treatments of as low as 1.3 with 80% power the experiment was designed to include six replicates of each condition. The order of sample processing was randomized with respect to treatment in order to avoid creating confounding batch effects. Cells from a human monocyte cell line (THP-1) were, stimulated with either Copaxone ^® , purported generics from several manufacturers including Polimunol by Synthon, or vehicle control (mannitol) for 6 hours. The 6 hour timepoint was selected because the greatest effects across all treatments were observed at this timepoint in the previous study described above in Example 1. RNA was extracted and expression profiled genome-wide using the Affymetrix U133 Plus 2.0 chip. Three batches of Copaxone ^® and one batch of Polimunol were comparatively tested in six replicates each. RNA processing was performed by Expression Analysis (NC, USA) .

Differentially-expressed probesets were identified across conditions using linear models for microarray data (LIMMA) . For comparing Copaxone ^® (''GA") and purported generic, comparisons were corrected for mannitol control (i.e., [GA vs mannitol] was compared to [purported generic vs mannitol] ) . Probesets were filtered by calls of presence on the chip for the relevant samples in the comparison (to be considered present at a given timepoint, a probeset was required to have on average a call of present or marginal across the relevant samples at that timepoint) . Probesets were mapped to genes using the U133 Plus 2.0 chip annotation from Affymetrix. Unless otherwise specified, all probesets called present for a gene showed the effect discussed above,- where all multiple probesets were present for a gene, p values are reported for the most significant probeset.

Upregulated and downregulated genes were analyzed separately for pathway enrichment, using DAVID [Huang, D. ., Sherman, B. T. & Lempicki, R. A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37 , 1-13 (2009)]. Pathway enrichment results were visualized using volcano plots, plotting -log p-values versus enrichment scores. For GA MOA, to obtain top-gene lists of appropriate size (tens- hundreds) for use with DAVID, an absolute-value fold-change cutoff of 1.5 and p-value cutoff of le-3 were utilized to obtain gene lists for pathway enrichment. For comparisons between GA and Polimunol, upregulated or downregulated genes with FDR-adjusted p-values<0.05 were used for pathway enrichment. DAVID runs were conducted on Sept. 12, 2014. Please note that the GO databases are updated daily (as noted on the GO site : www. geneontology. org/GO . downloads . ontology . shtml ) and therefore performing the same enrichments on the same genesets may yield slightly varying results depending on the rundate. Pathway p-values may change slightly between runs conducted at different times; the overall picture of enriched pathways, however, is expected to remain consistent . Genes differentially expressed between Copaxone ^® and mannitol control are enriched with a variety of pathways in Kegg and GO (molecular function (MP), biological process (BP), and cellular component (CC) ) , many of which affect immunological responses, demonstrating Copaxone ^® ' s complex mechanism of action, as shown in Figure 23. Pathways enriched among top probesets modulated by Copaxone ^® versus mannitol control are shown in Table 12. More than 80% of the pathways that enriched among top upregulated genes in the previous study were also enriched among top upregulated genes in the current study.

As an example at the individual gene level, IL1RN was significantly upregulated (adjusted p<2.8e-10), as shown in Figure 24, which is consistent with the previous study described in Example 1 above. This gene encodes for the protein IL-lra, which inhibits the activities of pro-inflammatory cytokines IL-la and IL-lb.

The probeset for IL10, which had been observed to be upregulated by Copaxone ^® above in Example 1, was called absent in this experiment, but was nominally upregulated (p < 0.029) . However, the IL10 receptor ILIORA was significantly upregulated (for the single probeset for this gene, which was called present) (adjusted p < 2.8e-14) .

Genes analyzed for pathway enrichment (Table 12), using DAVID (conducted September 12, 2014). Performing the same enrichments on the same genesets may yield slightly varying results depending on the run date (GO databases are updated daily: www . geneontology . org/GO . downloads . ontology. shtml ) .

Table 12. Human monocyte study: pathways significantly enriched among genes significantly upregulated by Copaxone ^® relative to mannitol at 6 hours

ı96

ı97

ı99

200

201

202

203

204

205

 211

213

214

215

216

218

219

220

223

224

226

The gene expression patterns induced by Copaxone ^® and Polimunol treatment were compared directly. The differential expression results were filtered based on the variability in observed control treatment effects relative to previous studies, to obtain a conservative subset of highest-confidence probesets. These analyses found that 27 highest- confidence probesets, representing 21 distinct genes, differed significantly by adjusted p value in expression between the two treatments (14 probesets downregulated, 13 upregulated by Polimunol relative to Copaxone ^® ) . The upregulated and downregulated probesets are illustrated in Table 13 and Table 14, respectively.

Table 13. Human monocyte study: probesets upregulated by Polimunol relative to Copaxone ^®

ID Gene raw . FC AveExpr P. Value adj .P.Val

202436 s at CYP1B1 1.328778115 •10.99251935 2.76E-15 1.51E-10

202435 s at CYP1B1 1.291947504 11.10690276 1.98E-11 2.70E-07

202434 s at CYP1B1 1.34300307 8.896124188 5.54E-10 3.79E-06

229055 at GPR68 1.233303306 7.906128859 3.58E-09 1.50E-05

202437 s at CYP1B1 1.283470087 11.35502759 5.53E-09 1.96E-05

212665 at TIPARP 1.170151206 9.316307674 2.29E-07 0.000543566

1554966_a_at DOC1 1.127401263 8.443050186 5.83E-07 0.001274168

204684 at NPTX1 1.121904593 10.50026157 4.27E-06 0.00556324

PDCD6

229354_at 1.082379299 10.56416164 8.47E-06 0.009858651

/// AHRR

206710 s at EPB41L3 1.17828072 6.683285506 3.11E-05 0.021766496

204135 at DOC1 1.093724798 8.540804821 4.46E-05 0.028883673

1569690 at CCDC36 1.140648392 5.595578016 5.04E-05 0.030714439

211067 s at GAS7 1.080052886 9.66677524 5.29E-05 0.031621345

Table 14. Human monocyte study: probesets downregulated by Polimunol relative to Copaxone ^®

The gene with the highest fold change among those upregulated by Polimunol relative to Copaxone ^® was CYP1B1 (adj p < 1.5e-10), a member of the cytochrome P450 superfamily of enzymes. All four present probesets for this gene in this study showed similar results, as exemplified in Table 13. As shown in Fig. 25a, CYP1B1 is significantly upregulated by Polimunol stimulation in human THP-1 monocyte cell line compared to Copaxone ^® stimulation at 6 hours. A second example is shown in Table 13 and Fig. 25b, a probeset for GPR68 which was also upregulated by Polimunol relative to Copaxone ^® (adj p < 1.5e-5) . Two probesets for the DOC1 gene were significantly upregulated by Polimunol relative to Copaxone, as shown in Table 13.

One of the probesets downregulated by Polimunol relative to Copaxone ^® was ADRB2, the gene encoding the beta- 2 adrenergic receptor. As shown in Figure 26, ADRB2 is significantly downregulated by Polimunol stimulation in human THP-1 monocyte cell line compared to Copaxone ^® stimulation at 6 hours. Discussion - Example 9

Copaxone ^® treatment was compared with treatment with the purported generic Polimunol (manufactured by Synthon) , as well as a mannitol control. More than 80% of the pathways that enriched among top upregulated genes in the previous study were also enriched among top upregulated genes in the current study. The results show concordance with the earlier study and confirm the gene expression patterns associated with Copaxone treatment of human monocytes - i.e. the complex, yet consistent mode of action of Copaxone ^® in this immunological cell type.

As an example at the individual gene level, IL1R was significantly upregulated (adjusted p 2.8e-10), consistent with the previous study described in Example 1. This gene encodes for the protein IL-lra, which inhibits the activities of pro- inflammatory cytokines IL-la and IL-lb.

Overall, the results demonstrated that the effects of the complex biological mechanism of Copaxone ^® observed in prior studies were mechanistically consistent with the effects observed in this study, corroborating the validity of this approach for studying glatiramoid functionality in treatment paradigms.

The study also identified significant differences between Copaxone ^® and Synthon' s Polimunol. The results show that 27 highest-confidence probesets, representing 21 distinct genes, differed significantly by adjusted p value in expression between the two treatments (14 probesets downregulated, 13 upregulated by Polimunol relative to Copaxone) .

The gene with the highest fold change among those upregulated by Polimunol relative to Copaxone ^® was CYP1B1 (adj p < 1.5e-10), a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism.

A second example is a probeset for GPR68 which was also upregulated by Polimunol relative to Copaxone ^® (adj p < 1.5e-5) . After traumatic brain injury, cerebral cortical astrocytes abundantly expressed GPR68, suggesting a role in reactive astrogliosis . Two probesets for the DOC1 gene were significantly upregulated by Polimunol relative to Copaxone ^® . DOC1 is also known as CDK2AP1, or cyclin-dependent kinase 2 associated protein 1. DOC1 has been implicated as a locus for susceptibility to MS. (International Multiple Sclerosis Genetics Consortium (IMSGC) , Genes Immun. , 2010) . One of the probesets downregulated by Polimunol relative to Copaxone ^® was ADRB2, the gene encoding the beta-2 adrenergic receptor. Agonists for this receptor have been reported to affect antigen cross- presentation by dendritic cells (Herve et al, J Immunol, 2013), alter cytokine secretion in human PBMC (Hilbert et al, Plos One, 2013), and change the proportions of myeloid cells in mouse brain under TNFc treatment (Laureys et al, J Neuroinflammation, 2014) . In addition, signaling via this receptor in FOXP3+ regulatory T cells has been shown to enhance the suppressive function of these cells (Guereschi et al, Eur J Immunol, 2013) . This functionality coupled with the observed expression levels of ADRB2 in Figure 26 warrants further investigation .

These initial studies show clear and significant differences between Polimunol and Copaxone ^® in terms of impact on genomic profiling, including expression of genes with relevance for safety. Follow-on experiments are currently underway in both THP-1 cells and other model systems to further elucidate the differences identified to date. Substantial differences between Polimunol and Copaxone ^® were also identified using physicochemical methods and biological methods. Therefore, the gene expression differences described here, albeit siibtle in terms of fold change, may represent chronic treatment effects that could have a clinically significant impact, and warrant further investigation in the interest of keeping MS patients safe.

Example 10

Differences in gene expression induced by Polimunol versus branded GA in mouse splenocyte gene expression studies

Immunological cells, particularly T cells, are critical to the antigenic mechanism of action of Copaxone ^® , thus post-treatment gene expression modulation needs to examine such relevant cell types, including lymphocytes .

As one approach to modeling these effects, a splenocyte system was utilized, in which mice were first immunized with either Copaxone ^® or Polimunol, and then sacrificed, having the splenocytes stimulated ex- vivo with Copaxone ^® , Polimunol, or medium. This model was used to simulate switching between medications compared with consistent use of one medicine or the other. A total of 157 samples were tested, and gene expression was measured using the Mouse Genome 430 2.0 Affymetrix chip.

Some similarities are observed between the genes modulated by Copaxone ^® in a mouse splenocyte model and in a human monocyte (THP-1) model: a prior study indicated that 1,378 genes were modulated by Copaxone ^® in both systems, while another 6,691 were modulated only in splenocytes and another 2,121 were modulated only in THP-1 cells (MSBoston Joint ACTRIMS-ECTRIMS 2014 Meeting, P282) . These findings indicate that the majority of the impact of glatiramoids is cell type and tissue specific, including different interactions with lymphocytes versus antigen presenting cells, and thus several different immunologically relevant model systems are required to study the various implications of treatment with this NBCD. Copaxone ^® -modulated genes Mechanism of Action (MoA)

Analyzing splenocytes from mice immunized by Copaxone ^® and later activated with Copaxone ^® , 16,647 probesets were significantly modulated relative to medium (8,342 upregulated and 8,305 downregulated) . The fact that over one third of the total probesets expressed in this tissue (i.e. 22,524 probesets called present on the chip) are significantly downregulated, and similarly over one third significantly upregulated, by Copaxone ^® treatment demonstrates the complexity of Copaxone ^® ' s mechanism of action in this model system. Copaxone ^® treatment upregulated key anti- inflammatory cytokines 1110 and 114 (adj p < 2.3e-24 and 5.1e-35, respectively; Figure 27a-b) as well as markers of regulatory T cells, Foxp3 and Gpr83 (adj p < 3.4e- 23 for Foxp3; adj p < 4.2e-33 and 9.0e-31 for the two Gpr83 probesets; Figure 27c-d) . Copaxone ^® downregulated pro- inflammatory cytokines, such as 1112a (adjusted p < 8.3e-31; Figure 27e) . Consistently similar effects were observed for both immunization conditions (p values given above correspond to Copaxone ^® immunization, and are within the same order of magnitude for immunization by Polimunol) . Copaxone ^® -modulated pathways

After imposing a conservative fold change filter of |FC| ≥ 2, 411 probesets are upregulated by Copaxone ^® relative to medium (in Copaxone ^® -immunized mice) , and these probesets enrich for 76 pathways. These pathways include relevant aspects of Copaxone ^® 's mechanism of action such as the cytokine-cytokine receptor interaction pathway identified previously in the THP-1 study for Copaxone mechanism of action (as well as differences observed with Polimunol) . Similarly, 485 downregulated probesets are detected, which enrich for 56 pathways. Both the upregulated and downregulated pathways are depicted in Figure 28. The full list of pathways entiched among top probesets modulated by Copaxone ^® relative to medium is provided in Table 15.

Table 15 : Pathways enriched among top probesets modulated by Copaxone ⁹ relative to medium in splenocytes from mice immunized with Copaxone ^® (Pathways enriched among top upregulated probesets listed first followed by pathways enriched among top downregulated probesets) .

Category Term C* Pvaiue Fofd Enrichm Dcnfan rit

GCrTiRM_ F_AU. 2.11E-11 kESG_MTHWAY 2.36E-11

GOTER JX AU 5.65 E- 11

GOTER _CC_ALL 2.17E-10

GCmRM_CC_AU. 4.2SE-10

G0RR J!P_AU. 1.66Ε-0» _*ATHWAY 1.67Ε-0Β

GOTE!*M_oP_ALL 1.98 E-06 eOTBtM_&P_AU. 3.49Ε-Οβ

L81E-CS 2.20E-05 2.SSE-06 4.30C-CB U 1.S4E-07 9J1334149 4.35E-OS

S 3.93E-07 1SL32913C2 7,33 E- 6

65 3 -H-0-7 L&473344J S.16E-0S

7 6.27E-0S 12 £270722 0.0002*55B

7 1.06E-Q5 11.910S527 000033*72

13 2.S9E-0S 5680S331 OOO03534S 10 2.7OE-06 B.09O3774B 0.00035JS1 IS 2 13E-05 3.995(5716 000037779

S 2.40E-OS 1ZL3556-2 0.0003S277

S 2.S6I-0O 3&40K9CS 0Ο003Ϊ457

9 3MX.-0S J5172249 Q 00031657 24 2.03E-06 3.13177103 000050318 13 «.S4£-0e 151130595 O 0O06S4O3 12 UIE-OS 5J33S8497 000110231 19 1.22E-05 3.35789938 000114199

19 1221-05 3357S9938 000114199

18 2.D7TH15 3.Ϊ779411 0.001731S5

7 2.01E-05 11ΛΒ39495 0.00177599 24 2-S7E-Q5 Z5&024775 0.00204526

GOTc R¾i_BP_ALL 8 2J6Z-05 rL5S628202 0.00204313

GOT! I¾M_5P_A11_ I! 2.75E-05 S.17062S-8 000208529

GOTERM_rP_ALL U 2J2E-05 4.46497247 000210856

GOTTI¾M_-?_ALL 5 3.4M-05 22.7S41SH 0.00231024

GGTEKMJW*_ALL 8 4JEE-05 Β.09Ο3774Ϊ 0.00 79017

GOT£R __- ⁿ _ALL S 52EE-05 7.17171861 000323223 GOTERM_Si*_AU. 5 5.2SE-05 7 S7171.il 0.00323223

GOTc K _&P_ALL GO004S5Z2-positive regulation of cellular proc ss 41 000014045 U3S2S92S O.0OS25294

€ΟΤ»Μ_οΡ_Α GO¾006952-defer.ie 18 0.0001494 2.18687478 0.00-46-21

«ncra _Bi>_AU. SttOOOts-29-Jipid meaboiic process 28 0.0001SS13 2_2430S674 0.01046917

GOTliS _ei>_Aa GO:OOfl6 t56^a«o ^ n^ oi« prc S 0.00019444 2124657S5 O.01OS2493

GOT RM_J1P_ ALL GOa ffia^t^Kl r e regulation of lymphocyte activation 10 00O0372S1 4.43964129 0.01839122

GOTcRM_S)>_AlL GOtf031399~regulation protein roodfkatton process 12 000036131 3.70237613 0JDlS39aS8

GOTERM~8.P~ALL G OOO«219-ceil 24 aoormssi 21240*1222 001*45504

&OTERM_Bf>_ALL GOO0u«91S-aaoptosis 23 000041493 225151871 001925699

24 a 00049S 22 2.20Ο9ΟΪ73 0.02O06939

10 0.00044S78 4.33413078 0.02013394 23 00004*402 22831191 0.02032437 12 a.O0O51i6 355187303 0.020MS6

10 000053242 423333704 0.02047943

6 000049453 8.737607*. 0020522S1

11 000048296 3.38809402 0.02058357

12 000059269 3.49504306 002223545

8 0.0006167 529551979 002512736

11 0.0007042 3.70808967 0.02 121-3 5 00007624S 11.3770933 0.02664025

10 000080674 400073611 002756213 23 O000BS0O4 2.1637056 002841182

42 0.0009007 166566595 0.0288702

9 000029543 5.1901528 0.02894292 20 000088925 232630662 002909335

Category Term Count Pvalue Fold Enrichm 6en$amini

GOTS M_ :_AU. G «044425~!T»n*fariepart 167 3.13E-1S LS3&62-01 790E-13

GOTER jXJsa GO:Q031224~ir«rin5ic to membrane 140 -15 1.77744709 UlE-12

QOTERM_CC_AU. GaoaiBCai-intefTaf to membrane 135 3.09E-14 -.7SS31M7 2 -12

SOTHRM_ F_ALL GOc0004872 "receptor activity 59 -15 107839222 ilOE-12

GOTERM_CC_AU. GO:cei-O20-rTwn*rarte 172 3.65E-12 1.50486701 2-32E-10

GOTERM_MF_AU.

GOTERM_MF_AlL

G DTERM_fi _AUL

GOTERM_MF_AU.

GC7T£R _AU.

GO cRM_CC_AUL

GOTERM_C _AU.

GcraaM_cc_AUL

GOTEH _ F_AiL

GOT£RM_CC_AU.

_PATHWAY

GOTERM _ALL

GCn¾R j_C_ALL

GOTWM_Bf_.AU.

GC r£RM_3P_ALL

GCrriHM_3P_AU.

GOTERM_BP_ALL

GOTBUM_OC

GOTERM_BP_AU.

GCfTER _BP_ALL

GOTERM_eu>_AUL

GOTERM_MF

G OTERM_BP

GOTERM_CC_ALL

GOT£RM_SP_AU.

GOTERM_f.!f_Aii

GOT£RM_8P_AU. GO:0007155~cell adhesion 20 2.74792344 0.0136546

G OTERM_5P_ GCTCO22610~tlidogI3l adhesion 20 OJ00O10998 2.74792344 0.0136546

GOTERM_SP_ALL Ga0007626l0OTno!ory behavior 11 0.0001342 3 56274248 0.01545668

GOTS M_Mf_AU. G ot»8201~bep«rin binding 7 0 O0024OS8 7.57520244 0.01587561

GQTERM_MF_AU. G oooiSTl-pattern binding S 0X 029954 5.99356677 0.01726258

G OTERM_MF GO:oa30247~polysacchariae binding B 0.O0O29954 5.99356677 0.01726258

GCJTER _BP_ALL :u0u69O9~phagOCyt05i5 3 0.00017473 65034188 0.01759075

GOTERM_SP_AU :0032501~rn-itice]luiar arganismal process 77 0.00017032 1-47960251 0.01828376

G OTERM_&p_ALL ~CW06954~irr!iannmatory response 14 000020677 3.41429487 0.O1957233

GOTERM_Sf_AU. :004233O-taxis 10 0JD0022296 4.72022333 0.01992884

. Garx»»35~chemotaH5 10 0.00022296 4.72022333 0.01992884

G OTER GO:0005578~proteinaceous extracellular matrix 9 0.00121751 4L19921S7S 0.0254587

G OTERM LL .00O7136~G-protejn coupled receptor protein signaling pathway 17 O.O0O35255 2.79500864 0.02970748

GCrrERM_MF_AI_L :C001664~G-protein-coupled receptor binding 7 0.00063894 6-39157706 0.03248313

GQTER _ F_ALL GO:0Coe009-chemokii» activity 6 0-0007267» 7.96B71945 0.03324267

GOTERM_BP_ALL G WXJOB037¾il recognition 000044777 177961539 0.03406274

GOTERM_BP_ALL GO:CC6O900" eukocyte migration 7 OJ00043774 &.82B5S974 0.03494842

G OTERM_ F_AJLL Ga0O42379-cherr«okine receptor binding 0.00090307 7.62225339 .03747238

G OTERM_M _ALL :0OQ493O~G-prQiein caupied receptor activity 12 0.0010892 3.24651533 .03Β2309·

GOTCRM_&P_AU. GO?004e583~Tegulat!on of response to stimulus 19 000053982 2.50469508 0.03909905

GCflERM_as GO0060326-cell chemotaxis 6 0JXX1571S2 S.36153846 0.03958S65

GOTERM_SP_AU. GO:0Q3O595~leulu cyte rfiemotaxis S 0.00057152 S.36153S46 0.03958565

GOTERM_MF_AU. G oao5102~receptor bincing 21 0.00105337 2.23938466 0.04001704

GOTERM_cc_AU. GQ0031012~e«racelfiilar rratnn 9 000218595 3 B392a571 00 1B5565

GOTERM _Aa GO:0Ou7165-5!gnaf transduction 51 0.00074467 1.58780278 0.04918842 Copaxone ^® MoA discussion

More than two thirds of the probesets expressed in the spleen were significantly modulated by Copaxone ^® treatment, and the top modulated probesets in either direction were enriched for many relevant pathways, including immune response and cytokine -cytokine receptor interaction pathways. Key anti- inflammatory cytokines, such as 1110 and 114, and regulatory T cell markers, such as Foxp3 and Gpr83, are upregulated by Copaxone ^® , while pro- inflammatory cytokines, such as 1112a, is downregulated by Copaxone ^® treatment in this model system, consistent with induction of a Thl to Th2 shift. Thus, these studies help to illustrate the complexity of Copaxone ^® ' s mechanism of action (impacting thousands of genes in over 100 different pathways) , and provide validation of the experimental system Polimunol and Copaxone ^® comparison: differentially expressed genes, under Copaxone ^® immunization

When splenocytes from Copaxone ^® - immunized mice were activated with Polimunol and compared to activation by Copaxone ^® (as reported in the prior section) , controlling for mannitol control, 223 probesets were found to be differentially expressed (208 were upregulated, 15 were downregulated) . The top 25 upregulated probesets by Polimunol versus Copaxone ^® are reported in Table 16, and include many interferon- induced genes as will be further discussed in the pathway enrichment section below. The 15 downregulated probesets by Polimunol versus Copaxone ^® are reported in Table 17.

Polimunol and Copaxone ^® comparison: differentially expressed genes, under Polimunol immunization

When splenocytes from Polimunol -immunized mice were activated with Copaxone ^® versus Polimunol, 431 probesets were found to be differentially expressed when both were corrected for medium (301 were upregulated, 130 were downregulated) . The top 25 upregulated probesets by Polimunol versus Copaxone ^® are reported in Table 18 and consistently with the reciprocal study design (prior paragraph) include many interferon induced genes, and the top 25 downregulated probesets by Polimunol versus Copaxone ^® are reported in Table 19.

Table 16: Top 25 probesets upregulated by Polimunol versus Copaxone ^® in splenocytes from Copaxone ^® - immunized mice

1421551_s_at j lfj202b .48 j3,02E-10

1451905_a_at Mxl 1.75 2.21E-14 4.98E-10

142l998_at jTor3a 1 1.29

Ifi202b ///

1457666_s_at LOC100044068 1.49 1.25E-13_ 1.41E-09

1424339^at ]¾-13 1ι¾ο?

1418293 at Ifit2 1.38 2.24E-13 1.69E-09

1423555 a at ]lfi44 1,62 ;2.85E-_13 Jli¾¾

1425917_at 1.63 4.06E-12 2.29E-08

14215?6_s_at J7.03E-08

1456164_at AW011738 1.20 2.32E-11 9.03E-08

jTpr3a , 1.25 .2.40Ε-Π liHal

I449455_at Hck 1.16 4.06E-11 1.33E-07

1448775_at LOCI 00862473 ^! 1.21 kl6E-ll 1 W3E-07

1438868_at Phfl ld 125 4.42E-11 1.33E-07

Tor3a l.41E-07

1434401_at Zcchc2 1.16 5.31E-11 _^ 1.4-1E-07

1450027_at Sdc3 1.25 1.14E-10 2.71 E-07

143533 l_at Pyhin L j U9 2.12E-10

1436120_at Setdb2 1.16 2.43E-10 5J21E-07

145133 _a_at .i 1-12 3.00E-10 ,6.14E-07

1424921_at Bst2 1.23 3.99E-10 7.83E-07

1419603_at i lfi204 1.44 5.16E-10 9.70E-07 ώ.1

1438037_at Herc6 1.27 6.06E-10 1.09E-06

1419026 Daxxfe 1.21 1

Table 17 : 15 probesets downregulated by Polimunol versus Copaxone" in splenocytes from Copaxone ^® -immun zed mice

1448107_x_at KM -134 _^ 2.21E-07 0.000114521

143977 l_s_at D13ERTD608E Ί

1415823_at Scd2 -1.35 3.68E-06 0.001275671

1442544_at j lghm ] 0.001916738

1415824 at Scd2 -1.31 2.36E-05 0.006376176

1415822 at Scd2 j-1.28; ]3.43E-05 0.008489827 1429100_at Ccdc71I -1.08 3.68E-05 0.008965532

1427756_x_at._ , 4,61Ε-05 0,010874062

1449325_at Fads2 -1.16 0.000104782 0.022291363

1416188_at | Gm2a _L :,, 0.0p0.10?828 0.023255206

1424567_at Tspan2 -1.13 0.00016899 0.033873925

0.000216398 0.042416254

Table 18 : Top 25 probesets upregulated by Polimunol versus Copaxone ^® in

1438004_at Papd7 1.19 9.92E-11 3.44E-07

142672 _. i_s_at . 1.12 j l.80E-10 5.81E-07

1426716_at Tdrd7 1.21 2.85E-10 8.56E-07

1419598_at Ms4a6d J.33

1420796_at Ahrr 1.47 1.38E-09 3.45E-06

1438148_at Cxcl3 1.68 6.34E-09 9.54E-06

1451905 a at _; 1.09E-08 1.54E-05. Table 19: Top 25 probesets downregulated by Polimunol versus Copaxone'" in

1451461_a_at Aldoc -1.60 3^75E-11 2.11E-07

1454757 s at ΙιδζϊΕ 3.44E-07

It is important to note that for either immunization (Copaxone ^® or Polimunol) , 1118 and its receptor I118rl are downregulated (and inhibitor I118bp is upregulated) by both of the activation treatments, Copaxone ^® and Polimunol. 1118 is downregulated significantly less by Polimunol than by Copaxone ^® (differential expression FDR p < 9e-6 (FC 1.20) with Copaxone ^® immunization and FDR p < 2e-9 (FC 1.26) for Polimunol immunization) . Downregulation of both 1118 and I118rl expression upon Copaxone ^® treatment was also reported in an earlier splenocyte study of similar design (Bakshi et al, 2013) . Boxplots of 1118 expression are shown in Figure 29. The probesets significantly entiched among top probesets modulated by Copaxone ^® relative to medium is provided in Table 20. Table 20 : Top probesets significantly differentially expressed between Polimunol and Copaxone ^® treatment (corrected for medium control) in splenocytes from Copaxone ^® -immunized mice.

Probes et Gene raw.FC AveExpr t P Value adj.P.Val B

1421551. s_3 lfi202b 1.47550912 9.16666894 10.5600946 6.69E-15 3.02E-10 22.5317107 1451905_ a_< Mxl 1.75432592 8.47709648 10.2249021 2.21 E-14 4.98E-10 21.4748998 1421998. at Tor3a 1,2928856 9.17160227 9.82507613 9.33E-14 1.40E-09 20.1932231 1457666. s_a tfi202b /// LC 1.49450011 8.60997583 9.74469879 1.25E-13 1.41E-09 19.9328881 1424339..at Oasll 1.46319835 9.8248556 9.60829298 2.05 E-13 1.69E-09 19.489091 1418293. at Ifft2 1.38359824 10.906172 9.5837092 2.24E-13 1.69E-09 19.4088447 1423555. a_< lft44 1.62258196 9.94187992 9.51838876 2.85E-13 1.84 E-09 19.1952407 1425917..at Ifi44l 1.6309207 8.85125178 8.79871072 4.06E-12 2-29E-08 16.8068255 1421596. s_a ffi44l 1.62779642 8.55050842 8.4667453 1.40E-11 7.03E- 8 15.6855236 1456164..at AW011738 1.19734234 6.98570845 8.33256611 2.32E-11 9.03 E-08 15.2292395 1450454. at Tor3a 1.25024933 8.74969803 8.32329605 2.40E-11 9.03 E-08 15.1976556 1449455. at Hck 1.1582816 10.9515022 8.18380999 4.06E-U 1.33 E-07 14.7215139 1448775. .at Gml6340 // 1.20618615 11.6014591 8.1770987 4.16E-11 1.33 E-07 14.6985633 1438868. at Phflld 1.2483759 10.329053 8.16092351 4.42E-11 1.33 E-07 14.6432337 1428660. s_aTor3a 1.248966 10.5033156 8.11568562 5.25E-11 1.41E-07 14.488379 1434401. at Zcchc2 1.15603797 10.8249905 8.1125305 5.31E-11 1.41E-07 14.4775726 1418191 at Uspl8 1.3S861948 11.5218281 7.91969756 1.10E-10 2.71E-07 13.8156858 1450027..at 5dc3 1.25031078 10.4588938 7.9099888 1.14E-10 2.71E-07 13.7822905 1435331 at Pyhinl 1.19292098 12.437413 7.74536994 2.12E-10 4-79E-07 13.2151145 1436120. at Setdb2 1.15959289 10.4269299 7.71019806 2.43E-10 5.21E-07 13.0937189 1451330. a_.lnpp5b 1.12122817 10.7773832 7.65452165 3.00E-10 6.14E-07 12.30141 1424921 at Bst2 1.22915197 11.6875461 7.578654S5 3.99E-10 7.83E-07 12.6390995 1419603. at lff204 1.43740773 7.15143963 7.51082104 5.16E-10 9.70E-07 12.4043263 1438037..at Herc6 1.27135334 10.4464057 7.46845772 6.06E-10 1.09E- 6 12.2576026 1419026. at Daxx 1.20586588 12.032791 7.44071108 6.74E-10 1.17E-06 12.1614627 1451567. a_iGml6340 // 1.14843448 12.2623403 7.42376782 7.18E-10 1.20E-06 12.1027407 1426716. at Tdrd7 1.17546145 9.815531S5 7.38758714 8.24E-10 1.33 E-06 11.9773091 1426774..at Parpl2 1.23323427 10.568185 7.32082974 1.06E-09 1.60E-06 11.7457533 1426276..at (fihl 1.25213306 10.3259786 7.3202472 1.Q6E-09 1.60E-06 11.7437321 1435665. at Trim30d 1.25197418 9.71194292 7.26872528 1.29E-09 1.88E-06 11.5649255 1431591. s_aGm9706 /// l 1.32351255 11.382458 7.17864536 1.82E-09 2.56E-06 11.2521346 1435330..at Pyhinl 1.20956064 9.18347439 7.12657207 2.22E-09 3.03 E-06 11.0712364 1438716..at Trim30d 1.23305159 7.93829998 7.11825503 2.29E-09 3.03E-06 11.0423392 1421008. at Rsad2 1.40087837 7.80703835 7.0280384 3.22E-09 4.15E-06 10.7288224 1421571. a_ Ly6d/// Ly6 1.12684658 13.613752 6.99594752 3.64E-09 4.56E-06 10.6172805 1435792. at Csprs /// Gm 1.187456 9.75936346 6.97563188 3.93E-09 4.76E-06 10.5466635 1423754. at [frtm3 1.19002363 12.4964655 6.96462013 4.10E-O9 4.76E-06 10.5083857 1457035. .at AI607873 1.33928347 5.46136565 6.96314834 4.12E-09 4.76E-06 10.5032697 1453939. x_eGm9706 1.28772667 8.70376747 6.95300697 4.2SE-09 4.83 E-06 10.468017 1420671. x_a s4a4c 1.11351765 13.1959702 6.9122537 5.00E-09 5.50E-06 10.326351 1426721 5_3Ήρβφ 1.12038515 10.8883102 6.87404388 5.77E-09 6.20E-06 10.1935268 1427059. at Tmeml84b 1.19049436 9.20535S9 6.80169576 7.60E-09 7.97E-06 9.94204892 1453196 a < Oasl2 1.34151303 10.6174821 6.77476842 8.41E-09 8.62E-06 9.84846205 1452231. x_ ndal 1.20215669 12.1489677 6.75397715 9.10E-09 9.12E-06 9.77620711 1417932. at 1118 1.2024199 8.58526778 6.73898284 9.63E-09 9.44 E-06 9.72410174 1420796. at Ahrr 1.35482305 6.39700067 6.68881415 l.lfiE-08 1.12E-05 9.54979119 1426906. at Mndal 1.22985583 12.0834069 6.68154198 1.20E-08 1.12E-05 952452794 1417244. a_< Irf7 1.29690765 11.8707637 6.66482592 1.28E-08 1.17E-05 9.46646104 1456494. a_ Trim30a ///l 1.24228874 10.5953269 6.66073405 1.29 E-oa 1.17E-05 9.45224793 1445897. s_z ffi35 1.09502194 13.2112571 6.64901185 1.35E-08 1.20E-05 9.41153295 1418115. s_aTorlaip2 1.09066644 11.3826254 6.63787659 1.41E-Q8 1.22E-05 9 37285954 1426670..at Agrn 1.16650332 8.38464727 6.61334752 1.55E-08 1.32E-05 9.28767938 1450783. at ffitl 1.31370421 11.6154892 6.57611523 1.78E-08 1.49E-05 9.15841659 1436058..at Rsad2 1.44054736 10.0892795 6.52152657 2.19E-08 1.76E-05 8.96897228 1460603. at Samd9l 1.09852241 13.0008563 6.48452217 2.52E-08 1.99E-05 8.84061078 1450484..a_cCrn k2 1.4069656 9.18452824 6.47037709 2.66E-08 2.06E-05 8.79155778 1452349. x_5 tR205 /// Mn 1.20045125 7.72773058 6.46703491 2.69E-08 2.06E-05 8.77996877 1435529. at Gml4446 1.28471375 11.9844626 6.46256796 2.74E-08 2.06E-05 8.76448031 1455581. x_cGm20559 1.13805761 11.6732978 6,44922028 2.aSE-0B 2.09E-05 8.71820419 1451860. _a_<Trim30a 1.18244967 12.1537452 6.36625749 3.94E-08 2.82E-05 8.43075121 1436562..at Ddx58 1.14667035 11.473735 6.36165042 4.00E-08 2.82E-05 8.41479807 1448380..at Lgals3bp 1.16298116 11.2244145 6.30367575 4.98E-08 3.40E-Q5 8-21414149 1449025. at Ifit3 1.3414478 11.8181697 6.30015076 5.05E-08 3.40E-05 8.20194708 1452087..at Epstil 1.11549904 11.2912312 6.24845347 6.13E-08 4.01E-05 8.02318829 1421009..at Rsad2 1.51117184 7.74253963 6.2035856 7.2SE-08 4.64E-05 7.86817911 1443698..at Xafl 1.18282113 11.9302802 6.20178329 7.30E-O8 4.54E-05 7.86195528 1442130..at Hsh2d 1.1709592 10.2697537 6.16886582 8.27E-08 5J.SE-05 7.7483219 1459151 x_ tft35 1.10594094 11.6543585 6.13185928 9.50E-08 5.87E-05 7.62066485 1436172..at Gm20559 1.1493816 11.5396111 6.07854249 1.15E-07 7.05 E-05 7.43692632 1448575..at »7r 1.09825437 11.0940999 6.07547051 1.17E-07 7.05 E-05 7.4263466 1452160..at TTparp 1.11979242 9.76721315 6.06904538 1.20E-07 7.13 E-05 7.40422136 1451050..at Nt5c3 1.16150561 10.6183063 6.05166841 1.28E-07 7.51E-05 7.34439991 1431095. _a_< Herc6 1.19901119 10.4733187 6.04385458 1.32E-07 7.63 E-05 7.31750846 1423681.at Ftsjd2 /// Rn 1.09083446 10.9815969 6.03884145 1.35E-07 7.68E-05 7.3002584 1449143..at Rtp4 1.24304662 7.42935297 6.02268936 1.43E-07 8.05 E-05 7.24469409 1437636..at Pydc4 1.33382761 8.19945237 6.01217359 1.49E-07 8.27E-05 7.20853136 1450495. _a_ _< lrkl 1.14444626 9.11777277 5.99801423 1.57E-07 8 9E-05 7.15985406 1450276 _a_cScin 1.26600893 8.7352575 5.99419456 1.59E-07 8 9E-05 7.14672584 1427091..at Znfxl 1.16622599 9.5503153 5.99232677 1.50E-07 8.59E-05 7.1403067 1432026..a_i Herc6 1.2332518 9.6340896 5.91285077 2.15E-07 0.00011289 6.86746993 1451777..at Ddx60 1.2572541 9.17655647 5.89999373 2.26E-07 0.00011573 6.82339016 1451655.at SlfnB 1.16818125 11.8030813 5.85259478 2.69E-07 0.00013591 6.6610318 1423071 _x_ 6720475J19F 1.12577119 8.9545691 5.84322799 2.79E-07 0.00013788 6.62897522 1450241. _a_ Evi2a 1.11124373 11.3075457 5.84097845 2.81E-07 0.00013788 6.62127789 1421217 _a_£ Lgals9 1.11289495 12.0356748 5.83616937 2.S6E-07 0.00013886 6.60482433 1424775..at Oasla 1.26381284 10.9682776 5.82921661 2.94E-07 0.00014098 6.58104095 1447851 _x_.AtplOa 1.13412363 9.35777039 5.81806601 3.06E-07 0.0Q01454 6.54290906

1451426..at Dhx58 1.27494236 10.5332943 5.79964551 3.28E-07 0.00015407 6.47994653 1452013..at AtplOa 1.16582075 7.25191599 5.74981475 3.95E-07 0.00018343 6.30981665 1438004..at Papd7 1.15866963 8.7651013 5.72747713 4.29E-07 0.00019722 6.23364804 1453757. at Herc6 1.25111898 9.09811412 5.64424695 5.83E-07 0.00026558 5.95039163 1456890..at Ddx58 - 1.20405595 8.33433728 5.63983971 5.93E-07 0.00026723 5.93541754 1416697..at Dpp4 1.1097733 9.72105276 5.63576616 6.01E-07 0.00026859 5.92157948 1422006..at Eif2ak2 1.23465729 9.21616067 5.61858421 6.41E-07 0.00028336 5.86323608 1424617..at !fi35 1.10413772 12.2660487 5.60315363 6.78E-07 0.00029704 5.8108739 1426278. at !fi27i2a 1.13356673 13.6135311 535624326 8.06E-07 0.00034964 5.65189199 1452676. a_cLOC1005051 1.11295467 9.74168879 533659908 8.67E-07 0.00037225 538541026 1451852..at Tcstv3 1.22404052 6.8712238 532210287 9.14E-07 0.00038891 5.53638704 1449366..at Mrnp8 1.22832664 9.31371883 530428037 9.76E-07 0.00041133 5.47615784 1425405. _a_ Adar 1.10728732 11.4786191 5.48996899 1.03E-06 0.0004295 5.42782879 1429570. at lkl 1.20072042 8.28523783 5.48602776 1.04E-06 0.00043175 5.4145249 1456288..at SlfnS 1.32340243 9.39871024 5.47997663 1.07E-06 0.00043504 5.3941035 1417961. _a_cTrini30a 1.17912824 12.8108758 5.47899844 1.07E-06 0.00043504 5.39080284 1444405..at Pydc4 1.32066484 5.20069324 5.43876125 1.24E-06 0.0004952 5.25516142 1435454. a_i Helz2 1.13249361 123204465 5.43239671 1.27E-06 0.00050243 5.23372972 1430530. _s_a Nmrall 1.17435967 9.31355989 5.37375224 1.57E-06 0.00061706 5.03656379 1438148..at Cxd3 1.69044193 7.09902456 5.35135811 1.71E-06 0.00065812 4.96142512 1422141 _s_a Csprs /// Gm 1.19436756 7.71681771 5.33738357 1.80E-06 0.00068662 4.91458012 1418116. _at Torlaip2 1.08075944 10.7447031 5.32686698 1.87E-06 0.00070743 4.87934914 1425065..at Oas2 1.28607157 10.4532534 5.32376691 1.39E-06 0.0007095 4.8S896748 1436778..at Cybb 1.1006634 12.2766584 5.29025539 2.13E-06 0.0007S482 4.75685109 1428346..at Trafdl 1.15659445 11.2650229 5.28308824 2.19E-Q6 0.0008091 4.73289875 1440522..at Chid 1.11707615 8.8938542 5.26963652 2.30E-06 0.00084269 4.68796879 1418580..at Rtp4 1.16283443 12.43898 5.25438045 2.43E-06 0.00088346 4.63705234 1425374..at Oas3 1.32020993 10.3330288 5.23952375 2.56E-06 0.00092489 4.58751022 1435840..x_. BC147527 1.21647215 7.14546794 5.20034393 2.95E-06 0.00104904 4.45705855 1459913..at TnfeflO 1.10617704 8.60982005 5.19467099 3.02E-06 0.00106241 4.43819454 1418346..at lnsl6 1.1375775 8.67983728 5.17515811 3.24E-06 0.00113118 4.3733569 1440299..at Mb21dl 1.08850433 8.S0638297 5.10764055 4.13 E-06 0.0014208 4.14959418 1452306..at Zfyve26 1.08114798 10.6819271 5.09739051 4.28E-06 0.00146298 4.11570542 1425008. _a_cGml6340/ / 1.14711446 8.2805057 5.07062975 4.71E-06 0.00159849 4.02733237 1426971 _at Uba7 1.0921264 113979875 5.05902098 4.91E-06 0.00165404 3.98904342 1427102..at Stfn4 1.4307997 10.9094731 5.02506971 5.55E-06 0.00184054 3.87722913 1447272.s_a AtplOa 1.16573994 8.48146745 5.00861675 5.S9E-06 0.00191674 3.82313389 1452161..at Tiparp 1.12341519 9.30889526 5.00763194 5.91E-06 0.00191674 3.81989785 1419668. _at Sgcb 1.11311815 8.08482712 4.99202128 6.25E-06 0.00201223 3.7686309 1452973. _at Ppmlk 1.06538857 103472337 4.97566869 6.62E-06 0.00211808 3.71498595 1440866.at Eif2ak2 1.27644426 8.72230965 4.96189632 6.96E-06 0.00220906 3.66985249 1425225.at Fcgr4 1.15148701 7.97090773 4.94964494 7.27E-06 0.00229151 3.62973994 1428843. _at 5-Mar 1.06276215 11.9004332 4.89939887 8.69E-06 0.00270208 3.46559327 1455500 at nf213 1.18104388 12.9664015 4.8925931 8.90E-06 0.00273916 3.44340567

1450322. s_aSlfn3 /// S!fiY 1.32138137 7.84711588 4.8916997 8.93E-06 0.00273916 3.4404939 1419569. a_< Esg20 1.21173809 11.9296506 4.86452698 9.83E-06 0.00299161 3.35202465 1451161. a_ Emrl 1.18065879 9.48930222 4.86302162 9.88E-06 0.00299161 3.3471287 1452348. s_a lfi204/// lfi2 1.22015123 10.6929234 4.85654465 1.01E-05 0.00304061 3.32606974 1451564. at Parpl4 1.13986145 12.0654567 4.85172709 1.03E-05 0.00307242 3.31041282 1418244..at Naa20 1.08893101 11.1644701 4.76808963 1.38E-05 0.00407322 3.03951865 1436899. at Zufsp 1.09784747 11.1470022 4.74873354 1.48E-05 0.00433173 2.97708107 1419599.5_c Ms4a6d 1.33981893 8.57140996 4.74664377 1.49E-05 0.0043355 2.97034589 1443621..at Xafl 1.16509294 7.24967566 4.74194912 1.51E-05 0.00437932 2.95521955 1436472. at SSfn9 1.11910501 8.38309804 4.73923193 1.53E-05 0.00439313 2.94646731 1453562. _a_« Nmrall 1.15341413 9.19098832 4.73002801 1.58E-05 0.00450863 2.91683543 1454809..at Ncoa7 1.09311088 10.3983869 4.7257237 1.60E-05 0.00454843 2.90298546 1436779..at Cybb 1.0941996 11.6457179 4.7126236 1.68E-05 0.00473241 2.86086374 1426970. _a_< Uba7 1.07523655 12.3984639 4.68910631 1.82E-05 0.00510655 2.78536262 1434139..at Parpll 1.09338753 10.840668 4.6805127 1.88E-05 0.00522983 2.75781068 1452178..at Parpl0/// Pl 1.10641059 11.7358548 4.66046456 2.01E-05 0.00552329 2.6936131 1417516. at Ddit3 1.07223921 9.94848573 4.66039944 2.02E-O5 0.00552329 2.69340478 1459973. _x_< Dpp4 1.14507385 7.63353457 4.65962457 2.02E-05 0.00552329 2.69092573 1422140..at Gm7609 1.16864971 8.39169472 4.63609019 2.19E-05 0.00595944 Z61571222 1417685..at Ankfyl 1.06791545 11.0934338 4.61188057 2.39E-05 0.00640602 2.53850302 1423627..at Nqol 1.16457475 6.67427154 4.59518149 2.53E-05 0.00674846 2.48534355 1451755. _a_<Apobecl 1.07861266 9.62528811 4.56307937 2.83E-05 0.00749855 2.38337634 1430700..a_cP!a2g7 1.18443125 10.1013856 4.56135068 2.84E-05 0.00749945 2.37789398 1438948. _x_cTspo 1.10391642 13_5941786 4.5571403 2-89E-Q5 0.0075653 2.36454478 1450291..s_a s4a4 1.12154489 12.4861899 4.55455972 2.91E-05 0.00758904 2.35636554 1419879. _s_aTrim25 1.09549971 12.1244381 4.5525076 2.93E-05 0.00759918 2.34986266 1428615..at Lparfi 1.07528364 9.93379264 4.54743285 2.98E-05 0.00768686 2.33378681 1416695. _at Tspo 1.0780893 12.4808237 4.54588597 3.0OE-O5 0.00768686 2.32888813 1424857. _a_ Trim3 a 1.11791554 10.7165118 4.53973664 3.06E-O5 0.00780763 2.30942125 1446457..at Ddx58 1.16007779 8.02122625 4.53347715 3.13E-05 0.00793348 2.28961716 1442640..at— 1.2168656 9.07831829 4.51929521 3.29E-05 0.00828496 2.24479093 1449078..at St3gaJ6 1.09165835 10.7727541 4.51684697 3.32E-05 0 0083088 2.23705863 1449591.at Casp4 1.10948228 11.1338558 4.50971919 3.40E-05 0.00846848 2.2145572 1418030..at Sko3al 1.08661497 9.54424904 4.49526041 3.57E-05 0.00880366 2.16895999 1416871..at Adam8 1.1193914 9.62857594 4.48900903 3.65E-05 0.0089462 2.14926531 1454668..at Ubr4 1.12814814 11.184894 4.48414411 3.71E-05 0.0089994 2.1339469 1442201..at— 1.1432126 9.81756401 4.47986246 3.77E-05 0.00908403 2.12047102 1436032..at— 1.21380001 11.1380493 4.47297003 3.86E-05 0.00925232 2.09878995 1454169. _a_i Epstil 1.12897335 10.1539562 4.45618995 4.09E-05 0.00974916 2.04606725 1434601..at Amigo2 1.13289174 9.38089015 4.42595648 4.53E-05 0.01075628 1.95129594 1448576..at H7r 1.10438001 9.35743301 4.3992231 4.96E-05 0.01166251 1.86773693 1421550. _a_cTri(Ti34a ///1 1.12211108 9.72957463 4.39764723 4.99E-05 0.01166465 1.86281845 1415713 _a_ _< Ddx24 1.06449185 113232541 4.37956906 5.31E-05 0.01234241 1.80645151 1419667.at Sg b 1.12646472 8.33509646 4.34873052 5.90E-05 0.01363746 1.71054358

1455227. at Ncehl 1.08446292 9.91489676 4.34099563 6.05E-O5 0.01392902 1.68653707 1418612. .at SJfnl 1.09272571 12.96439 4.32568503 6.38E-05 0.01459714 1.63907653 1452318. a Hspalb 1.19057538 7 25960902 4.30400323 6.86E-05 0.01562991 1.57200028 1427127. _c Hspalb 1.21832745 7.30468517 4.29624366 7.04E-05 0.01588217 1.54803323 1419598. at Ms4a6d 1.30010562 8.68960331 4.29561853 7.06E-05 0.01588217 1.54610327 1448303. .at Gpnmb 1.22944041 8.9049785 4.29482104 7.08E-05 0.01588217 1 4364139 1435660. .at LQC664787 1.08388982 8.74033836 4.29173015 7.15E-05 0.01596949 1.5341017 1422511 a_sOgfr 1.07234468 12.3938197 4J24109747 8.48E-05 0.01875548 1.37829561 1437176. .at Nlrc5 1.07682641 12.3735454 4.23337901 8.69E-05 0.01912232 1.35615536 1436633. at Gm 11772 1.14601474 4.72784952 4.22090965 9.08E-05 0.01980988 1.316422 1451082. .at Ftsjd2/// Rn 1.06640728 11.3628274 4.2204656 9.09E-05 0.01980988 1.31506267 1425974. .a_cTrim25 1.08480215 11.7657133 4.20895728 9.45E-05 0.02049028 1.27985683 1417876. .at Fcgrl 1.2323332 7.0806629 4.19894373 9.77E-05 0.0210878 1.24926191 1457069. .at Ascc3 1.11288948 9.43740297 4.19582127 9.87E-05 0.02120788 1.23972903 1429831 .at PikSapl 1.06680759 12.4737143 4.1806008 0.0001039 0.0222095 1.19331067 1449538. _a_cGcntl 1.11915617 8.47448492 4.14722631 0.00011614 0.02447684 1.09181994 1422005. .at Eif2ak2 1.19563857 9.53538322 4.12771094 0.00012393 0.02599698 1.03266263 1449875. _s_aH2-T10 /// H 1.04842787 12.8867189 4.11331035 0.00013 0.02714397 0.98909995 1418722. .at Ngp 1.11092189 12.7881149 4.10510418 0.00013359 0.02776429 0.96431022 1426133. _a_. Mftdl 1.10636222 10.1667831 4.07764709 0.00014629 0.03009875 0.88154944 1424354. .at Tmeml40 1.11754478 9.34810202 4.07577197 0.0001472 0.03009875 0.87590785 1423052. .at Arf4 1.05369833 12.3484921 4.06902312 0.00015052 0.03046771 0.35561388 1456251. .x_cTspo 1.1023499 11.1159008 4.06877418 0.00015065 0.03046771 0.85486562 1423986. _a_<Shisa5 1.04210813 14.2786011 4.03888346 0.00016625 0.03347242 0.76519512 1428378. .at Zc3havl 1.08752006 10.7288018 4.02875397 0.00017188 0.0343001 0.73488508 1420401. _a_i Ramp3 1.12512462 9.98404572 4.00377593 0.00018656 0.0370668 0.66031463 1460657. .at WnUOa 1.12684061 3.35987776 3.98317991 0.00019958 0.03947847 0.59901024 1424444. _a_i l60O014C10l 1.09898446 11.5959589 3.98018984 0.00020154 0.03969221 0 9012418 1428444. .at Asb2 1.13292232 8.24932226 3.95719355 0.00021725 0.04241625 0J5219O117 1439814. .at Atp8b4 1.11510444 9.33960673 3.95146957 0.00022134 0.04302868 030495269 1429588. .at 2810474O19 1.05637397 11.2428969 3.93455457 0.00023387 0.04526887 0.4549451 1433617 _s_s B4galt5 1.11846333 10.5599476 3.92169381 0.O0O24385 0.04679878 0.41700096 1431296 .at Gprl5 1.14301562 6.60205175 3.9193265 0.00024573 0.04695995 0.41002381

Probeset Gene raw.FC AveExpr P.Value adj.P.Val B 1454757. s_g |ff27ll -1.1515249 11.2428344 -6.5569053 1.92E-08 1 7E-05 9.09173948 1415837..at Klkl -1.4082454 7.5804401 -6.3275656 4.55E-08 3J.6E-05 8.29680484 1452956. a_< !ft27ll -1.1424326 10.7927481 -5.9606126 1.80E-07 9.56E-05 7.03136178 1448107. x_c Klkl -13445567 7.49119412 -5.9058876 2.21E-07 0.00011452 6.84359495 1439771. s_3 D13ERTD608 -1.2546842 8.36787505 -5.8507689 2.71E-07 0.00013591 6.65478212 1415823. .at Scd2 -1.3537166 10.2235672 -5.1396945 3.68E-06 0.00127567 4.25571056 1442544. .at Ighm -1.1737796 9.42424035 -5.0083987 5.89E-06 0.00191674 3.82241733 1415824. at S d2 -13093243 10.9433795 -4.6149411 2.36E-05 0.00637618 2.54825457 1415822. .at Scd2 -1.2780512 11.8313256 -4.5073901 3.43E-05 0.00848983 2.20720796 1429100. .at Ccdc71I -1.0849357 10.7147161 -4.4868075 3.68E-05 0.00896553 2.14233223 1427756. x_i lghm -1.1707153 9.14115987 -4.4212385 4.61E-05 0.01087406 1.93653267 1449325. .at Fads2 -1.1644392 8.52583689 -4.1780844 0.00010478 0.02229136 1.18564443 1416188. at Gm2a -1.0836296 10.9313169 -4.163994 0.00010983 0.02325521 1.1427593 1424567. .at Tspan2 -1.1339633 9.59951853 -4.0339051 0.00016899 0.03387392 0.75029377 1436131 .at Siglech -1.1248775 7.91450702 -3.9583983 0.0002164 0.04241625 0.52546999 Polimunal and Copaxone ^® comparison: differentially expressed pathways, under Copaxone ^® immunization

After imposing a conservative fold change filter of | FC | ≥ 1.2, 73 probesets are found to be upregulated by Polimunol relative to Copaxone ^® (medium-corrected, in Copaxone ^® - immunized mice) , and these probesets enrich for 22 pathways, including immune response and response to virus. These pathways may be relevant to Copaxone ^® ' s mechanism of action; several of these pathways are also enriched among probesets modulated by Copaxone ^® relative to control (e.g, immune response and immune system process) . A total of 6 downregulated probesets are detected, which do not enrich for pathways. The upregulated pathways are depicted in Figure 30 and the full list of pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® is provided in Table 21.

Table 21: Pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® (in Copaxone ^® -immunized mice) .

Category Term Count Pvalue Fold Enrichm Benjamini

GOTERM_BP_ALL ∞:0006955-immune response 438E-U 9.95074106 USEJQS

GOTERM_BP_AlL GO:000961≤~re5ponse to wrus S.15E-10 38.2602137 1.S4E-07

GOTERM_BP_ALL GO 0002376-immune system process S.29E-0S 5.57817311 9-3SE-06

G07EHM_BP_Ali GO:0051707~resporise to other organism 8.13E-08 14.9261116 L23E-05

GQTER _BP_ALL GO:0050896-Te5ponse to stimulus 1.3SE-07 3.37128932 1.25E-05

GOTERM_BP_AU. GO:0OO3S07~response to faiotic stimulus L27E-06 10.4567109 9.54E-05

60TEH BP ALL GO:CO51704~rrnjiti-orgar>isrn process US3E-05 10.113868 0.00010525

KEGG_PATHWAV mmu04622:RIG4-iike receptor signaling pathway 147E-05 27.2429078 0.00023467 EGG_PATHWAY rranu04e23:Cytoso6c ONA-sensing pathway 0.00031378 25.6083333 0.00250745

6QTERM_BP_AU. eO.-00 50S7~mnate immune response 0-00030987 14.6891892 0.01731968

60TEHM_ F_ALL G0:0001S32-mideos>de binding 16 0.00118391 2.41112097 0.02621825

GOTERM_ F_AU. (EO:OCB2559~attenyi ribonucleotide binding 16 0.00065903 2.54969114 0.02901942

G0TERM_MF_A1X GO 001833~purine nucleoside binding 16 0.00112323 2.42429649 0.02967043

GOTERM_BP_ALL GO:O0O6952~defense response 7 0.00OE06S5 6.34158823 0.02996091

GOTERM_MF_ALL 60:0030554~ader<yl nudeotide binding 16 0.00106069 2.4376168 0.03492727

GOTER _ F_AU- GO:OCB2553~ribonudeotide binding 17 0.00211744 2.18735104 0.03976457

GOTERM_MF_AU- GO:O032555~purine ribonudeotkie binding 17 0.00211744 Z1S735104 0.03976457

GOTERM_ F_AiL GO:0005524~ATP binding 16 0.00061962 2.55442924 0.04067708

GOTER _MF_AlL ∞ 30001730-2'-5'-olrgoaderiYl3te synthetase activity 3 0.0003357 99.8204082 004399453

GOTERM_ F_ALL GO:0017076~purme nucleotide binding 17 0.00310625 2.1090566 0.04526422

GOTFJRM_ F_AU. GO:O01G779-mjdeotidyrtrartsferase activity 5 0.00284393 823600727 0.04658368

GOTERM_MF_ALL GO:0003723~RMA binding 10 000371417 3.08659271 0.04863977

Polimunol/Copaxone ^® comparison: differentially expressed pathways, Polimunol immunization

In Polimunol -immunized mice, after imposing a fold change filter of I FC I ≥ 1.2, 77 probesets are upregulated by Polimunol relative to

Copaxone ^® (medium-corrected, in Polimunol- immunized mice) , and these probesets enrich for 10 pathways. These pathways are similar to those seen in the comparison for Copaxone ^® - immunized mice, and include pathways relevant to Copaxone ^® ' s mechanism of action such as immune response and immune system process pathways, as well as potentially concerning pathways such as response to virus. 22 downregulated probesets are detected, which do not enrich for pathways. The upregulated pathways are depicted in Figure 31 and provided in Table

Table 22 : Pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® (in Polimunol-immunized mice) .

Category Term Pvalue Fold E rictim Benjamin!

GOTERM BP AU. GO:0009615~response to vims 3 3.62E-09 31.4583979 1.93E-06

GOTERM_BP_ALi GQ:0009607~response to biotic stimulus 11 4.50E-OS 10-508349 1.20E-05

<30TERM_BP_ALL GQ:0051707~response to other organism 9 4.30E-07 12.2725806 5.73E-05

<30TERM_BP_ALl GQ:0050836~response to stimulus 23 3.87E-07 3.03594414 6.88E-05

GOTERM 8P ALL GO:0aS17D4~multi-argani5m process 10 7.S9E-07 9.23982999 8.03E-05

GOTERM_BP_ALL GO:0O06955""tmrnurte response 12 9.89E-07 6.54537634 8.78E-05

GOTERM BP AU. GO:0O02376~immune system process 12 0.0002277 3.66319331 0.O1719O59

GOTERM_CC_ALL GO:0044421~extracellular region part 7 0.00098754 5.86744639 0.03589677

60TERM_CC_AUL GO:00055?6~extraceihilar region 1Q 0.00051394 4.06619385 0.03732702

GOTERM_CC_AU GO:00G5615~extra cellular space 6 0.00178939 6.62813102 0.04321627

Polimunol and Copaxone ^® comparison: discussion

The fact that Polimunol modulates IL18 to a significantly different extent than Copaxone ^® , consistently, regardless of immunization agent is noteworthy and has potential implications for both safety and efficacy. IL18 is important for T helper cell differentiation, and IL18 levels are higher in serum from MS patients versus controls, as well as acute versus stable MS (Nicoletti et al, 2001) . The signaling pathway for IL-18 appears in Figure 32a. IL18 also induces IFNg expression and has been implicated in MS immunopathogenesis (Losy et al, 2001) . IL18 genetic variants have further been shown to affect MS risk (Celik et al, 2014; Thompson et al, 2007). Moreover, mice deficient for IL18 are resistant to EAE (Shi et al, J. Immunol., 2000) as shown in Figure 32b.

Intriguingly, a number of interferon-related genes are upregulated by Polimunol relative to Copaxone ^® in this model system. Figure 33 shows illustrated pathways of IFN Type I production (Trinchieri et al, J Exp Med, 2010), with overlay indicating genes including RIG-I, MDA5, and IRF7 upregulated by Polimunol versus Copaxone ^® . As the figure indicates, the upregulation of these genes would be consistent with an increase in type I interferon production. At the pathway level, the fact that a variety of immune-related pathways are enriched among the differentially expressed probesets, including ' ¹ immune system process" and ¹¹ response to virus," and that differential expression is seen for multiple genes affecting interferon signaling (e.g. leading to the significant enrichment of the RIG-I-like receptor signaling pathway in the comparison between Polimunol and Copaxone ^® in Copaxone ^® - immunized mice) , raises serious concerns for safety and efficacy.

Example 11

Differences in gene expression induced by Polimunol versus branded GA in human monocyte (THP-1) gene expression studies

The immunized mouse splenocyte model system has proved robust and informative in examining Copaxone ^® ' s mode of action, as well as in differentiating between seemingly similar FOGAs and Copaxone ^® [Bakshi et al, 2013; Towfic et al, 2014; FDA-2014-P-0933-0001 available at www . regulations . gov/# ! documentDetail ; D=FDA-2014-P-0933-0001 , and also described herein; and FDA-2013-P-1641-0001 available at www. regulations. gov/# ! documentDetail; D=FDA-2013-P-1641-0001, and also described herein. To follow up on these findings and test a human-source model system, THP-1 cells were utilized. The research community uses this human monocyte cell line to model the behavior of antigen-presenting cells . As described in further detail in the methods section below, THP-1 cells were utilized to (1) compare the genome-wide transcriptional impact of Copaxone ^® to that of a mannitol control, in order to shed additional light on Copaxone ^® ' s mechanism of action (MoA) , and to (2) compare the genome-wide transcriptional impact of Copaxone ^® to that of purported generics, including Polimunol. It is critical to methodologically pursue the MoA analyses first and independently of any subsequent investigations so as to ensure the validity and robustness of each experiment. To this end, at least three different batches of Copaxone ^® are tested and analyzed in comparison to control and to prior similar studies.

The study was performed in two repeats identical in design, reagents, drug lots, and technicians, performed on different days. Six replicate samples for each condition were utilized in each of the two experimental runs for a total of twelve replicates per condition, making this study well powered to detect changes in expression levels across conditions.

Copaxone ^® -modulated genes (MoA)

Copaxone ^® significantly upregulated 5296 probesets, and significantly downregulated 6819 probesets, out of >25,000 probesets called present on the chip. Consistent with previous studies (e.g. FDA-2014-P-0933- 0001 available at www. regulations . gov/# ! documentDetail; D=FDA-2014-P- 0933-0001, and also described herein) , the anti- inflammatory gene IL1RN was strongly upregulated by Copaxone ^® (all 3 IL1RN probesets that were called present in the study: FDR p values < 6.2e-21, 2.6e- 17, 8.0e-14); see Figure 34a-c.

IL10 was not upregulated significantly, but may have been difficult to detect because the single probeset on the chip was not present. IL10RA, representing the receptor necessary for IL10 signaling, was significantly upregulated (FDR p < 1.7e-21), indicating this pathway upregulated by Copaxone ^® , as expected. These results are consistent with the results of a prior study presented earlier, of which the currently discussed data represents two independent confirmatory datasets ( FDA-2014-P-0933-0001 available at www. regulations . gov/# ! documentDetail; D=FDA-2014-P-0933-0001, and also described herein) .

To test concordance with previous observations in the same model system, sets of top probesets modulated by Copaxone ^® were defined based on two prior THP-1 studies (FDA-2014-P-0933-0001 available at www . regulations . gov/# ! documentDetail; D=FDA-2014-P-0933-0001 , and also described herein) , by taking the intersection of the top probesets (subject to fold change (FC) filter of 1.5, treating up and downregulated probesets separately) modulated by Copaxone ^® across both prior datasets (see Table 23) . Significant enrichment of these sets by directionality was found in the present dataset among probesets upregulated by Copaxone ^® versus mannitol (FC ≥ 1.5) and probesets downregulated by Copaxone ^® versus mannitol (FC ≤ -1.5) by the hypergeometric test: 2.4e-10 and 7.6e-ll for up and downregulated sets, respectively.

Table 23: Top probesets modulated by Copaxone ^® are significantly enriched among the top probesets modulated by Copaxone ^® in prior THP- 1 studies.

Copaxone ^® -modulated pathways

Among the top probesets upregulated by Copaxone ^® with FC ≥ 1.3, 180 pathways were enriched. This includes immune response, immune system process, and cytokine-cytokine receptor interaction and regulation of B cell activation (as observed in prior THP-1 studies, e.g FDA-2014- P-0933-0001 available at www . regulations . gov/# ! documentDetail ; D=FDA- 2014-P-0933-0001, and also described herein) as well as coagulation, positive regulation of lymphocyte activation and proliferation, and positive regulation of B-cell activation and proliferation. The full list of pathways entiched among top probesets differentially expressed by Copaxone ^® relative to mannitol control in THP-1 cells is provided in Table 24.

Table 24: Pathways significantly enriched among top probesets differentially expressed by Copaxone ^® relative to mannitol control in THP-1 cells.

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Among the top probesets downregulated by Copaxone ^® with FC ≤ -1.3, six pathways were enriched. This includes developmental processes (as also seen in prior studies e.g. FDA-2014-P-0933-0001 available at www . regulations . gov/# ! documentDetail; D=FDA-2014-P-0933-0001, and also described herein), and cell-cell adhesion related pathways.

The top 25 pathways enriched among top upregulated probesets are shown in Table 25, and Figure 35 illustrates pathways enriched among top probesets differentially modulated by Copaxone ^® ( | FC | ≥ 1.3, FDR p < 0.05) . As an example of an enriched pathway anticipated to be relevant to Copaxone ^® mechanism of action, cytokine-cytokine receptor interaction, the individual genes modulated by Copaxone ^® involved in this pathway are depicted in Figure 36. Table 25: Top pathways enriched among top probesets upregulated by Copaxone ^®

GO Biological Process GO:0006950~response to stress 70 1.44E-07

GO Biological Process j GO:0042060~wound healing l iioi-oli

* Count refers to number of genes within the list of interest annotated to the pathway.

GO database: Ashburner, M. et al . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Wat. Genet. 25, 25-29 (2000) .

Kegg database: Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genea and genomes. Nucleic Acids Res. 28, 27-30 (2000) .

Copaxone MoA discussion The fact that 12,115 probesets are significantly modulated by Copaxone ^® relative to mannitol provides a window into the complexity of Copaxone ^® ' s mechanism of action on antigen-presenting cells. Despite the complexity and scope of this modulation, key genes known to be modulated by Copaxone ^® (such as IL1RN, IL10RA) appear in the expected directionality. These modulated genes are significantly enriched in immunology-related pathways which are known to be relevant for Copaxone ^® ' s mechanism of action. These two aspects combined together validate the design of the study and its ability to identify relevant aspects of a medicine's interaction with antigen-presenting cells .

Poli unol and Copaxone ^® comparison: differentially expressed genes Comparison of Polimunol versus Copaxone ^® treatment, corrected for Mannitol control expression [i.e. (Polimunol -Mannitol )- (Copaxone ^® - Mannitol)], resulted in 807 probesets differentially expressed with FDR-adjusted p < 0.05. Upon filtering for "present" calls only, 518 upregulated probesets and 289 downregulated probesets were detected. After conservative filtering out of highly variable probesets (i.e. the few previously identified to have differing behavior between THP- 1 studies, which removed 3.5% of the 807 probesets), 779 modulated probesets persist: 494 upregulated probesets and 285 downregulated probesets. After these filtering steps, the top 25 upregulated probesets are shown in Table 26, and the top 25 downregulated probesets are shown in Table 27.

Table 26: Probesets significantly upregulated in Polimunol versus

Table 27: Probesets significantly domregulated In Pollmunol versus Copaxone ^®

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35974_at LRMP .-1.12 1.69E-06

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at C50RF13 -1.12 1.96E-06 1

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24382 jrtJ-¾:. Λ&^ΖΔ2Ε . As observed in the earlier study of the same design (FDA-2014-P-0933- 0001 available at www. regulations . gov/# ! documentDetail; D=FDA-2014-P- 0933-0001, and also described herein) , Polimunol consistently upregulated CYPIBI relative to Copaxone ^® (all four probesets on chip: FDR p values 4.5e-ll, 3.6e-9, 1.6e-8, l.le-7, See Figure 37).

However, ADRB2 was not significantly downregulated by Polimunol relative to Copaxone ^® in the second set of studies (FC -1.06, nominal p 0.06) .

The probesets significantly differentially expressed between Polimunol and Copaxone ^® treatment (corrected for mannitol control) in THP-1 cells is provided in Table 28.

Table 28: Frobesets significantly differentially expressed between Polimunol and Copaxone' ⁸ treatment (corrected for mannitol control) in THP-1 cells.

Probeset Gene raw.FC Av Expr P .Value ad) P.Val B

212655_at TIPARP 1.18491814 9.07215527 11.883114 2.68E-17 1.47E-12 27.6284062 202436_s_atCYPlBl 1.40629663 103046627 10.7394789 1.64E-15 4.49E-11 23.9781074 224735_at CYBASC3 1.16280829 11.1371084 9.91592252 3.50E-14 6.37E-1Q 21.2319004 209921_at SLC7A11 1.34875797 8.01938606 9.38858221 2.57E-13 3.51E-09 19.4266298 202435_s_at CYPlBl 1.36824479 10.7674593 9.32190062 3.31E-13 3.62E-09 19.1959747 208937_s_at lDl 1.21578992 9.79600279 9.02417027 1.03E-12 9.43 E-09 18.1600689 202434_s_atCYPlBl 1.42360365 8.59154176 8.84918014 2.03E-12 1 8E-08 17.5468656 22S964_at PRDM1 1.24239601 8.33311381 8.72349013 3.29E-12 2.07E-08 17.1045709 223113_at TMEM138 1.1063561 11.1028453 8.71472552 3.40E-12 2.07E-08 17.0736735 230966_at IL4I1 1.32516688 8.36704038 8.31508719 1.60E-11 8.74E-08 15.657823 202Q14_at PPP1R15A 1.23664454 8.57467088 8.27614067 1.86E-11 9.24E-OS 15.5191648 2Q2437_s_at CYPIBI 1.34228274 11.0857103 8.20543116 2.45E-11 1.06E-07 15.2671479 37028_at PPP1R15A 1.18998338 9.10953004 8.19801576 2.52E-11 1.06E-07 15.2406986 39402_at I LIB 1.22916144 8.58599227 8.14511174 3.09E-11 1.21E-07 15.0518933 205O67_at IL1B 1.27678411 8.78154185 8.0777594 4.02E-11 1.47E-07 14.8112634 217678_at SLC7A11 1.28685305 7.69726333 7.93874264 6.91E-11 2.36E-07 14.3137409 216598_5_atCCL2 1.34792469 9.28596162 7.88363055 8.57E-11 2.67E-07 14.116209 203821_at HBEGF 1.23590003 9.26713046 7.87666898 8.80E-11 2.67E-07 14.0912465 201468_s_at NQOl 1.15576656 9.35668628 7.86152927 9.34E-11 2.69E-07 14.0369508 225252_at SRXN1 1.11737221 9.70265778 7.81446478 1.12E-10 3.07E-07 13.8680929 211307_s_at FCAR 1.27074012 7.1312048 7.77503632 L31E-10 3.41E-07 13.7265534 209928_s_at MSC 1.18769631 8.08116641 7.75739241 1.40E-10 3.48E-07 13.6631936 201266_at TXNRD1 1.06947321 11.9113637 7.6396293 2.22E-10 5.28E-07 13.239984 210519_s_at NQOl 1.13794807 10.6816859 7.50492043 3.76E-10 8.22E-07 12.7552954 212171_x_atVEGF 1.13674051 9.43661194 7.20421256 1.22E-09 2.46E-06 11.6719358 38037_at HBEGF 1.18482724 7.98711019 7.0523034 2.20E-09 4.14E-06 11.1244167 201118_at PGD 1.07758185 12.4845488 6.97857101 2.93E-09 5.34E-06 10.8587242 203045_at NINJ1 1.12384597 9.41715175 6.88585707 4.21E-09 7.19E-06 10.5247541 216250_s_at LPXN 1.24070246 10.2461732 6.84611362 4.91E-09 7.90E-06 10.3816492 210512_5_atVEGF 1.17453419 103171203 6.84606411 4.91E-09 7.90E-06 10.3814709 210592_s_atSATl 1.14616249 9.85711211 6.78833303 6.15E-09 9.16E-06 10.1736745 210095_s_at tGFBP3 1.26126777 7.77688369 6.7861051 6.20E-O9 9.16E-06 10.1656573 20S893_s_at DUSP6 1.23681965 10.7702231 6.7782857 6.39E-09 9.20E-06 10.1375206 202284_s_at CD N1A 1.12078798 10.6198443 6.75691033 6.95E-09 9.69E-06 10.0606157 209122_at ADFP 1.14098228 12.3228398 6.75171809 7.09E-09 9.69E-06 10.0419373 228937_at C130RF31 1.17921905 8.37907051 6.70099976 8.63E-09 1.15 E-05 9.8595365 201235_s_at BTG2 1.28386355 7.44589095 6.64539327 1.07E-08 1.39E-05 9.65967492 203927_at NFKBIE 1.12895866 9.72640239 6.63162768 1.13 E-08 1.44E-05 9.61021946 1553141_at C130RF31 1.19000046 6.93831195 6.55368898 1.53E-08 1.82E-05 9.33038387 220266_s_at LF4 L 1368523 8.46464122 6.55037647 1.55E-OS L82E-05 931849743 217995_at SQRDL 1.0793508 12.336991 6.54729812 1.57E-08 1.82E-05 9.30745172 207674_at FCAR 1.24494467 7.73429071 6.53420308 1.65 E-08 1.88E-05 9.26047019 46665 at SEMA4C 1.10637799 10.5657844 6.4481693 2.30E-08 2.53E-05 8.95205496 210264_at GPR35 1.11391738 8.72115064 6.44628003 2.32E-08 2.53 E-05 8.94528559 211668_s_at PlAU 1.11120293 9.2353654 6.42233001 2.54E-08 2.69E-05 8.85951421 205205_at RELB 1.16492706 7.34250559 6.42094346 2.56E-08 2.69E-05 8.85454977 203798_s_atVSN 1.16614475 7.2833092 6.41517707 2.61E-08 2.70E-05 8.83390503 219634_at CHST11 1.11031386 9.57653235 6.40091795 2.76E-08 2.75 E-05 8.78286459 201502_s_at NF BIA 1.14603586 11.2391775 6.40005102 2.77E-08 2.75 E-05 8.77976186 229055_at GPR68 1.14767352 7.68909756 6.36111525 3.22E-08 3.04E-05 8.64046681 212190_at SERP1NE2 1.12333317 9.662056 6.3519722 3.34E-08 3.04E-05 8.60777296 219386_s_at SLA F8 1.34835612 8.40890612 6.31827296 3.80E-08 3.41E-05 8.48732535 210513_s_atVEGF 1.15191285 8.36243556 6.28246816 4.36E-08 3.85E-05 8.35944956 211527_x_atVEGF 1.13731715 7.87125822 6.26106285 4.74E-08 4.11E-05 8.28305106 1555638_a_i SA SN1 1.16504788 8.69549173 6.24146956 5.11E-08 4.25 E-05 8.21315379 204470_at CXCU 1.35501196 7.67502936 6.24129687 5.11E-08 4.25 E-05 8.2125379 220935 _at CDK5RAP2 1.10875555 9.47138345 6.11902224 8.18E-08 6.48E-05 7.7771196 201236_s_at BTG2 1.39106574 9.51819834 6.10195957 8.73E-08 6.72E-05 7.71647403 228648_at LHG1 L13667657 10.1778893 6.09346129 9.02E-08 6.85E-05 7.68627977 212143_s_at tGFBP3 1.19756801 7.50292055 6.0375024 1.12E-07 8.26E-05 7.48764791 24Q076_at — 1.11560154 7.77294938 6.02250815 1.18E-07 8.63 E-05 7-43448169 215223_s_atSOD2 1.08832613 9.38708957 6.00345187 1.27E-07 9.16E-05 7.36694855 208S91_at DUSP6 1.20973898 11.4952332 5.99682168 1.31E-07 9.18E-05 7.34346158 228967_at EiFl 1.09256705 7.51282579 5.99430219 1.32E-07 9.18E-05 7.33453779 201489_at PPIF 1.07056711 11.9745223 5.98944612 1.34E-07 9.18E-05 731734011 2023S8_at RGS2 1.26773664 9.57646356 5.97863153 1.40E-07 9.45E-05 7.27905017 221903_s_at CYLD 1.09642353 9.26863731 5.97193254 1.44E-07 9.58E-05 7.25533872 1560228_at SNAI3 1.15060655 7.09991102 5.93825721 1.63E-07 0.0001076 7.13622321 227034_at ANK D57 1.22029842 7.32299473 5.88467981 2.00E-07 0.0001259 6.94699S81 200878_at EPAS1 1.12190973 8.895976 5.87823307 2.05E-O7 0.00012757 6.9242512 201OO5_at CD9 1.14821208 9.10086802 5.86983584 2.12E-07 0.00013023 6.S9463315 206026_s_at TNFA1 P6 1.19240437 5.36372703 5.85839211 2.21E-07 0.00013373 6.85428439 214290_s_at HIST2H2AA / 1.09794003 11.8199009 5.85526922 2.24E-07 0.00013373 6.84327656

222670. _at AFB 1.20369944 9.73888237 5.854147 2.25E-07 0.00013373 6.83932116

205153. _s_at CD40 1.13334093 8.72577521 5.82226469 2.54E-07 0.00014934 6.72701829

225390. _s_at KLF13 1.08054083 10.877664 5.78479854 2.93E-07 0.00016854 6.59522285

227080. at ZNF697 1.12343463 8.92012752 5.76864695 3.11E-07 0.000177 6.5384663

214056. .at MCL1 1.09148142 8.9472801 5.76468003 3.16E-07 0.000177 632453225

201739. .at SG 1.28779242 8.00577284 5.75044243 3.34E-07 0.00018189 6-47454023

201170. _s_at BHLHB2 1.09531573 9.50744497 5.74853964 3.36E-07 0.00018189 6.46786122

205633. _s_atALASl 1.08179152 11.5068057 5.74324623 3.43E-07 0.00018376 6.44928355

203665. .at H OX1 1.24623576 9.15770135 5.7289493 3.62E-07 0.00019209 639912762

203936. _s_at M P9 1.145748 8.56115455 5.70212398 4.01E-07 0.0002066 630510148

213988. _s_at SAT1 1.12993548 9.10813688 5.68515244 4.27E-07 0.00021822 6.24566986

225097. .at ΗΪΡ 2 1.16355832 9.37790876 5.66703291 4.57E-07 0.00023152 6.18226665

226218. .at — 1.2939063 6.28386762 5.66047476 4.69E-07 0.00023514 6.15933112

203939. .at T5E 1.19431475 7.2701384 5.6470707 4.93E-07 0.00024509 6-11247457

221S40_at PTPRE 1.10358333 8.99406461 5.64033312 5.06E-07 0.00024914 6.0889327 234994_at KIAA1913 1.26172422 6.19165569 5.61287248 5.61E-07 0.00026903 539305687 201169 _s_at BHUHB2 1.1138348 7.81678741 5.60701185 5.73E-07 0.00027264 537261084 223222_at 5LC25A19 1.06195494 11.1387437 5.60415209 5.80E-07 0.00027322 5.96263602 201250_s_atSLC2Al 1.07198576 9.45224146 5.58245393 6.29E-07 0.00029287 5.88699657 205770_at GSR 1.08507865 10.4221632 5.58115446 6.32E-07 0.00029287 5.88246909 211610_at KLF6 1.21373848 7.58295098 5.56973288 6.60E-07 0.00030315 5.84268743 217996_at PHLDA1 1.33234556 7.22644861 5.52201205 7.89E-07 0.00035373 5.6767135 204440_at CD83 1.09559915 9.65465598 5.51721887 8.04E-07 0.00035722 5.66006438 203751_x_atJUND 1.11709364 8.15242666 5.49344944 8.78E-07 0.00038425 5.57756091 220330_s_at SA SN1 1.16271877 9.59945919 5.48604123 9.03E-07 0.00038884 5.55186756 202644_s_at TNFAI P3 1.10355352 10.1094931 5.47992259 9.24E-07 0.00039474 5.53065412 203797 at VSNL1 1.10477681 8.15296158 5.47701685 9.34E-07 0.00039597 5.52058224

201069_at MMP2 1.10375779 8.40697176 5.45565127 1.01E-06 0.00042561 5.44657164 204653_at TFAP2A 1.17142932 7.72005745 5.44704422 1.05E-06 0.00043617 5.41678026 219385_at SLAMF8 1.21995297 7.92135191 5.44342079 1.06E-06 0.00043648 5.40424263 20S926_at NEU1 1.0B099136 10.7507527 5.44280336 1.06E-06 0.00043648 5.40210647 239412_at I F5 1.07460841 10.9779751 5.42713112 1.13E-06 0.00045596 5.34790799 223501_at L1103323 9.76378918 5.42513574 1.13E-06 0.00045596 5.34101078 201651 s_at PACSIN2 1.05371079 12.4689697 5.41770064 1.17E-06 0.00046511 5.31531719 214211_at FTHl 1.15283111 10.7669406 5.41590299 Π7Ε-06 0.00046511 5.30910659 202988_s_at RGSl 1.26703574 6.64018217 5.37761912 1.3SE-06 0.00052878 5.17698759 223303_at URP2 1.07136267 11.4584296 5.36688864 1.41E-06 0.00054258 5.14000695 36711_at MAFF 1.19353834 6.77574709 5.36039903 1.44E-06 0.00055196 5.11765264 203508_at TNFRSF1B 1.11118203 9.41800725 5.35852346 1.45E-06 0.00055196 5.1111935 227645_at PIK3R5 1.10436883 8.17453287 5.33951385 U56E-06 O.O0G5S83 5.04576711 218501_at ARHGEF3 1.11215762 8.30700755 5.31477003 1.71E-06 0.00063184 4.96071299 209606_at PSCDBP 1.18667973 7.12974957 5.30711238 1.76E-06 0.00064569 4.93441572 1555756_a CLEC7A 1.21395231 6.44819327 5.2975806 1.82E-Q6 0.00066446 4.90169919 229354 at PDCD6///AJ 1.08957565 10.3878046 5.29027036 1.87E-06 0.00067819 4.87662042

233955_x_atCXXC5 1.07971604 12.6052495 5.27206493 2.00E-06 0.00071277 4.81421221 203887_s_atTHBD 1.14864911 11 807825 5.27153474 2.01E-06 0.00071277 4.81239575 233540_s_atCD 5RAP2 1.08483341 10.2227011 5.26920484 2.03E-06 0.00071431 4.80441408 209774_x_atCXCL2 1.33797035 6.42227624 5.26653762 2.05E-06 0.00071677 4.79527824 210845_s_at PIAUR 1.12269107 10.7660847 5.26173913 2.08E-06 0.0007209 4.77884607 225980_at C140RF43 1.0793459 9.21104798 5.23040107 2.34E-06 0.00079874 4.67165036 219039_at SE A4C 1.11139871 9.52722178 5.2215591 2.41E-06 0.0008154 4.64144331 228754_at SLC6A6 1.11066199 9.56424888 5.21977863 2.43E-06 0.0008154 4.63536267 222062_at 1127 RA 1.14734393 8.84896859 5.21600492 2.47E-06 0.0008189 4.62247702 208892_s_at DUSP6 1.19436158 11.0841436 5.21531302 2.47E-Q6 0.0008189 4.62011481 204684_at NPTX1 1.28533088 9.73612701 5.20831506 2.54E-06 0.00083526 4.59622895 208373_s_at P2RY6 1.06697743 9.65819159 5.20192905 Z60E-Q6 0.00084937 4.57444113 218856_at TNFRSF21 1.11783326 11.1389024 5.20052327 2.61E-Q6 0.00084937 4.56964607 204436 at PLE HQ1 1.09698664 9.3889143 5.19357309 2.68E-06 0.0008652 4.54594574

212227_ x_at EIFl 1.05443994 12.7811739 5.19230534 2.69E-06 0.0008652 4.54162382 223125. s_atC10RF21 1.11079328 10.4937493 5.18218325 2.79E-06 0.00089281 4.50712903 217997_ at PHLDAl 1.26744571 6.13655327 5.17537259 2.86E-06 0.0009049 4.48393197 204912. at !UORA 1.12420434 9.40611087 5.17279988 2.89E-06 0.00090826 4.47517201 218417. s_atFU2Q489 1.08815767 9.3505492 5.15361341 3.10E-O6 0.0009514 4.4098898 203888. at THBD 1.15159161 10.9696824 5.15288486 3.11E-06 0.0009514 4.40741251 205419..at EBI2 1.18216692 9.40684523 5.1527513 3.11E-06 0.0009514 4.4069584 228708. at RAB27B 1.18815027 7.90684935 5.15257387 3.11E-06 0.0009514 4.40635511 200644. at MARCKSL1 1.10690452 11.028723 5.15248432 3.11E-06 0.0009514 4.40605064 202021. x_at EiFl 1.05923104 12.6600822 5.1394264 3.27E-06 0.00099262 4.36167177 211653. x_atAKRlC2 1.12714868 8.13501584 5.12100436 3.50E-O6 0.00104753 4.29912857 209882. at Rin 1-10219332 10.0435725 5.12025544 3.51E-06 0.00104753 4.29658764 201467. _s_at Q01 1.11423301 9.57842418 5.10680582 3.68E-06 0.00109451 425097758 225842. at PHLDAl 1.16531676 7.08579562 5.09284521 3.88E-06 0.00114573 4.20367946 220091..at SLC2AS 1.11656636 9.02115478 5.08631413 3.97E-06 0.00116392 4.18156801 200920. s_at BTG1 1.06979743 10.8993308 5.08304104 4.02E-06 0.00116392 4.17049051 222703. s_atYRDC 1.06438343 10.3475422 5.08288187 4.02E-06 0.00116392 4.1699519 201490. sjat PPIF 1.05947022 113950549 5.07132874 4.19E-06 0.00120065 4.13087206 218223..sjatPLEKHQl 1.12093336 9.10575582 5.06452081 4.30E-O6 0.00122451 4.10785829 201851. at SH3GL1 1.07901872 9.65074195 5.02668705 4.94E-06 0.00138427 3.98016723 228124. at ABHD12 1.09977731 7.66951417 5.01836495 5.09E-O6 0.00141465 3.95212649 218559. js_at MAFB 1.22135659 10.2200187 5.01793255 5.1QE-06 0.00141465 3.95066998 228696. at SLC 5A3 1.12825933 7.72464342 5.01306718 5.19E-06 0.00143268 3.93428488 223660. at AD0RA3 1.13136045 7.77795316 4.98586352 5.73E-06 0.00155048 3.84277934 220066. at CARD15 1.12730802 7.8810279 4.98180156 5.81E-06 0.0015658 3.82913191 238542. at ULBP2 1.10589961 7.94992924 4.9769201 5.92E-06 0.00158601 3.81273664 224480. _s_at LPAAT-THEXi 1.20881651 3.02630766 4.96873318 6.1QE-06 0.00162593 3.78525289 207469. sjat PlR 1.10472357 9.02435046 4.96686989 6.14E-06 0.00162902 3.77900012 202241. at TRIBl 1.67898747 9.30574701 4.94914352 6.55E-0S 0.00172797 3.71955903 204975. at EMP2 1.07979325 8.71044082 4.94102597 6.74E-06 0.00176349 3.69236569 226354. at LACTB 1.06792187 9.9828876 4.93326158 6.93E-06 0.00179962 3.66637136 226022..at SASH1 1.07960243 112682799 4.93280332 6.95E-06 0.00179962 3.66483764 228869..at SLIC1 1.07164715 9.82112889 4.92528486 7.14E-06 0.00184057 3.63968244 203752. jsjatJUNO 1.08201127 11.8110521 4.92340249 7.19E-06 0.00184446 3.63338672 212130. x_at E!Fl 1.055S8847 12.6471904 4.91712987 7.35E-06 0.00187608 3.6124142 219593. at 5LC15A3 1.08615216 8.63335571 4.91416769 7.43E-06 0.00187608 3.60251376 236570. at ZNF366 1.23552697 5.63015267 4.91397465 7.43E-06 0.00187608 3.60186863 213236..at SASH1 1.09881243 10.3511094 4.91356632 7.45E-06 0.00187608 3.60050408 225609..at GSR 1.08973861 9.95822522 4.90544456 7.67E-06 0.00192315 3.57337186 205891..at AD0RA2B 1.11169386 9.89367673 4.87112294 8.68E-06 0.00216282 3.45890752 228438..at TRPA1 1.12226677 3.86862388 4.87039478 8.70E-O6 0.00216282 3.45648245 226372..at CHST11 1.08446345 11.0281604 4.8686604 8.76E-Q6 0.00216654 3.45070693 204961 s_at NCFl///LO 1.09199637 10.3669364 4.86594187 8.84E-06 0.00217803 3.44165575 212124 at RA117 1.09160138 9.61628437 4.84935418 9.39E-06 0.00230182 3.38647153

2Q4341_at TRIM16 ///T 1.10230923 3.04807245 4.83779913 9.79E-08 0.0023573 3.34807425

233857_s_atASB2 1.10322519 6.77376513 4.82807168 1.01E-05 0.00243053 3.31577846

205479_s_at PLAU 1.08239048 9.99849286 4.82413541 1.03E-O5 0.00244373 3.30271717

202252_at RAB13 1.04918345 12.5262785 4.81495419 1.06E-05 0.00251476 3.27226887

204363_at F3 1.13756401 8.52817386 4.80950401 1.08E-O5 0.00254245 3.25420514

226389_s_at RAPGEF1 1.09449369 10.0900401 4.80799583 1.09E-05 0.00254533 3.24920801

238893_at LOC338758 1.19879171 8.45854652 4.79847311 L13E-05 0.00260733 3.21767044

1559399_s_a ZCCHC10 1.08397924 9324417 4.79836233 1.13E-05 0.00260733 3.21730369

213281_at J UN 1.32929059 8.21180845 4.79539679 1.14E-OS 0.00260733 3.20748765

35150_at CD40 1.0785382 10.2548276 4.7810706 1.20E-05 0.00272195 3.16010228

237252_at THBD 1.17836626 8.93981242 4.7780675 1.21E-05 0.00274002 3.15017657

204908_s_at BCL3 1.15086138 7.37503762 4.76630513 1.26E-05 0.00282288 3.11132484

200884_at CKB 1.07535296 9.92747723 4.76403187 1.28E-05 0.00282288 3J.0382067

222996_s_atO XC5 1.07526087 11.470336 4.7S122287 1.29E-05 0.0028399 3.09455008

209949_at NCF2 1.0957522 12.1194106 4.75475484 1.32E-OS 0.00289468 3.07321208

214175_x_at PDUM4 1.10938746 10.0654194 4.75115423 1.34E-05 0.00292045 3.06133B91

211924_s_at PLAUR 1.11165511 9.95057637 4.74398245 1.37E-05 0.00298199 3.0377008

208786_s_at MAP1LC3B 1.06211193 10.0695592 4.71562836 1.52E-05 0.00321787 2.94439234

2U005_at LAT 1.08938993 7.96306748 4.71210161 1.54E-05 0.00324053 2.93280287

205681_at BCL2A1 1.21178632 7.93446379 4.70888129 1.55E-05 0.00326531 2S2222355

239529_at C5ORF20 1.07787194 9.92848977 4.70651414 1.57E-05 0.00328034 231444905

211564_s_at PDLIM4 1.14599993 9.5625589 4.69674734 1.62E-05 0.00338345 2.88238905

216834_at RGS1 1.23977301 8.08711615 4.69312858 1.64E-05 0.00341426 2.87051745

205468_s_at IRF5 1.07554402 9.22742578 4.6798859 1.72E-05 0.00356532 2.82710733

201465_s_atJUN 1.4322588 3.69995542 4.64844489 1.92E-05 0.00391212 2.72425354

2Q4059_s_at El 1.12987509 10.6613264 4.64336736 1.96E-05 0.0039684 2.70767146

219926_at POPDC3 1.14627403 7.07974513 4.62989868 2.06E-05 0.00414687 2.66372393

203217_s_at 5T3GAL5 1.09010335 8.64299026 4.61328701 2.18E-05 0.00431813 2.60959806

203140_at B S 1.09370126 9.0972S992 4.60731699 2.23E-05 0.00435798 2.59016685

223394_at SERTAD1 1.09520636 8.8545176 4.60661454 2.23E-05 0.00435798 238788125

1555832_s_a KLF6 1.3281372 9.3646245 4.60196013 2.27E-05 0.00439877 2.57274081

202181_at KIAA0247 1.06968044 10.7870044 4.59786925 2.30E-05 0.00444699 2.55943906

215346_at CD40 1.11448836 7.24866952 4.58843542 2.38E-05 0.00458129 2.52878443

1554036_at 2BT324 1.18706647 7.29410595 4.57607014 2.49E-05 0.00473788 2.48864674

227345_at TNFRSF10D 1.11676877 7.04849796 437591796 2.49E-05 0.00473788 2.48815304

23S638_at SLC37A2 1.13101655 3.61062051 4.57336536 2.51E-05 0.00474087 2.47987348

221841_s_at UF4 1.10113355 10.8767227 4.57011234 2.54E-05 0.00474759 2.469325

219256_s_atSH3TCl 1.11536627 7.53451496 4.56946119 2.54E-05 0.00474759 2.46721395

1555950_a_<CD55 1.09152724 10.0342225 4.56489196 2.59E-05 0.00479572 2.45240406

2Q4702_s_at FE2L3 1.12411725 7.17327917 436338707 2.60E-05 0.00479572 2.44752785

227811_at FGD3 1.06629472 10.1971288 4.56331445 2.60E-05 0.00479572 2.44729254

205505_at GCNT1 1.07750113 9.23709484 4.55594632 2.67E-05 0.00487889 2.42342858

224397_s_atT TCl /// L< 1.0620857 9.26567514 4.550558 2.72E-05 0.0049228 2.40598784

201642 at IFNGR2 1.05959086 11.6162722 434471501 2.78E-05 0.00499333 2.38708599

20650S_at T FSF7 1.05574374 11.4883906 4.54463083 2.78E-05 0.00499333 2.38681375 208O91_s_at ECOP 1.04916375 11.1694214 4.54122019 2.81E-05 0.00502048 2.37578563 200797_s_at MCU 1.07430577 12.8237735 4.53733476 2.85E-05 0.00507286 236322689 224516_s_atCXXC5 1.06346079 12.1814931 4.5350953 2.S7E-05 0.0050963 2.35599058 202838_at FUCA1 1.08015905 8.59058103 4.52576753 2.97E-05 0.00521504 2.32586748 218902_at NOTCH1 1.07544712 10.0281701 4.51751651 3.05E-05 0.00535088 2.29924525 1556314_a_j— 1.19283635 8.47221892 4.51444845 3.09E-05 0.00539144 2.2893517 212552_at HPCALl 1.05856719 11.9497308 4.51088571 3.13E-05 0.00541251 2-27786684 220307_at CD244 1.06735723 10.3372156 4.50054668 3.24E-05 0.00557134 2.24456149 1555827_at CCNU 1.31890926 6.17504609 4.49891525 3.26E-0S 0.00558567 2-23930934 205349_at GNA15 1.06857174 8.74643664 4.49799127 3.27E-05 0.00558624 2.23633511 210785_s_at C10RF38 1.10692612 9.80722622 4.4919076 3.34E-05 0.00568834 2.21675923 209568_s_at RGU 1.09184408 7.96502675 4.49062407 3.35E-05 0.00568834 2.21263071 212298_at NRP1 1.20491357 7.7598722 4.49014314 3.36E-05 0.00568834 2.21108391 223145_s_at C6ORFI66 1.05608761 11.4884714 4.48713202 3.40E-05 0.00573078 2-20140111 204257_at FADS3 1.09493945 8.41951964 4.48151372 3.46E-05 0.0058264 2.18334247 202686_s_atAXL 1.09254285 3.17667586 4.47347755 3.56E-05 0.0059656 2.15753052 216080_s_at FADS3 1.09835074 8.00176994 4.46781128 3.63E-05 0.00601925 2J.3934359 223392_s_atTSHZ3 1.06527254 7.90879098 4.46593878 3.66E-05 0.00604039 2.13333582 55093_at CSGLCA-T 1.06274155 9.78511615 4.4616716 3.71E-05 0.00611247 2J.1964927 234351_x_atTRPSl 1.08022797 8.01237377 4.45917263 3.74E-05 0.00612832 2.11163694 212882_at KLHL18 1.05377934 9.17946015 4.45890277 3.75E-05 0.00612832 2.11077186 230698_at — 1.13801592 5.25817407 4.45834849 3.75E-05 0.00612832 2.10899501 1553142_at C130RF31 1.22937031 5.40269403 4.45539446 3.79E-05 0.0061733 2.09952717 215195_at PR CA 1.07061108 8.15580417 4.4501435 3.86E-05 0.0062686 2.08270483 223305_at MGC13379 1.04781374 10.291887 4.44708307 3.91E-05 0.00631099 2.07290452 212681_at EPB41L3 1.16483529 6.50195379 4.44605331 3.92E-05 0.00631099 2.06960767 212225_at EfFl 1.29978025 8.27092573 4.42703387 4.19E-05 0.00665515 2.00878036 235299_at — 1.16674528 5.45895742 4.42210056 4.26E-05 0.00675057 1.993023 221658_s_at SI_21R 1.1069911 6.7874754 4.41756867 4.33E-05 0.00681813 1 7855514 223276_at MST150 1.04156368 11.4183626 4.40792637 4.47E-05 0.00696979 1.9477961 218280_x_at HIST2H2AA / 1.08743247 10.2812164 4.40125238 4.58E-05 0.00711271 1.92652478 218647_s_at¥RDC 1.06300514 9.78941527 4.38080776 4.92E-05 0.00752763 1.86146015 2185B9_at P2RY5 1.1167465 8.63436917 4.37437741 5.03E-05 0.00764929 1.S4102585 207535_s_at NFKB2 1.10079929 6.90974535 4.37295025 5.05E-05 0.00764929 1.8364926 230925_at APBB11P 1.06629311 12.0575087 4.35935406 5.29E-05 0.00795107 1.79334155 481D6_at FU20489 10637033 9.15515486 4.35698216 5.34E-05 0.00799448 1.78582038 210872_x_at GAS7 1.08154753 7.70819207 4.35585799 5.36E-05 0.00800363 1.78225642 204359 at FLRT2 1.14647669 7.31270266 4.35162998 5.44E-05 0.00806509 1.76885628

235457_at MAML2 111934624 7.88052648 4.35157862 5.44E-05 0.00806509 1.76869354 209239_at NFKB1 1.06667957 9.95829149 4.34970949 5.47E-05 0.00808685 1.76277161 57163_at ELOVU. 1.03977111 11.2971996 4.34572593 5.55E-05 0.00815484 1.75015477 218145 at TRIB3 1.05938261 11.0204954 4.33624331 5.73E-05 0.00835029 1.7201439

211776 s at EPB41L3 1.13532577 6.97220625 4.3357415 5.74E-05 0.00835029 1.71855664

203455_s_atSATl 1.1106924 10.2329144 4.32750295 5.91E-05 0.00843913 1.69251066 207S71_x_at C10RF38 1.09650304 9.82311518 4.32655202 5.93E-05 0.00843913 1.68950588 211661_x_at PTAFR 1.09097156 8.56515505 4.32283339 6.00E-05 0.00852559 1.67775875 201590_x_atANXA2 1.0821024 12.5151345 4.29910185 6.51E-05 0.00910791 1.60290884 202071_at SDC4 1.10346382 9.40347252 4.29057952 6.71E-05 0.00933036 1.57607916 208983_s_at PECAM1 1.05734731 11.7319933 4.28529786 6.83E-05 0.00945271 1.55946497 205098_at CCR1 1.06303521 11.4600607 4.28157126 6.92E-05 0.00952594 134774856 200839_s_atCTSB 1-0495602 12.4472914 4.27935833 6.97E-05 0.00952643 134079356 205503 at PTP 14 1.114491D1 5.88707054 4.27156243 7.16E-05 0.00973541 131630622

204998_ s_atATF5 1.09981149 9.30480593 4.26739042 7.26E-05 0.00985086 130321093 208961 s_at KLF6 1.23937112 8.76862028 4.26084325 7.43E-05 0.00997486 1.48267336 211962_s_atZFP36Ll 1.14336043 7.45775693 4.25626247 7.54E-05 0.01008195 1.46831355 223502_s_at T FSF13B 1.09556837 9.8619397 4.25432078 7.59E-05 0.01008195 1.46222911 212062_at ATP9A 1.12049998 7.42652014 4.24093141 7.95E-05 0.01044325 1.42031066

222165. _x_atC90RF16 1.06651407 9.91796752 4.24002979 7.97E-05 0.01044325 1.41749035 201926_ _s_at CD55 1.09241207 9.80032696 4.23706219 8.05E-05 0.01046218 1.40820968 214446_at ELL2 1.08240974 7.5600877 4.23640074 8.07E-05 0.01046218 1.40614158 205713 at FTGB7 1.05295759 9.27615896 4.23403904 8.14E-05 0.01049314 139875869 216504_s_at SLC39A8 1.10938409 7.59501292 4.23284649 8.17E-05 0.01049314 1.3950315 221799_at CSGLCA-T 1.07612526 9.24334654 4.23263401 8.18E-05 0.01049314 1.39436746 1554406_a_ _< CLEC7A 1.10481365 7.94057206 4.23125877 3.21E-05 0.01051774 1.39007005 41644_at SASH1 1.07635742 10.9010644 4.22769131 8.31E-05 0.01058985 1.3789256 238669_at PTGS1 1.10119423 8.07043819 4.21299805 8.74E-05 0.01101178 133307571 211571_s_atCSPG2 1.11087565 8.5143978 4.21117973 8.80E-05 0.01105461 1.32740739 203702_s_atTTLL4 1.05712621 8.43342998 4.2038303 9.Q2E-05 0.01130824 1.30450953 209906_at C3AR1 1.12163622 7.99304364 4.19174628 9.40E-05 0.01159647 126690537 221752_at SSH1 1.06296062 8.5565014 4.18795524 9.52E-05 0.011693 3_25511957 204655_at CCL5 1.08067913 11.8965338 4.18339572 9.67E-05 0.01179566 1_24095201 1555788_a_cTHIB3 1.07151286 9.51438422 4.18231045 9.70E-05 0.01181277 1.23758099 209160_at AKR1C3 1.14905554 5.73155063 4.17829766 9.B3E-05 0.0118711 1.22512056 224783_at FA 100B 1.05774261 9.77579353 4.17654931 9.89E-05 0.0118964 1.21969356 203549_s_at LPL 1.05114008 12.062737 4.17631113 9.90E-05 0.0118964 L21895431 230343_at — 1.0958987 7.39528117 4.17213744 0.00010041 0.01203929 U2060O404 201925_s_atCD55 1.12915465 9.47556264 4.16888144 0.00010152 0.01212964 1.19590588 214581_x_at TNFRSF21 1.11185517 9.56118012 4.16612537 0.00010247 0.01220649 1.18736144 215813_s_at PTGS 1.05554211 10.1951822 4.16354389 0.00010337 0.0122868 1.17936091 39582_at CYLD 1.07942531 7.63563499 4.16212948 0.00010387 0.01231894 1.17497847 219890_at CLEC5A 1.14451027 8.86385658 4.15970971 0.00010472 0.01239328 1.16748282 22421S_s_atTRPSl 1.10873593 7.212934 4.15691737 0.00010572 0.01243643 1.15883589 207275_s_atACSLL 1.06382835 10.2365501 4.15687886 0.00010573 0.01243643 1.15871663 1560485_at HIVEP1 1.09963892 6.29901302 4.14268989 0.00011092 0.01282144 1.11482542 224967_at UGCG 1.07551513 9.81750879 4.13803967 0.00011267 0.01294212 1.1004579 235479_at CPEB2 1.05886438 8.76040386 4.13334561 0.00011447 0.01305473 1.08596354 205323 s at MTFl 1.05603723 9.75949747 4.13204585 0.00011497 0.01305473 1.08195167

202643_s_at TNFAIP3 1.09192276 8.84841512 4.13157653 0.00011516 0.01305473 1.0805032 202948_at ILIRI 1.11651018 6.61849267 4.13003859 0.00011575 0.01305473 1.07575731 205469_s_atlRF5 1.05102073 11.1050752 4.12871511 0.00011627 0.01305473 1.07167395 211676_s_at lFNGRl 1.05547086 11.597122 4.11880246 0.00012022 0.01335977 1.04111224 226039_at MGAT4A 1.06778678 10.4027019 4.10156128 0.0001274 0.01404306 0.98804884 213763_at H!P 2 1.10105649 7.77301596 4.09563418 0.00012996 0.01425665 0.96983433 222877_at NRP2 L15705726 5.02483818 4.09527073 0.00013012 0.01425665 0.96871786 228186_s_at SP03 1.14318575 5.7292516 4.09151825 0.00013176 0.01437971 035719398 228640_at — 1.18540594 4.77536947 4.08751237 0.00013355 0.01454523 0.94489812 1558404_at 3C6442421 1.23417115 5.05041215 4.08679741 0.00013387 0.01455116 0.94270427 1554966_a_ _< DOC1 1.09595173 8.58722147 4.0855338 0.00013444 0.01456531 0.93882738 209803_s_at PHLDA2 1.09168215 8.97143045 4.08488393 0.00013473 0.01456531 0.93683375 1555759 a iCCL5 1.08590053 12.3665501 4.08473429 0.0001348 0.01456531 0.93637472 205322. s_at MTF1 1.06116697 9.07418068 4.07720028 0.00013824 0.01490832 0.91327536 204197. s_at RUNX3 1.07101524 9.2606011 4.075793 0.0001389 0.01494692 0.90896318 224785. at FA IOOB 1.06028293 9.68830224 4.07291553 0.00014024 0.01494692 0.90014852 204011. at SPRY2 1.07921096 9.36460861 4.06326541 0.00014485 0.01535236 0.87061139 218673 s_atAT67 1.0429976 10.1275004 4.063176 0.00014489 0.01535236 0.87033789 244434 at — 1.20479383 5.19908075 4.05858303 0.00014713 0.01555469 0.85629319 203313. s_atTGIF 1.07792023 9.34545441 4.05661779 0.0001481 0.01555469 0.85028636 214057 at ai 1.08299074 8.45324848 4.05637551 0.00014822 0.01555469 0.84954593 201473 at um 1.18429728 8.79340992 4.05365798 0.00014957 0.01564376 0.84124255 203234 at UPPl 1.11194547 9.00007417 4.05220054 0.0001503 0.01565768 0.83679059 223126 s_atC10RF21 1.0962014 8.74641324 4.05101842 0.0001509 0.01565768 0.83318028 203604 at ZNF516 1.06761148 9.49503774 4.05097313 0.00015092 0.01565768 0.83304199 219398 at CI DEC 1.06603998 7.6766591 4.05011563 0.00015135 0.01567285 0.83042347 241418 at — 1.11426423 6.19780118 4.04745294 0.00015271 0.01578293 0.82229445 239845 at — 1.14637752 5.55035202 4.04641564 0.00015324 0.01580779 0.81912842 214010 s_atATP9B 1.05604217 8.49566348 4.04162949 0.0001557 0.01601409 0.80452591 201063 .at RCN1 1.05280589 9.82235338 4.02360178 0.00016534 0.01680334 0.74960812 226064 _s_at DGAT2 1.05258611 9.74527668 4.00179079 0.00017778 0.01786795 0.68334514 212419 .at C10ORF56 1.07773109 8.71242101 3.99856112 0.0001797 0.01799441 0.67355005 201199 _s_at PSMDl 1.03812334 11.768617 3.99425825 0.00018228 0.01820614 0.66050691

1554691_a PACS1 2 1.05020015 10.5255625 3.98851731 0.00018579 0.01843526 0.64311668 213503_x_atANXA2 1.07802407 12.4262407 3.98512527 0.00018789 0.01856568 0.63284816 225386_s_at HNRPLL 1.04770359 11.2270978 3.98475235 0.00018812 0.01856568 0.63171954 219093_at FU20701 1.14335282 6.49529551 3.98380226 0.00018871 0.01858124 0.62884438 212657_s_at IL1RN 1.06064344 10.3261013 3.97849886 0.00019206 0.01881842 0.61280238 215411_s_at T AF3 IP2 1.04746131 9.60905229 3.97606781 0.00019361 0.01893656 0.60545275 224828_at CPEB4 1.11148606 6.94793798 3.97135657 0.00019665 0.01908993 0.59121672 208309_s_at MALT1 1.07563121 7.84016779 3.95900453 0.00020485 0.01975315 0.55393702 211219_s_at l_HX2 1.07519303 8.41763861 3.95580414 0.00020702 0.01992792 0.54428847 208619_at DDB1 1.04094564 10.905059 3.9493717 0.00021147 0.02022705 0.52490916 212659 s at ILLRN 1.06314743 8.36939546 3.94913045 0.00021164 0.02022705 0,52418269

204401_at KCN 4 1.0819664 10.2570594 3.94621319 0.00021368 0.02031839 031539986 203922_s_atCYBB 1.09189933 9.03066782 3.94421507 0.00021509 0.02041722 030938632 225955_at ETRNL /// 1 1.12640184 9.30736877 3.94080195 0.00021753 0.02054128 0.49911817 223019_at C90RF88 1.11519595 8.77056793 3.93913081 0.00021873 0.02061912 0.49409247 225372_at C10ORF54 1.11079316 7.82556013 3.93618776 0.00022086 0.02074849 0.48524461 225368_at HIPK2 1.10811883 10.9436109 3.93081197 0.00022481 0.02104628 0.46909267 227255_at KIAA15Q5 3L17158338 9.78973377 3.92552212 0.00022875 0.02130693 0.45321112 238604_at ECOP 1.07570947 9.50546921 3.92153082 0.00023178 0.02151518 0-44123614 206171_at ADO R A3 1.12468497 8.70914475 3.92097723 0.0002322 0.02151785 0.43957576 200748_s_at FTHl 1.09484808 13.0211632 3.91978982 0.00023311 0.02156547 0.43601482 204858_s_at ECGFl 1.07328226 10.0994132 3.91907356 0.00023366 0.0215798 0.43386711 226534_at KITLG 1.07330296 9.3627121 3.90512624 0.00024461 0.02229014 0.3920904 225407_at MBP 1.05793961 113278556 3.90258448 0.00024666 0.02243941 038448614 216594_x_at AKR1C1 1.08731511 8.97660025 3.90054274 0.00024832 0.02255267 0.37837983 242157_at — 1.10450816 7.85915836 3.89900755 0.00024957 0.02262757 0.37378967 203104_at CSF1R 1.066843 11.2558738 3.89852024 0.00024997 0.02262757 037233286 201471_s_atSQ5TMl 1.05817603 11.064824 3.8911549 0.00025608 0.02302792 0.35032669 201565_s_at ID2 1.05840103 12.351258 3.88999177 0.00025705 0.02306893 0.34685365 201412_at LRP10 1.0522513 10.0558306 3.8879203 0.0002588 0.0231589 0.34066984 208982_at PECAM1 1.04940273 12-4408294 3.88579521 0.00026061 0.02324451 0.33432794 242302_at APRIN 1.09399636 6.08366862 3.88405566 0.0002621 0.02333917 032913805 201920_at SLC20A1 1.0505388 11.1251381 3.87844015 0.00026696 0.02365634 031239348 214084_x_at LOC648998 / 1.07297813 9.87462439 3.87717059 0.00026807 0.02367801 0.30860978 202804_at ABCC1 1.05325862 10.0332207 3.86552597 0.00027847 0.02439924 0.27393816 228532_at C10RF162 1.06940145 105010812 3.86494651 0.00027899 0.02440633 0.2722144 210773_s_at FPRU 1.096511 8.0656375 3.86209224 0.0002816 0.02456545 0.26372575 204620_s_atCSPG2 1.09556927 10.356296 3.S56133S9 0.00028713 0.02491902 0.24601655 227067_x_at NOTCH2NL 1.0532533 10.0530487 3.85320299 0.00028989 0.02507868 0.23731212 226368_at CHST11 1.07195471 9.52648879 3.8487656 0.00029411 0.02532955 0.22413996 213142_x_at LOC54103 1.06311548 10.4211815 3.84869575 0.00029418 0.02532955 0.22393268

217992 _s_at EFHD2 1.06506856 11.6374518 3.84358776 0.00029911 0.02567362 0.20878091 221571_at TRAF3 1.06383739 9.65844518 3.84232271 0.00030035 0.02570473 0.20503022 225207_at PDK4 1.13997001 6.99602651 3.84205117 0.00030061 0.02570473 0.20422522 201191_at PITPNA 1.07930886 8.54956136 3.33764717 0.00030495 0.02584057 0.19117405 219412_at RAB38 1.09786171 8.08626906 3.83442124 0.00030817 0.0260019 0.18161959 50221_at TFEB 1.06697604 9.57832583 3.83038439 0.00031224 0.02622405 0.16966997 206140_at LHX2 1.06574569 9.81614566 3.82420766 0.00031857 0.02659987 0.15140014 226545_at CD109 1.07280592 9.51243783 3.82411952 0.00031866 0.02659987 0.15113954 1552486_s. c LACTB 1.08525899 8.38629859 3.82306652 0.00031975 0.0266503 0.1480267 228368_at ARHGAP20 1.14164081 7.83168691 3.81871004 0.00032431 0.02696861 0.13515348 238727_at LOC440934 1.11497925 7.08620645 3.8125927 0.00033081 0.02730892 0,11709143 225283_at ARRDC4 1.04969035 9.71669678 3.8080796 0.00033569 0.02759937 0J.0377592 201S95_at EXT1 1.09076481 6.49400167 3.80540237 0.00033861 0.02779804 0.09588293 231496 at FCAMR 1.09935645 7.04227829 3.79899562 0.00034571 0.02829583 0.07700546

217741_s_at ZFAND5 1.03867699 11.247246 3.79602954 0.00034904 Q.02S48348 0.06827223 226075_at SPSB1 1.09367375 6.41796675 3.79131798 0.0003544 0.02879199 0.0544079 1569136_at GAT4A 1.18908532 6.30607913 3.78721234 0.00035914 0.02909023 0.04233483 AFFX-HU ISSTATl 1.06320305 9.76660865 3.78614824 0.00036038 0.02914726 0.03920699 206157_at PTX3 1.13951692 9.77811771 3.77291403 0.00037611 0.02998389 0.00034936 204899_s_atSAP3Q 1.05454489 9.10790083 3.7723175 0.00037683 0.02998389 -0.0014002 210427_x_at A XA2 1.07331631 123352054 3.77202707 0.00037719 0.02998389 -0.002252 210357js_atSMOX 1.08311104 8.03967009 3.7719322 0.0003773 0.02998389 -0.0025302 225530_at MOB L2A 1.04391552 103141996 3.76923042 0.0003806 0.03009487 -0.010452 234976_x_at SLC4A5 1.0654205 8.11158064 3.76817676 0.0003819 0.03011937 -0.0135404 225115_at HIP 2 1.08936992 8.35503513 3.76532698 0.00038542 0.03026716 -0.0218911 212561_at AB6IP1 1.05486737 10.6159658 3.76463655 0.00038628 0.03026716 -0.0239136 233177_s_at PNKD 1.05881097 8.90692004 3.7603318 0.00039167 0.03054886 -0.0365193 205926_at IL27RA 1.08811794 8.50082949 3.75788045 0.00039478 0.03074707 -0.0436938 203940_s_atVASHl 1.10205097 8.93929781 3.75557481 0.00039772 0.03085591 -0.0504392 230634_x_at LOC113179 1.06907966 7.85469698 3.75508795 0.00039834 0.03085591 -0.0518633 219994_at APBB1IP 1.07862342 8.79352106 3.75501728 0.00039843 0.03085591 -0.05207 211139_5_atNABl 1.07131493 8.72031957 3.74646937 0.00040954 0.0314976 -0.0770544 201707_at PEX19 1.04709872 103748471 3.74254693 0.00041473 0.03166964 -0.0885078

209933. s_atCD300A 1.06497364 9.72572801 3.74177958 0.00041576 0.03168935 -0.0907476 203233_at IL4R 1.07541642 8.96600013 3.74112983 0.00041662 0.03168935 -0.092644 212724_at RND3 1.10102105 7.85276337 3.73595709 0.0004236 0.03207812 -0.1077338

218260_at C190RF58 1.05658126 9.52851385 3.72698571 0.00043597 0.03278903 -0.1338755 202779_s_at UBE2S /// LC 1.03653716 12,7522175 3.71585925 0.00045179 0.03383761 -0.1662444 204589_at NUAK1 1.08993672 6.703S9618 3.71372502 0.00045488 0.0339596 -0.1724466 200078_s_atATP6V0B 1.0264003 13.5385773 3.71309911 0.0004558 0.0339596 -0.1742651

202192_ s_at GAS 7 1.07358071 9.32496946 3.71302712 0.0004559 0.0339596 -0.1744742 242705 _x_at— 1.050541 9.41748882 3.71038947 0.00045976 0.03410795 -0.1821356 218611_at IER5 1.07040021 11,1112341 3.70562135 0.00046683 0.0343816 -0.1959768 239598_s_atAYTLl 1.0605954 9.78054544 3.70535414 0.00046723 0.0343816 -0.1967522 219456_s_at iN3 1.07330011 7.90448799 3.70257871 0.00047139 0.03464126 -0.2048036 211572_s_at SLC23A2 1.07618941 7.04729666 3.70142012 0.00047314 0.03470886 -0.2081635 212502_at C10ORF22 1.04307648 9.95312582 3.70033342 0.00047478 0.03475049 -0.2113144 201251_at PK 2 1.04329421 13.0859336 3.69894945 0.00047688 0.03485776 -0.2153264 204135_at DOC1 1.07274599 8.83386998 3.69578905 0.00048172 0.03516424 -0.2244847 219944_at RSNL2 1.08504226 7.05512921 3.69481629 0.00048322 0.03517085 -0.2273027 210018_x_atMALTl 1.06841222 7.99947523 3.69389329 0.00048464 0.03517085 -0.229976 236220_at — 1.14920843 4.26492324 3.69312582 0.00048583 0.03517085 -0.2321986

213935_at ABHD5 1.07822608 6.87154542 3.69294217 0.00048612 0.03517085 -0.2327305

227420_at TNFAIP8L1 1.06654551 a.06189779 3.69281506 0.00048631 0.03517085 -0.2330985

219496_at A RD57 1.13993106 6.53387141 3.6910586 0.00048905 0.03532176 -0.2381S39

214743_at cum 1.06965625 9.94412122 3.68791266 0.00049398 0.0355839 -0.2472886

1554544_a_ <MBP 1.07318708 10.1607524 3.6870054 0.00049541 0.03564002 -0.2499134

218614_at C120RF35 1.06691348 10.0756991 3.68269534 0.00050226 0.03608547 -0.2623776

2Q5147_x_at NCF4 1.03578282 11.8404339 3.6799098 0.00050674 0.03617329 -0.2704283 223852_s_atSTK40 1.07352861 8.47342374 3.67987641 0.00050679 0.03617329 -0.2705248 204834_at FGL2 1.15453451 8.63307396 3.67701847 0.00051142 0.03645638 -0.2787809 36994_at ATP6V0C 1.03052612 13.09078 3.6758467 0.00051333 0.03649744 -0.2821648 1555168_a_iCALNl 1.07042924 7.3789421 3.66717734 0.00052769 0.03716608 -0.3071804 203388_at ARR82 1.05764941 9.38740578 3.66559438 0.00053035 0.03717544 -0.3117441 214054_at DO 2 1.07678197 11.2259885 3.66223375 0.00053604 0.03752644 -0.321429 212096_s_at MTUSl 1.11473269 7.49260762 3.6528896 0.00055218 0.03845937 -0.3483291 225480_at C1QRF122 1.04930018 10.1940995 3.65080013 0.00055586 0.03866588 -0.3543385 20170O_at CCND3 1.04752925 12.8929574 3.64778851 0.00056119 0.03888847 -0.3629964 218399_s_atCDCA4 1.03865826 10.9812294 3.64588211 0.00056459 0.03907466 -0.3684747 212003_at C10RF144 1.05223728 9.96851324 3.64185086 0.00057185 0.03942724 -0.3800532 205099_s_atCCRl 1.07264855 9.06024264 3.63132179 0.00059123 0.04045726 -0.4102577 201422_at 1FI30 1.05859805 11.1928984 3.63012447 0.00059347 0.04050934 -0.413689 227220_at NFXtl 1.05892434 8.69171722 3.62491347 0.00060333 0.04097752 -0.4286146 213923_at RAP2B 1.05181562 11.5158708 3.62050346 0.00061179 0.04138559 -0.4412357 242538_at TFDP1 1.06598341 8.25495776 3.61714555 0.00061831 0.04163319 -0.4508394 211855_s_at SLC25A14 1.04783376 8.87468082 3.61205543 0.00062832 0.04220328 -0.4653867 205462_s_at HPCALl 1.0537572 10.6818738 3.60669792 0.00063902 0.04273699 -0.4806845 213649_at SFRS7 1.10439275 9.36601754 3.60651451 0.00063939 0.04273699 -0.4812079 225701_at AKNA 1.052602 8.96472073 3.60207226 0.00064841 0.04315666 -0.4938812 217691_x_at SLC16A3 1.06195853 9.25873814 3.60186431 0.00064883 0.04315666 -0.4944742 225375_at C170RF32 1.04600249 10.3975791 3.59958371 0.00065351 0.04336219 -0.5009765 206710_s_at EPB41L3 1.10596585 7.40730158 3.59798029 0.00065681 0.04347608 -0.5055465 204393_s_atACPP 1.05975941 8.04387684 3-59438387 0.00066429 0.04381176 -0.5157924 244536_at TP53BP2 1.18627513 7.50015327 3.58918064 0.00057525 0.04421781 -0.5306045 219183_s_at PSCD4 1.04907356 10.1644303 3.58716888 0.00067953 0.04438865 -0.5363279 226267_at JDP2 1.0662635 8.31398002 3.5828349 0.00068885 0.04454185 -0.548651 202111_at SLC4A2 1.06505371 9.07129828 3.58192152 0.00069082 0.04454185 -0.5512469 205128_x_at PTGSl 1.05569773 10.4322081 3.58162573 0.00069147 0.04454185 -0.5520875 227107_at — 1.05069658 9.99172727 3.57890951 0.00069739 0.0448057 -0.5598043 2044S9_s_atCD44 1.06303314 10.62276 3.57845421 0.00069838 0.04481711 -0.5610975 224733_at CMT 3 1.05905507 10.6346875 3.57586316 0.00070409 0.04507716 -0.5684547 229045_at SLIC1 1.07967634 7.89386361 3.57233315 0.00071192 0.04541946 -0.5784727 242414_at QPRT 1.05189094 10.2463166 3.56946163 0.00071836 0.04561726 -0.5866174 227948_at FGD4 1.09161868 7.2001949 3.55996253 0.00074006 0.04665922 -0.6135311 207610_s_at E R2 1.10912425 6.51140397 3.55918695 0.00074185 0.04665922 -0.6157265 2383S9_s_at— 1.08307842 8.36785016 3.55808Q73 0.00074443 0.04672969 -0.6188574 202295_s_atCrSH 1.0545204 12.0343467 3-55490548 0.00075186 0.04706777 -0.6278407 213134_x_at BTG3 1.04181201 11-0553855 3.55329658 0.00075565 0.04706777 -0.6323906 2G4495_s_at 0.50RF39 1.06073223 9.19429662 3.55321693 0.00075584 0.04706777 -0.6326159 225631_at KIAA1706 1.09137745 7.01050123 3.55021925 0.00076296 0.04734911 -0.6410896 217168_s_at HERPUDl 1.03983791 11.6835542 3.54664359 0.00077153 0.04764859 -0.6511914 203658 at 5LC25A20 1.04561479 9.46245075 3.54654461 0.00077177 0.04764859 -0.6514709

226735_at FU9O013 1.05055665 9.2921795 3.54448273 0.00077675 0.04781967 -0.657293

212372_at MYH10 1.06171907 9.0082261 3.53720879 0.00079459 0.04864948 -0.6778151

214769_at 1.06476746 8.52685941 3.53521138 0.00079955 0.04873518 -0.6834457

225408_at MBP 1 0628553 8.95772417 3.53415379 0.00080219 0.04881373 -0.6864262

222900_at 1.05686661 9.96719959 3.53260926 0.00080606 0.04891403 -0.690778

1562475_at DKFZP68601 1.08348486 8.1338617 3.53084868 0.0008105 0.04912864 -0.6957371

226629_at SLC43A2 1.09818747 7.92209671 3.5269652 0.00082036 0.04956322 -0.7066702

204174_at ALOX5AP 1.04445917 12.5979593 3.52653085 0.00082147 0.04956322 -0.7078925

211D67_s_at GAS7 1.06066251 9.58135451 3.52629694 0.00082207 0.04956322 -0.7085508

204157_s_at K1AAG999 1.06020492 8.89537432 3.52624693 0.0008222 0.04956322 -0.7086915

211026_s at MGU 1.05773402 7.85103089 3.52322146 0.00082998 0.04986733 -0.7172027 Probes et Gene raw.FC AveExpr P.Value adj.P.Vai B

204614_at 5ERPINB2 -1.1547768 12.4744252 -7.4528925 4.60E-10 9.68E-07 1 5679S41

211421_s_at ET -1.1345252 9.30328848 -7.1113218 1.75E-09 3.41E-06 11.3371247

207725_at POU4F2 -1.1644052 9.97790101 -6.9339707 3.49E-09 6.15 E-06 10.6980464

208206_s_at RASGRP2 -1.1124445 10.5120774 -6.549181 1.56E-08 1.82E-05 9.31420762

218971_s_at HSPC049 -1.1502366 9.26509596 -6.353404 3.32E-08 3.04E-05 8.6128924

222799_at H5PC049 -1.1678019 8.76549992 -6.2405739 5.13E-08 4.25 E-05 8.20995923

219463_at C20ORF103 -1.1066514 11.1578088 -6.1792066 6.49E-08 5.22E-05 7.99126082

21SS58_at DEPDC6 -1.1739709 8.39313128 -6.1048654 8.64E-08 6.72E-05 7.72680015

214539_at SERPINB10 -1.1393961 9.05047781 -6.0524221 1.06E-07 7.91E-05 7.54057412

225510_at OAF -1.0795282 10.1352866 -5.9010298 1.S8E-07 0.00012109 7.0047035

228855_at LOC645919 -1.1276666 10-7515984 -5.8846827 2.00E-07 0.0001259 6.94700615

20O799_at HSPA1A -1.0946162 10.8594511 -5.7859004 2.92E-07 0.00016854 6.59909626

206643_at HAL -1.1136035 9.45516733 -5.7636924 3.17E-07 0.000177 6.52106329

44790_s_at C130RF18 -1.1118604 11.1923769 -5.7586514 3.23E-07 0.00017859 6.50336066

202441_at 5PFH1 -1.0851805 11.4291926 -5.6315658 5.23E-07 0.00025521 6.05830953

206O34_at 5ERPINB8 -1.080288 10.6134257 -5.5518212 7.06E-07 0.00032156 5.78034465

203685_at SCL2 -1.1572394 9.68186938 -5.5344339 7.53E-07 0.00034041 5.71987917

216733_s_atGATM -1.0919977 10.6962606 -5.5025531 8.49E-07 0.00037436 5.60914785 224428_s_at CDCA7 -1.0723261 11.8097904 -5.4896239 8.91E-07 0.0003867 536429181 201310_s_at C50RF13 -1.1126729 11.785614 -5.4263444 1.13E-06 0.00045596 5.34518843 213361_at TDRD7 -1.1610606 10.9747672 -5.391919 1.28E-05 0.00050496 5.22630402 219714_s_at CACNA2D3 -1.0949691 10.9314712 -5.3685146 1.40E-OS 0.00054258 5.14560908 35974_at LR P -1.1227255 8.47924836 -5.3181301 1.69E-06 0.00062826 4.97225553 201309_x_atC5ORF13 -1.1203829 9.89153948 -5.2776918 1.96E-06 0.00070587 4.83349392 243S24_at — -1.1826717 8.98902905 -5.2561294 2.13E-0S 0.00073085 4.75964206 226117_at T!FA -1.0706362 10.6431699 -5.2203927 2.43 E-06 0.0008154 4.6374596S 210986_s_atTPMl -1.0953979 11.1982 -5.1779859 2.S4E-06 0.00090145 4.49283173 235275_at OXCT2 -1.167218 12.4747234 -5.1258467 3.43E-06 0.0010376 4.31556088 203178_at GAT -1.1772979 9.84150408 -5.0826986 4.02E-0S 0.00116392 4.16933171 223062_s_at PSAT1 -1.0966737 10.8142971 -5.0731123 4.17E-06 0.00119913 4.13690304 227921_at — -1.0939212 9.03133919 -5.0296725 4.S8E-06 0.00137633 3.9903064 225673_at MYAD -1.O710199 12.4026311 -5.0110829 5.23E-06 0.00143582 3.92760413 2109S7_x_a-TPMl -1.0747681 11.0724469 -5.008451 5.28E-06 0.0014424 3 1874425 220252_x_at CXORF21 -1.1107929 11.2367599 -4.990621 5.63E-06 0.00153146 3.85876875 212175_s_atAK2 -1.0635824 12.0933996 -4.9479609 6.57E-05 0.00172797 3.71559637 213931_at ID2 /// ID2B -1.5575806 8.63155658 -4.8451866 9.53E-06 0.00231585 3.37261839 206116_s_atTPMl -1.0886322 10.541027 -4.8397732 9.72E-06 0.00235097 3.35463151 225421_at ACY1L2 -1.1026709 10.2401371 -4.8246433 1.03E-05 0.00244373 3.30440211 2281S8_at — -1.0980344 9.30046163 -4.8130876 1.07E-05 0.00252076 3.26608136 1553436_at UC19 -1.1317348 7.84569387 -4.796243 1.14E-05 0.00260733 3.21028822 223165_s_at IHPK2 -1.0812006 8.49238402 -4.7744158 1.23E-05 000276466 3.13811043 217521_at — -1.0843722 8.45544985 -4.7662509 1.27E-05 0.00282288 3.11114575 214787 at DENN04A -1.1130314 8.79367689 -4.743088 1.37E-05 0.00298199 3.03475381

212765_at CAMSAP1U -1.0863982 9.42505575 -4.7345547 1.42E-05 0.0030621 3.00664977

210254_at MS4A3 -1.0500477 12.8157054 -4.7261168 1.46E-05 0.00314327 2.9788805

233176_at — -1.1278256 8.19196857 -4.7198778 1.49E-05 0.00318888 235836149

223344_s_at MS4A7 -1.0542376 11.6140787 -4.6615341 1.84E-05 0.00376871 2.7670363

219951_s_at C20ORF12 -1.0986972 9.36939485 -4,6610806 1.84E-05 0.00376871 2.76555328

224358_s_at MS4A7 -1.0737805 10.2934393 -4.6288589 2.06E-05 0.00414687 2.66033365

209822_s_atVLDLR -1.0809314 10.4822858 -4.6256973 2.09E-05 0.00417816 2.65002641

1554892_a_« MS4A3 -1.0607494 11.9760309 -4.6180329 2.14E-05 0.00427729 2.62505295

224916_at LOC340061 -1.0659077 11.5293213 -4.6084907 2.22E-05 0.00435798 2.59398619

219607_s_at MS4A4A -1.0618962 10.8982797 -4.6084529 2.22E-05 0.00435798 239386325

220112_at A RD55 -1.0892108 8.61196167 -4.6022914 2.27E-05 0.00439877 237381817

202158_s_atCUGBP2 -1.071327 10.2596168 -4.5821696 2.43E-05 0.00466718 230843969

229638_at IRX3 -1.0842058 12.4826855 -4.5731157 2.51E-05 0.00474087 2.47906391

1557359_at LOC285758 -1.0922204 9.92033734 -4.5727867 2.51E-05 0.00474087 2.47799688

1555037_a_z lDHl -1.0626668 11.297782 -4362743 2.61E-05 0.00479572 2.4454411

235936_at LOC254559 -1.0942156 7.69992263 -4.5533045 2.69E-05 0.0048917 2.41487632

217196 _s_atCA SAPlLl -1.0905855 8.32441354 -4.5428721 2.79E-05 0.0050078 2.38112639 225786_at LOC2S4702 -1.1841367 9.55400971 -4310983 3.12E-05 0.00541251 2.27818048 203221 at TLE1 -1.0725652 10.2194004 -4.504306 3.20E-O5 0.00551587 2.25666737

218507_at HK32 -1.0603259 10.2529741 -4.4729944 3.57E-05 0.0059656 2.1559794

223952_x_at DHHS9 -1.0842606 123366028 -4.4456627 3.92E-Q5 0.00631099 2.0683571

224929_at LOC340061 -1.0551654 11.6690807 -4.4386464 4.02E-05 0.00644802 2.04590464

209485_ _s_atOS8PUA -1.0832594 8.89666819 -4.4376043 4.04E-05 0.00645252 2.04257108 222369_at NAT11 -1.0773853 9.63846481 -4.4294999 4.15E-05 0.00661759 2.01666018 210279 at GP 18 -1.1061684 9.71898614 -4.4206221 4.28E-05 0.00676572 138830241

206542_s_atSMARCA2 -1.0665392 10.093152 -4.4164022 4.34E-05 0.00682612 1.97483232

228055_at NAPSB -1.1406853 10.0636876 -4.411431 4.42E-05 0.00690524 135897232

206088_at LOC474170 -1.1642536 5.60881351 -4.3987993 4.62E-05 0.00715313 1.91871021

1555728_a_i MS4A4A -1.0619928 10.814275 -4.3884831 4.79E-05 0.00739242 1.8858698

229159_at K1AA0960 -1.1638873 7.81943811 -4.378427 4.96E-05 0.00756868 1.85389295

212071_s_atSPTBNl -1.0802737 10.3524809 -4.3710543 5.08E-05 0.00767831 1.83047131

224009_x_at DHRS9 -1.0883843 12.9995564 -4.3451551 5.56E-05 0.00815484 1.74834735

219471_at C130RF18 -1.082994 11.244718 -4.3449394 5.56E-05 0.00815484 1.74766447

204674_at LR P -1.0754387 9.48836985 -4.3365053 5.73 E-05 0.00835029 1.72097259

225594_at ZF -1.0660997 8.44053993 -4.3348185 5.76E-05 0.00835466 1.71563729

64900_at CHST5 ///AS -1.0783605 7.454203S5 -4.3330734 5.80E-05 0.00836918 1.71011893

218326_s_at LGR4 -1.1055598 7.35402657 -4.3327777 5.S0E-O5 0.00836918 1.70918383

204639_at ADA -1.0663173 8.71406105 -4.3311807 5.83E-05 0.00839318 1.70413466

220416_at ATP8B4 -1.0560097 10.8651277 -4.3288715 5.88E-05 0.00843796 1.69683558

226255_at ZBTB33 -1.056353 11.34447 -4.3186727 6.09E-05 0.00862606 1.66462107

204548_at 5TAR -1.0828983 8.71225533 -4.3131689 6.21E-05 0.00876809 1.64725213

207865_s_at BMP8B -1.1309201 9.46800068 -4.3117307 6.24E-05 0.00878832 1.64271524

244447_at KLF10 -1.3134824 7.8071422 -4.2828862 6.89E-05 0.00950707 1.55188213

224837 at FOXP1 -1.0552487 11.2859527 -4.279807 6.96E-05 0.00952643 134220361

201689_s_atTPD52 -1.0726713 9.3965084 -4.2740096 7.10E-05 0.00967829 1.52399041 212097_at CAV1 -1.0973744 8.37508938 -4.2610503 7.42E-05 0.00997486 1.48332253 1557570_a_< LOC285084 -1.0977131 8.27009497 -4.2541445 7.60E-05 0.01008195 1.46167694 201690_s_atTPD52 -1.073115 103093023 -4.2504384 7.69E-05 0.01016104 1.45006755 214920 at K1AA0960 -1.1291766 9.28547078 -4.2405995 7.96E-05 0.01044325 1.41927233

226431_at ALS2C 13 -1.0804181 8.88019612 -4.2395927 7.98E-05 0.01044325 1.4161231

227629_at PRLR -1.1385104 7.04094281 -4.2375147 8.04E-05 0.01046218 1.40962463

57540_at RB S -1.0889358 8.11543924 -4.2362686 8.G8E-05 0.01046218 1.40572847

228455_at SLC16A4 -1.2438773 7.61141506 -4.2334573 8.15E-05 0.01049314 1.39694035

242511_at ST3GAL3 -1.0989987 7.9960706 -4.2291028 8.27E-05 0.01057053 1.38333428

225619 at SIA1N1 -1.1432234 8.6802401 -4.227198 8.33E-05 0.01058985 1.37738486

213737_x_atGOLGA8G //, -1.0557244 13.4113502 -4.2214214 8.49E-05 0.01077515 1.35935067 224486_s_at C150RF41 -1.0809669 9.42072522 -4.2192321 8.56E-05 0.01083061 1.35251877 2304S0_at P1WIL4 -1.0659842 10.6705451 -4.2178649 8.60E-05 0.01085599 1.34825366 225224_at C20O F112 -1.0767769 9.19255558 -4.1971114 9.23E-05 0.01151643 1.28359413 219799_s_at DH S9 -1.0873546 12.5296658 -4.1953591 9.2SE-05 0.01155875 1.27814225 202979_s_atZF -1.0920673 9.89384482 -4.1942804 9.31E-05 0.01157478 1.27478664 206461_x_at MTlH -1.0392307 11.9250301 -4.1935006 9.34E-05 0.01157914 1.27236118 201675_at AKAP1 -1.0615779 10.8983992 -4.1859946 9.58E-05 0.01174461 1.24902648 227949_at PHACTR3 -1.0599385 10.7921228 -4.1808322 9.75E-05 0.01184572 1.2329899 237265_at C160RF73 -1.0739194 9.90657205 -4.1786481 9.82E-05 0.0118711 1.22620861 235758_at PNMA6A -1.0679142 8.36962585 -4.1782399 9.84E-05 0.0118711 1.22494122 1554298_a_< WDR49 -1.168549 7.28424515 -4.1685361 0.00010161 0.01212964 1J.9514511 230OO8_at IAA096Q -1.1023476 9.40901508 -4.156767 0.00010577 0.01243643 1J.5837023 215771_x_atRET -1.0639479 8.73407172 -4.1514318 0.00010769 0.01258151 1.14185786 204301_at BTBD11 -1.0665649 10.3597689 -4.1465423 0.00010949 0.01271022 1.12673448 2OlO36_s_at HA0H -1.0465759 10.8776177 -4.1465262 0.00010949 0.01271022 1.12668456 223044_at SLC4QA1 -1.0799265 8.72509702 -4.1435626 0.00011059 0.01281082 1.11752261

205996_ _s_atAK2 -1.0533596 11.6545132 -4.1314862 0.00011519 0.01305473 1.08022438 213894_at KIAA0960 -1.0975098 9.74897241 -4.1307312 0.00011549 0.01305473 1.07789445 235823_at LOC197322 -1.0867032 7.00344771 -4.1303782 0.00011562 0.01305473 1.07680534 212593 s_at PDCD4 -1.0784075 9.6202895 -4.1277406 0.00011665 0.01305473 1.06866759 227254_at — -1.0878832 8.8387562 -4.1270419 0.00011693 0.01305473 1.06651244 218082_s_at UBPl -1.061315 11.2875622 -4.1236056 0.00011829 0.01317223 1.05591605 221648_s_at C10RF121 -1.0625223 9.30594001 -4.1122294 0.00012291 0.01363084 1.02086816 225883_at ATG16L2 -1.0866743 8.95908959 -4.1072117 0.000125 0.01380676 1.0054261 222388_s_atVPS35 -1.0544103 10.9995649 -4.096001 0.0001298 0.01425665 0.9709611 208636 at ACTN1 -1.0393569 12.61059 -4.0933116 0.00013097 0.01432201 0.96270059

204165_at WASF1 -1.0621996 10.2583762 -4.0742957 0.0001396 0.01494692 0.9043759 239963_at -1.2400451 9.0375203 -4.0742228 0.00013963 0.01494692 0.9041527 227055_at ETTL7B -1.0860464 10.9882916 -4.0733051 0.00014006 0.01494692 0.90134178 229700_at LOC148203 -1.0769984 9.16397658 -4.0732431 0.00014009 0.01494692 0.90115181 225720_at SYNP02 -1.093531 8.22312673 -4.0689427 0.00014212 0.01511757 0.88798401 233782 at WDR68 -1.0892946 7.81601785 -4.0571162 0.00014785 0.01555469 0.85180964

226438_at TBP -1.0674478 9.28796451 -4.0535202 0.00014964 0.01564376 0.84082167 200672_x_atSPTBNl -1.0717572 7.97282842 -4.0518568 0.00015048 0.01565768 053574084 228625_at CITED4 -1.0665343 12.4781742 -4,0414018 0.00015582 0.01601409 0.80383153 223704_s_at D RT2 -1.0966738 7.49852282 -4.038741 0.00015721 0.01612655 0.79571762 223136_at AJG1 -1.0602864 11.4123181 -4.0340714 0.00015968 0.01634893 0.78148555 218168_s_atCABCl -1.05636 10.9814373 -4.0298906 0.00016192 0.01654732 0.76875062 219056_at R ASEH2B -1.0587835 9.59474393 -4.0293131 0.00016223 0.01654826 0.76699214 1553955_at LOC129285 -1.0626958 9.65678818 -4.0249191 0.00016462 0.01676095 0.75361657 216336_x_at T1M -1.0417674 11.497183 -4.0083934 0.00017392 0.01757723 0.70338342 209O07_s_at C10RF63 -1.0860359 10.6932184 -4.0033033 0.00017689 0.01782313 0.68793375 204959_at MNDA -1.0681514 11.9635641 -4.003101 0.00017701 0.01782313 0.68732013 232722_at RNASET2 -1.121936 6.4751986 -3.9998645 0.00017892 0.0179496 0.67750249 201924_at AFF1 -1.0636204 10.9900787 -3.9938919 0.0001825 0.01820614 0-65939689 205268_s_atADD2 -1.0749965 8.29295849 -3.9894046 0.00018524 0.01841452 0.64580364 217892_s_at U Al -1.0674835 9.77391533 -3.9742552 0.00019477 0.0190165 0.59997453 225610_at UHRF2 -1.0478186 11.8006338 -3.9712363 0.00019673 0.01908993 0.5908533 213888_s_at TRAF3 IP3 -1.0732522 10.3053256 -3.9709396 0.00019692 0.01908993 0.58995707 209879_at SELPLG -1.0891682 9.91966583 -3.9695775 0.00019781 0.0191422 0.58584343 226630_at C14ORF106 -1.0672553 9.79100795 -3361139 0.00020341 0.01964899 0.56037434 225455_at TADA1L -1.0580187 10.2337996 -3.9517012 0.00020985 0.02016419 0.5319252 15S4352_s_2 DENND4A -1.0590459 9.89217484 -3.9498502 0.00021113 0.02022705 0.52635021 227805_at — -1.0725811 7.97633184 -3.9486352 0.00021198 0.02022705 0.52269151 204849_at TCFL5 -1.0508793 10.0777273 -3.9473794 0.00021286 0.02027564 0.51891058 212174_at A 2 -1.0435458 12.5602536 -3.9427886 0.00021611 0.02047123 0.50509441 243431_at BTBD14A -1.1988342 7.54359435 -3.9340968 0.00022239 0.02085605 0-4789607 1558027_s__ PRKAB2 -1.0672869 8.44162128 -3.9261915 0.00022825 0.02129633 0.45522005 220615_s_at MLSTD1 -1.0704751 11.0839465 -3.9246829 0.00022939 0.0213295 0.45069271 220116_at KCMN2 -1.0475679 10.7237831 -3.9161743 0.00023589 0.02174968 0.42517604 201193_at !DHl -1.0387181 11.9734806 -3.9122575 0.00023895 0.02199427 0.41344031 2257S2_at MSRB3 -1.0704 8.85357731 -3.9114057 0.00023962 0.02201882 0.41088889 218270_at MRPL24 -1.041775 10.7168033 -3.9080124 0.0002423 0.02219357 0.40072844 1559139_at NOC2L -1.1614047 7.69426499 -3.9079762 0.00024233 0.02219357 0.4006202 201841_s_at HSPBl -1.0441743 13.4381243 -3.9073471 0.00024283 0.02220226 0.39873692 1559189_at TTC9C -1.1233947 6.22264013 -3.9060463 0.00024387 0.02226003 0.39484371 205944_s_atCLTCU -1.0767087 9.59502778 -3.8960537 0.000252 0.0227332 0.36496078 2ia532_s_at FU20152 -1.0975951 7.14515674 -3.8958965 0.00025213 0.0227332 0.36449103 205659_at HDAC9 -1.0805755 9.52806368 -3.8955883 0.00025238 0.0227332 0.36356988 228056_s_at NAPSB -1.133171 8.05318337 -3.8864469 0.00026006 0.02323287 0.33627243 208158_s_at OSBPL1A -1.0689057 8.96913414 -3.8834664 0.0002626 0.0233462 0.32738037 241024_at CSORF147 -1.130088 5.62544192 -3.8775071 0.00026777 0.02367801 0.30961257 212859_x_at MTlE -1.0360762 12.3752245 -3.8735521 0.00027126 0.02392114 0.29782945 219498_s_at BCLllA -1.0732492 8.13793041 -3.8714456 0.00027313 0.0240476 0.29155627 215095_at ESD -1.1487406 5.82227073 -3.8696858 0.00027471 0.02414738 0.28631705 203253 s at HtSPPDl -1.0681144 10.4329202 -3.8669778 0.00027715 0.02432282 0.2782577

213416_at ITSA4 -1.0669742 10.3810332 -3.8619771 0.00028171 0.02456545 0.26338338 1557283_a_;ZNF519 -1.1068414 5.33423642 -3.8586267 0.00028481 0.02479593 0.25342411 230424_at C50RF13 -1.129586 6.85369311 -3.8555889 0.00028764 0.02492377 0.24439825 230550_at M54A6A -1.0527231 11.5245536 -3.8469498 0.00029586 0.02543398 0.21875242 1555963_x_. B3GNT7 -1.0971417 7.71455009 -3.8417726 0.00030089 0.02570473 0.20339936 203518_at LYST -1.0508267 12.5285349 -3.8410237 0.00030162 0.02572727 0.20117947 229084_at CNTN4 -1.1046924 8.60627464 -3.8396872 0.00030294 0.02579917 0.19721855 200912_s_at EIF4A2 -1.0342758 13.3848401 -3.8372855 0.00030531 0.02584057 0.19010257 243514_at — -1.1677325 8.64926127 -3.834963 0.00030763 0.02599628 0.18322394 156Q495_at— -1.0868663 7.91686834 -3.8289949 0.00031366 0.02626207 0.16555845 209539_at ARHGEF6 -1.0428012 11.4186716 -3.8184713 0.00032456 0.02696861 0.13444828 211980_at COL4A1 -1.0583579 8.52391992 -3.8156429 0.00032755 0.02717595 0.1260953

222538 s atAPPt -1.0538895 9.69059359 -3.8135376 0.0003298 0.02730892 0.11988026 217540_at -1.0829555 9.09428634 -3.8128923 0.00033049 0.02730892 0.11797567 231950_at ZNF658 -1.0895471 8.18062639 -3.8089596 0.00033473 0.02756221 0.10637231 221900 at COL8A2 -1.0731684 10.4949814 -3.8010969 0.00034336 0.02814612 0.0831949 229033_s_at MUM1 -1.0955974 7.47621492 -3.798449 0.00034632 0.02830357 0.0753956 201688_s_atTPD52 -1.0610401 9.71085633 -3.7945851 0.00035068 0.02857425 0.0640208 209960_at HGF -1.1259855 5.57784014 -3.7926895 0.00035283 0.02870722 0.05844274 232232_s_at SLC22A16 -1.0425388 113170133 -3.785579 0.00036104 0.02915779 0.03753396 223470_at PIG -1.0448041 10.782124 -3.7837211 0.00036321 0.02924694 0.03207456 218540_at THTPA -1.0678164 9.37118811 -3.782058 0.00036517 0.02936123 0.0271889 226773_at — -1.0599901 8.73474937 -3.7794255 0.00036829 0.02956841 0.0194579 238098_at — -1.1114847 5.09426112 -3.778084 0.00036989 0.02961164 0.01551954 217707_x_at 5MARCA2 -1.0808866 103195127 -3.7780645 0.00036991 0.02961164 0.01546237 212993_at — -1.0777658 10.0764962 -3.7708097 0.00037867 0.03004896 -0.0058219 229123_at — -1.0812886 7.27161787 -3.7693556 0.00038045 0.03009487 -0.010085 235036_at UX1L -1.0722631 8.44284176 -3.7689888 0.0003809 0.03009487 -0.0111601 1557261_at WHDC1L1 //j -1.1135936 8.0995202 -3.7678412 0.00038231 0.03011937 -0.Q145238 228904_at HOXB3 -1.0881045 7.40156866 -3.7669423 0.00038342 0.03016331 -0:0171583

201381 _x atCACYBP -1.0345348 12.6646023 -3.7613837 0.00039034 0.03049295 -0.0334251 224800_at WDFY1 -1.0460265 11.2146548 -3.7556441 0.00039763 0.03085591 -0.0502365 228497_at SLC22A15 -1.0528433 10.2806063 -3.7504565 0.00040432 0.03126767 -0.0654047 218376_s_at ICA LI -1.063991 10.8151846 -3.7464229 0.0004096 0.0314976 -0.0771901 214997_at GOLGAl -1.1629895 5.40289373 -3.7438471 0.000413 0.03166964 -0.084712

232168. _x_at MACFl -1.1118803 7.19380131 -3.7436429 0.00041327 0.03166964 -0.0853084 215143_at FU36166 -1.1403943 5.25780477 -3.7428445 0.00041434 0.03166964 -0.0876391 229712_at S APC3 -1.1504135 5.48415471 -3.7427571 0.00041445 0.03166964 -0.0878942 2Q8910_s_atClQBP -1.0363862 12.212373 -3.7403131 0.00041772 0.03172049 -0.0950274 223343 at MS4A7 -1.0576569 11.3702217 -3.7294854 0.O0Q43249 0.03261559 -0.1265955

216007_at CLST 2 -1.1573199 5.8326347 -3.7201011 0.00044569 0.03342695 -0.153911 218477_at TME 14A -1.0520488 11.0359972 -3.7120317 0.00045735 0.03401174 -0.1773659 225716_at -1.0488569 12.276306 -3.711697 0.00045784 0.03401174 -0.1783381 229934_at -1.1078549 9.5045234 -3.7090958 0.00046167 0.03418201 -0.1858919

226O20_s_at OABX /// O W -1.0604674 9.19536151 -3.7080794 0.00046317 0.03418201 -0.1888427

231300. at LOC90835 -1.0706749 8.05881715 -3.7080185 0.00046326 0.03418201 -0.1890194

225431. x_atACYlL2 -1.1051561 9.95149452 -3.6951992 0.00048263 0.03517085 -0.2261934

239503. at — -1.1019241 6.4612666 -3.6931957 0.00048572 0.03517085 -0.2319963

208747. s_atClS -1.0897058 7.74085712 -3.6813511 0.00050442 0.03616953 -0.2662632

210658. s_atGGA2 -1.0464213 10.9126279 -3.6763333 0.00051254 0.03648841 -0.2807596

207405. _s_at RAD17 -1.0614693 9.75893285 -3.6739986 0.00051636 0.03662349 -0.2875005

218792. _s_at BSPRY -1.0964707 7.1685673 -3.6700784 0.00052284 0.037029 -0.2988132

224838. .at FOXP1 -1.0451305 11.003461 -3.666886 0.00052818 0.03716608 -0.3080204

208956. _atDUT -1.0305575 13.3123909 -3.6657787 0.00053004 0.03717544 -0.3112129

210375. .at PTGER3 -1.122068 4.90394615 -3.6657484 0.00053009 0.03717544 -0.3113002

233252. _5_atST BP -1.0460631 9.42442497 -3.6597179 0.00054034 0.03777915 -0.3286758

202309. .at MTHFDl -1.0363875 113356701 -3.6479618 0.00056088 0.03888847 -0.3624982

212510. .at GPD1L -1.0564567 9.5177254 -3.6426294 0.00057044 0.03942724 -0.3778178

232242. .at C3DRF14 -1.1397197 5.05025398 -3.6421706 0.00057127 0.03942724 -0.3791352

203335. .at PHYH -1.0509077 9.47404929 -3.6414392 0.00057259 0.03942897 -0.3812352

225876. .at NPAL3 -1.0545782 8.47639608 -3.6399342 0.00057533 0.03956752 -0.3855556

226038. _at LONRF1 -1.0686626 8.27265094 -3.6331772 0.00058777 0.04027091 -0.4049391

241466. .at MTL5 -1.0881094 7.2321193 -3.630577 0.00059262 0.04050197 -0.4123921

232702. _at RABGAP1L -1.1084819 7.2641058 -3.629559 0.00059453 0.04053125 -0.4153094

228157. _at ZNF207 -1.1331898 9.20083267 -3.628722 0.00059611 0.04058804 -0.4177074

220892. _s_at PSATl -1.0539762 10.5575882 -3.6260997 0.00060107 0.04087498 -0.4252181

211987. _at TDP2B -1.0376579 11.6916878 -3.6237021 0.00060564 0.04108363 -0.4320824

207636 at SERPINI2 -1.1147369 8.32640727 -3.6221365 O.O0O6OB54 0.04123615 -0.4365631

1555702_a_< ST3GAL3 -1.0571721 11.469985 -3.6202073 0.00061236 0.04138559 -0.4420828 208967_s_atAK2 -1.0444004 11.8885466 -3.6083697 0.00063567 0.04259196 -0.4759123 227233_at TSPAN2 -1.0933291 4.88565746 -3.6039803 0.00064452 0.04297454 -0.488439 1561488_at — -1.0791431 8.42185259 -3.5998639 0.00065293 0.04336219 -0.5001777 232034_at LOC203274 -1.1061415 8.7194472 -3.59871 O.O0O65531 0.04342891 -0.5034667 210817_s_at CALCOC02 -1.0381701 11-2547695 -3.5973152 0.00065819 0.04351451 -0.5074419 20B990_s_at HNRPH3 -1.0433996 11.010468 -3.5949274 0.00066315 0.04378974 -0.5142443 205550_s_at BRE -1.042758 10.1098377 -3.5935936 0.00066594 0.0438679 -0.518043 218461_at ATPBD1C -1.044665 10.8560567 -3.5S8935 0.00067577 0.04421781 -0.5313034 203774_at MTR -1.0520755 10.5810662 -3.5887762 0.00067611 0.04421781 -0.5317553 1554791_a_ FU23861 -10S02S14 7.25343472 -3.5862528 0.00068149 0.0444105 -0.5389334 227662_at SYNP02 -1.0748437 9.18363146 -3.5850906 0.00068398 0.04451989 -0.5422384 235374_at MDH1 -1.1308822 8.18431482 -3.584254 0.00068578 0.04454185 -0.5446169 211929_at HNRPA3 -1.0599635 11.1782682 -3.5S31072 0.00068826 0.04454185 -0.5478769 236421_at A RD45 -1.1046422 7.81492792 -3.5820889 0.00069046 0.04454185 -0.5507713 222423_s_at LARS -1.044671 11.3066627 -3.5819545 0.00069075 0.04454185 -0.551153 218404_at SNX10 -1.0542239 10.5371703 -3.5819241 0.00069082 0.04454185 -0.5512396 225845_at ZBTB44 -1.0510504 10.114137 -3.5792352 0.00069667 0.0448057 -0.5588792 228O30_at — -1.1453293 8.222179 -3.5744486 0.00070722 0.04522467 -0.5724699 205543 at HSPA4L -1.0619155 10.0871911 -3.5711304 0.00071461 0.04550224 -0.5818846

222786_at CHST12 -1.0953465 8.08550285 -3.5710089 0.00071489 0.04550224 -0.5822293 226148_at ZBTB44 -1.044973 10.9431965 -3.5699976 0.00071716 0.04559364 -0.5850975 220007_at ETTL8 -1.0742738 7.97164029 -3.568486 0.00072056 0.04570388 -0.5893838 2320 9_at — -1.1055172 3.71843028 -3.5666355 0.00072475 0.04591638 -0.5946293 225639_at SKAP2 -1.0513915 10.9430745 -3.5623166 0.00073462 0.04643409 -0.6068655 201432_at CAT -1.029344 13.2389426 -3.5605892 0.00073861 0.04663198 -0.611757 243366_s_atCERKL -1.0677271 9.52062508 -3.5590761 0.00074211 0.04665922 -0.6160402 239163_at UBE2B -1.115315 5.28263677 -3.5589302 0.00074245 0.04665922 -0.6164534 239911_at — -1.1157309 6.92640942 -3.5564148 0.00074832 0.04692001 -0.6235711 239841_at C70RF24 -1.1067027 8.40613863 -3.5537484 0.00075458 0.04706777 -0.6311131 213510_x_at LOC220594 -1.0787105 9.26871882 -3.5532589 0.00075574 0.04706777 -0.6324971 203446_S_atOCRL -1.0590145 8.52928391 -3.5522168 0.00075821 0.04716146 -0.6354436 220900_at HJ12078 -1.2242895 4.04470354 -3.550766 0.00076165 0.04732199 -0.6395446 222427_s_at LARS -1.0327116 11,8350021 -3.5464813 0.00077192 0.04764859 -0.6516498 213908_at WHDC1U //, -1.106503 7.49688229 -3.54639 0.00077214 0.04764859 -0.6519076 235170_at ZNF92 -1.0701713 10.4753161 -3.5440334 0.00077784 0.04781967 -0.6585616 205804_s_at TRAF3 IP3 -1.0645947 10.430865 -3.5397143 0.0007884 0.04837904 -0.6707492 227865_at C9ORF103 -1.0549476 9.09854389 -3.537566 0.0007937 0.04864948 -0.6768078 201769_at CUNT1 -1.0404695 11,3472898 -3.5358759 0.0007979 0.04872219 -0.6815728 1555962_at B3GNT7 -1.0816315 8.07026497 -3.5328566 0.00080544 0.04891403 -0.6900812 244O50_at PTPLAD2 -1.0466927 10.2444943 -3.5293148 0.00081438 0.04930933 -0.7000563 1554704 at ATP8B3 -1.0775601 9.03671576 -3.5253989 0.00082438 0.04963954 -0.7110776

Polimunol and Copaxone ^® comparison: differentially expressed pathways In order to identify pathways differentially expressed by Polimunol compared with Copaxone ^® , the input probesets had to comply not only with the conservative steps described above (resulting in a set of 779 differentially expressed probesets) , but also with a fold change threshold of | FC | 1.1. Pathway enrichment analysis employed the N1H DAVID platform, resulting in 137 pathways enriched among top probesets upregulated by Polimunol relative to Copaxone ^® . Pathways significantly enriched among top probesets differentially expressed between Polimunol and Copaxone in THP-1 cells are listed in Table 29.

Table 29: Pathways significantly enriched among top probesets differentially expressed between Polimunol and Copaxone ^® in THP-1 cells .

Category Term Count Pvalue Fold Enrichment Benjamin!

GOTERM BP ALL GO:00O9605~response to external stimulus 34 1.25E-12 4.242127482 2.13E-09

GOTERM Bl> ALL GO :005089 ~response to stimulus 66 1.47E-11 2J21777115 125E-0B

GOTERM BP ALL GO-O009611~response to wounding 24 1.1OE-10 5.226859152 6 6E-0B

GO:0051239~regu ration of multicellular organtsmal

GOTE M BP ALL process 30 2.36E-09 3.546434111 1.22E-06

GOTERM BP ALL GO 00O6950~response to stress 45 3.97E-09 2.520092B1 USE-OB

GOTERM_CC_ALL GO:QO05576"extr3tel3ular region 32 1.62E- S 3.124422358 2-46E-06

GOTERM BP ALL GO:0002376~inimune system process 31 9.B E-09 3.264522306 2.79E-06

GOTE M MF ALL GO:00O4838**transmembrane receptor activity 21 7.19E-OB 4L2773191S2 9.08E-06

GOTERM MF ALL GO"0004872~rece tor activity 30 6.09E-OB 3.099OB2935 1.15E-U5

GOTERM BP ALL GO:00O5S55~immune response 23 6.20E-OB 3.925650193 1-5 E-05

KEGG PATHWAY sa(M060:CytokB e-cyto¾ate receptor interaction 14 2.08E-O7 6.063 19076 1.92E-05

GOTERM MF ALL G O Q0O4B l~s i goal transducer activity 37 5.51E-0B 2.B480B9319 2.09E-O5

GOTERM MF ALL GO:0O6O0S9~rnoleeu!ar transducer activity 37 5.S1E-OS 2.648089319 2.09E-0S

GOTERM BP ALL GO:00O6952~defense response 21 1-12E-Q7 4.15637457 2-37E-05

GOTERM BP ALL GO OOS2879~re»u!ation of localization 22 1-5SE-07 3.S85957066 2.98E-05

GOTERM MF ALL GO:0a3O247~polysaccharide binding 10 4.26E-07 10.281O8466 4.04E-05

GOTERM MF ALL GO:0O01871~pattefn binding 10 4.26E-07 10.28108-156 4.04 E-05

GOTERM CC ALL GO 00G5615~e:rtracellular space 17 6.BOE-07 4.6263B8S91 S.17E-05

GOTERM BP ALL GO 0C-t»5S3~r emulation of response to stimulus 19 3.0S.E-O7 4.32390456 5.23E-05

GOTERM CC ALL GO.00-4421~e:<traceUular region part IS 2-56E-06 3.750331428 9.73E-05

GOTERM CC ALL GO::aoo5SBS~ plasma membrane 51 1.99E-06 1.918590604 0.00010059

GOTERM BP ALL GO:005O794~regulatian of cellular process 97 7.60E-O7 1.431262036 000010778

GOTERM BP ALL GO:0O42127~re(ulation of eel proliferation 25 8.8SE-07 3.138545339 0.00010788

GO.0OO7I66~ceII surface receptor linked signal

GOTERM BP ALL transduction 30 S.25E-07 2.737037737 0.000108

GOTERM BP ALL GO:0COG954r inflammatory response 15 7.41E-07 5.299032363 0.0001146

GOTERM BP ALL GO 0O 222 l~response to chemical stimulus 33 1.27E-0S 2.509579282 0.0O0134S7

GOTERM BP ALL GO:0050789~regulation of biological process 93 1.24E-06 1.405153361 0.00014066

GOTERM BP Alt i3O:OO650O7~biological regulation 101 2.B1E-06 1.374157191 □ 00023327

GOTERM BP ALL <-Q:004S584~pesitive regulation of response to stimulus 13 2JSE-06 3.72397(92 0.0O023S4S

GO:0002eS4~positive regulation of immune system

GOTERM BP ALL process 13 237E-OS 5.682799215 O.0OO2A311

GOTERM BP ALL GO 000156a~bk3od vessel development 13 4.31E-06 5.410336239 0.00036654

GOTERM BP ALL GO:000194 ~vasculature devekipment 13 4.97E-06 5.337223587 0.00038399 TE M BP ALL GO:OOd2C60-wourvd healing 11 4.S9E-06 6.683846154 00O039593

GOTERM BP ALL GOS0*85i9"negative regulation of biological process 41 6.24E-06 2.055488241 0.00040825

GOTERM BP ALL GO 0048514.*"blaod vessel morphogenesis 12 6.15E-06 5.786879787 0.DO041817

GOTERM BP ALL GO.O002682~regulation oC immune system process 16 5-94E-06 4.154682924 0.00042096

GOTERM BP ALL GO:0OO7165~5ignal transduction 45 5.71E-06 1.962B8636 00O042219

GOTERM BP ALL GO 0050793~regulation of developmental process 21 7.97E-06 3.166270454 0.0004676

GOTERM BP ALL GO:0O4873l~system development 41 7.80E-06 2.037000612 0,00047369

GOTERM BP ALL GO 0050776"*re¾ulation of immune response 12 7.72E-06 5.652301187 0.00048624

GO :0O5124O~ positive regulation of multicellular

GOTERM BP ALL organ ismal process 12 1.19E-05 5.401017801 0.0006771

GOTERM BP ALL GO:0060341~regulation of cellular localization 11 2.31E-05 5.61667744 0.00126569

GOTERM BP ALL GO:O03250l~mufticetlular organismal process 55 2.47 E-05 1.69297015 0.00131208 GOTERM BP ALL GO:OOG2703- regulation of leukocyte mediated immunity 7 3.08E-05 11.1930438 0.00158406

GOTERM MF AU GOiOOOSSse-giycosam ogfycan binding S 2.69E-05 8.933908046 0.0020367

GO:0048646~anatomical structure formation involved in

GOTERM BP ALL morphogenesis 14 5.46E-05 3.902162058 0.00272943

GOTERM BP ALL G0:004ia66-negative regulation of apoptosis 15 8.17E-05 3.519048519 0.00396163

GOt JQi60*"nucleotide receptor activity, G-protein

GOTERM MF ALL coupled 5 6.34E-05 21.59027778 0.00399 S02

GO:0045028~purinergic nucleotide receptor activity, G-

GOTERM MP ALL pratein coupled 5 6.31E-05 21.59027778 0.00399*02

GO-QO43069~rtegat†ve regulation of programmed cell

GOTERM BP ALL death IS 9.24E-05 3.47875407 0.00423954

KEGS PATHWAY hsaO4610:Complement and coagulation cascades 6 9.3 IE-OS 12.09974425 0.00427423

GOTERM BP ALL GO 0060548- negative regulation of cell death 15 963E-05 3 «5526569 0.00429948

GQTERM_BP_AUL GO:Q04BB56"anatom»cal structure development 41 9.18E-05 1.834500551 0.00433037

GOTERM BP ALL GO:0O01525~angsogenesis 9 Q.0OO10467 6-076223776 0.00444135

GOTERM BP ALL GO:0O0ia 19" positive regulation of cytokine production S 0.0O010299 7.255192569 0.00448212

GO:0048G60~reguSation of smooth musde cell

GOTERM BP ALL proliferation 6 0.00011139 12.15244755 0.00461078

GOTERM BP ALL GO:0O4SSia~ ositive regulation of baotagital process 40 o.oooiiais 1.834331706 0.00477377

GOTERM BP ALL GO:O032502~deveiapmental process 48 0.00013028 1.687839938 0.00514072

GOTERM BP ALL GO :00O7275~rn unicellular organtsmal develapment 44 O.OOO 14296 1.743991169 0.00551191

GOTERM BP ALL G0MO10033~respon5e to organic substance 20 0.0OO14322 2.665010428 O.0O558755

GOTERM BP ALL GO.00O9617~response to bacterium 9 0.00015325 5.756422525 0.0056515

GOTERM MF ALL GO 0016502-nudeatide receptor activity 5 0.00010797 19.0502451 0.00582884

GOTERM MF ALL GQ:0Q01614~purinergk nucleotide receptor activity 5 0.0O0I0797 19.0502451 0.00582884

GOTERM BP ALL GOrDQ32496~respon5e to Hpopoiy saccharide 7 0.0OO16B53 8.339914987 0.00608127

GOTERM BP AIL GO:0O4S765~reeulation of angiogenesis 6 0.00017834 11.04767959 0.00630065

GOTERM CC ALL GO 0O31226~intrinsic to plasma membrane 21 0.0OO2QS51 2.513724996 0.00631924

GOTERM BP ALL GO:0O S5l3~organ development 31 O.0O0182S5 2.027588128 0.00633147

GOTERM BP ALL SO:0O5170 ~response to other organism 11 0.00021593 4.312158809 0.00731991

GOTERM BP ALL GO:0O5l270-regulation of ceM motion 10 O.OOO 22502 4.78442817 0.00741176

GOTERM BP ALL GO:0031099~regeneration 6 O.OOO 23762 10.41638362 0.00774377

GOTERM_MF_ALL GO:uO30246~carbohydrate binding 11 0.00017696 4.425336439 0.00834919

GOTERM CC ALL GO:0OOSsr?"integral to plasma membrane 20 Q.0O047736 2.436305529 0.01031444

GOTERM BP ALL GO 0030334"regul ation of ceB migration 9 0.0O034S68 5.110842429 0.01092533

GOTERM BP ALL GO OO51049-re¾ulation of transport 13 O.0QQ34269 3.464513557 0.01094009

GOTERM BP ALL GQ:0OO2237~response to molecule of bacterial origin 7 0.0OO37BB3 7.209079057 0.01165013

GO:0OO71i6"G-protein coupled receptor protein

GOTERM BP ALL signaling pathway 13 0.00040141 3.404780564 0.01170574

GOTERM BP ALL GO aoo2697~regutation of immune effector process 7 O.0O041534 7.088927739 0.01170818

GOTERM CC ALL GO OO16O20~membrane 32 0.00046587 1.342587724 0.01173539

GO :0OO2B2 "regulation of adaptive immune response

based on somatic recombination of immune receptors

GOTERM BP ALL built from imrnuna globulin superfamiry domains 6 O.0O039991 9.348036579 0.011S65E5

GOTERM BP ALL GO:0OO9968~ negative regulatian of signal transduction 10 0.0OO41443 4.403060707 0.01187952

GOTERM BP ALL GO 0044057~regulation of system process 10 0.00041443 4.403060707 0.01187952

GOTERM_BP_ALL GO:0051Q46~regufation of secretion 8 0.00039574 5.B5660123 0.01195094

GOTERM_BP_ALl GO 005077S~posrtrve regulation of immune response a 0.00039574 5 85660123 0.01195094

GQTERM_BP_ALL G O :00O69 5~chem otaxis s 0.0O04S788 5.718798848 0.01248643

GOTERM BP ALL GO:004233O~taxis 8 0.00045788 5.718798:848 0.01248643

GOTEHM BP ALL. GO:0002B19~regulation of adaptive immune response s 00004511 9 114335664 0.01250293

GOTERM_BP_ALL GO:Q051101~regu!ation of DNA bindinj 8 0.OO049175 5.652301187 0.01319259

GOTERM_BP ALL GO:0O48523~negatwe regulation of ceJiular process 34 0.0O0S0059 1.834738973 0.01321981

GOTERM BP ALL GO:oa09653~anatom>caI structure morphogenesis 24 0.00055741 2.16C 3512 0.01448509

GOTERM BP ALL GO:0O«)134'"regulation of response to stress 11 0.OO057O31 3.819340659 0 01459518

GOTERM Mf ALL GO 0019955~cytakine binding 7 0.0O0354B6 7 312836022 0 01483488

GOTERM_BP_ALL GO:Q042981~reguIation of apoptosis 22 Q.OOO60362 2.254248281 0.01521241

GOTERM CC ALL GO:OQ3l224~intrinsic to membrane 60 0.00085774 1452927379 0.01617187

GOTERM BP ALL GO:00400l2~*regulaTion of locomotion 9 Q.0O067325 4634407965 0 01670569

GOTERM BP ALL GO:0043067"-regulation of programmed cell death 22 0.00068835 2.231668165 00168318

GOTERM BP ALL GO:001094i~regulation of ceH death 22 0.0007188 2 224241649 0.01732135

GOTERM BP ALL GO:001O648~negative regulation of cell communication 10 0.00076041 4.05O815851 0.01781109

GOT-BM_BP_ALL GO:0O0iai7~regulation of cytokine production 9 Q.00075248 4.557167832 0.01787284

GOTERM BP ALL GO :0030154~ce)l differentiatian 28 0.0O084S05 1.942171983 0.01952917

GO:000246C~adaptrve immune response based on

somatic recombination of immune receptors built from

aOTERM_BP_ALL immunoglobulin superfamily domains S 0.00086878 7.925509273 0.0197B0S7

GOTERM BP ALL GO:a002250~adaptrve immune response 6 0.00086878 7.925509273 001978057

GOTERM BP ALL GO 0O850Oa-regulation of biologica! quality 27 0.00088955 1.969484297 0.01998171

GOTERM BP ALL GO:000177S-cell activation 11 0.0009539 3.57424928 a02059711

GOTERM SP ALL GO:0051223~regulation of protein transport 7 0.0OO95132 6.076223776 0.0208168

GOTERM BP ALL GO:0048869~ceilular developmental process 29 0.0O094798 1.89677599 0.02100365

KEGG PATHWAY h5a04621:fJOD-like receptor signaling pathway 7 0.00076766 6.125971143 Q.02327548

GOTERM_CC_ALL GO:0O33256~l~i<appao/NF-*appae complex 3 0.CO140853 475647651 0.02352421

GOTERM BP ALL GO OOo2694~regulation of leukocyte activation 8 0.0011427 4.910079819 0.02431771

GOTERM_BP_ALL GO:005OB17~coagufation S 0.00116213 7.440274012 0.02442105

GOTERM_BP_ALL GO:00075S6~blood coagulation S 0.00116213 7 440274012 0.02442105

GOTERM_BP_ALL GO;0006916~anti-apoptosii 10 0.00120323 3.79763986 0.02466543

GOTERM BP ALL GO:00O9607~response to biotic stimulus 12 0.0O120O13 3.212100675 002490264

GOTERM_BP_ALL GO:00OS285""negative r egulation of cell proliferation 12 0.0012435 3.198012514 0.02517972

GOTERM MF ALL GO:Q0O4930"*G-prarein coupled receptor activity 9 0.0O06S792 4.626488095 0.02574405

GOTERM CC ALL GO :00099S6~ceil surface 10 0.001793 35928663 0.02690939

GOTERM BP ALL GO:CKU4070~response to organic cycBc substance 7 0.0O136752 5.671142191 0.02733082

GOTERM BP ALL GOX)040011~locomotiOR 12 0.00148086 3.129385636 0.028SS62B

G :00702CU~reguiation of establishment of protein

GOTERM BP ALL localization 7 0.0014651 5.596521899 0.02891444

GOTERM BP ALL GO:0046649~lymphocyte activation 9 0.00154141 4.08104582 0.02971013

GO:003l32S~positive regulation of cellular taxsyntheoc

GOTERM BP ALL process 17 0.00162069 2.413453369 0.03052477

GOTERM BP ALL GO:005Q865~regulation of cell activation 8 0.00161108 4.62950383 0.03068591

GOTERM BP ALL GO :OOC7626~locomotory behavior 9 0.00169408 4.02103044 0.0311S615

These pathways include a variety of immune related pathways expected to be relevant to Copaxone ^® ' s mechanism of action, including immune- related pathways such as the cytokine-cytokine receptor interaction pathway (adjusted p < 1.9e-5) that was also enriched among probesets modulated by Copaxone ^® (see above) , and positive regulation of cytokine production (adjusted p < 0.004) . These pathways also include inflammation related pathways, such as inflammatory response (adjusted p < 0.0001), NOD-like receptor signaling (adjusted p < 0.02), and response to lipopolysaccharide (adjusted p < 0.006) . The top 25 pathways are listed in Table 30, and the key pathways are illustrated in Figure 38. The specific genes in the cytokine-cytokine receptor interaction pathway are depicted in Figure 39.

Table 30: Top 25 pathways significantly enriched among top probesets differentially expressed between Polimtinol and Copaxone

GO:0007166~cell surface receptor

GO Biological Process linked signal transduction 30 0.000108003

GO Biological Process response 15 jQ£QJH 4j6pJ Polimunol and Copaxone ^® comparison: discussion

Once demonstrated to be robustly designed as shown in the MoA subsection, and upon applying conservative statistical approaches, hundreds of genes are differentially expressed in human monocytes following activation with Polimunol compared to activation with Copaxone ^® . In and of itself, the fact that so many genes are differentially expressed immediately calls into question the "sameness" of Polimunol and suggests that its biological impact on human antigen presenting cells differs significantly from Copaxone ^® . This stands in sharp contrast to the lack of differences between the three different lots of Copaxone ^® tested in parallel, under blinding, in the same experiment (in the three possible pairwise comparisons between Copaxone ^® lots, for two of the comparisons zero significant probesets were observed, and for the third a single probeset passed FDR with adjusted p value of 0.044) . Moreover, the fact that the differentially expressed genes are enriched in key biological pathways such as "immune response" further supports the biological relevance of the observed differences. Finally, the fact that many of the pathways enriched among the differentially expressed genes are relevant to Copaxone ^® ' s mechanism of action, such as cytokine-cytokine receptor interactions, and relevant to potential safety concerns, such as inflammatory response and response to lipopolysaccharide pathways, together raise serious concerns regarding the safety and efficacy of Polimunol. In fact, the response to lipopolysaccharide pathway was also enriched among genes differentially expressed by another purported generic, Probioglat (Figure 40) . Out of the 137 pathways enriched among probesets upregulated by Polimunol relative to Copaxone ^® , 37 of these pathways were also enriched in the prior comparison with Probioglat (out of 64 total pathways seen for

Probioglat) . Of note, the introduction of Probioglat in Mexico was associated with a 3 -fold increase in adverse events and a 7-fold increase in relapses as detailed in Teva's seventh Citizen Petition (FDA-2014-P-0933-0001 available at www . regulations . gov/# ! documentDetail; D=FDA-2014-P-0933-0001 , and also described herein) .

Discussion — Example 10-11

Copaxone ^® has long provided a safe and effective treatment option for multiple sclerosis patients, operating through a complex set of mechanisms that have gradually been elucidated through extensive research that continues to this day.

Methods for comparing two small molecule medicines to determine therapeutic equivalence are well established, and standards for evaluating biologies are also rapidly becoming available. However, for non-biological complex drugs (NBCDs) such as glatiramer acetate the level of evidence needed to determine equivalence remains an unresolved question and a subject of ongoing research by the scientific community. Teva is an active participant in such research, conducting a steady program of experiments to characterize Copaxone ^® and compare it to various glatiramoids marketed outside the United States and Europe as purported generics. Such characterization studies are critical to ensure that patients with multiple sclerosis (MS) continue to receive adequate medicines that are efficacious and safe .

One key aspect of the public discourse on non-biological complex drugs concerns the role of clinical trials. Well-controlled clinical trials of appropriate duration (typically 2 years) using standard endpoints such as annualized relapse rate (ARR) are an important means for investigating the safety and efficacy of medicines for MS, yet clinical studies not meeting those criteria distract from the essential question of "sameness" and risk creating a false sense of security for a purported generic. In recent months, Synthon has publicly reported clinical results for a follow-on glatiramoid purported to be a generic form of Copaxone ^® , yet the trial results raise significant questions regarding its validity [as detailed in Appendix 2 of FDA-2014-P-0933-0001 available at www. regulations .gov/# ! documentDetail; D=FDA-2014-P-0933-0001, and also described herein] . For instance, given the sample size of GATE (Copaxone ^® =357 , Placebo=84) , the probability of showing any level of annualized relapse rate (ARR) reduction (i.e. clinical efficacy) in the reference, well-established drug Copaxone ^® , using results from prior adequate, randomized, placebo-controlled studies with Copaxone ^® was high (>90%). Yet, a statistically unlikely result of no effect in reducing ARR was recorded for the Copaxone ^® arm in the GATE study, attesting to the lack of assay sensitivity. It is critical to know whether the trial had assay sensitivity (i.e., could have distinguished an effective drug from an ineffective one) . Thus, if the active control (Copaxone ^® in the case of GATE study) had no effect at all in the trial (i.e., did not have any of its well-established, expected effect) , then finding even a very small difference between control and test drug is meaningless, providing no evidence that the test drug is effective. Lastly, the rate of adverse events leading to discontinuation was 2.4 fold higher in the Synthon product arm than in the Copaxone ^® arm (12 vs 5) . Overall, the many shortcomings of the design and conduct of the GATE study render its findings unreliable . Teva is continuously conducting experiments to further elucidate Copaxone ^® ' s complex mechanism of action, and working towards the discovery of validated biomarkers, which have yet to be identified. Teva then seeks to compare Copaxone ^® ' s profile to that of all purported generics marketed globally. Synthon' s Polimunol was recently introduced to clinical practice in Argentina, and has since been studied by Teva extensively through a variety of characterization methods, each providing a small window into specific characteristics of this complex medicine. For instance, genome-wide transcriptional studies were employed in carefully selected model systems informative of certain aspects of the biological impact of an immunological medicine. To compare the ex-vivo biological effect of Copaxone ^® and Polimunol in mouse lymphocytes following prior in vivo immunization, mouse splenocytes were utilized, which embody the key cell type impacted by antigenic presentation. Additionally, to compare the immediate biological effects of Copaxone ^® and Polimunol in antigen- presenting cells, which are key to the mode of action of an antigen in mediating T-helper cell immune response, a human monocyte (THP-1) cell line was utilized. In both model systems significant differences in gene expression profiles were detected between Copaxone and Polimunol, regardless of the immunization sequence or array randomization scheme. In mouse splenocytes, the fact that significant and consistent differences in gene expression profiles are observed between splenocytes ex-vivo activated with Polimunol and splenocytes activated with Copaxone ^® , regardless of whether the mice were initially in vivo immunized with Copaxone or initially immunized with Polimunol, further emphasizes the robustness of the differences in biological impact of these two medicines on many genes . These hundreds of affected genes participate in immunologically relevant pathways and highlight potential clinical implications of overly stimulated or under- regulated immunological mechanisms relevant to the response and well- being of MS patients. For instance, IL18, which has been implicated in the pathogenesis of MS, is downregulated significantly less effectively by Polimunol than by Copaxone ^® . IL18 is important for T helper cell differentiation, and influences IFNg expression, suggesting that the impact of each medicine on T cells (which play an important role in Copaxone ^® ' s mechanism of action) is significantly different. The importance of IL18 via its actions in inducing Thl responses (which is attributed, at least partially, to induction of IFNg production by natural killer (NK) cells) , was underscored in a study in the mouse model of MS, autoimmune encephalomyelitis (EAE) . Mice deficient for IL18 were observed to be resistant to EAE, and treatment of these mice with IL18 restored the ability to generate a Thl response, while treatment of mice wild-type for IL18 increased ΕΆΕ disease severity (Shi et al, J. Immunol., 2000) . IL18 antibodies as well as the naturally expressed IL18 inhibitor, IL18BP (which was upregulated by Copaxone treatment in this study) , have been proposed as potential therapeutic agents against neuroinflamination (Felderhoff-Mueser et al, Trends Neurosci, 2005).

Similarly, key type I interferon pathway production pathway genes including RIG-I, MDA5 , and IRF7 are all significantly upregulated by Polimunol relative to Copaxone ^® . This increased interferon signaling with Polimunol treatment further increases concerns about possible adverse events including flu-like symptoms in Polimunol-treated patients. As noted in Trinchieri et al, 2010, "IFN produced during viral infection, other pathological conditions, or in the presence of DNA released by dying cells may mediate unwanted toxicity or induce pathological damage and inflammatory or autoimmune syndromes (Pascual et al. , 2010) ." In human monocytes, many of the pathways enriched among the genes differentially expressed between Copaxone ^® and Polimunol are relevant to Copaxone ^® ' s mechanism of action (such as cytokine-cytokine receptor interaction) , and relevant to potential safety concerns (such as inflammatory response and response to lipopolysaccharide pathways) . The same response to lipopolysaccharide pathway was also enriched among genes differentially expressed by another purported generic, Probioglat. This is particularly concerning because the introduction of another purported generic to Copaxone ^® , Probioglat in Mexico was associated with a 3-fold increase in adverse events and a 7-fold increase in relapses as detailed in Teva's seventh Citizen Petition (FDA-2014-P-0933-0001 available at www. regulations . gov/# ! documentDetail; D=FDA-2014-P-0933-0001, and also described herein) . The gene expression findings suggest that regardless of the many issues in the design and conduct of Synthon' s GATE study that render the results unreliable, the study itself was premature because it was conducted on a glatiramoid that is almost certainly not equivalent to Copaxone ^® . Together, these data warrant further investigation, and emphasize the need for clinical trials following upon the establishment of quality and pharmaceutical equivalence, specifically multi-year safety studies with standard clinical endpoints for MS, to ensure the safety and well-being of multiple sclerosis patients. How best to determine whether a differently manufactured glatiramoid is as safe and effective as Copaxone ^® remains an unresolved question that is also the subject of active research. One such differently manufactured glatiramoid, Synthon' s Polimunol, purports to have been tested in a clinical study (GATE) , yet the trial results are of questionable validity and raise more questions than answers, as detailed in Appendix 2 of FDA-2014-P-0933-0001 available at www. regulations. gov/# ! documentDetail; D=FDA-2014-P-0933-0001, and also described herein] . Beyond the extensive flaws in the design and conduct of the GATE study that render the results unreliable, the study itself was premature because the equivalence of Synthon' s glatiramoid with Copaxone ^® had not been conclusively established, and data from a full battery of high resolution physicochemical and gene expression studies support the conclusion that Sython' s glatiramoid and Copaxone ^® are not equivalent .

The newest gene expression studies first reported in this document find extensive and significant differences between the gene expression profiles modulated by Synthon' s Polimunol and the profiles modulated by Copaxone ^® , in both human monocytes and mouse splenocytes . Both of these studies employ a whole genome based approach, looking across the entire expression array in an unbiased fashion, in model systems capturing differing, relevant aspects of Copaxone ^® effect.

In mouse splenocytes, 223 probesets were significantly differentially expressed between Copaxone ^® and Polimunol in Copaxone ^® -immunized mice, and 431 probesets were significantly differentially expressed between Copaxone ^® and Polimunol in Polimunol- immunized mice. In both immunization conditions, IL18 was downregulated to a significantly greater extent by Copaxone ^® than Polimunol, raising concerns about Polimunol' s reduced effectiveness in suppressing this MS-associated cytokine. As described above, IL18 is known to affect helper T cell differentiation, an important aspect of Copaxone ^® ' s mechanism of action, and to induce IFNg expression, and has been implicated in MS pathogenesis. IL18 induces proinflammatory Thl responses and has been implicated in a number of neurodegenera ive and neuroinflammatory contexts including MS (Felderhpff -Mueser et al, Trends Neurosci, 2005) .

The probesets differentially expressed between Copaxone ^® and Polimunol enriched to 22 pathways for Copaxone ^® immunization, and 10 pathways for Polimunol immunization. Many of these pathways overlapped, including immune response and response to virus. The fact that there are many significant differences between the gene expression patterns induced in splenocytes by Polimunol and Copaxone ^® , regardless of whether those splenocytes are from mice immunized with Polimunol or with Copaxone ^® , further emphasizes the robustness of the observed differences between these two medicines. Moreover, Polimunol upregulates a number of interferon- related genes, including RIG- I, MDA5, and IRF7, suggesting the possibility of increased type I interferon signaling with Polimunol treatment. An increase in type I interferon is concerning, and could lead to possible adverse events such as flu-like symptoms.

In human monocytes, 779 probesets were differentially expressed, with 137 pathways enriched among the probesets upregulated by Polimunol relative to Copaxone ^® . Differentially expressed genes included CYP1B1 and IL1B, and the pathways enriched among the differentially expressed probesets included cytokine-cytokine receptor interactions and response to lipopolysaccharide . The enrichment in the response to lipopolysaccharide (LPS) pathway is particularly concerning, because the same prototypic pro- inflammatory pathway was also enriched among genes differentially expressed by the purported generic Probioglat, and the introduction of Probioglat in Mexico was associated with a 3- fold increase in adverse events (and a 7-fold increase in relapses) as described in Teva's seventh Citizen Petition (FDA-2014-P-0933-0001 available at www . regulations . gov/# ! documentDetail; D=FDA-2014-P-0933- 0001, and also described herein) . Whether a similar phenomenon potentially underlies the higher adverse event rate (~2.4-fold increase) observed in Synthon's GATE trial warrants further investigation.

Taken together, the new data introduced here demonstrates that the genes and pathways modulated by Synthon's Polimunol differ significantly and extensively from those modulated by Copaxone ^® . These data are in line with Teva's report of significant differences observed in various state-of-the-art physicochemical analyses detailed in a November comment to CP Docket FDA-2014-P-0933 (available at www.noticeandcomment.com/FDA-2014-P-0933-fcol-41234.aspx) .

The biology underlying the differences detailed herein provide potential mechanistic hypotheses for differential efficacy and for the increase in adverse events leading to discontinuations as reported by Synthon with Polimunol relative to Copaxone ^® in the GATE study. Several striking biological differences stand out including levels of inflammatory cytokine genes such as IL18, interferon genes, and pro- inflammatory pathways such as response to lipopolysaccharide. These findings warrant further investigation, and raise substantial concerns for the safety and well-being of patients treated with Synthon's Polimunol. The data further illustrates the imminent need for guidelines specific to NBCD, and specifically to glatiramoids . The gene expression changes described in this document, together with physicochemical differences between Polimunol and Copaxone ^® described in a November 13, 2014 comment to CP Docket FDA-2014-P-0933-0020 (available at www.noticeandcomment.com/FDA-2014-P-0933-fcol-

41234. aspx), support the conclusion that Synthon's Polimunol is not therapeutically equivalent or similar to Copaxone ^® .

More generally, to establish whether a follow on glatiramoid has comparable safety and effectiveness to Copaxone ^® , it must first be established that the glatiramoid is the same as Copaxone ^® using a full battery of orthogonal methodologies including assays that detect high- resolution physicochemical properties and functionally relevant biological properties, including genome-wide gene expression analyses in immunologically relevant model systems including systems modeling antigen presenting cells and systems modeling T cells. Only when an applicant has demonstrated equivalence on these biological and physicochemical methods should they proceed to establish therapeutic comparability through an adequately powered, at least 2 -year clinical trial using a widely accepted clinical endpoint such as annualized relapse rate.

Example 12

Gene expression studies of a human monocyte cell line identify dissimilarities between differently manufactured glatiramoids

Protein levels at 24h are consistent with upregulation of pro- inflammatory mRNA markers by Probioglat versus GA treatment at 6h

Protein concentration was tested in the same experiment at the 24h timepoint in order to validate upregulation of pro-inflammatory markers by Probioglat versus GA. Taking into consideration the fact that differences observed at the mRNA level do not necessarily translate to protein concentration differences, and may reflect regulatory processes, a Luminex kit measuring the concentrations of a panel of 45 chemokines and cytokines (in pg/ml) was employed. The Bio- Plex Human Chemokine (Bio Rad kit) and the Luminex Performance Assay (R&D kit) were utilized. Protein concentrations were measured in a single replicate at 24 hours, a timepoint estimated to correspond to the time when the mRNA signals observed at 6 hours may have been translated to protein. Of the five genes tested by qRT-PCR, three were represented on the Luminex panel: CCL5, CXCL10, and MMP9. All three showed higher concentrations in the Probioglat samples than the

GA samples (fold changes 1.5, 2.3, and 1.4, respectively; Figure 45) consistent with the directionality of the gene expression data (FIGS. 4A-D) . Two other genes discussed above, IL10 and CCL2, were also present on the Luminex panel and also showed higher concentration levels in Probioglat relative to GA (fold changes 1.8 and 1.3, respectively; Figure 45) , consistent with the directionality observed at the mRNA level (Figure 41d-e) .

Key genes upregulated by Probioglat compared to GA were validated in primary human monocytes

While immortalized cell lines are widely utilized in biological research and provide various advantages including uniformity and accessibility, it is important to confirm that the changes introduced by the immortalization process do not alter the key results. Therefore, top findings from the expression data were further tested in primary monocytes from healthy human donors using the sensitive method of qRT-PCR . Nine genes (CCL2, CCL5, CXCL10, MMP1 , MMP9, CD9, ICAM1 , IL10, IL1RN) were chosen for testing based on the findings reported above from the THP-1 monocyte cell line. In primary monocytes from a healthy donor with 6 replicates, the majority of the tested genes exhibited the expected directionality of expression differences between Probioglat and GA. Five of these nine genes passed statistical significance (Figure 42). These genes included IL1RN, and the proinflammatory CCL2, CCL5, CXCL10 and MMP9 (p values < 0.01 and 0.009, 0.029, 0.02, and 0.009, respectively).

Discussion — Example 12

Protein concentrations tested in the same experiment at the 24h timepoint were consistent with the findings observed at the mRNA level, supporting the reported findings and indicating an inflammation-related biological impact at the protein level. An independent follow-on study in primary human monocytes tested nine inflammation and MS-related genes by qRT-PCR, finding that five of these genes were statistically significantly upregulated by Probioglat relative to GA. These included IL1RN, which is relevant to Copaxone mechanism of action. In addition, CCL2, CCL5, CXCL10, and MMP9 were all seen to be upregulated significantly and consistently at both the mRNA and protein level in THP-1 cells, as well as confirmed by qRT- PCR in primary human monocytes. These genes act in pro-inflammatory pathways and have been implicated as relevant to MS susceptibility and severity, as described above.

The complex picture of genomic signatures described here underscores the intricate relationships between immune processes, effects of treatment on the associated pathways and the differing responses of each immune cell type. Consistent with previous evidence from other systems and cell types (Huang et al, Nucleic Acids Res. 2009), differences are consistently observed between GA and differently- manufactured glatiramoids, although their nature depends on the biological context of the tested model. Further, many of these differences affect molecules relevant to drug MOA and MS disease pathoetiology, particularly relating to inflammatory signatures. Genes significantly upregulated by Probioglat relative to GA were significantly enriched for inflammatory pathways and included key proinflammatory genes.

These findings have identified significant differences that warrant further investigation, especially in light of the observed clinical effects of Probioglat's introduction. The Teva Patient Support Program in Mexico records numbers of adverse events, including during the years 2012 and 2013 (Table 31; Figure 46) , for which a similar number of patients were tracked (1618 patients in 2012; 1552 in 2013) . Probioglat was first introduced in January 2013; subsequently, each time a patient's prescription was filled, it could be with either Probioglat or GA. In 2013 versus 2012 (during which only branded GA was marketed) , numbers of adverse events, and relapses specifically, increased more than 3-fold (from 125 to 380) and 7-fold (from 8 to 59) , respectively (Table 31; Figure 46) , representing statistically- significant increases (p<2.2e-29 and p<3e-ll, respectively). The gene- expression differences observed herein warrant careful investigation, through studies comparing GA to candidate generics in meaningful settings, most comprehensively including clinical trials.

Table 31: Reported Adverse Events and Relapses in Teva's Patient Support Program, 2012-2013.

* Singfe tailed p-value by Fisher's Exact test comparing the number of adverse events and relapses in 2012 < 2013. Example 13

Validation of Key mRNA-Based Findings by Secreted Protein Analyses

To evaluate effects of Copaxone at the protein level, and assess the extent to which differences observed at the mRNA level (using micaroarry and qRT-PCR) were further consistent with effects observed at the level of the translated proteins, levels of 42 secreted cytokines and chemokines were measured using Luminex technology, analyzing the supernatant of THP-1 cells (human monocyte cell line) stimulated for 24 hours with Copaxone, FOGA, or mannitol control.

After applying statistical significance threshold, Synthon's Polimunol treatment increased the levels of 23 proteins (out of 39 having sufficient measurements to test for this comparison) relative to Copaxone, while Probioglat treatment increased the levels of 31 proteins (out of 40 having sufficient measurements to test for this comparison) relative to Copaxone (Table 32) .

SECRETED PROTEIN ANALYSES

Measurements were also undertaken at the protein level, in order to assess the biological relevance of the observed gene expression differences. Levels of a panel of secreted cytokines and chemokines were measured via Luminex from THP-1 cells stimulated with branded GA, Polimunol, or Probioglat.

Cells from the THP-1 human monocyte cell line were incubated with branded GA, FOGA (Polimunol or Probioglat) , or vehicle control (mannitol) for 24 hours. This time point was chosen in order to reflect translation of mRNA expression patterns observed in the same study design at 6 hours post stimulation. Supernatants were collected and assayed for the concentration of selected proteins using a Luminex assay. A total of 5 biological replicates per condition were utilized. Data (concentrations in pg/mL) were compared using a two-sided t-test with equal variance, and corrected for multiple hypothesis testing using Benj amini-Hochberg correction. To calculate the fold change between the protein expression levels with FOGA and with GA, GA values were averaged together and compared to the average value for FOGA (average FOGA expression level/average GA expression level) . Polimunol versus Copaxone

Polimunol treatment significantly increased the levels of 23 proteins (out of 39 having sufficient measurements to test for this comparison). These include IFNg, TNFa, MIP-la (CCL3 ) , IL-8 (CXCL8), and IL-10 (Figure 47; adjusted p values as shown) . Many of these proteins were also increased in level by Copaxone treatment relative to mannitol control. Consistent with the result observed at the mRNA expression level, secreted levels of MMP-9, MCP-1 (CCL2 ) , RANTES (CCL5) , Gro-a (CXCL1) , and IL-lb were increased with Polimunol treatment relative to GA (Figure 48; adjusted p values as shown) . Of note, CCL2 was not modulated by GA relative to control, while it was increased by Polimunol treatment relative to GA.

A number of important differences in secreted protein level are observed for Polimunol relative to Copaxone, including levels of IFNg, TNFa, IL-8, and MIP-la. IFNg is the major cytokine that drives the pro- inflammatory Thl T-cell response, and is both implicated in MS and known to be relevant to Copaxone mechanism of action (Gilli et al 2012; Tumani et al 2011) . TNFa is a major cytokine directing inflammatory responses, and polymorphisms in this gene have been reported to influence MS susceptibility (Rahmanian et al, 2014) . The chemokine IL-8 (CXCL8) has been implicated in MS disease progression and risk, and proposed as a biomarker for MS (Lund et al, 2004; Kelland et al, 2011; Almasi et al, 2013; Tomioka et al, 2014) . MIP-la (Macrophage Inflammatory Protein 1-alpha; CCL3) is another proinflammatory chemokine with relevance to MS (Zhang et al, Brain, 2000; Aung et al, 2010) .

Differences are also observed in the level of secreted IL-10. IL-10 is an anti -inflammatory cytokine important for Th2 polarization, and has been implicated in the mechanism of action of Copaxone (Vieira at al. Glatiramer acetate (copolymer-1, Copaxone) promotes Th2 cell development and increased IL-10 production through modulation of dendritic cells. J. Immunol. 1950 170, 4483-4488 (2003); Kim, H. J. et al . Type 2 monocyte and microglia differentiation mediated by glatiramer acetate therapy in patients with multiple sclerosis. J ^" . Immunol..1950 172 , 7144-7153 (2004); Weber, M. S. et al . Type II monocytes modulate T cell -mediated central nervous system autoimmune disease. Nat. Med. 13 , 935-943 (2007)) . The observed differences in levels of each of these five proteins with Polimunol versus Copaxone treatment confirm the gene level reports by microarray as described (Kolitz et al, Sci Rep, 2015, in press) . As detailed above, CCL2 and RANTES (CCL5) are inflammatory chemoattractants with known relevance to MS (Allie et al 2005; Mahad et al 2006) , and MMP-9 is a pro- inflammatory matrix metalloproteinase extensively implicated in MS (Rosenberg 2005; Romme Christensen et al 2013; Kouwenhoven et al 2002; Waubant et al 2006; Milward et al 2008) . The biological relevance of these genes is discussed at length in Section 6.2. Gro-a (CXCL1) is another chemokine implicated in MS and MS models (Glabinski et al 1998; Rumble et al, J Exp Med, 2015) , and IL-lb is a proinflammatory cytokine important for inflammasome signalling, with numerous connections to MS in the literature (Prins et al 2013; Rossi et al 2014; Murta et al 2015) .

Overall the proteomic data complements the microarray data and confirms the robustness of the detected signatures. These observations substantiate the concerns raised by upregulation of proinflammatory cytokines and associated pathways.

Probioglat versus Copaxone

Key differences between Probioglat and Copaxone were identified using microarray in THP-1 cells, then tested in primary monocytes, confirming the relevance of the cell line model. To see whether these gene expression differences translated into differences at the protein level, indicating biological relevance, secreted protein levels were measured from THP-1 cells treated with Copaxone or Probioglat.

Probioglat treatment significantly increased the levels of 31 proteins (out of 40 having sufficient measurements to test for this comparison) . These include IFNg, TNFa, MIP-la (CCL3) , IL-8 (CXCL8) , and IL-10 (Figure 49; adjusted p values as shown) . The clear biological relevance of these proteins to disease or to GA response is also described above. Many of these proteins were also increased in level by GA treatment relative to mannitol control. Consistent with results observed at the mRNA expression level (Kolitz et al, Sci Rep 2015, in press), the 31 proteins also include MMP-9, IP-10 (CXCL10) , MCP-1 (CCL2) and RANTES (CCL5) (Figure 50; adjusted p values as shown). Of note, CCL2 was not modulated by GA relative to control, while it was increased by Probioglat treatment relative to GA. Secreted levels of several key proteins were observed to differ with Probioglat treatment relative to Copaxone, including IFNg, TNFa, IL- 8, and MIP-la. As discussed in the previous section, each of these genes has important roles in inflammation and/or MS (Gilli et al 2012; Tumani et al 2011; Rahmanian et al, 2014; Lund et al, 2004; Kelland et al, 2011; Almasi et al, 2013; Tomioka et al, 2014; Zhang et al, Brain, 2000; Aung et al, 2010) . The level of secreted IL-10 also differs between Probioglat and Copaxone treatment. As described in the previous section, IL-10 is an anti- inflammatory cytokine important for Th2 polarization, and implicated in Copaxone mechanism of action (Vieira at al . 2003; Kim, H. J. et al . 2004; Weber, M. S. et al . 2007) .

As described above, CCL2, RANTES (CCL5) and IP-10 (CXCL10) are all inflammatory chemoattractants with relevance to MS (Allie et al 2005; Mahad et al 2006; Peperzak et al 2013; Thamilarasan et al 2013), and MMP-9 is a pro- inflammatory matrix metalloproteinase implicated in MS (Rosenberg 2005; Romme Christensen et al 2013; Kouwenhoven et al 2002; Waubant et al 2006; Milward et al 2008) . As described in FDA-2014-P- 0933; Kolitz et al, Sci Rep, 2015, in press; and above, the genes coding for these proteins were also demonstrated to be induced to differing degrees by Probioglat and Copaxone in both the THP-1 model system and in primary human monocytes . The biological relevance of these genes is discussed at length above.

Thus, the protein analyses further supported the observation of inflammation-related differences between Probioglat and Copaxone, consistent with the clinical observations of increased rates of adverse events and relapses .

Table 32 : Proteins and genes significantly differentially expressed between Polimunol and Copaxone ^® treatment and between Probloglat and Copaxone ^® treatment in THP- 1 human monocytes.

Polimunol vs Copaxone Probioglat vs Copaxone

Gene Beniamini Beniamini

Protein FC p.value p.value

symbol D value D value

MIP-la CCL3 1.37 3.59E-09 1.40E-07 1.56 1.58E-11 5.62E-10

M P-9 P9 1.42 8.69E-09 1.69E-07 1.44 7.40E-09 3.70E-08

MDC CCL22 1.13 1.63E-07 2.12E-06 1.24 2.81E-11 5.62E-10

CCL24 CCL24 1.15 2.39E-07 2.33E-06 1.25 2.31E-10 2.84E-09

CX3CL1 CX3CL1 1.28 2.28E-06 1.78E-05 1.64 3.15E-09 1.80E-08

MIP-3a CCL20 1.28 4.73 E-06 2.65E-05 1.72 2.84E-10 2.84E-09

MCP-1 CCL2 1.16 4.75E-06 2.65E-05 1.26 2.48E-05 5.23E-05

TNF-a TNF 1.23 1.16E-05 5.64E-05 1.29 7.81E-07 2.08E-06

IL-8 IL8 1.21 2.40E-05 1.04E-04 1.30 6.39E-07 1.83E-06

MCP-4 CCL13 1.21 4.98E-05 1.94E-04 1.44 2.66E-09 1.77E-08

ANTES CCL5 1.19 6.70E-05 2.38E-04 1.34 1.15E-08 5.13E-08

IL-lb IL1B 1.22 1.30E-04 4.22E-04 1.43 2.53E-07 8.44E-07

MCP-2 CCL8 1.19 1.76E-04 5.27E-04 1.50 7.15E-10 5.72E-09

IL-10 IL10 1.25 2.99E-04 8.34E-04 1.36 1.07 E-05 2.53E-05

l-TAC CXCL11 1.21 8.60E-04 2.24E-03 1.40 3.03E-05 6.06E-05

CXCL13 CXCL13 1.31 1.35E-03 3.25E-03 1.68 9.06E-08 3.30E-07

IP- 10 CXCL10 1.28 1.42E-03 3.25E-03 1.64 5.88E-08 2.35E-07

MCP-3 CCL7 1.43 5.11E-03 1.11E-02 1.57 1.38E-03 2.21E-03

CCL1 ecu 1.20 5.73E-03 1.18E-02 1.26 1.57E-03 2.35E-03

CXCL1 CXCL1 1.10 1.19E-02 2.32E-02 1.22 1.32E-05 2.93E-05

INF-g IFNg 1.18 1.32E-02 2.45E-02 1.42 1.05 E-05 2.53E-05

CCL26 CCL26 1.16 1.91E-02 3.39E-02 1.32 1.59E-03 2.35E-03

IF MIF 1.23 2.86E-02 4.85E-02 1.38 5.54E-04 1.01E-03

IL-16 IL16 1.12 3.15E-02 5.13E-02 1.25 9.01E-05 1.72E-04

IL-6 IL6 1.19 3.37E-02 5.26E-02 1.33 1.06E-03 1.84E-03

CXCL6 CXCL6 1.18 4.02E-02 6.03E-02 1.16 6.56E-02 7.96E-02

TEC CCL25 1.11 5.67E-02 8.19E-02 1.44 3.77E-07 1.16E-06

GM-CSF CSF2 1.22 9.66E-02 1.35E-01 1.30 4.65E-02 5.81E-02

IL-2 IL2 1.16 l.llE-01 1.49E-01 1.34 1.20E-03 2.00E-03

MPIF-1 CCL23 1.05 2.48E-01 3.22E-01 1.02 6.91E-01 7.47E-01

MIP-3b CCL19 1.11 2.72E-01 3.42E-01 1.25 1.93E-02 2.57E-02

SDF-la+b CXCL12 1.05 3.41E-01 4.15E-01 1.07 2.55E-01 2.92E-01

CXCL2 CXCL2 1.17 4.06E-01 4.80E-01 1.65 2.85E-03 4.07E-03

MIG CXCL9 1.07 4.43E-01 5.08E-01 1.31 5.46E-03 7.54E-03

CCL11 CCL11 0.99 4.61E-01 5.13E-01 1.00 8.61E-01 9.06E-01

CXCL5 CXCL5 0.93 5.16E-01 5.59E-01 0.79 3.05 E-02 3.94E-02

MIP-ld (M CCL15 0.97 5.45E-01 5.74E-01 1.00 9.22E-01 9.22E-01

SCYB16 CXCL16 1.01 6.77E-01 6.94E-01 1.02 5.44E-01 6.05E-01

CCL21 CCL21 1.01 8.27E-01 8.27E-01 1.00 8.96E-01 9.19E-01

IL-4 IL4 NA NA NA 1.26 1.62E-01 1.91E-01

TARC CCL17 0.76 NA NA 1.39 NA NA

CCL27 CCL27 NA NA NA NA NA NA Noseworthy JH, Lucchinetti C, Rodriguez M, Weinshenker BG . Multiple sclerosis. N Engl J Med 2000; 343:938-52.

Guideline on clinical investigation of medicinal products for the treatment of multiple sclerosis EMEA, London 16 September 2006.

Bjartmar C, Fox RJ. Pathological mechanisms and disease progression of multiple sclerosis: therapeutic implications. Drugs of Today 2002; 38:17-29.

Fleming JO. Diagnosis and management of multiple sclerosis. 1st ed. New York: Professional communications, Inc., 2002.

Anderson DW, Ellenberg JH, Leventhal CM et al . Revised estimate of the prevalence of multiple sclerosis in the United States. Ann Neurol 1992; 31:333-36.

Compston A, Lassmann H, McDonald I. The story of multiple sclerosis. In: Compston A, Confavreux C, Lassman H, Mcdonald I, Miller D, Noseworthy JH, Smith K, Wekerle H, editors. McAlpine's Multiple Sclerosis. London: Churchill Livingstone; 2006. p. 3- 68.

Revel M., Pharmacol. Ther., 100(1) :49-62 (2003).

Copaxone ^® (glatiramer acetate injection) (2012) Teva Pharmaceutical Industries, Ltd Petach-Tikva, Israel : Rev-2/209.

Varkony H, et al. (2009) The glatiramoid class of immunomodulator drugs. Expert Opin Pharmacother 10:657-668.

Filippi M, et al. (2001) Glatiramer acetate reduces the proportion of new MS lesions evolving into "black holes". Neurology 57:731-733. Kipnis J, Schwartz M (2002) Dual action of glatiramer acetate (Cop-1) in the treatment of CNS autoimmune and neurodegenerative disorders. TRENDS in Molecular Medicine 8:319-323.

Teitelbaum D, Aharoni R, Arnon R, Sela M (1988) Specific inhibition of the T-cell response to myelin basic protein by the synthetic copolymer Cop 1. Proc Natl Acad Sci U S A 85:9724- 9728.

Putheti P, Soderstrom , Link H, Huang YM (2003) Effect of glatiramer acetate (Copaxone ^® ) on CD4+CD25high T regulatory cells and their IL-10 production in multiple sclerosis. J NeuroImmunol 144:125-131.

Stadelmann C, et al. (2002) BDNF and gpl45trkB in multiple sclerosis brain lesions: neuroprotective interactions between immune and neuronal cells? Brain 125:75-85.

Ford C, et al . (2010) Continuous long-term immunomodulatory therapy in relapsing multiple sclerosis: results from the 15- year analysis of the US prospective open-label study of glatiramer acetate. Mult Scler 16:342-350.

Aharoni R, Teitelbaum D, Arnon R, Sela M (1999) Copolymer 1 acts against the immunodominant epitope 82-100 of myelin basic protein by T cell receptor antagonism in addition to major histocompatibility complex blocking. Proc Natl Acad Sci U S A 96: 634-639.

Arnon R, Aharoni R (2004) Mechanism of action of glatiramer acetate in multiple sclerosis and its potential for the development of new applications. Proc Natl Acad Sci U S A 101 Suppl 2:14593-14598.

Teitelbaum D, Aharoni R, Sela M, Arnon R (1991) Cross-reactions and specificities of monoclonal antibodies against myelin basic protein and against the synthetic copolymer 1. Proc Natl Acad Sci U S A 88:9528-9532.

Webb C, Teitelbaum D, Arnon , Sela M (1973) In vivo and in vitro immunological cross-reactions between basic encephalitogen and synthetic basic polypeptides capable of suppressing experimental allergic encephalomyelitis. Eur J Immunol 3:279-286.

Duda PW, et al . (2000) Human and murine CD4 T cell reactivity to a complex antigen: recognition of the synthetic random polypeptide glatiramer acetate. J Immunol 165:7300-7307.

Duda PW, et al. (2000) Glatiramer acetate (Copaxone) induces degenerate, Th2-polarized immune responses in patients with multiple sclerosis. J Clin Invest 105:967-976.

Brenner T, et al. (2001) Humoral and cellular immune responses to Copolymer 1 in multiple sclerosis patients treated with Copaxone. J Neuroimmunol 115:152-160.

Aharoni R, Teitelbaum D, Sela M, Arnon R (1997) Copolymer 1 induces T cells of the T helper type 2 that crossreact with myelin basic protein and suppress experimental autoimmune encephalomyelitis. Proc Natl Acad Sci U S A 94:10821-10826.

Wiesemann E, et al. (2003) Correlation of serum IL-13 and IL-5 levels with clinical response to Glatiramer acetate in patients with multiple sclerosis. Clin Exp Immunol 133:454-460.

Aharoni R, Teitelbaum D, Sela M, Arnon R (1998) Bystander suppression of experimental autoimmune encephalomyelitis by T cell lines and clones of the Th2 type induced by copolymer 1. J Neuroimmunol 91:135-146.

Aharoni R, et al. (2003) Glatiramer acetate-specific T cells in the brain express T helper 2/3 cytokines and brain-derived neurotrophic factor in situ. Proc Natl Acad Sci U S A 100:14157- 14162. Miller A, et al . (1998) Treatment of multiple sclerosis with copolymer-1 (Copaxone) : implicating mechanisms of Thl to Th2/Th3 immune-deviation. J Neuroimmunol 92:113-121.

Neuhaus O, et al. (2000) Multiple Sclerosis: Comparison of copolymer-l-reactive T cell Lines from treated and untreated subjects reveals cytokine shift From T helper 1 to T helper 2 cells. Proceedings of the National Academy of Sciences 97:7452- 7457.

Venken K, et al . (2008) Natural naive CD4+CD25+CD1271ow regulatory T cell (Treg) development and function are disturbed in multiple sclerosis patients: recovery of memory Treg homeostasis during disease progression. J Immunol 180:6411-6420.

Haas J, et al. (2009) Glatiramer acetate improves regulatory T- cell function by expansion of naive CD4 (+) CD25 (+) FOXP3 (+) CD31 (+) T-cells in patients with multiple sclerosis. J Neuroimmunol 216:113-117.

Hong J, et al. (2005) Induction of CD4+CD25+ regulatory T cells by copolymer-I through activation of transcription factor Foxp3. Proc Natl Acad Sci U S A 102:6449-6454.

Weber MS, et al . (2007) Type II monocytes modulate T cell- mediated central nervous system autoimmune disease. Nat Med 13:935-943.

Xu D, et al. (1998) Selective expression and functions of interleukin 18 receptor on T helper (Th) type 1 but not Th2 cells. J Exp Med 188:1485-1492.

Jee Y, et al. (2007) CD4 (+) CD25 (+) regulatory T cells contribute to the therapeutic effects of glatiramer acetate in experimental autoimmune encephalomyelitis. Clin Immunol 125:34-42.

Windhagen A, et al. (1998) Cytokine secretion of myelin basic protein reactive T cells in patients with multiple sclerosis. J Neuroimmunol 91:1-9.

Neuhaus O, et al. (2000) Multiple sclerosis: comparison of copolymer-1- reactive T cell lines from treated and untreated subjects reveals cytokine shift from T helper 1 to T helper 2 cells. Proc Natl Acad Sci U S A 97:7452-7457.

Chen M, et al. (2001) Glatiramer acetate induces a Th2-biased response and crossreactivity with myelin basic protein in patients with MS. Mult Scler 7:209-219.

Franciotta D, et al . (2003) Interferon gamma and interleukin 4 producing T cells in peripheral blood of multiple sclerosis patients undergoing immunomodulatory treatment. J Neurol Neurosurg Psychiatry 74:123-126.

Weder C, et al. (2005) Clinical and immune responses correlate in glatiramer acetate therapy of multiple sclerosis. Eur J Neurol 12:869-878.

Sanna A, et al. (2006) Glatiramer acetate reduces lymphocyte proliferation and enhances IL-5 and IL-13 production through modulation of monocyte-derived dendritic cells in multiple sclerosis. Clin Exp Immunol 143:357-362.

Kipnis J, Avidan H, Caspi R, Schwartz M (2004) Dual effect of CD4+CD25+ regulatory T cells in neurodegeneration: a dialogue with microglia. Proc Natl Acad Sci U S A 101 Suppl 2:14663- 14669.

Tennakoon DK, et al. (2006) Therapeutic induction of regulatory, cytotoxic CD8+ T cells in multiple sclerosis. J Immunol 176:7119- 7129.

Praksova P, et al . (2012) Immunoregulatory T cells in multiple sclerosis and the effect of interferon beta and glatiramer acetate treatment on T cell subpopulations . J Neurol Sci 319:18- 23.

Achiron A, et al. (2009) Molecular profiling of glatiramer acetate early treatment effects in multiple sclerosis . Dis Markers. 27 (2) :63-73.

Dunning MJ, Smith ML, Ritchie ME, Tavare S (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics 23:2183-2184.

Sharan R, Maron- atz A, Shamir R (2003) CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 19:1787-1799.

Sugimoto N (2006) Foxp3-dependent and -independent molecules specific for CD25+CD4+ natural regulatory T cells revealed by DNA microarray analysis. International Immunology 18:1197-1209.

Subramanian N, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102:15545-15550.

Weber M. S. et al. (2007) Type II monocytes modulate T cell- mediated central nervous system autoimmune disease. Nature Medicine 13:935-943.

Wang Z. (2006) Role of IFN-g in induction of Foxp3 and conversion of CD4+CD25- f cells to CD4+ Tregs . Journal of Clinical Investigation, doi : 10.1172/JCI25826.

^• Hong J. et al. (2005) Induction of CD4+CD25+ regulatory T cells by copolymer-I through activation of transcription factor Foxp3. Proc Natl Acad Sci USA 102:64 9-6454.

Burger D. et al. (2009) Glatiramer acetate increases IL-l receptor antagonist but decreases T cell-induced IL-lp in human monocytes and multiple sclerosis. Proceedings of the National Academy of Sciences 106:4355-4359.

Ingersoll M. A. et al. (2010) Comparison of gene expression profiles between human and mouse monocyte subsets. Blood 115, el0-el9.

Nylander A. and Hafler D. A. (2012) Multiple sclerosis. Journal of Clinical Investigation 122:1180-1188.

Dhib-Jalbut S. et al . (2012) in ECTRIMS.

Bar-Or A. et al. (2003) Analyses of all matrix metalloproteinase members in leukocytes emphasize monocytes as major inflammatory mediators in multiple sclerosis. Brain 126:2738-2749.

Pul R. et al. (2012) Glatiramer Acetate Increases Phagocytic Activity of Human Monocytes In Vitro and in Multiple Sclerosis Patients. PLoS ONE 7, e51867.

Anis S. et al. (2013) in AAN.

Anis S. et al. (2010) in ECTRIMS.

Bolstad B. M., preprocessCore : A collection of pre-processing functions .

Johnson W. E. et al. (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. BiostatS 118- 127.

Leek J. T. et al., sva: Surrogate Variable Analysis .

Ho J. W. K. et al. (2008) Differential variability analysis of gene expression and its application to human diseases. Bioinformatics 24:i390-398. 64. Quackenbush J. (2002) Microarray data normalization and transformation. Nature Genetics 32:496-501. Pavlidis P. (2003) Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31:282-289.

Benjamini Y. and Hochberg Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B (Methodological) 289-300.

Smyth G. K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. StatAppl Genet Mol Biol 3, Article3.

Smyth G. K. (2005) In Bioinformatics and Computational Biology Solutions Using R and Bioconductor, R. Gentleman, V. Carey, S. Dudoit, R. Irizarry, W. Huber, Eds. (Springer, New York) 397-420.

Gentleman R. C. et al. (2004) Bioconductor: Open software development for computational biology and bioinformatics . Genome Biology 5, R80.

Reich . et al. (2006) GenePattern 2.0, Nature Genetics 38:500- 501.

Saeys Y. et al . (2007) A review of feature selection techniques in bioinformatics . Bioinformatics 23:2507-2517.

Zheng Y. et al. (2007) Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature 445:936- 940.

Eppig J. T. et al . (2012) The Mouse Genome Database (MGD) : comprehensive resource for genetics and genomics of the laboratory mouse. Nucleic Acids Res 40 : D881-D886.

Ashburner, M . , Ball, C.A., Blake, J.A. , Botstein, D., Butler, H., Cherry, J.M., Davis, A. P., Dolinski, K. , Dwight, S.S., Eppig, J.T., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29. Benita Y. et al . (2010) Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Blood 115:5376-5384.

Painter M. W. et al. (2011) Transcriptomes of the B and T lineages compared by multi-platform microarray profiling. Immunol 186:3047-3057.

Bakshi, S., Chalifa-Caspi, V., Plaschkes, I., Perevozkin, I., Gurevich, M., and Schwartz, R. (2013). Gene expression analysis reveals functional pathways of glatiramer acetate activation. Expert Opinion on Therapeutic Targets 17, 351-362.

Felderhoff-Mueser, U., Schmidt, O.I., Oberholzer, A., Buhrer, C, and Stahel, P.F. (2005). IL-18: a key player in neuroinflanunation and neurodegeneration? Trends in Neurosciences 28, 487-493.

Huang, D.W., Sherman, B.T., and Lempicki, R.A. (2008). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols 4, 44-57.

Johnson, .E., Li, C, and Rabinovic, A. (2007). Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118-127.

Kanehisa, M. , and Goto, S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28, 27-30.

Karakas Celik, S., Oz, Z.S., Dursun, A., Unal, A., Emre, U., Cicek, S., and Keni, F. . (2014). Interleukin 18 gene polymorphism is a risk factor for multiple sclerosis. Molecular Biology Reports 41, 1653-1658.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD (2013) . sva: Surrogate Variable Analysis. Losy, J., and Niezgoda, A. (2001). IL-18 in patients with multiple sclerosis. Acta Neurologica Scandinavica 104, 171-173.

Nicoletti, F., Di Marco, . , Mangano, K. , Patti, F., Reggio, E., Nicoletti, A., Bendtzen, K. , and Reggio, A. (2001). Increased serum levels of interleukin-18 in patients with multiple sclerosis. Neurology 57, 342-344.

Orr, M. , and Liu, P. (2009). Sample Size Estimation while Controlling False Discovery Rate for Microarray Experiments Using the ssize.fdr Package. The R Journal 1/1.

Shi, F.-D., Takeda, K. , Akira, S., Sarvetnick, . , and Ljunggren, H.-G. (2000) . IL-18 Directs Autoreactive T Cells and Promotes Autodestruction in the Central Nervous System Via Induction of IFN- by NK Cells. The Journal of Immunology 165, 3099-3104.

Smyth, G.K. (2004) . Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3, Article3.

Thompson, S.R., and Humphries, S.E. (2007). Interleukin-18 genetics and inflammatory disease susceptibility. Genes and Immunity 8, 91-99.

Towfic, F . , Funt, J.M., Fowler, K.D., Bakshi, S., Blaugrund, E., Artyomov, M.N., Hayden, M.R., Ladkani, D . , Schwartz, R. , and Zeskind, B. (2014). Comparing the Biological Impact of Glatiramer Acetate with the Biological Impact of a Generic. PLoS ONE 3, e83757.

Trinchieri, G. (2010) . Type I interferon: friend or foe? Journal of Experimental Medicine 207, 2053-2063.