WO/2019/161126 | NOVEL GENE CLASSIFIERS AND USES THEREOF IN NON-MELANOMA SKIN CANCERS |
WO/2000/052204 | GENE EXPRESSION IN BLADDER TUMORS |
WO/2023/015149 | TREATMENT OF NON-SMALL CELL LUNG CANCER WITH POZIOTINIB |
SHAH MANISH (US)
KOTLOV NIKITA (RU)
MELIKHOVA DARIA (RU)
GUSAKOVA MARIIA (RU)
SAMARINA NAIRA (RU)
PODSVIROVA SVETLANA (RU)
TYCHININ DMITRY (RU)
BOSTONGENE LLC (RU)
WEILL CORNELL MEDICAL COLLEGE (US)
UNIV CORNELL (US)
KUDRYASHOVA OLGA (RU)
SHAH MANISH (US)
KOTLOV NIKITA (RU)
MELIKHOVA DARIA (RU)
GUSAKOVA MARIIA (RU)
SAMARINA NAIRA (RU)
PODSVIROVA SVETLANA (RU)
TYCHININ DMITRY (RU)
CN112133365A | 2020-12-25 | |||
US20200273543A1 | 2020-08-27 |
CHO JUNHUN ET AL: "Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability", ESMO OPEN : CANCER HORIZONS, vol. 3, no. 3, 1 January 2018 (2018-01-01), London, pages e000326, XP055931360, ISSN: 2059-7029, DOI: 10.1136/esmoopen-2018-000326
O'DONNELL JAKE S ET AL: "Cancer immunoediting and resistance to T cell-based immunotherapy", NATURE REVIEWS CLINICAL ONCOLOGY, NATURE, NY, US, vol. 16, no. 3, 6 December 2018 (2018-12-06), pages 151 - 167, XP036706114, ISSN: 1759-4774, [retrieved on 20181206], DOI: 10.1038/S41571-018-0142-8
MA ET AL., ONCOL LETT, vol. 11, no. 5, May 2016 (2016-05-01), pages 2959 - 2964
HENNEQUIN ET AL., ONCOLMMUNOLOGY, vol. 5, 2016, pages 2
VAUGHT ET AL., CANCER EPIDEMIOL BIOMARKERS PREV, vol. 21, no. 2, February 2012 (2012-02-01), pages 253 - 5
VAUGHTHENDERSON, IARC SCI PUBL, no. 163, 2011, pages 23 - 42
NICOLAS L BRAYHAROLD PIMENTELPALL MELSTEDLIOR PACHTER: "Near-optimal probabilistic RNA-seq quantification", NATURE BIOTECHNOLOGY, vol. 34, 2016, pages 525 - 527
BIOINFORMATICS, vol. 20, no. 3, 12 February 2004 (2004-02-12), pages 307 - 15
RITCHIE MEPHIPSON BWU DHU YLAW CWSHI WSMYTH GK: "limma powers differential expression analyses for RNA-sequencing and microarray studies", NUCLEIC ACIDS RES., vol. 43, no. 7, 20 April 2015 (2015-04-20), pages e47
WAGNER ET AL., THEORY BIOSCI, vol. 131, 2012, pages 281 - 285
BARBIE ET AL., NATURE, vol. 462, no. 7269, 5 November 2009 (2009-11-05), pages 108 - 112
SAUTES-FRIDMAN ET AL., NAT REV CANCER, vol. 19, 2019, pages 307 - 325
CLAIMS What is claimed is: 1. A method for identifying, based at least in part on a gastric cancer (GC) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk of having gastric cancer, whether the subject is likely to respond to an immunotherapy, the method comprising: using at least one computer hardware processor to perform: (a) obtaining RNA expression data for the subject, the RNA expression data indicating RNA expression levels for at least some genes in each group of at least some of a plurality of gene groups listed in Table 1; (b) generating a GC TME signature for the subject using the RNA expression data, the GC TME signature comprising gene group scores for respective gene groups in the at least some of the plurality of gene groups, the generating comprising: determining the gene group scores using the RNA expression levels; (c) identifying, using the GC TME signature and from among a plurality of GC TME types, a GC TME type for the subject; and (d) identifying, using the GC TME type of the subject, whether or not the subject is likely to respond to the immunotherapy. 2. The method of claim 1, wherein the RNA expression data further indicates second RNA expression levels for at least some genes in each group of at least some of a second plurality of gene groups listed in Table 2, wherein the GC TME signature further comprises second gene group scores for respective gene groups of the at least some of the second plurality of gene groups, and wherein the generating further comprises determining the second gene group scores using the second RNA expression levels. 3. The method of claim 1, wherein the RNA expression data further indicates second RNA expression levels for at least some genes in each group of at least some of a second plurality of gene groups listed in Table 2, and the method further comprises: (e) generating a second GC TME signature for the subject using the RNA expression data, the second GC TME signature comprising second gene group scores for respective gene groups in the at least some of the second plurality of gene groups, the generating comprising: determining the second gene group scores using the second RNA expression levels. 4. The method of any one of claims 1 to 3, wherein obtaining the RNA expression data for the subject comprises obtaining sequencing data previously obtained by sequencing a biological sample obtained from the subject. 5. The method of claim 4, wherein the sequencing data comprises at least 1 million reads, at least 5 million reads, at least 10 million reads, at least 20 million reads, at least 50 million reads, or at least 100 million reads. 6. The method of claim 4 or 5, wherein the sequencing data comprises whole exome sequencing (WES) data, bulk RNA sequencing (RNA-seq) data, single cell RNA sequencing (scRNA-seq) data, or next generation sequencing (NGS) data. 7. The method of claim 4 or 5, wherein the sequencing data comprises microarray data. 8. The method of any one of claims 1 to 7, further comprising: normalizing the RNA expression data to transcripts per million (TPM) units prior to generating the GC TME signature. 9. The method of any one of claims 1 to 8, wherein obtaining the RNA expression data for the subject comprises sequencing a biological sample obtained from the subject. 10. The method of claim 9, wherein the biological sample comprises gastrointestinal tissue of the subject, optionally wherein the biological sample comprises tumor tissue of the subject. 11. The method of any one of claims 1 to 10, wherein the RNA expression levels comprise RNA expression levels for at least three genes from each of at least two of the following gene groups: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 12. The method of any one of claims 1 to 11, wherein the RNA expression levels comprise RNA expression levels for each of the genes from each of the following gene groups: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 13. The method of any one of claims 1 to 12, wherein the RNA expression levels comprise RNA expression levels for at least three genes from each of at least two of the following gene groups: (a) MHC I group: HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, NLRC5, TAPBP; (b) MHC II group: HLA-DRA, HLA-DRB1, HLA-DMA, HLA-DPA1, HLA-DPB1, HLA- DMB, HLA-DQB1, HLA-DQA1, CIITA; (c) Coactivation molecules group: CD28, CD40, TNFRSF4, ICOS, TNFRSF9, CD27, CD80, CD86, CD40LG, CD83, TNFSF4, ICOSLG, TNFSF9, CD70; (d) Effector cells group: IFNG, GZMA, GZMB, PRF1, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B; (e) T cell traffic group: CXCL9, CXCL10, CXCL11, CX3CL1, CCL3, CCL4, CX3CR1, CXCL16, CXCR6; (f) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (g) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (h) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (i) M1 signature group: NOS2, TNF, IL1B, SOCS3, CMKLR1, IRF5, IL12A, IL12B, IL23A; (j) Antitumor cytokines group: TNF, IFNB1, IFNA2, CCL3, TNFSF10, IL21; (k) Checkpoint inhibition group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, TIGIT, VSIR; (l) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (m) Neutrophil signature group: MPO, ELANE, PRTN3, CTSG, CXCR1, CXCR2, FCGR3B, CD177, FFAR2, PGLYRP1; (n) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (o) M2 signature group: IL10, MRC1, MSR1, CD163, CSF1R, IL4I1, SIGLEC1, CD68; (p) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (q) Angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PGF, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5; (r) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (s) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 14. The method of any one of claims 1 to 13, wherein determining the gene group scores comprises: determining a respective gene group score for each of at least two of the following gene groups, using, for a particular gene group, RNA expression levels for at least three genes in the particular gene group to determine the gene group score for the particular group, the gene groups including: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 15. The method of any one of claims 1 to 14, wherein determining the gene group scores comprises: determining a respective gene group score for each of the following gene groups, using, for each gene group, RNA expression levels for each of the genes in each gene group to determine the gene group score for each particular group, the gene groups including: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 16. The method of claim 15, wherein determining the gene group scores comprises determining a first score of a first gene group using a single-sample GSEA (ssGSEA) technique from RNA expression levels for at least some of the genes in one of the following gene groups: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 17. The method of any one of claims 1 to 16, wherein determining the gene group scores comprises determining the gene group scores, using a single-sample GSEA (ssGSEA) technique, from RNA expression levels for each of the genes in each of the following gene groups: (i) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (ii) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (iii) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (iv) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (v) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (vi) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (vii) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (viii) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 18. The method of any one of claims 1 to 17, wherein determining the gene group scores comprises: determining a respective gene group score for each of at least two of the following gene groups, using, for a particular gene group, RNA expression levels for at least three genes in the particular gene group to determine the gene group score for the particular group, the gene groups including: (a) MHC I group: HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, NLRC5, TAPBP; (b) MHC II group: HLA-DRA, HLA-DRB1, HLA-DMA, HLA-DPA1, HLA-DPB1, HLA- DMB, HLA-DQB1, HLA-DQA1, CIITA; (c) Coactivation molecules group: CD28, CD40, TNFRSF4, ICOS, TNFRSF9, CD27, CD80, CD86, CD40LG, CD83, TNFSF4, ICOSLG, TNFSF9, CD70; (d) Effector cells group: IFNG, GZMA, GZMB, PRF1, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B; (e) T cell traffic group: CXCL9, CXCL10, CXCL11, CX3CL1, CCL3, CCL4, CX3CR1, CXCL16, CXCR6; (f) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (g) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (h) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (i) M1 signature group: NOS2, TNF, IL1B, SOCS3, CMKLR1, IRF5, IL12A, IL12B, IL23A; (j) Antitumor cytokines group: TNF, IFNB1, IFNA2, CCL3, TNFSF10, IL21; (k) Checkpoint inhibition group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, TIGIT, VSIR; (l) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (m) Neutrophil signature group: MPO, ELANE, PRTN3, CTSG, CXCR1, CXCR2, FCGR3B, CD177, FFAR2, PGLYRP1; (n) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (o) M2 signature group: IL10, MRC1, MSR1, CD163, CSF1R, IL4I1, SIGLEC1, CD68; (p) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (q) Angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PGF, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5; (r) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (s) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 19. The method of claim 18, wherein determining the gene group scores comprises determining the gene group scores, using a single-sample GSEA (ssGSEA) technique, from RNA expression levels for at least some of the genes in each one of the following gene groups: (a) MHC I group: HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, NLRC5, TAPBP; (b) MHC II group: HLA-DRA, HLA-DRB1, HLA-DMA, HLA-DPA1, HLA-DPB1, HLA- DMB, HLA-DQB1, HLA-DQA1, CIITA; (c) Coactivation molecules group: CD28, CD40, TNFRSF4, ICOS, TNFRSF9, CD27, CD80, CD86, CD40LG, CD83, TNFSF4, ICOSLG, TNFSF9, CD70; (d) Effector cells group: IFNG, GZMA, GZMB, PRF1, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B; (e) T cell traffic group: CXCL9, CXCL10, CXCL11, CX3CL1, CCL3, CCL4, CX3CR1, CXCL16, CXCR6; (f) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (g) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (h) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (i) M1 signature group: NOS2, TNF, IL1B, SOCS3, CMKLR1, IRF5, IL12A, IL12B, IL23A; (j) Antitumor cytokines group: TNF, IFNB1, IFNA2, CCL3, TNFSF10, IL21; (k) Checkpoint inhibition group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, TIGIT, VSIR; (l) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (m) Neutrophil signature group: MPO, ELANE, PRTN3, CTSG, CXCR1, CXCR2, FCGR3B, CD177, FFAR2, PGLYRP1; (n) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (o) M2 signature group: IL10, MRC1, MSR1, CD163, CSF1R, IL4I1, SIGLEC1, CD68; (p) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (q) Angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PGF, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5; (r) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (s) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 20. The method of any one of claims 1 to 19, wherein determining the gene group scores comprises determining the gene group scores, using a single-sample GSEA (ssGSEA) technique, from RNA expression levels for each of the genes in each of the following gene groups: (a) MHC I group: HLA-A, HLA-B, HLA-C, B2M, TAP1, TAP2, NLRC5, TAPBP; (b) MHC II group: HLA-DRA, HLA-DRB1, HLA-DMA, HLA-DPA1, HLA-DPB1, HLA- DMB, HLA-DQB1, HLA-DQA1, CIITA; (c) Coactivation molecules group: CD28, CD40, TNFRSF4, ICOS, TNFRSF9, CD27, CD80, CD86, CD40LG, CD83, TNFSF4, ICOSLG, TNFSF9, CD70; (d) Effector cells group: IFNG, GZMA, GZMB, PRF1, GZMK, ZAP70, GNLY, FASLG, TBX21, EOMES, CD8A, CD8B; (e) T cell traffic group: CXCL9, CXCL10, CXCL11, CX3CL1, CCL3, CCL4, CX3CR1, CXCL16, CXCR6; (f) NK cells group: NKG7, CD160, CD244, NCR1, KLRC2, KLRK1, CD226, GZMH, GNLY, IFNG, KIR2DL4, EOMES, GZMB, FGFBP2, KLRF1, SH2D1B, NCR3; (g) T cells group: TBX21, ITK, CD3D, CD3E, CD3G, TRAC, TRBC1, TRBC2, CD28, CD5, TRAT1; (h) B cells group: CD19, MS4A1, TNFRSF13C, CR2, TNFRSF17, TNFRSF13B, CD22, CD79A, CD79B, BLK, FCRL5, PAX5, STAP1; (i) M1 signature group: NOS2, TNF, IL1B, SOCS3, CMKLR1, IRF5, IL12A, IL12B, IL23A; (j) Antitumor cytokines group: TNF, IFNB1, IFNA2, CCL3, TNFSF10, IL21; (k) Checkpoint inhibition group: PDCD1, CD274, CTLA4, LAG3, PDCD1LG2, BTLA, HAVCR2, TIGIT, VSIR; (l) Treg group: FOXP3, CTLA4, IL10, TNFRSF18, CCR8, IKZF4, IKZF2; (m) Neutrophil signature group: MPO, ELANE, PRTN3, CTSG, CXCR1, CXCR2, FCGR3B, CD177, FFAR2, PGLYRP1; (n) MDSC group: IDO1, ARG1, IL10, CYBB, PTGS2, IL4I1, IL6; (o) M2 signature group: IL10, MRC1, MSR1, CD163, CSF1R, IL4I1, SIGLEC1, CD68; (p) Cancer associated fibroblast (CAF) group: LGALS1, COL1A1, COL1A2, COL5A1, ACTA2, FAP, LRP1, CD248, COL6A1, COL6A2, COL6A3, COL11A1, CXCL12, FBLN1, LUM, MFAP5, MMP3, MMP2, PDGFRB, PDGFRA, FN1, COL1A1, COL1A2, COL4A1, COL3A1, VTN, LGALS7, LGALS9, LAMA3, LAMB3, LAMC2, TNC, COL5A1, COL11A1, LGALS3, CA9, MMP9, MMP2, MMP1, MMP3, MMP12, MMP7, MMP11, PLOD2, ADAMTS4, ADAMTS5, LOX; (q) Angiogenesis group: VEGFA, VEGFB, VEGFC, PDGFC, CXCL8, CXCR2, FLT1, PGF, KDR, ANGPT1, ANGPT2, TEK, VWF, CDH5; (r) Proliferation rate group: MKI67, ESCO2, CETN3, CDK2, CCND1, CCNE1, AURKA, AURKB, E2F1, MYBL2, BUB1, CCNB1, MCM2, MCM6; and (s) Lgr5 ISC group: ABTB2, AFAP1L1, APCDD1, ARHGEF4, ARNT2, AXIN2, BCL2, BEX1, BEX2, CAP2, CCDC46, CYP2E1, DGKG, DLGAP1, DTL, DYNC2H1, EPHA4, FAM64A, FGFR4, FMNL2, FSTL1, GRAMD1A, GRK4, IGF1R, IGFBP4, IL17RD, KIF12, KIF26B, KLHL13, LDHB, LGR5, LIFR, LOC285141, MDFIC, MPP3, NPNT, PITPNC1, PLP1, RASSF4, RNF157, SCN2B, SEPT6, SERTAD4, SLC1A2, SLC38A4, SLCO3A1, SLIT2, SOAT1, SORBS2, SOX4, TACC1, TMEM182, TNFRSF19, UTRN, ZNF141, ZNF273, ZNF493, ZNF626, ZNF678, ZNF680, ZNF714, ZNF85, ZNF92, ZNF93. 21. The method of any one of claims 1 to 20, wherein generating the GC TME signature further comprises normalizing the gene group scores, wherein the normalizing comprises applying rank estimation and/or median scaling to the gene group scores. 22. The method of any one of claims 1 to 21, wherein the plurality of GC TME types is associated with a respective plurality of GC TME signature clusters, wherein identifying, using the GC TME signature, and from among a plurality of GC TME types, the GC TME type for the subject comprises: associating the GC TME signature of the subject with a particular one of the plurality of GC TME signature clusters; and identifying the GC TME type for the subject as the GC TME type corresponding to the particular one of the plurality of GC TME signature clusters to which the GC TME signature of the subject is associated. 23. The method of claim 22, further comprising generating the plurality of GC TME signature clusters, the generating comprising: obtaining multiple sets of RNA expression data by sequencing biological samples from multiple respective subjects, each of the multiple sets of RNA expression data indicating RNA expression levels for at least some genes in each of the at least some of the plurality of gene groups listed in Table 1; generating multiple GC TME signatures from the multiple sets of RNA expression data, each of the multiple GC TME signatures comprising gene group scores for respective gene groups in the plurality of gene groups, the generating comprising, for each particular one of the multiple GC TME signatures, determining the GC TME signature by determining the gene group scores using the RNA expression levels in the particular set of RNA expression data for which the particular one GC TME signature is being generated; and clustering the multiple GC signatures to obtain the plurality of GC TME signature clusters. 24. The method of claim 23, wherein the clustering comprises dense clustering, spectral clustering, k-means clustering, hierarchical clustering, and/or an agglomerative clustering. 25. The method of claim 24, wherein the hierarchical clustering is performed using a Louvain community detection algorithm. 26. The method of any one of claims 23 to 25, further comprising: updating the plurality of GC TME signature clusters using the GC TME signature of the subject, wherein the GC TME signature of the subject is one of a threshold number GC TME signatures for a threshold number of subjects, wherein when the threshold number of GC TME signatures is generated the GC TME signature clusters are updated. 27. The method of claim 26, wherein the threshold number of GC TME signatures is at least 50, at least 75, at least 100, at least 200, at least 500, at least 1000, or at least 5000 GC TME signatures. 28. The method of claim 27, wherein the updating comprises applying dense clustering, spectral clustering, k-means clustering, hierarchical clustering, and/or agglomerative clustering. 29. The method of claim 28, wherein the hierarchical clustering is performed using a Louvain community detection algorithm. 30. The method of any one of claims 23 to 29, further comprising: determining an GC TME type of a second subject, wherein the GC TME type of the second subject is identified using the updated GC TME signature clusters, wherein the identifying comprises: determining an GC TME signature of the second subject from RNA expression data obtained by sequencing a biological sample obtained from the second subject; associating the GC TME signature of the second subject with a particular one of the plurality of the updated GC TME signature clusters; and identifying the GC TME type for the second subject as the GC TME type corresponding to the particular one of the plurality of updated GC TME signature clusters to which the GC TME signature of the second subject is associated. 31. The method of any one of claims 1 to 30, wherein the plurality of a plurality of GC TME types comprises: GC TME type A, GC TME type B, GC TME type C, GC TME type D, and GC TME type E. 32. The method of any one of claims 1 to 31, further comprising: identifying the subject as having tertiary lymphoid structures (TLS) when the subject is identified as having GC TME type E. 33. The method of any one of claims 1 to 32, further comprising: identifying the subject as having an increased likelihood of having a good prognosis, optionally, as measured by overall survival (OS) or progression-free survival (PFS), when the subject is identified as having GC TME type E. 34. The method of any one of claims 3 to 33, wherein the RNA expression levels for genes in the second plurality of gene groups comprise RNA expression levels for at least three genes from each of at least two of the following gene groups: (i) Th17 signature group: IL17F, IL17A, IL26, IL22, RORC, BATF, IL23R, CCR6; (ii) Gamma-delta (γΔ) T cells group: TRGC1, TRDC, TRDV2, TRGC2, TRDV1; (iii) Tumor suppressor group: LATS1, LATS2, FBXW7, BAP1, KLF4, SASH1, CASP3, MLKL, SOCS1; (iv) Oncogenes group: KRAS, AKT1, EGFR, PIK3CA, PIK3CB, MYC, VAV3, MET, CCND1, INPPL1, CHD1L, RACGAP1; (v) Myc targets group: AIMP2, BYSL, CBX3, CDK4, DCTPP1, DDX18, DUSP2, EXOSC5, FARSA, GNL3, GRWD1, HK2, HSPD1, HSPE1, IMP4, IPO4, LAS1L, MAP3K6, MCM4, MCM5, MPHOSPH10, MRTO4, MYBBP1A, MYC, NDUFAF4, NIP7, NOC4L, NOLC1, NOP16, NOP2, NOP56, NPM1, PA2G4, PES1, PHB, PLK1, PLK4, PPAN, PPRC1, PRMT3, PUS1, RABEPK, RCL1, RRP12, RRP9, SLC19A1, SLC29A2, SORD, SRM, SUPV3L1, TBRG4, TCOF1, TFB2M, TMEM97, UNG, UTP20, WDR43, WDR74; (vi) Th2 signature group: IL4, IL5, IL13, IL10, GATA3, CCR4; and (vii) Th1 signature group: IFNG, IL2, CD40LG, IL21, TBX21, STAT4, IL12RB2. 35. The method of claim 34, wherein the RNA expression levels for genes in the second plurality of gene groups comprise RNA expression levels for each of the genes from each of the following gene groups: (i) Th17 signature group: IL17F, IL17A, IL26, IL22, RORC, BATF, IL23R, CCR6; (ii) Gamma-delta (γΔ) T cells group: TRGC1, TRDC, TRDV2, TRGC2, TRDV1; (iii) Tumor suppressor group: LATS1, LATS2, FBXW7, BAP1, KLF4, SASH1, CASP3, MLKL, SOCS1; (iv) Oncogenes group: KRAS, AKT1, EGFR, PIK3CA, PIK3CB, MYC, VAV3, MET, CCND1, INPPL1, CHD1L, RACGAP1; (v) Myc targets group: AIMP2, BYSL, CBX3, CDK4, DCTPP1, DDX18, DUSP2, EXOSC5, FARSA, GNL3, GRWD1, HK2, HSPD1, HSPE1, IMP4, IPO4, LAS1L, MAP3K6, MCM4, MCM5, MPHOSPH10, MRTO4, MYBBP1A, MYC, NDUFAF4, NIP7, NOC4L, NOLC1, NOP16, NOP2, NOP56, NPM1, PA2G4, PES1, PHB, PLK1, PLK4, PPAN, PPRC1, PRMT3, PUS1, RABEPK, RCL1, RRP12, RRP9, SLC19A1, SLC29A2, SORD, SRM, SUPV3L1, TBRG4, TCOF1, TFB2M, TMEM97, UNG, UTP20, WDR43, WDR74; (vi) Th2 signature group: IL4, IL5, IL13, IL10, GATA3, CCR4; and (vii) Th1 signature group: IFNG, IL2, CD40LG, IL21, TBX21, STAT4, IL12RB2. 36. The method of claim 34 or 35, wherein determining the gene group scores comprises determining a first score of a first gene group using a single-sample GSEA (ssGSEA) technique from second RNA expression levels for at least some of the genes in one of the following gene groups: (i) Th17 signature group: IL17F, IL17A, IL26, IL22, RORC, BATF, IL23R, CCR6; (ii) Gamma-delta (γΔ) T cells group: TRGC1, TRDC, TRDV2, TRGC2, TRDV1; (iii) Tumor suppressor group: LATS1, LATS2, FBXW7, BAP1, KLF4, SASH1, CASP3, MLKL, SOCS1; (iv) Oncogenes group: KRAS, AKT1, EGFR, PIK3CA, PIK3CB, MYC, VAV3, MET, CCND1, INPPL1, CHD1L, RACGAP1; (v) Myc targets group: AIMP2, BYSL, CBX3, CDK4, DCTPP1, DDX18, DUSP2, EXOSC5, FARSA, GNL3, GRWD1, HK2, HSPD1, HSPE1, IMP4, IPO4, LAS1L, MAP3K6, MCM4, MCM5, MPHOSPH10, MRTO4, MYBBP1A, MYC, NDUFAF4, NIP7, NOC4L, NOLC1, NOP16, NOP2, NOP56, NPM1, PA2G4, PES1, PHB, PLK1, PLK4, PPAN, PPRC1, PRMT3, PUS1, RABEPK, RCL1, RRP12, RRP9, SLC19A1, SLC29A2, SORD, SRM, SUPV3L1, TBRG4, TCOF1, TFB2M, TMEM97, UNG, UTP20, WDR43, WDR74; (vi) Th2 signature group: IL4, IL5, IL13, IL10, GATA3, CCR4; and (vii) Th1 signature group: IFNG, IL2, CD40LG, IL21, TBX21, STAT4, IL12RB2. 37. The method of any one of claims 34 to 36, wherein determining the gene group scores comprises determining the gene group scores, using a single-sample GSEA (ssGSEA) technique, from RNA expression levels for each of the genes in each one of the following gene groups: (i) Th17 signature group: IL17F, IL17A, IL26, IL22, RORC, BATF, IL23R, CCR6; (ii) Gamma-delta (γΔ) T cells group: TRGC1, TRDC, TRDV2, TRGC2, TRDV1; (iii) Tumor suppressor group: LATS1, LATS2, FBXW7, BAP1, KLF4, SASH1, CASP3, MLKL, SOCS1; (iv) Oncogenes group: KRAS, AKT1, EGFR, PIK3CA, PIK3CB, MYC, VAV3, MET, CCND1, INPPL1, CHD1L, RACGAP1; (v) Myc targets group: AIMP2, BYSL, CBX3, CDK4, DCTPP1, DDX18, DUSP2, EXOSC5, FARSA, GNL3, GRWD1, HK2, HSPD1, HSPE1, IMP4, IPO4, LAS1L, MAP3K6, MCM4, MCM5, MPHOSPH10, MRTO4, MYBBP1A, MYC, NDUFAF4, NIP7, NOC4L, NOLC1, NOP16, NOP2, NOP56, NPM1, PA2G4, PES1, PHB, PLK1, PLK4, PPAN, PPRC1, PRMT3, PUS1, RABEPK, RCL1, RRP12, RRP9, SLC19A1, SLC29A2, SORD, SRM, SUPV3L1, TBRG4, TCOF1, TFB2M, TMEM97, UNG, UTP20, WDR43, WDR74; (vi) Th2 signature group: IL4, IL5, IL13, IL10, GATA3, CCR4; and (vii) Th1 signature group: IFNG, IL2, CD40LG, IL21, TBX21, STAT4, IL12RB2. 38. The method of any one of claims 34 to 37, wherein the identifying in (c) is performed using the second GC TME signature. 39. The method of any one of claims 34 to 38, wherein the identifying in (d) is performed using the second GC TME signature. 40. The method of any one of claims 1 to 39, further comprising: identifying the subject as having an increased likelihood of responding to an immunotherapy when the subject is assigned GC TME type B. 41. The method of any one of claims 1 to 39, further comprising: identifying the subject as having an increased likelihood of responding to an immunotherapy when the subject is assigned GC TME type E. 42. The method of claim 40 or 41, wherein the subject is Microsatellite Stable (MSS). 43. The method of any one of claims 40 to 42, wherein the subject is Epstein Barr virus (EBV) low or EBV negative. 44. The method of any one of claims 1 to 43 further comprising: administering an immunotherapy to the subject. 45. The method of any one of claims 1 to 44, wherein the immunotherapy comprises a PD1 inhibitor, optionally pembrolizumab. 46. A method for predicting disease control rate (DCR) to an immunotherapy of a subject, the method comprising: using at least one computer hardware processor to perform: (i) identifying the GC TME of the subject using the method of any one of the preceding claims; and (ii) identifying the subject as likely to have an increased DCR when the subject is assigned GC TME type B or GC TME type E relative to subjects having GC TME type A, GC TME type C, or GC TME type D. 47. The method of claim 46, wherein the immunotherapy comprises a PD1 inhibitor, optionally pembrolizumab. 48. The method of claim 46 or 47, wherein the DCR of a subject having GC TME type B is greater than 50%. 49. The method of claim 46 or 47, wherein the DCR of a subject having GC TME type E is greater than 50%. 50. The method of any one of claims 46 to 49, wherein the subject is Microsatellite Stable (MSS). 51. The method of any one of claims 46 to 50, wherein the subject is Epstein Barr virus (EBV) low or EBV negative. 52. The method of any one of claims 46 to 51, further comprising administering an immunotherapy to the subject. 53. A system, comprising: at least one computer hardware processor; and at least one computer-readable storage medium storing processor-executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform a method for identifying, based at least in part on a gastric cancer (GC) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk, of having a gastric cancer, whether the subject is likely to respond to an immunotherapy, the method comprising: (a) obtaining RNA expression data for the subject, the RNA expression data indicating RNA expression levels for at least some genes in each group of at least some of a plurality of gene groups listed in Table 1; (b) generating a GC TME signature for the subject using the RNA expression data, the GC TME signature comprising gene group scores for respective gene groups in the at least some of the plurality of gene groups, the generating comprising: determining the gene group scores using the RNA expression levels; (c) identifying, using the GC TME signature and from among a plurality of GC TME types, a GC TME type for the subject; and (d) identifying, using the GC TME type of the subject, whether or not the subject is likely to respond to the immunotherapy. 54. At least one computer-readable storage medium storing processor-executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform a method for identifying, based at least in part on a gastric cancer (GC) tumor microenvironment (TME) type for a subject having, suspected of having, or at risk, of having a gastric cancer, whether the subject is likely to respond to an immunotherapy, the method comprising: (a) obtaining RNA expression data for the subject, the RNA expression data indicating RNA expression levels for at least some genes in each group of at least some of a plurality of gene groups listed in Table 1; (b) generating a GC TME signature for the subject using the RNA expression data, the GC TME signature comprising gene group scores for respective gene groups in the at least some of the plurality of gene groups, the generating comprising: determining the gene group scores using the RNA expression levels; (c) identifying, using the GC TME signature and from among a plurality of GC TME types, a GC TME type for the subject; and (d) identifying, using the GC TME type of the subject, whether or not the subject is likely to respond to the immunotherapy. 55. A system, comprising: at least one computer hardware processor; and at least one non-transitory computer-readable storage medium, storing processor executable instructions that, when executed by the at least one computer hardware processor, cause the at least one computer hardware processor to perform a method for predicting disease control rate (DCR) to an immunotherapy of a subject, the method comprising: (i) identifying the GC TME of the subject using the method of any one of the preceding claims; and (ii) identifying the subject as likely to have an increased DCR when the subject is assigned GC TME type B or GC TME type E relative to subjects having GC TME type A, GC TME type C, or GC TME type D. 56. At least one non-transitory computer-readable storage medium, storing processor executable instructions that, when executed by at least one computer hardware processor, cause the at least one computer hardware processor to perform a method for predicting disease control rate (DCR) to an immunotherapy of a subject, the method comprising: (i) identifying the GC TME of the subject using the method of any one of the preceding claims; and (ii) identifying the subject as likely to have an increased DCR when the subject is assigned GC TME type B or GC TME type E relative to subjects having GC TME type A, GC TME type C, or GC TME type D. |
In some embodiments, expression data from a subject is further analyzed after a GC TME type has been assigned. The disclosure is based, in part, on secondary GC TME signatures, which can used for identifying a shift in a subject’s TME type and/or subject’s shift in response to an immunotherapy. In some embodiments, a second GC TME signature is generated using RNA expression levels for genes in the plurality of gene groups listed in Table 2. In some embodiments, the second GC TME signature comprises RNA expression levels for at least three (e.g., at least 2, 3, 4, 5, between 2 and 10 and any integer therebetween, or more than 10) genes from each of at least two of the following gene groups: (i) Th17 signature group; (ii) Gamma-delta (γΔ) T cells group; (iii) Tumor suppressor group; (iv) Oncogenes group (v) Myc targets group; (vi) Th2 signature group; and (vii) Th1 signature group. In some embodiments, the second GC TME signature comprises RNA expression levels for each of the genes from each of the following gene groups: (i) Th17 signature group; (ii) Gamma-delta (γΔ) T cells group; (iii) Tumor suppressor group; (iv) Oncogenes group (v) Myc targets group; (vi) Th2 signature group; and (vii) Th1 signature group. The gene group scores of the second GC TME signature may be determined using gene set enrichment (GSEA) (e.g., using a single sample GSEA technique). For example, in some embodiments, ssGSEA is performed on RNA expression data using one or more (e.g., 1, 2, 3, 4, 5, 6, or 7) gene groups listed in Table 2. In some embodiments, each gene group of Table 2 comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, or more) genes listed in Table 2. In some embodiments, the additional analysis comprises performing ssGSEA on the Th17 gene group and gamma-delta T cells (γΔ T cells) gene group to produce a Th17 signature and a Gamma-delta (γΔ) T cell signature. Aspects of GSEA and ssGSEA are described herein. In some embodiments, the additional analysis comprises performing cell deconvolution analysis and/or histological analysis (e.g., by assessing Lauren subtypes) of the expression data. In some embodiments, determining one or more additional signatures (e.g., a second GC TME signature) comprises determining a respective gene group score for each of at least one of the following gene groups, using, for a particular gene group, RNA expression levels for at least two genes in the particular gene group to determine the gene group score for the particular group, the gene groups including: (i) Th17 signature group: IL17F, IL17A, IL26, IL22, RORC, BATF, IL23R, CCR6; (ii) Gamma-delta (γΔ) T cells group: TRGC1, TRDC, TRDV2, TRGC2, TRDV1; (iii) Tumor suppressors group: LATS1, LATS2, FBXW7, BAP1, KLF4, SASH1, CASP3, MLKL, SOCS1; (iv) Oncogenes group: KRAS, AKT1, EGFR, PIK3CA, PIK3CB, MYC, VAV3, MET, CCND1, INPPL1, CHD1L, RACGAP1; (v) MYC targets group: AIMP2, BYSL, CBX3, CDK4, DCTPP1, DDX18, DUSP2, EXOSC5, FARSA, GNL3, GRWD1, HK2, HSPD1, HSPE1, IMP4, IPO4, LAS1L, MAP3K6, MCM4, MCM5, MPHOSPH10, MRTO4, MYBBP1A, MYC, NDUFAF4, NIP7, NOC4L, NOLC1, NOP16, NOP2, NOP56, NPM1, PA2G4, PES1, PHB, PLK1, PLK4, PPAN, PPRC1, PRMT3, PUS1, RABEPK, RCL1, RRP12, RRP9, SLC19A1, SLC29A2, SORD, SRM, SUPV3L1, TBRG4, TCOF1, TFB2M, TMEM97, UNG, UTP20, WDR43, WDR74; (vi) Th2 signature group: IL4, IL5, IL13, IL10, GATA3, CCR4; and (vii) Th1 signature group: IFNG, IL2, CD40LG, IL21, TBX21, STAT4, IL12RB2 Table 2: List of Gene Groups, the left column providing the name of the Gene Group and the right column providing examples of genes in the Gene Group. It should be noted that the names of the gene groups shown in Table 2 appear in some of the figures (e.g., Figs.15, 16, 18, and 19) with “_” instead of spaces due to how the graphics were generated. For example, “Th17 signature” appears as “Th17_signature” in those figures. Also “MYC targets” is labeled “MYC_targets_2” in the figures. As described above, aspects of the disclosure relate to determining an GC TME signature for a subject. That signature may include gene group scores (e.g., gene group scores generated using RNA expression data for gene groups listed in Table 1 and/or Table 2). Aspects of determining of GC TME signatures is described next with reference to FIG.3. In some embodiments, a GC TME signature comprises gene group scores generated using a gene set enrichment analysis (GSEA) technique to determine a gene group score for one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) gene groups listed in Table 1. In some embodiments, a GC TME signature comprises gene group scores generated using a gene set enrichment analysis (GSEA) technique to determine a gene group score for eight or more (e.g., 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) gene groups listed in Table 1. In some embodiments, each gene group score is generated using a gene set enrichment analysis (GSEA) technique, using RNA expression levels of at least some genes in the gene group. In some embodiments, using a GSEA technique comprises using single-sample GSEA. Aspects of single sample GSEA (ssGSEA) are described in Barbie et al. Nature.2009 Nov 5; 462(7269): 108–112, the entire contents of which are incorporated by reference herein. In some embodiments, ssGSEA is performed according to the following formula: where r i represents the rank of the ith gene in expression matrix, where N represents the number of genes in the gene set (e.g., the number of genes in the first gene group when ssGSEA is being used to determine a gene group score for the first gene group using expression levels of the genes in the first gene group), and where M represents total number of genes in expression matrix. Additional, suitable techniques of performing GSEA are known in the art and are contemplated for use in the methods described herein without limitation. In some embodiments, a GC TME signature is calculated by performing ssGSEA on expression data from a plurality of subjects, for example expression data from one or more cohorts of subjects, such as GSE15459, GSE34942, GSE26253, GSE62254, GSE13861, GSE26901, GSE29272, GSE84437, GSE26899, GSE28541, GSE113255, PRJEB25780, SRP219269, and TCGA – stomach samples (e.g., STAD TCGA project), in order to produce a plurality of enrichment scores. FIG.3 depicts an illustrative example of how gene group scores may be determined as part of act 108 of process 100. As shown in the example of FIG.3, a “GC TME signature” comprises multiple gene group scores 320 determined for respective multiple gene groups. Each gene group score, for a particular gene group, is computed by performing GSEA 310 (e.g., using ssGSEA) on RNA expression data for one or more (e.g., at least two, at least three, at least four, at least five, at least six, etc., or all) genes in the particular gene group 300. For example, as shown in FIG.3, a gene group score (labelled “Gene Group Score 1”) for gene group 1 (e.g., the Treg group) is computed from RNA expression data for one or more genes in gene group 1. As another example, a gene group score (labelled “Gene Group Score 2”) for gene group 2 (e.g., the T cells group) is computed from RNA expression data for one or more genes in gene group 2. As another example, a gene group score (labelled “Gene Group Score 3”) for gene group 3 (e.g., the NK cells group) is computed from RNA expression data for one or more genes in gene group 3. As another example, a gene group score (labelled “Gene Group Score 4”) for gene group 4 (e.g., the B cells group) is computed from RNA expression data for one or more genes in gene group 4. As another example, a gene group score (labelled “Gene Group Score 5”) for gene group 5 (e.g., the MDSC group) is computed from RNA expression data for one or more genes in gene group 5. As another example, a gene group score (labelled “Gene Group Score 6”) for gene group 6 (e.g., the CAF group) is computed from RNA expression data for one or more genes in gene group 6. As another example, a gene group score (labelled “Gene Group Score 7”) for gene group 7 (e.g., the Proliferation rate group) is computed from RNA expression data for one or more genes in gene group 7. As another example, a gene group score (labelled “Gene Group Score 8”) for gene group 8 (e.g., the Lgr5 ISC group) is computed from RNA expression data for one or more genes in gene group 8. Although the example of FIG.3 shows that the gene expression group score includes eight gene group scores for a respective set of eight gene groups, it should be appreciated that in other embodiments, the first gene expression signature may include scores for any suitable number of groups (e.g., not just 8; the number of groups could be fewer or greater than 8). As indicated by the vertical ellipsis in FIG.3, determining gene group scores of a GC TME signature may comprise determining gene group scores for 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more gene groups using RNA expression data from one or more respective genes in each respective gene group, as aspects of the technology described herein are not limited in this respect. In another example, a GC TME signature may include scores for only a subset of the gene groups listed in Table 1 above. As another example, the gene expression group score may include one or more scores for one or more gene groups other than those gene groups listed in Table 1 (either in addition to the score(s) for the groups in Table 1 or instead of one or more of the scores for the groups in Table 1, for example the gene groups listed in Table 2). In some embodiments, RNA expression levels for a particular gene group may be embodied in at least one data structure having fields storing the expression levels. The data structure or data structures may be provided as input to software comprising code that implements a GSEA technique (e.g., the ssGSEA technique) and processes the expression levels in the at least one data structure to compute a score for the particular gene group. The number of genes in a gene group used to determine a gene group score may vary. In some embodiments, all RNA expression levels for all genes in a particular gene group may be used to determine a gene group score for the particular gene group. In other embodiments, RNA expression data for fewer than all genes may be used (e.g., RNA expression levels for at least two genes, at least three genes, at least five genes, between 2 and 10 genes, between 5 and 15 genes, or any other suitable range within these ranges). In some embodiments, RNA expression levels for a particular gene group may be embodied in at least one data structure having fields storing the expression levels. The data structure or data structures may be provided as input to software comprising code that is configured to perform suitable scaling (e.g., median scaling) to produce a score for the particular gene group. In some embodiments, ssGSEA is performed on expression data comprising three or more (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20) gene groups set forth in Table 1. In some embodiments, each of the gene groups separately comprises one or more (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, or more) genes listed in Table 1. In some embodiments, a GC TME signature is produced by performing ssGSEA on all 20 of the gene groups in Table 1, each gene group including all listed genes in Table 1. In some embodiments, one or more (e.g., a plurality) of enrichment scores are normalized in order to produce a GC TME signature for the expression data (e.g., expression data of the subject or of a cohort of subjects). In some embodiments, the enrichment scores are normalized by median scaling. In some embodiments, the enrichment scores are normalized by rank estimation and median scaling. In some embodiments, median scaling comprises clipping the range of enrichment scores, for example clipping to about -1.0 to about +1.0, -2.0 to about +3.0, -3.0 to about +3.0, -4.0 to +4.0, -5.0 to about +5.0. In some embodiments, median scaling produces a GC TME signature of the subject. In some embodiments, a GC TME signature of a subject processed using a clustering algorithm to identify a GC tumor microenvironment type (e.g. a GC TME type). In some embodiments, the clustering comprises unsupervised clustering. In some embodiments, the unsupervised clustering comprises a dense clustering approach. In some embodiments, the unsupervised clustering comprises a hierarchical clustering approach. In some embodiments, clustering comprises calculating intersample similarity (e.g., using a Pearson correlation coefficient that, for example, may take on values in the range of [-1,1]), converting the distance matrix into a graph where each sample forms a node and two nodes form an edge with a weight equal to their Pearson correlation coefficient, removing edges with weight lower than a specified threshold, and applying a Louvain community detection algorithm to calculate graph partitioning into clusters. In some embodiments, the optimum weight threshold for observed clusters was calculated by employing minimum DaviesBouldin, maximum Calinski-Harabasz, and Silhouette techniques. In some embodiments, separations with low-populated clusters (< 5% of samples) are excluded. In some embodiments, a GC TME signature of a subject is compared to pre-existing clusters of GC TME types and assigned a GC TME type based on that comparison. Some aspects of determining gene group scores for gene groups are also described in U.S. Patent Publication No.2020-0273543, entitled “SYSTEMS AND METHODS FOR GENERATING, VISUALIZING AND CLASSIFYING MOLECULAR FUNCTIONAL PROFILES”, the entire contents of which are incorporated by reference herein. Generating GC TME Signature and Identifying TME Type As described herein, FIG.1 illustrates the determination of a subject’s GC TME signature, identification of the subject’s GC TME type using the GC TME signature, and identification of whether the subject is likely to respond to an immunotherapy based on the identified GC TME type. As described herein, in some embodiments, one of a plurality of different GC TME types may be identified for the subject using the GC TME signature determined for the subject using the techniques described herein. In some embodiments, the GC TME type comprises GC TME type A, GC TME type B, GC TME type C, GC TME type D, and GC TME type E, as described herein and further below. In some embodiments, each of the plurality of GC TME types is associated with a respective GC TME signature cluster in a plurality of GC TME signature clusters. The GC TME type for a subject may be determined by: (1) associating the GC TME signature of the subject with a particular one of the plurality of GC TME signature clusters; and (2) identifying the GC TME type for the subject as the GC TME type corresponding to the particular one of the plurality of GC TME signature clusters to which the GC TME signature of the subject is associated. FIG.4 shows an illustrative GC TME signature 400. In some embodiments, the GC TME signature comprises at least eight gene group scores for the following gene groups: NK cell group, T cell group, B cell group, Treg cells group, MDSC group, CAF group, Proliferation rate group, and the Lgr5 ISC group. However, it should be appreciated, that a GC TME signature may include fewer scores than the number of scores shown in FIG.4 (e.g., by omitting scores for one or more of the gene groups listed in Table 1) or more scores than the number of scores shown in FIG.4 (e.g., by including scores for one or more other gene groups in addition to or instead of the gene groups listed in Table 1). In some embodiments, a GC TME signature may be embodied in at least one data structure comprising fields storing the gene group scores part of the GC TME signature. In some embodiments, the GC TME signature clusters may be generated by: (1) obtaining GC TME signatures (using the techniques described herein) for a plurality of subjects; and (2) clustering the GC TME signatures so obtained into the plurality of clusters. Any suitable clustering technique may be used for this purpose including, but not limited to, a dense clustering algorithm, spectral clustering algorithm, k-means clustering algorithm, hierarchical clustering algorithm, and/or an agglomerative clustering algorithm. For example, intersample similarity may be calculated using a Pearson correlation. A distance matrix may be converted into a graph where each sample forms a node and two nodes form an edge with a weight equal to their Pearson correlation coefficient. Edges with weight lower than a specified threshold may be removed. A Louvain community detection algorithm may be applied to calculate graph partitioning into clusters. To mathematically determine the optimum weight threshold for observed clusters minimum DaviesBouldin, maximum Calinski- Harabasz, and Silhouette techniques may be employed. Separations with low-populated clusters (< 5% of samples) may be excluded. Accordingly, in some embodiments, generating the GC TME signature clusters involves: (A) obtaining multiple sets of RNA expression data obtained by sequencing biological samples from multiple respective subjects, each of the multiple sets of RNA expression data indicating RNA expression levels for genes in a first plurality of gene groups (e.g., one or more of the gene groups in Table 1); (B) generating multiple GC TME signatures from the multiple sets of RNA expression data, each of the multiple GC TME signatures comprising gene group scores for respective gene groups, the generating comprising, for each particular one of the multiple TME signatures: (i) determining the GC TME signature by determining the gene group scores using the RNA expression levels in the particular set of RNA expression data for which the particular one GC TME signature is being generated, and (ii) clustering the multiple GC signatures to obtain the plurality of GC TME signature clusters. The resulting GC TME signature clusters may each contain any suitable number of GC TME signatures (e.g., at least 10, at least 100, at least 500, at least 500, at least 1000, at least 5000, between 100 and 10,000, between 500 and 20,000, or any other suitable range within these ranges), as aspects of the technology described herein are not limited in this respect. The number of GC TME signature clusters in this example is five. And although, in some embodiments, it may be possible that the number of clusters is different, it should be appreciated that an important aspect of the present disclosure is the inventors’ discovery that GC may be characterized into five types based upon the generation of GC TME signatures using methods described herein. For example, as shown in FIG.4, a subject’s GC TME signature 400 may be associated with one of five GC TME clusters: 402, 404, 406, 408, and 410. Each of the clusters 402, 404, 406, 408and 410 may be associated with respective GC TME type. In this example, the GC TME signature 400 is compared to each cluster (e.g., using a distance-based comparison or any other suitable metric) and, based on the result of the comparison, the GC TME signature 400 is associated with the closest GC signature cluster (when a distance-based comparison is performed, or the “closest” in the sense of whatever metric or measure of distance is used). In this example, GC TME signature 400 is associated with GC TME Type Cluster 5410 (as shown by the consistent shading) because the measure of distance D5 between the GC TME signature 400 and (e.g., a centroid or other point representative of) cluster 410 is smaller than the measures of the distance D1, D2, D3, and D4 between the GC TME signature 400 and (e.g., a centroid or other point(s) representative of) clusters 402, 404, 406, and 408, respectively. In some embodiments, a subject’s GC TME signature may be associated with one of five GC TME signature clusters by using a machine learning technique (e.g., such as k-nearest neighbors (KNN) or any other suitable classifier) to assign the GC TME signature to one of the four GC TME signature clusters. The machine learning technique may be trained to assign GC TME signatures on the meta-cohorts represented by the signatures in the clusters. In some embodiments, GC TME types include GC TME type A, GC TME type B, GC TME type C, GC TME type D, and GC TME type E. The GC TME types described herein may be described by qualitative characteristics, for example high signals for certain gene expression signatures or scores or low signals for certain other gene expression signatures or scores. In some embodiments, a “high” signal refers to a gene expression signal or score (e.g., an enrichment score) that is at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9- fold, 10-fold, 20-fold, 50-fold, 100-fold, 1000-fold, or more increased relative to the score of the same gene or gene group in a subject having a different type of GC. In some embodiments, a “low” signal refers to a gene expression signal or score (e.g., an enrichment score,) that is at least 1-fold, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 20-fold, 50-fold, 100-fold, 1000-fold, or more decreased relative to the score of the same gene or gene group in a subject having a different type of GC TME. Without wishing to be bound by any theory, the tumor microenvironment of GC may contain variable numbers of immune cells, stromal cells, blood vessels and extracellular matrix. In some embodiments, “GC TME type A” is characterized by “Mesenchymal, EMT” type. In some embodiments, GC TME type A (mesenchymal) type is characterized by having the highest LGR5+ stem cell signature relative to any other GC TME types. In some embodiments, GC TME type A GC subjects also have high stromal compartment gene group signatures, for example cancer-associated fibroblasts (CAF) and angiogenesis, relative to other GC TME types. In some embodiments, GC TME type A subject are characterized by high levels of pro- tumor cytokines and medium immune compartment signatures. In some embodiments, GC TME type A subjects have low tumor proliferation rates (relative to other GC TME types). In some embodiments, type A GC tumors are diffuse (by e.g. as assessed by Lauren classification). GC TME type A has been observed, in some embodiments, to be the most aggressive GC TME type, and subjects having GC TME type A have been observed in some embodiments to have worse prognosis (e.g., by overall survival (OS)) relative to other GC TME types. In some embodiments, “GC TME type B” is also referred to as “Immune-enriched, non- fibrotic (IE)” type. In some embodiments, GC TME type B (IE) is characterized by high levels of immune-active infiltrate with a significant number of effector cells and NK cells relative to other GC TME types. In some embodiments, GC TME type B subjects have the highest tumor mutational burden (TMB). In some embodiments, subjects having GC TME type B have been observed to have better prognosis (e.g., by overall survival (OS)) relative to other GC TME types. In some embodiments, “GC TME type C” is also referred to as “Fibrotic” or “immune non-inflamed” type. In some embodiments, GC TME type C is characterized by a highly fibrotic tumor microenvironment with dense collagen formation. In some embodiments, GC TME type C is characterized by minimal lymphocyte infiltration with elevated angiogenesis, relative to other GC TME types. In some embodiments, Cancer-associated fibroblasts (CAFs) signatures are abundant in GC TME type C. In some embodiments, GC TME type C is characterized by a high level of both protumor and antitumor cytokines. In some embodiments, subjects having GC TME type C have a poorer prognosis (e.g., as measured by OS) than subjects having other GC TME types. In some embodiments, GC TME type D is also referred to as “Immune desert” type. In some embodiments, GC TME type D is characterized by the highest malignant cell percentage relative to other GC TME types. In some embodiments, GC TME type D is characterized by minimal or complete absence of leukocyte/lymphocyte infiltration (e.g., relative to other GC TME types). In some embodiments, GC TME type D is characterized by a high level of tumor proliferation rate relative to other GC TME types. In some embodiments, GC TME type E is also referred to as “B-cell enriched” type. In some embodiments, GC TME type E is characterized by high levels of immune infiltrate with a significant number of B-cells, relative to other GC TME types. In some embodiments, GC TME type D is characterized by having a low proliferation rate relative to other GC TME types. In some embodiments, subjects having GC TME type E have been observed to have better prognosis (e.g., by overall survival (OS)) relative to other GC TME types. Tables 3, 4, 5, 6, and 7 below describe examples of GC TME signatures and gene group scores produced by ssGSEA analysis and normalization (e.g., median scaling) of expression data from one or more GC subjects. Table 3: Statistics of GC TME signatures of samples having GC TME type A. The statistics in the table show, for each gene group score in the GC TME signature, the mean, minimum, maximum, 25th percentile, 50th percentile, and 75% percentile values.
Table 4: Statistics of GC TME signatures of samples having GC TME type B. The statistics in the table show, for each gene group score in the GC TME signature, the mean, minimum, maximum, 25th percentile, 50th percentile, and 75% percentile values.
Table 5: Statistics of GC TME signatures of samples having GC TME type C. The statistics in the table show, for each gene group score in the GC TME signature, the mean, minimum, maximum, 25th percentile, 50th percentile, and 75% percentile values. Table 6: Statistics of GC TME signatures of samples having GC TME type D. The statistics in the table show, for each gene group score in the GC TME signature, the mean, minimum, maximum, 25th percentile, 50th percentile, and 75% percentile values. Table 7: Statistics of GC TME signatures of samples having GC TME type E. The statistics in the table show, for each gene group score in the GC TME signature, the mean, minimum, maximum, 25th percentile, 50th percentile, and 75% percentile values.
In some embodiments, the present disclosure provides methods for identifying a subject having, suspected of having, or at risk of having GC as having an increased likelihood of having a good prognosis (e.g., as measured by overall survival (OS) or progression-free survival (PFS). In some embodiments, the method comprises determining a GC TME type of the subject as described herein. In some embodiments, the methods comprise identifying the subject as having a decreased risk of GC progression relative to other GC TME types when the subject is assigned GC TME type E. In some embodiments, “decreased risk of GC progression” may indicate better prognosis of GC or decreased likelihood of having advanced disease in a subject. In some embodiments, “decreased risk of GC progression” may indicate that the subject who has GC is expected to be more responsive to certain treatments. For instance, “decreased risk of GC progression” indicates that a subject is at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% likely to experience a progression-free survival event (e.g., relapse, retreatment, or death) than another GC patient or population of GC patients (e.g., patients having GC, but not the same GC TME type as the subject). In some embodiments, the methods further comprise identifying the subject as having an increased risk of GC progression relative to other GC TME types when the subject is assigned a GC TME type other than GC TME type E. In some embodiments, “increased risk of GC progression” may indicate less positive prognosis of GC or increased likelihood of having advanced disease in a subject. In some embodiments, “increased risk of GC progression” may indicate that the subject who has GC is expected to be less responsive or unresponsive to certain treatments and show less or no improvements of disease symptoms. For instance, “increased risk of GC progression” indicates that a subject is at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100% more likely to experience a progression-free survival event (e.g., relapse, retreatment, or death) than another GC patient or population of GC patients (e.g., patients having GC, but not the same GC TME type as the subject). The disclosure is based, in part, on the recognition that subjects having certain GC TME types (e.g., GC TME type E) are characterized as having (or being more likely to have) tertiary lymphoid structures (TLS), compared to subjects having other types of GC TME. Tertiary lymphoid structures are ectopic lymphoid organs that develop in non-lymphoid tissues at sites of chronic inflammation including tumors, for example as described by Sautès-Fridman et al. Nat Rev Cancer 19, 307–325 (2019). In the context of certain cancers (e.g., gastric cancers) the presence of TLS is associated with an improved subject prognosis. Accordingly, in some embodiments, subjects identified as having GC TME type E have an increased likelihood of having PFS or increased overall survival (OS) relative to subjects having other GC TME types. In some embodiments, the methods described herein comprise the use of at least one computer hardware processor to perform the determination. In some embodiments, the present disclosure provides a method for providing a prognosis, predicting survival, or stratifying patient risk of a subject suspected of having, or at risk of having GC. In some embodiments, the method comprises determining a GC TME type of the subject as described herein. Updating GC TME Clusters Based on New Data Techniques for generating GC TME clusters are described herein. It should be appreciated that the GC TME clusters may be updated as additional GC TME signatures are computed for patients. In some embodiments, the GC TME signature of the subject is one of a threshold number GC TME signatures for a threshold number of subjects. In some embodiments, when the threshold number of GC TME signatures is generated the GC TME signature clusters are updated. For example, once a threshold number of new GC TME signatures are obtained (e.g., 1 new signature, 10 new signatures, 100 new signatures, 500 new signatures, any suitable threshold number of signatures in the range of 10-1,000 signatures), the new signatures may be combined with the GC TME signatures previously used to generate the GC TME clusters and the combined set of old and new GC TME signatures may be clustered again (e.g., using any of the clustering algorithms described herein or any other suitable clustering algorithm) to obtain an updated set of GC TME signature clusters. In this way, data obtained from a future patient may be analyzed in a way that takes advantage of information learned from patients whose GC TME signature was computed prior to that of the future patient. In this sense, the machine learning techniques described herein (e.g., the unsupervised clustering machine learning techniques) are adaptive and learn with the accumulation of new patient data. This facilitates improved characterization of the GC TME type that future patients may have and may improve the selection of treatment for those patients. Therapeutic Indications Aspects of the disclosure relate to methods of identifying or selecting a therapeutic agent for a subject based upon determination of the subject’s GC TME type. The disclosure is based, in part, on the recognition that subjects having GC TME type B or GC TME type E have an increased likelihood of responding to certain therapies (e.g., an immunotherapy) relative to subjects having other GC TME types. The inventors have surprisingly discovered that determination of GC TME type E or GC TME type B patients are likely to respond to immunotherapy independent of their MSS/MSI or EBV status. In some aspects, the disclosure provides a method for predicting disease control rate (DCR) to an immunotherapy of a subject, the method comprising determining the GC TME type of the subject, and identifying the subject as likely to have an increased DCR when the subject is assigned GC TME type B or GC TME type E relative to subjects having GC TME type A, GC TME type C, or GC TME type D. As used herein, “disease control rate” or “DCR” refers to the percentage of patients with advanced or metastatic cancer who have achieved complete response, partial response, and stable disease to a therapeutic intervention. In some embodiments, a subject determined to have GC TME type B or GC TME type E has a DCR greater than 50% (e.g., at least 50%, 60%, 70%, 80%, 90%, 95%, or 99%) for an immunotherapy. In some embodiments, the immunotherapy comprises a PD1 inhibitor. Examples of PD1 inhibitors include but are not limited to pembrolizumab, nivolumab, cemilimab, JTX-4014, camrelizumab, sintilimab, tisleizumab, toripalimab, dostarlimab, AMP-224, and AMP-514. In some embodiments, the immunotherapy comprises pembrolizumab. The disclosure is based, in part, on the recognition that certain subjects having GC TME type B or GC TME type E may have a higher likelihood of responding to an immunotherapy (e.g., pembrolizumab) even if that subject has previously been characterized as Epstein-Barr virus (EBV)-low and/or microsatellite stable (MSS). This is surprising because such patients have previously been observed to be low responders to immunotherapies. Aspects of the disclosure relate to methods of treating a subject having (or suspected or at risk of having) GC based upon a determination of the GC TME type of the subject. In some embodiments, the methods comprise administering one or more (e.g., 1, 2, 3, 4, 5, or more) therapeutic agents to the subject. In some embodiments, the therapeutic agent (or agents) administered to the subject are selected from small molecules, peptides, nucleic acids, radioisotopes, cells (e.g., CAR T-cells, etc.), and combinations thereof. Examples of therapeutic agents include chemotherapies (e.g., cytotoxic agents, etc.), immunotherapies (e.g., immune checkpoint inhibitors, such as PD-1 inhibitors, PD-L1 inhibitors, etc.), antibodies (e.g., anti- HER2 antibodies), cellular therapies (e.g. CAR T-cell therapies), gene silencing therapies (e.g., interfering RNAs, CRISPR, etc.), antibody-drug conjugates (ADCs), and combinations thereof. In some embodiments, a subject is administered an effective amount of a therapeutic agent. “An effective amount” as used herein refers to the amount of each active agent required to confer therapeutic effect on the subject, either alone or in combination with one or more other active agents. Effective amounts vary, as recognized by those skilled in the art, depending on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size, gender and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons, or for virtually any other reasons. Empirical considerations, such as the half-life of a therapeutic compound, generally contribute to the determination of the dosage. For example, antibodies that are compatible with the human immune system, such as humanized antibodies or fully human antibodies, may be used to prolong half-life of the antibody and to prevent the antibody being attacked by the host's immune system. Frequency of administration may be determined and adjusted over the course of therapy, and is generally (but not necessarily) based on treatment, and/or suppression, and/or amelioration, and/or delay of a cancer. Alternatively, sustained continuous release formulations of an anti-cancer therapeutic agent may be appropriate. Various formulations and devices for achieving sustained release are known in the art. In some embodiments, dosages for an anti-cancer therapeutic agent as described herein may be determined empirically in individuals who have been administered one or more doses of the anti-cancer therapeutic agent. Individuals may be administered incremental dosages of the anti-cancer therapeutic agent. To assess efficacy of an administered anti-cancer therapeutic agent, one or more aspects of a cancer (e.g., tumor microenvironment, tumor formation, tumor growth, or GC TME types, etc.) may be analyzed. Generally, for administration of any of the anti-cancer antibodies described herein, an initial candidate dosage may be about 2 mg/kg. For the purpose of the present disclosure, a typical daily dosage might range from about any of 0.1 µg/kg to 3 µg /kg to 30 µg /kg to 300 µg /kg to 3 mg/kg, to 30 mg/kg to 100 mg/kg or more, depending on the factors mentioned above. For repeated administrations over several days or longer, depending on the condition, the treatment is sustained until a desired suppression or amelioration of symptoms occurs or until sufficient therapeutic levels are achieved to alleviate a cancer, or one or more symptoms thereof. An exemplary dosing regimen comprises administering an initial dose of about 2 mg/kg, followed by a weekly maintenance dose of about 1 mg/kg of the antibody, or followed by a maintenance dose of about 1 mg/kg every other week. However, other dosage regimens may be useful, depending on the pattern of pharmacokinetic decay that the practitioner (e.g., a medical doctor) wishes to achieve. For example, dosing from one-four times a week is contemplated. In some embodiments, dosing ranging from about 3 µg /mg to about 2 mg/kg (such as about 3 µg /mg, about 10 µg /mg, about 30 µg /mg, about 100 µg /mg, about 300 µg /mg, about 1 mg/kg, and about 2 mg/kg) may be used. In some embodiments, dosing frequency is once every week, every 2 weeks, every 4 weeks, every 5 weeks, every 6 weeks, every 7 weeks, every 8 weeks, every 9 weeks, or every 10 weeks; or once every month, every 2 months, or every 3 months, or longer. The progress of this therapy may be monitored by conventional techniques and assays and/or by monitoring GC TME types as described herein. The dosing regimen (including the therapeutic used) may vary over time. When the anti-cancer therapeutic agent is not an antibody, it may be administered at the rate of about 0.1 to 300 mg/kg of the weight of the patient divided into one to three doses, or as disclosed herein. In some embodiments, for an adult patient of normal weight, doses ranging from about 0.3 to 5.00 mg/kg may be administered. The particular dosage regimen, e.g., dose, timing, and/or repetition, will depend on the particular subject and that individual's medical history, as well as the properties of the individual agents (such as the half-life of the agent, and other considerations well known in the art). For the purpose of the present disclosure, the appropriate dosage of an anti-cancer therapeutic agent will depend on the specific anti-cancer therapeutic agent(s) (or compositions thereof) employed, the type and severity of cancer, whether the anti-cancer therapeutic agent is administered for preventive or therapeutic purposes, previous therapy, the patient's clinical history and response to the anti-cancer therapeutic agent, and the discretion of the attending physician. Typically, the clinician will administer an anti-cancer therapeutic agent, such as an antibody, until a dosage is reached that achieves the desired result. Administration of an anti-cancer therapeutic agent can be continuous or intermittent, depending, for example, upon the recipient's physiological condition, whether the purpose of the administration is therapeutic or prophylactic, and other factors known to skilled practitioners. The administration of an anti-cancer therapeutic agent (e.g., an anti-cancer antibody) may be essentially continuous over a preselected period of time or may be in a series of spaced dose, e.g., either before, during, or after developing cancer. As used herein, the term “treating” refers to the application or administration of a composition including one or more active agents to a subject, who has a cancer, a symptom of a cancer, or a predisposition toward a cancer, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve, or affect the cancer or one or more symptoms of GC, or the predisposition toward GC. Alleviating GC includes delaying the development or progression of the disease, or reducing disease severity. Alleviating the disease does not necessarily require curative results. As used therein, “delaying” the development of a disease (e.g., a cancer) means to defer, hinder, slow, retard, stabilize, and/or postpone progression of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individuals being treated. A method that “delays” or alleviates the development of a disease, or delays the onset of the disease, is a method that reduces probability of developing one or more symptoms of the disease in a given time frame and/or reduces extent of the symptoms in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a number of subjects sufficient to give a statistically significant result. “Development” or “progression” of a disease means initial manifestations and/or ensuing progression of the disease. Development of the disease can be detected and assessed using clinical techniques known in the art. Alternatively, or in addition to the clinical techniques known in the art, development of the disease may be detectable and assessed based on other criteria. However, development also refers to progression that may be undetectable. For purpose of this disclosure, development or progression refers to the biological course of the symptoms. “Development” includes occurrence, recurrence, and onset. As used herein “onset” or “occurrence” of a cancer includes initial onset and/or recurrence. Examples of the antibody anti-cancer agents include, but are not limited to, alemtuzumab (Campath), trastuzumab (Herceptin), Ibritumomab tiuxetan (Zevalin), Brentuximab vedotin (Adcetris), Ado-trastuzumab emtansine (Kadcyla), blinatumomab (Blincyto), Bevacizumab (Avastin), Cetuximab (Erbitux), ipilimumab (Yervoy), nivolumab (Opdivo), pembrolizumab (Keytruda), atezolizumab (Tecentriq), avelumab (Bavencio), durvalumab (Imfinzi), and panitumumab (Vectibix). Examples of an immunotherapy include, but are not limited to, a PD-1 inhibitor or a PD- L1 inhibitor, a CTLA-4 inhibitor, adoptive cell transfer, therapeutic cancer vaccines, oncolytic virus therapy, T-cell therapy, and immune checkpoint inhibitors. Examples of radiation therapy include, but are not limited to, ionizing radiation, gamma- radiation, neutron beam radiotherapy, electron beam radiotherapy, proton therapy, brachytherapy, systemic radioactive isotopes, and radiosensitizers. Examples of a surgical therapy include, but are not limited to, a curative surgery (e.g., tumor removal surgery), a preventive surgery, a laparoscopic surgery, and a laser surgery. Examples of the chemotherapeutic agents include, but are not limited to, R-CHOP, Carboplatin or Cisplatin, Docetaxel, Gemcitabine, Nab-Paclitaxel, Paclitaxel, Pemetrexed, and Vinorelbine. Additional examples of chemotherapy include, but are not limited to, Platinating agents, such as Carboplatin, Oxaliplatin, Cisplatin, Nedaplatin, Satraplatin, Lobaplatin, Triplatin, Tetranitrate, Picoplatin, Prolindac, Aroplatin and other derivatives; Topoisomerase I inhibitors, such as Camptothecin, Topotecan, irinotecan/SN38, rubitecan, Belotecan, and other derivatives; Topoisomerase II inhibitors, such as Etoposide (VP-16), Daunorubicin, a doxorubicin agent (e.g., doxorubicin, doxorubicin hydrochloride, doxorubicin analogs, or doxorubicin and salts or analogs thereof in liposomes), Mitoxantrone, Aclarubicin, Epirubicin, Idarubicin, Amrubicin, Amsacrine, Pirarubicin, Valrubicin, Zorubicin, Teniposide and other derivatives; Antimetabolites, such as Folic family (Methotrexate, Pemetrexed, Raltitrexed, Aminopterin, and relatives or derivatives thereof); Purine antagonists (Thioguanine, Fludarabine, Cladribine, 6-Mercaptopurine, Pentostatin, clofarabine, and relatives or derivatives thereof) and Pyrimidine antagonists (Cytarabine, Floxuridine, Azacitidine, Tegafur, Carmofur, Capacitabine, Gemcitabine, hydroxyurea, 5-Fluorouracil (5FU), and relatives or derivatives thereof); Alkylating agents, such as Nitrogen mustards (e.g., Cyclophosphamide, Melphalan, Chlorambucil, mechlorethamine, Ifosfamide, mechlorethamine, Trofosfamide, Prednimustine, Bendamustine, Uramustine, Estramustine, and relatives or derivatives thereof); nitrosoureas (e.g., Carmustine, Lomustine, Semustine, Fotemustine, Nimustine, Ranimustine, Streptozocin, and relatives or derivatives thereof); Triazenes (e.g., Dacarbazine, Altretamine, Temozolomide, and relatives or derivatives thereof); Alkyl sulphonates (e.g., Busulfan, Mannosulfan, Treosulfan, and relatives or derivatives thereof); Procarbazine; Mitobronitol, and Aziridines (e.g., Carboquone, Triaziquone, ThioTEPA, triethylenemalamine, and relatives or derivatives thereof); Antibiotics, such as Hydroxyurea, Anthracyclines (e.g., doxorubicin agent, daunorubicin, epirubicin and relatives or derivatives thereof); Anthracenediones (e.g., Mitoxantrone and relatives or derivatives thereof); Streptomyces family antibiotics (e.g., Bleomycin, Mitomycin C, Actinomycin, and Plicamycin); and ultraviolet light. In some aspects, the disclosure provides a method for treating gastric cancer, the method comprising administering one or more therapeutic agents (e.g., one or more anti-cancer agents, such as one or more chemotherapeutic agents) to a subject identified as having a particular GC TME type, wherein the GC TME type of the subject has been identified by method as described by the disclosure. In some embodiments, a subject has been identified as having GC TME type A, GC TME type B, GC TME type C, GC TME type D, or GC TME type E. In some embodiments, a subject has been identified as having GC TME type B or GC TME type E. The disclosure is based, in part, on the inventors’ recognition that subjects having certain GC TME types are likely to respond well to certain immunotherapies (e.g., immune checkpoint inhibitors, such as pembrolizumab). In some embodiments, the therapeutic agent comprises pembrolizumab when the subject has been identified as having GC TME type E or GC TME type B. Dosages of pembrolizumab are well known, for example 200 mg every 3 weeks or 400 mg every 6 weeks, by infusion over 30 minutes. Aspects of the disclosure are based on the inventors’ recognition that subjects having certain GC TME types are unlikely to respond well to certain GC therapies, such as immunotherapeutic agents. Thus, in some embodiments, the therapeutic agent comprises a therapeutic agent other than an immunotherapy when the subject has been identified as having a GC TME type C or GC TME type A. Examples of other gastric cancer therapies include but are not limited to Cyramza (Ramucirumab), Docetaxel, Doxorubicin Hydrochloride, Enhertu (Fam- Trastuzumab Deruxtecan-nxki), 5-FU (Fluorouracil Injection), Fam-Trastuzumab Deruxtecan- nxki, Fluorouracil Injection, Herceptin (Trastuzumab), Keytruda (Pembrolizumab), Lonsurf (Trifluridine and Tipiracil Hydrochloride), Mitomycin, Ramucirumab, Taxotere (Docetaxel), Trastuzumab, and Trifluridine and Tipiracil Hydrochloride. Reports In some aspects, methods disclosed herein comprise generating a report for assisting with the preparation of recommendation for prognosis and/or treatment. The generated report can provide summary of information, so that the clinician can identify the GC TME type or suitable therapy. The report as described herein may be a paper report, an electronic record, or a report in any format that is deemed suitable in the art. The report may be shown and/or stored on a computing device known in the art (e.g., handheld device, desktop computer, smart device, website, etc.). The report may be shown and/or stored on any device that is suitable as understood by a skilled person in the art. In some embodiments, methods disclosed herein can be used for commercial diagnostic purposes. For example, the generated report may include, but is limited to, information concerning expression levels of one or more genes from any of the gene groups described herein, clinical, and pathologic factors, patient’s prognostic analysis, predicted response to the treatment, classification of the GC TME environment (e.g., as belonging to one of the types described herein), the alternative treatment recommendation, and/or other information. In some embodiments, the methods and reports may include database management for the keeping of the generated reports. For instance, the methods as disclosed herein can create a record in a database for the subject (e.g., subject 1, subject 2, etc.) and populate the specific record with data for the subject. In some embodiments, the generated report can be provided to the subject and/or to the clinicians. In some embodiments, a network connection can be established to a server computer that includes the data and report for receiving or outputting. In some embodiments, the receiving and outputting of the date or report can be requested from the server computer. Computer Implementation An illustrative implementation of a computer system 1300 that may be used in connection with any of the embodiments of the technology described herein (e.g., such as the method of FIG.1) is shown in FIG.13. The computer system 1300 includes one or more processors 1310 and one or more articles of manufacture that comprise non-transitory computer- readable storage media (e.g., memory 1320 and one or more non-volatile storage media 1330). The processor 1310 may control writing data to and reading data from the memory 1320 and the non-volatile storage device 1330 in any suitable manner, as the aspects of the technology described herein are not limited to any particular techniques for writing or reading data. To perform any of the functionality described herein, the processor 1310 may execute one or more processor-executable instructions stored in one or more non-transitory computer-readable storage media (e.g., the memory 1320), which may serve as non-transitory computer-readable storage media storing processor-executable instructions for execution by the processor 1310. Computing device 1300 may also include a network input/output (I/O) interface 1340 via which the computing device may communicate with other computing devices (e.g., over a network), and may also include one or more user I/O interfaces 1350, via which the computing device may provide output to and receive input from a user. The user I/O interfaces may include devices such as a keyboard, a mouse, a microphone, a display device (e.g., a monitor or touch screen), speakers, a camera, and/or various other types of I/O devices. The above-described embodiments can be implemented in any of numerous ways. For example, the embodiments may be implemented using hardware, software, or a combination thereof. When implemented in software, the software code can be executed on any suitable processor (e.g., a microprocessor) or collection of processors, whether provided in a single computing device or distributed among multiple computing devices. It should be appreciated that any component or collection of components that perform the functions described above can be generically considered as one or more controllers that control the above-discussed functions. The one or more controllers can be implemented in numerous ways, such as with dedicated hardware, or with general purpose hardware (e.g., one or more processors) that is programmed using microcode or software to perform the functions recited above. In this respect, it should be appreciated that one implementation of the embodiments described herein comprises at least one computer-readable storage medium (e.g., RAM, ROM, EEPROM, flash memory or other memory technology, CD-ROM, digital versatile disks (DVD) or other optical disk storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices, or other tangible, non-transitory computer-readable storage medium) encoded with a computer program (i.e., a plurality of executable instructions) that, when executed on one or more processors, performs the above-discussed functions of one or more embodiments. The computer-readable medium may be transportable such that the program stored thereon can be loaded onto any computing device to implement aspects of the techniques discussed herein. In addition, it should be appreciated that the reference to a computer program which, when executed, performs any of the above-discussed functions, is not limited to an application program running on a host computer. Rather, the terms computer program and software are used herein in a generic sense to reference any type of computer code (e.g., application software, firmware, microcode, or any other form of computer instruction) that can be employed to program one or more processors to implement aspects of the techniques discussed herein. The foregoing description of implementations provides illustration and description but is not intended to be exhaustive or to limit the implementations to the precise form disclosed. Modifications and variations are possible in light of the above teachings or may be acquired from practice of the implementations. In other implementations the methods depicted in these figures may include fewer operations, different operations, differently ordered operations, and/or additional operations. Further, non-dependent blocks may be performed in parallel. It will be apparent that example aspects, as described above, may be implemented in many different forms of software, firmware, and hardware in the implementations illustrated in the figures. Further, certain portions of the implementations may be implemented as a “module” that performs one or more functions. This module may include hardware, such as a processor, an application-specific integrated circuit (ASIC), or a field-programmable gate array (FPGA), or a combination of hardware and software. EXAMPLES Example 1: Identification of Gastric Cancer Tumor Microenvironment (TME) This example describes an illustrative technique for generating an GC TME signature for a subject from RNA expression data for the subject, according to some embodiments of the technology described herein. The produced GC TME signature reflects and/or indicates the abundance of both the malignant and microenvironment (TME) cell subpopulations and the activity of tumor-promoting and tumor-suppressive processes occurring within a tumor, and constitutes a personalized tumor map. The generated GC TME signature for the subject is used to identify an GC TME type for the subject from among five GC TME types: GC TME type A, GC TME type B, GC TME type C, GC TME type D, and GC TME type E. Aspects of some of the steps of the process described in this example are described in further detail herein including with reference to FIGs.1-4 above. RNA expression data (including both RNA-seq and microarray expression data) were obtained from multiple public databases. Data were subjected to basic quality control (QC) measures. For example, outlier samples and samples with signs of RNA degradation were excluded. Preprocessing of expression data included normalization and log-transformation. For microarrays normalization is performed automatically using gcrma package. RNA-seq data was subsequently normalized to TPM (transcript per million) units. TPM normalization techniques are described in Wagner et al. (Theory Biosci. (2012) 131:281–285), which is incorporated by reference herein in its entirety. TPM normalization may be performed using a software package, such as, for example, the gcrma package. Aspects of the gcrma package are described in Wu J, Gentry RIwcfJMJ (2021). “gcrma: Background Adjustment Using Sequence Information. R package version 2.66.0.”, which is incorporated by reference in its entirety herein. In some embodiments, RNA expression level in TPM units for a particular gene may be calculated according to: The GC TME type determined for a subject is determined using a GC TME signature. The GC TME signature includes gene group scores (e.g., one or more of the gene groups described in Table 1) obtained using ssGSEA. The gene group scores in the GC TME signatures were calculated from log-transformed RNA expression valued. The ssGSEA was performed according to the following formula: where ri represents the rank of the ith gene in expression matrix, where N represents the number of genes in the gene set (e.g., the number of genes in the first gene group when ssGSEA is being used to determine a score for the first gene group using expression levels of the genes in the first gene group), and where M represents total number of genes in expression matrix. Additional, suitable techniques of performing GSEA are known in the art and are contemplated for use in the methods described herein without limitation. In some embodiments, a GC signature is calculated by performing ssGSEA on expression data from a plurality of subjects, for example expression data from one or more cohorts of subjects. After calculation, the scores were scaled using rank estimation and median-scaling, which was important for removing undesirable batch effects and to enable all the datasets to be combined together. Median scaling consisted of estimating median and MAD (median absolute deviation) for each signature within each dataset, and applying the formula xi- median(x)/MAD(x). After GC TME signatures were calculated according to the above for multiple patients, unsupervised clustering was performed to generate GC TME clusters. To classify a new sample, it is grouped together with the dataset used to get the GC TME type. Scores are calculated for the sample and scaled together with the selected cohort. After that the sample type, can be predicted by applying a machine learning model (e.g., K-nearest neighbor, “knn”) trained on the scaled metacohort. In this example, inter-sample similarity was calculated using Pearson correlation. The distance matrix was converted into a graph where each sample formed a node and two nodes formed an edge with a weight equal to their Pearson correlation coefficient. Edges with weight lower than a specified threshold were removed. The Louvain community detection algorithm was applied to calculate graph partitioning into clusters. To mathematically determine the optimum weight threshold for observed clusters, minimum DaviesBouldin, maximum Calinski- Harabasz, and Silhouette techniques were employed. Separations with low-populated clusters (< 5% of samples) were excluded. This analysis resulted in the generation of five (5) GC TME signature clusters, corresponding to five (5) GC TME types. Example of Characterizing GC TME types Using the aforementioned approach on several publicly available cancer data sets, five distinct types of GC were observed (FIG.5A). To identify GC TME types, a meta-cohort of gene expression data was collected from public datasets. GC TME signatures comprising twenty gene group scores were used to estimate different biological processes in each of the samples. Genes included in each gene group are described in Table 1. To overcome batch effect from different datasets, rank estimation and median scaling transformation were used prior to clustering, which led to identification of the five GC TME types. Examples of processes for identifying GC TME types are described in FIG. 1. Using unsupervised clustering, five stable GC TME types were identified (FIG.5A): Immune Enriched/Non fibrotic (type B), Depleted (type D), Mesenchymal/EMT (type A), Fibrotic (type C), and “B cell-enriched” (type E). FIG.5B provides a heatmap of pairwise signature correlation for the gene groups listed in Table 1. Data indicate the gene group scores for the NK cells group, T cells group, B cells group, Treg group, MDSC group, CAF group, Proliferation rate group, and Lgr5 ISC group may facilitate typing the GC TME of a subject. Accordingly, in some embodiments, a GC TME signature may include gene group scores for these gene groups. Though, in other embodiments, one or more gene scores for one or more other gene groups may be used in addition to or instead of these gene group scores. GC TME type E is characterized by the following features: low or medium stromal/vascularized component (e.g., lower than GC TME types A and C), medium or high immune component (e.g., similar to GC TME type B), highest B cell signal (e.g., of all GC TME types), and low or medium neoplasm properties (e.g., low expression level of Proliferation rate and Oncogenes signatures, higher level of Tumor suppressors signature, relative to other GC TME types). In some embodiments, GC TME type is prognostic for patient outcome. An analysis between GC TME types was performed and compared to TCGA histological data. FIG.6 provides selected process signature comparisons across GC TME types. Data indicates that while GC TME types A and C have the highest Angiogenesis and stromal (CAF = Cancer- associated fibroblasts) signals, GC TME type E represents the highest B cells signal and similar T cell signals. FIG.7 provides an exemplary heatmap of gastric cancer TME type gene group signatures and cell deconvolution across the samples. For RNA-seq samples, high B cell content was also supported by a cell deconvolution algorithm-based analysis. This algorithm allows reconstructing cell composition from bulk RNA-seq data and estimating the percentage of different cell types (fibroblasts, B cells, T cells, macrophages, etc.). GC TME type E samples proved the highest B cells percentage (FIG.5A). Medians and cumulative distribution function (CDF) for each signature in each GC TME type are provided below in Tables 8 and 9. Table 8: Median signature values by TME types in Gastric Cancer
Table 9: Mean cumulative distribution function (CDF) of signatures values by TME types in Gastric Cancer
Using TCGA histology data, immune infiltration and stromal compartments were compared in samples belonging to different GC TME types (FIG.8A). Samples of GC TME types A and C had high stromal content. GC TME type D samples had desert immune, low fibroblast composition, and high tumor cellularity. GC TME type B and E samples, on the contrary, showed high immune infiltration. Remarkably, GC TME type E samples also showed the existence of germinative centers/tertiary lymphoid structures (TLSs) - ectopic lymphoid organs that develop in non-lymphoid tissues (shown by the arrow in FIG.8A). FIGs.8B-8F show graphic representations of relative cell type content of different GC TME types. FIG.8B shows a representation of the relative cell type content of GC TME type A, which is characterized by WNT-activation, and the prevalence of LGR5+ stem cells.; type A was also associated with a low tumor proliferation rate. Cancer-associated fibroblasts are often observed. Signs of epithelial-mesenchymal transition (EMT) were present. Subjects having GC TME type A have been observed to have a poor prognosis. FIG.8C shows a representation of the relative cell type content of GC TME type B, which is characterized by high levels of tumor-infiltrating immune cells, including cytotoxic effector cells. This type has the highest tumor mutational burden (TMB). High PD-L1 expression is commonly observed. This GC TME type is often responsive to immunotherapy and associated with good prognosis. FIG.8D shows a representation of the relative cell type content of GC TME type C, which is associated with high fibrosis and dense collagen formation. This type is also characterized by minimal lymphocyte infiltration (non-inflamed) with intense angiogenesis. Cancer-associated fibroblasts (CAF) are abundant. High levels of both protumor and antitumor cytokines have been observed. This GC TME type is associated with poor prognosis. FIG.8E shows a representation of the relative cell type content of GC TME type D, which is characterized by the highest percentage of malignant cells, while leukocyte/lymphocyte infiltration is only minimal or completely absent. A high tumor proliferation rate has been observed. This GC TME type is associated with good prognosis. FIG.8F shows a representation of the relative cell type content of GC TME type E, which is characterized by the presence of tertiary lymphoid structures (TLS), and high levels of immune infiltrate with a significant number of B cells. A low tumor proliferation rate has been observed. This GC TME type is associated with good prognosis. Certain GC TME types were found to be associated with malignant properties: Mesenchymal A type comprised the majority of the studied metastatic samples and was characterized by the highest signal of LGR5+ stem cell signature. TLSs have been observed in various cancers: colorectal cancer, lung cancer, clear-cell renal cell carcinoma, sarcoma, urothelial bladder cancer, and others. The existence of TLS may provide additional opportunities in treatment decision making. For example, it has been observed that TLS-positive samples in primary gastrointestinal stromal tumors demonstrated better postoperative outcomes. Analysis of overall survival (OS) and progression-free survival (PFS) revealed better prognosis for GC TME type E compared with stromal enriched and WNT activated GC TME types A and C (FIG.9). Samples of GC TME types B, E and D had the best overall survival rates. Example 2: Additional embodiments Association of STAD TME types with EBV, MSI, TMB Status GC is histologically classified into intestinal, diffuse and the mixed types, and into four molecular types based on genetic profiling (i.e., microsatellite instable (MSI), EBV positive, chromosomal instable, and genomically stable). Here, samples with various statuses of EBV, MSI, and tumor mutational burden (TMB) across the GC TME types were examined. FIG.10 shows comparison of MSS and MSI samples in different GC TME types. As shown in FIG.10, most MSI samples were located in GC TME type B (i.e., immune enriched), indicating that subjects having GC TME type B may have a higher likelihood of responding to therapies such as immunotherapies. FIGs.11A-11B show mutation burden across the GC TME types in the TCGA cohort. As shown in FIG.11A, immune enriched type has the highest mutation load (ML) in comparison to all other GC TME types. However, in the ACGR cohort, the highest malignant cell content (i.e., purity or cellularity) and ploidy were observed in the immune depleted type, GC TME type D (FIG.11B, left). Additional studies were conducted to examine the EBV status of the TCGA cohorts across all GC TME types. FIG.12 shows strong relationships between EBV-positive status (i.e., “1.0") and GC TME type B and E (immune enriched and B cell enriched, respectively). The overall results confirmed that subjects who have GC TME types B and E would be determined to have increased likelihood of having a good prognosis and/or progression-free survival (PFS). Example 3: Th17 and γδ T cells signatures for GC typing After identification of the five GC TME types, additional gene group scores were evaluated, including Th17 (T helper 17) and γδ T cells gene group scores; and gene group scores for Tumor suppressors, Oncogenes, MYC targets, Th2, and Th1. The additional gene groups used to produce the additional GC TME signatures are described in Table 2. Comparative analysis revealed higher γδ T cells signal in immune enriched GC TME types (B and E) and the lowest signal in immune desert subtype. Th17 was higher in all these three types and has the lowest signal in Mesenchymal, WNT-activated subtype A (FIG.14). The combination of the novel Th17 and γδ T cells signatures with the GC TME types of the TCGA cohort is shown in FIG.15. Dynamic changes of the GC TME types may correlate with response to chemotherapy. Example 4: Immunotherapy Immunotherapy for gastric cancer has shown promising results, indicating better response in Epstein-Barr virus (EBV)-positive samples or in microsatellite-unstable/instability (MSI) samples (or samples with high mutation burden) than other cancer types. The GC typing (particularly for types E and B) may identify responders to immunotherapy among a large population of patients having conventional biomarkers associated with an adverse response to immunotherapy (e.g., microsatellite stable (MSS) and EBV-negative). Analysis of the TCGA cohort revealed that the majority of EBV positive samples belonged to E and B types; MSI samples were also mostly located in type B (FIG.16). Indeed, 54 samples from a total 69 B-type samples in the TCGA cohort were EBV positive or MSI with high mutation burden. Fifteen samples are EBV negative and microsatellite stable (MSS) but still these samples may be better responders for immunotherapy. In type E more than a half of samples are EBV negative and MSS (FIG.16). Using a public dataset, response to immunotherapy was investigated in metastatic gastric cancer (2nd or 3rd line of pembrolizumab) across different GC TME types, considering their EBV and MSS status. It was observed that patients from types B and E had a higher Disease Control Rate (DCR): 9/9 for type B and 3/4 for type E, while other subtypes had lower: type A - 3 /6, type C - 4 /11 and type D – 1/4. Next, all patients with well-known markers for immunotherapy treatment were excluded: MSI samples and EBV positive samples. Interestingly, B and E types still included higher percentages of responders (FIG.17). All metrics were calculated for different groups and are presented in Table 10. Table 10
According to the data in FIGs.16 and 17, and Table 10, GC TME typing serves as a predictive parameter independent from MSI/MSS and EBV status. Although MSI and EBV-high patients are consistent responders to immunotherapy (Table 10), a significant percentage of MSS and EBV-low patients could still show better response rates if they belong to E- and B- subtypes (FIG.17). Since more than half of E-type patients from TCGA cohort were MSS and EBV- negative (FIG.16) GC typing may allow covering this large group of patients who previously escaped from the responder category. E- and B-type metastatic gastric cancer patients have a higher disease control rate (DCR) in response to immunotherapy (2nd or 3rd line of pembrolizumab), regardless of MSI and EBV status. All the five described subtypes were found in Cabazi-cohort (FIG.18). All subtypes have similar distribution of samples from gastric, GEJ and esophagus. The cohort comprises samples of different biopsy sites, including metastatic samples. Interestingly, the most metastatic samples (5/9) were identified as Mesenchymal, WNT-activated type (type A). In addition, these five type A metastatic samples have the highest signal of LGR5+ stem cell signature, hence the highest tumor stemness potential. Metastatic samples were also observed in types E and D. For nine samples from the Cabazi-cohort both pre- and post-treatment biopsies were sequenced in order to identify their GC TME type and analyze the impact of treatment on type- switching. Two of these samples retained their initial GC TME type after treatment (both samples had Immune desert D type). The other seven samples showed various GC TME type switching. Interestingly, the only one partial responder to cabazitaxel in this group changed fibrotic type C to Immune enriched type B (FIG.19). Table 11: Exemplary NCBI Accession Numbers for genes listed in Table 1.
Table 12: Exemplary NCBI Accession Numbers for genes listed in Table 2.
EQUIVALENTS Having thus described several aspects and embodiments of the technology set forth in the disclosure, it is to be appreciated that various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be within the spirit and scope of the technology described herein. For example, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described herein, and each of such variations and/or modifications is deemed to be within the scope of the embodiments described herein. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation many equivalents to the specific embodiments described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described. In addition, any combination of two or more features, systems, articles, materials, kits, and/or methods described herein, if such features, systems, articles, materials, kits, and/or methods are not mutually inconsistent, is included within the scope of the present disclosure. The above-described embodiments can be implemented in any of numerous ways. One or more aspects and embodiments of the present disclosure involving the performance of processes or methods may utilize program instructions executable by a device (e.g., a computer, a processor, or other device) to perform, or control performance of, the processes or methods. In this respect, various inventive concepts may be embodied as a computer readable storage medium (or multiple computer readable storage media) (e.g., a computer memory, one or more floppy discs, compact discs, optical discs, magnetic tapes, flash memories, circuit configurations in Field Programmable Gate Arrays or other semiconductor devices, or other tangible computer storage medium) encoded with one or more programs that, when executed on one or more computers or other processors, perform methods that implement one or more of the various embodiments described above. The computer readable medium or media can be transportable, such that the program or programs stored thereon can be loaded onto one or more different computers or other processors to implement various ones of the aspects described above. In some embodiments, computer readable media may be non-transitory media. The terms “program” or “software” are used herein in a generic sense to refer to any type of computer code or set of computer-executable instructions that can be employed to program a computer or other processor to implement various aspects as described above. Additionally, it should be appreciated that according to one aspect, one or more computer programs that when executed perform methods of the present disclosure need not reside on a single computer or processor, but may be distributed in a modular fashion among a number of different computers or processors to implement various aspects of the present disclosure. Computer-executable instructions may be in many forms, such as program modules, executed by one or more computers or other devices. Generally, program modules include routines, programs, objects, components, data structures, etc. that perform particular tasks or implement particular abstract data types. Typically the functionality of the program modules may be combined or distributed as desired in various embodiments. Also, data structures may be stored in computer-readable media in any suitable form. For simplicity of illustration, data structures may be shown to have fields that are related through location in the data structure. Such relationships may likewise be achieved by assigning storage for the fields with locations in a computer-readable medium that convey relationship between the fields. However, any suitable mechanism may be used to establish a relationship between information in fields of a data structure, including through the use of pointers, tags or other mechanisms that establish relationship between data elements. When implemented in software, the software code can be executed on any suitable processor or collection of processors, whether provided in a single computer or distributed among multiple computers. Further, it should be appreciated that a computer may be embodied in any of a number of forms, such as a rack-mounted computer, a desktop computer, a laptop computer, or a tablet computer, as non-limiting examples. Additionally, a computer may be embedded in a device not generally regarded as a computer but with suitable processing capabilities, including a Personal Digital Assistant (PDA), a smartphone, a tablet, or any other suitable portable or fixed electronic device. Also, a computer may have one or more input and output devices. These devices can be used, among other things, to present a user interface. Examples of output devices that can be used to provide a user interface include printers or display screens for visual presentation of output and speakers or other sound generating devices for audible presentation of output. Examples of input devices that can be used for a user interface include keyboards, and pointing devices, such as mice, touch pads, and digitizing tablets. As another example, a computer may receive input information through speech recognition or in other audible formats. Such computers may be interconnected by one or more networks in any suitable form, including a local area network or a wide area network, such as an enterprise network, and intelligent network (IN) or the Internet. Such networks may be based on any suitable technology and may operate according to any suitable protocol and may include wireless networks, wired networks or fiber optic networks. Also, as described, some aspects may be embodied as one or more methods. The acts performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed in which acts are performed in an order different than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments. All definitions, as defined and used herein, should be understood to control over dictionary definitions, definitions in documents incorporated by reference, and/or ordinary meanings of the defined terms. The indefinite articles “a” and “an,” as used herein in the specification and in the claims, unless clearly indicated to the contrary, should be understood to mean “at least one.” The phrase “and/or,” as used herein in the specification and in the claims, should be understood to mean “either or both” of the elements so conjoined, i.e., elements that are conjunctively present in some cases and disjunctively present in other cases. Multiple elements listed with “and/or” should be construed in the same fashion, i.e., “one or more” of the elements so conjoined. Other elements may optionally be present other than the elements specifically identified by the “and/or” clause, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc. As used herein in the specification and in the claims, the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements. This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified. Thus, as a non-limiting example, “at least one of A and B” (or, equivalently, “at least one of A or B,” or, equivalently “at least one of A and/or B”) can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc. In the claims, as well as in the specification above, all transitional phrases such as “comprising,” “including,” “carrying,” “having,” “containing,” “involving,” “holding,” “composed of,” and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transitional phrases “consisting of” and “consisting essentially of” shall be closed or semi-closed transitional phrases, respectively. The terms “approximately,” “substantially,” and “about” may be used to mean within ±20% of a target value in some embodiments, within ±10% of a target value in some embodiments, within ±5% of a target value in some embodiments, within ±2% of a target value in some embodiments. The terms “approximately,” “substantially,” and “about” may include the target value.
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