TREATMENT METHODS FOR PANCREATIC TUMORS

ASSOCIATED WITH THE WORST PROGNOSIS

CROSS-REFERENCE TO RELATED APPLICATION

[0001] This application claims priority to US provisional application serial no. 62/620,332 filed on January 22, 2018, which is incorporated herein by reference in its entirety as if fully set forth herein.

FIELD OF THE DISCLOSURE

[0002] The current disclosure provides treatment methods selective for pancreatic tumors associated with the worst prognosis of all pancreatic tumor subtypes identified to date. The treatment methods utilize cyclin-dependent kinase 7 (CDK7) inhibitors. The pancreatic subtypes susceptible to the treatments can be identified utilizing gene array panels and/or reduced surface expression of NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6).

REFERENCE TO SEQUENCE LISTING

[0003] The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 18-028-WO-PCT_ST25.txt. The text file is 68.6 KB, was created on January 22, 2019, and is being submitted electronically via EFS-Web.

BACKGROUND OF THE DISCLOSURE

[0004] Pancreatic cancer is the seventh highest cause of death from cancer worldwide. The cancer is highly lethal because it grows and spreads rapidly, and is often not diagnosed until late stages, when the cancer is already locally advanced or has spread to other parts of the body. Most pancreatic cancer begins in the cells that line the ducts of the pancreas. Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths in the United States, with a 5-year survival rate of <5% and a median survival of 6 months.

[0005] Surgery can offer a path to cure pancreatic cancer, but given the cancer’s aggressive nature, surgery is only a possible treatment route for 20% of new cases. Chemotherapy and radiotherapy are other options to manage pancreatic cancer but have historically provided limited benefit at best. Numerous clinical trials have failed to identify therapeutic agents that are effective for PDAC patients. One reason for these failures may be because significant molecular differences between PDAC tumors introduce heterogeneity into PDAC populations.

[0006] Analysis of global gene expression in pancreatic tumors and tumor cell lines has allowed classification of PDAC into three subtypes based upon a 62-gene signature called PDAssigner: classical, exocrine-like, and quasi-mesenchymal-PDA (QM-PDA) (Collisson EA et al. (2011) Nature medicine 17(4): 500-503). The three subtypes are prognostic for survival after tumor resection, with individuals having classical subtype tumors faring the best and individuals having QM-PDA subtype tumors faring the worst. Further, whole genome sequencing and gene expression analysis in a more recent study identified four subtypes: pancreatic progenitor, immunogenic, abnormally differentiated endocrine exocrine (ADEX), and squamous (Bailey P et al. (2016) Nature 531(7592): 47-52). Similar to the Collisson 2011 study, the four subtypes in the Bailey 2016 study were prognostic for patient survival and indicated that: the pancreatic progenitor and immunogenic subtypes resembled the classical subtype; the ADEX subtype resembled the exocrine-like subtype; and the squamous subtype resembled the QM-PDA subtype. As seen for the QM-PDA subtype in the Collisson 2011 study, the prognosis for survival for patients having squamous subtype tumors was the poorest compared to the other subtypes. While these genetic underpinnings of PDAC subtypes are being elucidated, there remains a need to identify drugs that are effective to target and treat PDAC tumor subtypes.

SUMMARY OF THE DISCLOSURE

[0007] The current disclosure provides that cyclin-dependent kinase 7 (CDK7) inhibitors are effective to target and treat PDAC subtypes with currently the poorest prognosis. In particular embodiments, the pancreatic tumors that can be effectively targeted and treated with CDK7 inhibitors are pancreatic ductal adenocarcinoma (PDAC), with the subtype QM-PDA, as characterized by PDAssigner, a 62-gene panel. In particular embodiments, the PDAC tumor subtype is squamous. In particular embodiments, the PDAC tumor subtype is characterized by reduced expression of the NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6 ^|0W ). In particular embodiments, the CDK7 inhibitor is a selective covalent inhibitor of CDK7 selected from THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001. Thus, the disclosure provides therapies that can be selectively targeted to PDAC subtypes with poor prognosis for survival.

BRIEF DESCRIPTION OF THE DRAWINGS

[0008] FIGs. 1A-1 E (FIG. 1A), Model for SIRT6 loss in Pancreatic ductal adenocarcinoma (PDAC) pathogenesis. (FIG. 1 B), Relative expression of SIRT6 as measured by real-time PCR (RT-PCR) in the indicated PDAC cell lines. Black bars = Classical /SIRT6 ^high PDAC cell lines, grey bars = QM-PDA /SIRT6 ^|0W PDAC cell lines. (FIG. 1C), Proliferation curves for quasi-mesenchymal (QM)- PDA /SIRT6 ^|0W (grey), compared with Classical /SIRT6 ^high (black) PDAC cell lines treated with increasing doses of Gemcitabine (FIG. 1C) and THZ1 (FIG. 1 D). (FIG. 1 E), THZ1 IC50 of THZ1 in Classical versus QM-PDA (left) and SIRT6 ^hi9h versus SIRT6 ^|0W PDAC cell lines.

[0009] FIGs. 2A-2D. (FIG. 2A), Western blots for RNA polymerase II (RNAPII) phosphorylation of serine 5 (PS5) and 7 (PS7) and cleaved caspase 3 (CC3) in QM-PDA /SIRT6 ^|0W (grey), compared with Classical /SIRT6 ^hi9h (black) treated with increasing doses of THZ1. (FIG. 2B), Apoptosis assay showing % apoptosis in QM-PDA /SIRT6 ^|0W (grey) and Classical /SIRT6 ^hi9h (black) as measured by Annexin V & PI positive cells with increasing doses of THZ1. White and black bars = Classical /SIRT6 ^h ' ^9h SUIT2 cell line, light and dark grey bars = QM-PDA /SIRT6 ^|0W Panc3.27 cell line. (FIG. 2C), Proliferation of QM-PDA /SIRT6 ^|0W cells with knockout of CDK7 (grey) compared to vector (sgEGFP) control. (FIG. 2D), Western blot showing partial knockout of CDK7.

[0010] FIGs. 3A-3D. Western blots for MYC and CC3 (FIG. 3A) and RT-PCR for MYC (FIG. 3B) in QM-PDA /SIRT6 ^|0W (grey), compared with Classical /SIRT6 ^hi9h (black) PDAC cell lines treated with increasing treatment time of THZ1. In FIG. 3B, Black bars = Classical /SIRT6 ^hi9h ASPC-1 cell line, checkered bars = Classical /SIRT6 ^hi9h SUIT2 cell line, dark grey bars = QM-PDA /SIRT6 ^|0W BxPC3 cell line, light grey bars = QM-PDA /SI RT6 ^|0W Panc3.27 cell line. (FIG. 3C), Proliferation of QM-PDA /SIRT6 ^|0W cells with knockout of MYC (grey) compared to vector (sgEGFP) control. (FIG. 3D), Western blot showing knockout of MYC.

[0011] FIGs. 4A, 4B. (FIG. 4A), QM-PDA /SIRT6 ^|0W cell line, BxPc3 xenograft tumor volume after treatment with 10mg/kg THZ1 (grey) by IP compared to DMSO control (black). (FIG. 4B), Tumor weight of DMSO or THZ1 treated BxPc3 xenografts.

[0012] FIGs. 5A, 5B. (FIG. 5A), RNA-seq data in QM-PDA /SIRT6 ^|0W cell lines (Panc3.27 and BxPc3) and Classical /SIRT6 ^hi9h cell line (SUIT2) comparing THZ1 treatment (100ng for 6hrs) to DMSO control. Venn diagram showing significantly downregulated genes from each comparison, segregating genes by logFC. (FIG. 5B), Gene set enrichment analysis (GSEA) plots. Note: the top pathway enriched was the same for both QM-PDA /SIRT6 ^|0W cell lines, but this gene set was not enriched in the Classical /SIRT6 ^hi9h cell line.

[0013] FIGs. 6A-6D. Prior art heat maps from Collisson et al. (2011) (FIGs. 6A-6C) and Bailey et al. (2016) (FIG. 6D) showing: (FIG. 6A), three subtypes of PDAC in distance-weighted discrimination (DWD)-merged UCSF and GSE15471 (Badea L et al. (2008) Hepatogastroenterology 55: 2016-2027) PDAC microarray data sets using the PDAssigner gene set. (FIG. 6B), three subtypes of PDAC in a DWD-merged core clinical and human PDAC cell line microarray data sets using the PDAssigner gene set. (FIG. 6C) three subtypes of PDAC in a DWD-merged core clinical and mouse PDA cell line microarray data sets using PDAssigner gene set. (FIG. 6D) overlap of the 4 classes identified in Bailey et al. (2016) and Collisson et al. (2011) classification. The bars on the side of FIGs. 6A-6C denote PDAssigner genes upregulated in classical (violet), QM-PDA (gray) and exocrine-like (green).

[0014] FIG. 7 shows representative sequences supporting the disclosure (SEQ ID NOs: 1-22).

DETAILED DESCRIPTION

[0015] Pancreatic cancer is the seventh highest cause of death from cancer worldwide. The cancer is highly lethal because it grows and spreads rapidly, and is often not diagnosed until late stages, when the cancer is already locally advanced or has spread to other parts of the body. Most pancreatic cancer begins in the cells that line the ducts of the pancreas. Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related deaths in the United States, with a 5-year survival rate of <5% and a median survival of 6 months.

[0016] Surgery can offer a path to cure pancreatic cancer, but given the cancer’s aggressive nature, surgery is only a possible treatment route for 20% of new cases. Chemotherapy and radiotherapy are other options to manage pancreatic cancer but have historically provided limited benefit at best. Numerous clinical trials have failed to identify therapeutic agents that are effective for PDAC patients. One reason for these failures may be because significant molecular differences between PDAC tumors introduce heterogeneity into PDAC populations.

[0017] Analysis of global gene expression in pancreatic tumors and tumor cell lines has allowed classification of PDAC into three subtypes based upon a 62-gene signature called PDAssigner: classical, exocrine-like, and quasi-mesenchymal-PDA (QM-PDA) (Collisson EA et al. (2011) Nature medicine 17(4): 500-503). The three subtypes are prognostic for survival after tumor resection, with individuals having classical subtype tumors faring the best and individuals having QM-PDA subtype tumors faring the worst. Further, whole genome sequencing and gene expression analysis in a more recent study identified four subtypes: pancreatic progenitor, immunogenic, abnormally differentiated endocrine exocrine (ADEX), and squamous (Bailey P et al. (2016) Nature 531(7592): 47-52). Similar to the Collisson 2011 study, the four subtypes in the Bailey 2016 study were prognostic for patient survival and indicated that: the pancreatic progenitor and immunogenic subtypes resembled the classical subtype; the ADEX subtype resembled the exocrine-like subtype; and the squamous subtype resembled the QM-PDA subtype. The pancreatic progenitor subtype includes preferential expression of genes involved in early pancreatic development, such as Forkhead Box A2 (FOXA2), Forkhead Box A3 (FOXA3), Pancreatic and Duodenal Homeobox 1 (PDX1), and (Motor Neuron and Pancreas Homeobox 1 (MNX1), while the immunogenic subtype includes upregulated immune networks including pathways involved in acquired immune suppression. The ADEX subtype includes upregulation of genes that regulate networks involved in KRAS activation (gene encoding K-Ras GTPase involved in RAS/MAPK pathway), exocrine (e.g., Nuclear Receptor subfamily 5 group A member 2 ( NR5A2 ) and Recombination Signal Binding Protein for Immunoglobulin Kappa J Region Like (, RBPJL )), and endocrine differentiation (e.g., Neuronal Differentiation 1 ( NEUROD1 ) and NK2 Homeobox 2 ( NKX2-2 )). As seen for the QM-PDA subtype in the Collisson 2011 study, the prognosis for survival for patients having squamous subtype tumors was the poorest compared to the other subtypes. While these genetic underpinnings of PDAC subtypes are being elucidated, there remains a need to identify drugs that are effective to target and treat PDAC tumor subtypes.

[0018] The current disclosure provides that cyclin-dependent kinase 7 (CDK7) inhibitors are effective to target and treat the PDAC subtypes with currently the poorest prognosis. In particular embodiments, the pancreatic tumors that can be effectively targeted and treated with CDK7 inhibitors are pancreatic ductal adenocarcinoma (PDAC), with the subtype QM-PDA, as characterized by PDAssigner, a 62-gene panel. In particular embodiments, the PDAC tumor subtype is squamous, as characterized by prevalence of adenosquamous carcinomas and four core gene programs (GP2, GP3, GP4, and GP5). In particular embodiments, the PDAC tumor subtype is characterized by reduced expression of the NAD+-dependent histone deacetylase Sirtuin 6 (SIRT6 ^|0W ). In particular embodiments, the CDK7 inhibitor is a selective covalent inhibitor of CDK7 selected from THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001. Thus, the disclosure provides therapies that can be selectively targeted to PDAC subtypes with poor prognosis for survival. As disclosed herein, the selective CDK7 inhibitors are not indicated for or effective to treat other PDAC subtypes (i.e., classical, exocrine-like, pancreatic progenitor, immunogenic, or ADEX) or PDAC with SIRT6 ^h '9 ^h .

[0019] Aspects of the current disclosure are now described in more detail as follows: (i) the QM- PDA subtype; (ii) the squamous subtype; (iii) the SIRT6 subtype; (iv) CDK7 and its inhibitors; (v) L-Myc inactivators; (vi) compositions; (vii) methods of use; and (viii) kits.

[0020] (i) The QM-PDA subtype. As discussed above, a 62-gene panel called PDAssigner can be used to identify three PDAC subtypes: classical, exocrine-like, and QM-PDA. The classical subtype has high expression of adhesion-associated and epithelial genes, and the QM-PDA sub- type shows high expression of mesenchyme-associated genes. The exocrine-like subtype shows relatively high expression of tumor cell-derived digestive enzyme genes (Collison et al. (2011), supra). The 62 genes are listed in Table 1.

[0021] Table 1. List of 62 genes present in PDAssigner.

Adapted from Collisson et al. (2011), supra.

[0022] In particular embodiments, a QM-PDA subtype of PDAC can be identified by the upregulation of one or more genes selected from those listed in Table 2 relative to a reference tissue or sample. The reference can include a different PDAC subtype or a healthy tissue.

[0023] Table 2. Exemplary genes from PDAssigner that can be upregulated in QM-PDA subtype of PDAC.

[0024] In particular embodiments, a QM-PDA subtype of PDAC can be identified by the upregulation of one or more genes selected from ones listed in Table 2 and normal or downregulated expression of one or more genes selected from those listed in Table 3 relative to a reference tissue or sample. The reference can include a different PDAC subtype or a healthy tissue.

[0025] Table 3. Exemplary genes from PDAssigner that can be upregulated in classical or exocrine like, but normal or downregulated in QM-PDA subtype of PDAC.

[0026] In particular embodiments, up- and downregulation of one or more genes of PDAssigner can be assayed by quantitative Northern blot, quantitative reverse transcription (RT)-PCR, real time quantitative RT-PCR, oligonucleotide or cDNA microarrays, EST sequencing, RNA sequencing, differential display, SAGE (Serial Analysis of Gene Expression), RAGE (Rapid Analysis of Gene Expression), MPSS (Massively Parallel Signature Sequencing), FISH (Fluorescence In Situ Hybridization) and oligonucleotide bead arrays.

[0027] In particular embodiments, up- and downregulation of one or more genes of PDAssigner can be assayed by gene expression microarrays as described in Collisson et al. (2011), supra. A representative protocol to determine gene expression from microarrays disclosed in Collisson et al. (2011) is the following: After tissue dissection and processing, RNA from tumor tissues can be extracted from formalin fixed, paraffin embedded dissected tissues and processed using a phenol- chloroform technique (Response Genetics, Los Angeles, CA: U.S. 6,248,535). Human cell line mRNA can be extracted from exponentially growing cultures using RNAeasy columns (Qiagen, Germantown, MD). After two rounds of RNA amplification, cRNA from PDAC tissue samples and/or human PDAC cell lines can be synthesized and hybridized to a microarray, e.g., Affymetrix Human GeneChip® U133Plus2.0 (Affymetrix, Santa Clara, CA).

[0028] Processing of microarrays can be done in the following manner. Robust multiarray analysis (RMA) can be performed using the affy package from the R-based Bioconductor Project (Gentleman RC et al. (2004) Genome Biol 5: R80). The quality of microarrays can be assessed using normalized unsealed standard error (NUSE) (Bolstad BM et al. Quality control of Affymetrix GeneChip data in Bioinformatics and Computational Biology Solutions using R and Bioconductor (eds. Gentleman R et al. (Springer, New York, 2005)). Arrays with a NUSE score of > 1+0.25 or < 1-0.25 can be removed.

[0029] Statistical analyses can include the following. The coefficient of variation of a variable (x) can be defined as standard_deviation(x)/mean(x). The usual unbiased estimators can be used to compute the standard deviation and the mean of metagene expression (for each sample and each metagene) across initial conditions. The coefficient of variation is an indicator of consistency except when mean(x) is extremely small. To circumvent the small-mean-value problem, the coefficient of variation as a least-squares estimate of the slope of mean(x) vs. standard deviation(x) can be computed for each metagene across all of the samples, yielding one coefficient of variation for each metagene. The Collison data provided compelling evidence in support of k = 3 clusters for merged core clinical datasets. The three pertinent coefficients of variation were: 0.047, 0.038 and 0.058 (i.e. one for each of the 3 metagenes). Hence, the results from different initial conditions (or model fits) were within roughly 6% across all 3 metagenes.

[0030] (ii) The squamous subtype. In particular embodiments, CDK7 inhibitors are effective to target and treat the squamous subtype of PDAC tumors. Four subtypes of PDAC tumors were resolved by analysis of RNA seq data for 96 tumors with high epithelial content and array-based mRNA expression profiles of 232 PDACs encompassing the full range of tumor cellularity (Bailey P et al. (2016), supra). The squamous subtype is characterized by poor prognosis. In particular embodiments, the squamous subtype is characterized by four core gene programs (GP): (1) GP2, including gene networks involved in squamous differentiation, upregulated expression of TR63DN (an isoform of tumor protein p63, a member of the p53 family of transcription factors) and its target genes, inflammation, hypoxia response, and metabolic reprogramming; (2) GP3: genes involved in extracellular matrix (ECM) and transforming growth factor beta (TGF-b) signaling; (3) GP4: genes involved in proliferation; and (4) GP5: genes involved in MYC pathway activation, autophagy, and RNA processing. Many of these genes are highly expressed in the C2-squamous- like class of tumors of breast, bladder, lung and head and neck cancer defined in the Cancer Genome Atlas (TCGA) pan-cancer studies (Hoadley KA et al. (2014) Cell 158: 929-944). In particular embodiments, the squamous subtype of PDAC is associated with mutations in TP53 (tumor suppressor protein p53) and KDM6A (lysine demethylase 6A), which interacts with activating signal cointegrator-2 (ASC-2)-containing (ASCOM) complex constituents MLL2 (Mixed Lineage Leukemia 2, a lysine methyltransferase 2D) and MLL3 (Mixed Lineage Leukemia 3, a histone H3 lysine 4 (H3K4) lysine methyl transferase). In particular embodiments, the squamous subtype of PDAC is associated with high TR63DN expression and its target genes. In particular embodiments, squamous tumors are enriched for activated a6b1 and a6b4 integrin signaling, and activated EGF signaling. In particular embodiments, the squamous subtype of PDAC is associated with hypermethylation and concordant downregulation of genes that govern pancreatic endodermal cell-fate determination (e.g., PDX1 (Pancreatic And Duodenal Homeobox 1 (transcriptional activator of several genes, including insulin, somatostatin, glucokinase, islet amyloid polypeptide, and glucose transporter type 2); MNX1 (Motor Neuron And Pancreas Homeobox 1 , a transcription factor); GATA6 (GATA Binding Protein 6, a member of a small family of zinc finger transcription factors that play an important role in the regulation of cellular differentiation and organogenesis during vertebrate development); HNF1B (HNF1 Homeobox B, a member of the homeodomain-containing superfamily of transcription factors that functions in nephron development and regulates development of the embryonic pancreas)). Thus, in particular embodiments, the squamous subtype of PDAC is characterized by downregulation of expression of one or more genes or corresponding proteins selected from PDX1 , MNX1 , GATA6, and HNF1 B.

[0031] In particular embodiments, the one or more pathways involved in squamous differentiation, upregulated expression of TR63DN and its target genes, inflammation, hypoxia response, and metabolic reprogramming includes genes associated with: direct p53 effectors; a6b1 and a6b4 integrin signaling; transcriptional targets of r63DN; EGF receptor (ErbB1) signaling pathway; cytokine-cytokine receptor interaction; p73 transcription factor network; PDGFR-b signaling pathway; PI3K-Akt signaling pathway; and/or HIF-1-a transcription factor network. In particular embodiments, the squamous subtype of PDAC can be identified by the upregulation of one or more genes listed in Table 4.

[0032] Table 4. Exemplary genes associated with core gene program GP2 (from Bailey et al. 2016, supra) that can be upregulated in the squamous subtype of PDAC

[0033] In particular embodiments, the one or more pathways involved in ECM and TGF-b signaling includes genes associated with: TGF-b signaling pathway; signaling by PDGF; signaling by VEGF; Ras signaling pathway; focal adhesion; integrin signaling pathway; extracellular matrix organization; ECM-receptor interaction; PI3K-Akt signaling pathway; urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling; basal cell carcinoma; Wnt signaling network; and/or angiopoietin receptor Tie2-mediated signaling. In particular embodiments, the squamous subtype of PDAC can be identified by the upregulation of one or more genes listed in Table 5.

[0034] Table 5. Exemplary genes associated with core gene program GP3 (from Bailey et al. 2016, supra) that can be upregulated in the squamous subtype of PDAC

[0035] In particular embodiments, the one or more pathways involved in proliferation includes genes associated with: mitotic prophase; aurora B signaling; S phase; meiotic synapsis; mitotic prometaphase; ATR signaling pathway; cell cycle checkpoints; DNA damage/telomere stress induced senescence; cell cycle; mitotic G1-G1/S phases; synthesis of DNA; E2F transcription factor network; and/or DNA replication. In particular embodiments, the squamous subtype of PDAC can be identified by the upregulation of one or more genes listed in Table 6.

[0036] Table 6. Exemplary genes associated with core gene program GP4 (from Bailey et al. 2016, supra) that can be upregulated in the squamous subtype of PDAC

[0037] In particular embodiments, the one or more pathways involved in MYC pathway activation, autophagy, and RNA processing includes genes associated with: targets of C-MYC transcriptional activation; proteasome; regulation of mRNA stability by proteins that bind AU-rich elements; mitotic metaphase and anaphase; synthesis of DNA; protein folding; mitochondrial protein import; regulation of DNA replication; processing of capped intron-containing pre-mRNA; ribosome; metabolism of amino acids and derivatives; ribosome biogenesis in eukaryotes; and/or spliceosome. In particular embodiments, the squamous subtype of PDAC can be identified by the upregulation of one or more genes listed in Table 7.

[0038] Table 7. Exemplary genes associated with core gene program GP5 (from Bailey et al. 2016, supra) that can be upregulated in the squamous subtype of PDAC

Symbol;Acc:HGNC:9536]

[0039] In particular embodiments, up- and downregulation of one or more genes associated with the squamous subtype of PDAC tumors can be assayed by RNA sequencing (RNA seq) and/or mRNA expression microarrays as described in Bailey et al. (2016), supra. A representative protocol for RNA seq disclosed in Bailey et al. (2016) is the following: Total RNA library preparation. RNA Seq libraries can be generated using the lllumina TruSeq Stranded Total RNA LT sample preparation kit (with Ribo-Zero Gold) (lllumina, San Diego, CA, Part no. RS-122-2301 and RS- 122-2302), according to the standard manufacturer’s protocol (Part no. 15031048 Rev. D April 2013), except they can be made in an automated high-throughput fashion using Perkin Elmer’s (Waltham, MA) Sciclone G3 NGS Workstation (Product no. SG3-31020-0300). The ribosomal depletion step can be performed on 1 pg of total RNA using Ribo-Zero Gold before a heat fragmentation step aimed at producing libraries with an insert size between 120-200 bp. cDNA can then be synthesized from the enriched and fragmented RNA using Superscript II Reverse Transcriptase (Invitrogen, Waltham, MA, Catalog no. 18064) and random primers. The resulting cDNA can be converted into double-stranded DNA in the presence of dUTP to prevent subsequent amplification of the second strand and thus maintain the strandedness of the library. Following 3' adenylation and adaptor ligation, libraries can be subjected to 15 cycles of PCR to produce RNA seq libraries ready for sequencing. Prior to sequencing, RNA seq libraries can be qualified via the Perkin Elmer LabChip GX with the DNA High Sensitivity LabChip kit (Perkin Elmer, Waltham, MA, Part no. CLS760672). Quantification of libraries for clustering can be performed using the KAPA Library Quantification Kit - lllumina/Universal (KAPA Biosystems, Charlestown, MA, Part no. KK4824) in combination with the Life Technologies (Waltham, MA) Viia 7 real time PCR instrument.

[0040] Library sequencing. Libraries can be sequenced using the lllumina HiSeq 2000/2500 system with TruSeq SBS Kit v3 - HS (200-cycles) reagents (lllumina, San Diego, CA, Part no. FC-401-3001) to generate paired-end 101 bp reads. RNA-seq analysis. Sequencing reads can be mapped to transcripts corresponding to ensemble 70 annotations using RSEM34. RSEM data can be normalized using TMM (weighted trimmed mean of M-values) as implemented in the R package‘edgeR’. For downstream analyses, normalized RSEM data are converted to counts per million (c.p.m.) and log2 transformed (Robinson MD et al. (2010) Bioinformatics 26: 139-140). Genes without at least 1 c.p.m. in 20% of the sample can be excluded from further analysis.

[0041] A representative protocol for microarray analysis disclosed in Bailey et al. (2016) is the following: Tumor RNA can be assayed using Human HT-12 v4 Expression BeadChips as per manufacturer’s instructions (lllumina, San Diego, CA) and analyzed as previously described (Nones K et al. (2014) Int. J. Cancer 135: 1110-1118). Batch correction can be performed using the R package‘sva’ (Leek JT et al. (2012) Bioinformatics 28: 882-883).

[0042] Additional representative protocols for microarray analysis disclosed in Bailey et al. (2016) are discussed below.

[0043] Pan-cancer 12 data and squamous assignment. Platform corrected input data can be obtained from Synapse as part of the Pan-Cancer 12 data freeze (syn1715755) (Hoadley et al. (2014), supra). Pan-cancer 12 subtype assignments can also be obtained from Synapse (syn1889916) and sample sizes, as indicated, used for statistical comparisons.

[0044] (iii) The SIRT6 subtype. In particular embodiments, CDK7 inhibitors are effective to target and treat PDAC tumors with down-regulated SIRT6. Sirtuin 6 (SIRT6) is a nicotinamide adenine dinucleotide (NAD)+-dependent histone deacetylase that removes acetyl groups from histone 3 lysine 9 (H3K9) and histone 3 lysine 56 (H3K56) motifs and has pleiotropic functions including glucose homeostasis, maintenance of genome stability, and suppression of cellular transformation. SIRT6 inactivation accelerates PDAC progression and metastasis via upregulation of Lin28b, a negative regulator of the let-7 microRNA. SIRT6 loss results in histone hyperacetylation at the Lin28b promoter, Myc recruitment, and pronounced induction of Lin28b and downstream let-7 target genes, HMGA2, IGF2BP1 , and IGF2BP3 (Kugel S et al. (2016) Cell 165, 1401-1415).

[0045] Assays to measure expression of SIRT6 mRNA include gene expression assays described above. Assays to measure SIRT6 protein include quantitative Western blot, ELISA, 2D gels, gas or liquid chromatography, mass spectrometry, and immunohistochemistry.

[0046] In particular embodiments, the level of SIRT6 protein can be assayed by immunohistochemistry. In particular embodiments, immunohistochemistry can be performed as described in Fitamant et al. (2015) Cell Reports 10(10): 1692-1707 and Kugel et al. (2016), supra.

[0047] A representative immunohistochemistry protocol is the following: Tissue samples can be fixed overnight in 4% buffered formaldehyde, embedded in paraffin, and sectioned (5 pm thickness). Unstained slides can be deparaffinized in xylenes (two treatments, 3 min each), rehydrated sequentially in ethanol (2 min in 100%, 2 min in 95%, 2 min in 80%), and washed for 3 min in water. Slides can be incubated for 20 min with 3% H ₂ O ₂ at room temperature to block endogenous peroxidase activity and rinsed twice with water (3 min each). Endogenous peroxidase activity can be blocked by incubating deparaffinized tissue sections with 3% Hydrogen Peroxide (20 min; Fisher Scientific, Waltham, MA), and antigen retrieval can be performed by boiling in 10 mM sodium citrate buffer (20 min, 95°C, pH 6). Sections can be blocked 1 hour in TBS-0.05 % Tween 20 (Fisher Scientific, Waltham, MA)-10% Normal Goat Serum (Cat#5425, Cell Signaling Technology, Danvers, MA), and incubated overnight at 4°C with primary antibody. A primary anti-SIRT6 antibody that can be used is a rabbit monoclonal D8D12 antibody available from Cell Signaling Technology, Danvers, MA (Cat#12486). The anti-SIRT6 antibody can be used at a dilution of 1 :300 for mouse tissues and 1 :200 for human tissues. Specimens can be then washed three times for 3 min each in PBST and incubated with biotinylated secondary antibodies (1 :200, Vector Laboratories, Burlingame, CA) in blocking solution for 45 min at room temperature, followed by catalyzed signal amplification using the Vectastain Elite ABC kit (30 min; Vector Laboratories, Burlingame, CA). Specimens can then be washed three times in TBS-0.05 % Tween 20 and treated with ABC reagent (Cat#PK-6100, Vectastain ABC kit, Vector Laboratories, Burlingame, CA) for 30 min, followed by three washes for 3 min each. Finally, slides can be stained for peroxidase for 1-2 min with the DAB (di-aminebenzidine) substrate kit (SK-4100, Vector Laboratories, Burlingame, CA), washed with water and counterstained with haematoxylin. Stained slides can be photographed with an Olympus DP72 microscope. Immunohistochemistry can be scored semi quantitatively, in a blinded fashion by a pathologist on a 0 (no staining) to 3 (strongest intensity) scale based on the intensity of reactivity. A score of 0 can be considered SIRT6 ^|0W , while scores of 1-3 can be considered SIRT6 ^hi9h .

[0048] One of ordinary skill in the art will appreciate that measuring expression of genes of PDAssigner, genes associated with gene networks characterizing the squamous subtype of PDAC, or SIRT6 can include measuring the expression of a gene or measuring the amount of its encoded protein in the methods of the present disclosure.

[0049] In particular embodiments, one of ordinary skill in the art can determine sequences of genes and proteins associated with PDAssigner or the squamous subtype of PDAC. The following representative examples are provided: HK2 (QM-PDA subtype, SEQ ID NOs: 1 and 2), MUC13 (classical subtype, SEQ ID NOs: 3 and 4), PNLIP (exocrine-like subtype, SEQ ID NOs: 5 and 6), r63DN (upregulated in squamous subtype of PDAC, SEQ ID NOs: 7-16), PDX1 (downregulated in squamous subtype of PDAC, SEQ ID NOs: 17 and 18), and GATA6 (downregulated in squamous subtype of PDAC, SEQ ID NOs: 19 and 20).

[0050] A gene can refer to a unit of inheritance that occupies a specific locus on a chromosome and includes transcriptional and/or translational regulatory sequences and/or a coding region and/or non-translated sequences (/.e., introns, 5' and 3' untranslated sequences). In particular embodiments, genes can include mRNA, cDNA and coding sequences. The term further can include all introns and other DNA sequences spliced from the mRNA transcript, along with variants resulting from alternative splice sites. Nucleic acid sequences encoding proteins can be DNA or RNA that directs the expression of protein or RNA. These nucleic acid sequences may be a DNA strand sequence that is transcribed into RNA or an RNA sequence that is translated into protein. The nucleic acid sequences include both the full-length nucleic acid sequences as well as non-full-length sequences derived from the full-length protein or RNA. In particular embodiments, the term“gene” includes various sequence polymorphisms, mutations, and/or sequence variants. In particular embodiments, the sequence polymorphisms, mutations, and/or sequence variants do not affect the function of the encoded transcript. A coding sequence is any nucleotide sequence that contributes to the code for the product of a gene. A non-coding sequence thus refers to any nucleic acid sequence that does not contribute to the code for the product of a gene. In particular embodiments, genes may include not only coding sequences but also non-coding regulatory regions such as promoters, enhancers, and termination regions.

[0051] Variants of gene and protein sequences disclosed or described herein are also included. In particular embodiments, a protein can include one or more insertions, one or more deletions, one or more amino acid substitutions (e.g., conservative amino acid substitutions or non conservative amino acid substitutions), or a combination of the above-noted changes, when compared with the disclosed or described proteins (e.g., SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, and 22). An insertion, deletion or substitution may be anywhere in a protein disclosed or described herein, including at the amino- or carboxy-terminus or both ends of this region, provided that the expression of the modified protein can still be used to determine whether a PDAC subject has QM-PDA PDAC, squamous PDAC, or SIRT6 ^low PDAC. A“conservative substitution” involves a substitution found in one of the following conservative substitutions groups: Group 1 : Alanine (Ala), Glycine (Gly), Serine (Ser), Threonine (Thr); Group 2: Aspartic acid (Asp), Glutamic acid (Glu); Group 3: Asparagine (Asn), Glutamine (Gin); Group 4: Arginine (Arg), Lysine (Lys), Histidine (His); Group 5: Isoleucine (lie), Leucine (Leu), Methionine (Met), Valine (Val); and Group 6: Phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp).

[0052] Additionally, amino acids can be grouped into conservative substitution groups by similar function or chemical structure or composition (e.g., acidic, basic, aliphatic, aromatic, sulfur- containing). For example, an aliphatic grouping may include, for purposes of substitution, Gly, Ala, Val, Leu, and lie. Other groups containing amino acids that are considered conservative substitutions for one another include: sulfur-containing: Met and Cysteine (Cys); acidic: Asp, Glu, Asn, and Gin; small aliphatic, nonpolar or slightly polar residues: Ala, Ser, Thr, Pro, and Gly; polar, negatively charged residues and their amides: Asp, Asn, Glu, and Gin; polar, positively charged residues: His, Arg, and Lys; large aliphatic, nonpolar residues: Met, Leu, lie, Val, and Cys; and large aromatic residues: Phe, Tyr, and Trp. Additional information is found in Creighton (1984) Proteins, W.H. Freeman and Company.

[0053] Variants of the protein or nucleic acid sequences disclosed herein also include sequences with at least 70% sequence identity, 80% sequence identity, 85% sequence, 90% sequence identity, 95% sequence identity, 96% sequence identity, 97% sequence identity, 98% sequence identity, or 99% sequence identity to a protein or nucleic acid sequence described or disclosed herein.

[0054] “% sequence identity” refers to a relationship between two or more sequences, as determined by comparing the sequences. In the art, "identity" also means the degree of sequence relatedness between sequences as determined by the match between strings of such sequences. "Identity" (often referred to as "similarity") can be readily calculated by known methods, including those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, NY (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, NY (1994); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, NJ (1994); Sequence Analysis in Molecular Biology (Von Heijne, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Oxford University Press, NY (1992). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR, Inc., Madison, Wisconsin). Multiple alignment of the sequences can also be performed using the Clustal method of alignment (Higgins and Sharp CABIOS, 5, 151- 153 (1989) with default parameters (GAP PENALTY=10, GAP LENGTH PENALTY=10). Relevant programs also include the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wisconsin); BLASTP, BLASTN, BLASTX (Altschul, et al., J. Mol. Biol. 215:403-410 (1990); DNASTAR (DNASTAR, Inc., Madison, Wisconsin); and the FASTA program incorporating the Smith- Waterman algorithm (Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992, 111-20. Editor(s): Suhai, Sandor. Publisher: Plenum, New York, NY. Within the context of this disclosure it will be understood that where sequence analysis software is used for analysis, the results of the analysis are based on the "default values" of the program referenced. "Default values" will mean any set of values or parameters, which originally load with the software when first initialized.

[0055] "Up-regulation" or“up-regulated” means an increase in the presence of a protein and/or an increase in the expression of its gene. “Down-regulation” or“down-regulated” means a decrease in the presence of a protein and/or a decrease in the expression of its gene.

[0056] Obtained expression values for genes and/or proteins disclosed or described herein can be compared to a reference level. Reference levels can be obtained from one or more relevant datasets. A "dataset" as used herein is a set of numerical values resulting from evaluation of a sample (or population of samples) under a desired condition. The values of the dataset can be obtained, for example, by experimentally obtaining measures from a sample and constructing a dataset from these measurements. As is understood by one of ordinary skill in the art, the reference level can be based on e.g., any mathematical or statistical formula useful and known in the art for arriving at a meaningful aggregate reference level from a collection of individual datapoints; e.g., mean, median, median of the mean, etc. Alternatively, a reference level or dataset to create a reference level can be obtained from a service provider such as a laboratory, or from a database or a server on which the dataset has been stored.

[0057] A reference level from a dataset can be derived from previous measures derived from a population. A "population" is any grouping of subjects or samples of like specified characteristics. The grouping could be according to, for example, clinical parameters, clinical assessments, therapeutic regimens, disease status, severity of condition, etc.

[0058] In particular embodiments, conclusions are drawn based on whether a sample value is statistically significantly different or not statistically significantly different from a reference level. A measure is not statistically significantly different if the difference is within a level that would be expected to occur based on chance alone. In contrast, a statistically significant difference or increase is one that is greater than what would be expected to occur by chance alone. Statistical significance or lack thereof can be determined by any of various methods well-known in the art. An example of a commonly used measure of statistical significance is the p-value. The p-value represents the probability of obtaining a given result equivalent to a particular datapoint, where the datapoint is the result of random chance alone. A result is often considered significant (not random chance) at a p-value less than or equal to 0.05.

[0059] In particular embodiments, values obtained about expression of genes and/or proteins disclosed or described herein and/or other dataset components can be subjected to an analytic process with chosen parameters. The parameters of the analytic process may be those disclosed herein or those derived using the guidelines described herein. The analytic process used to generate a result may be any type of process capable of providing a result useful for classifying a sample, for example, comparison of the obtained value with a reference level, a linear algorithm, a quadratic algorithm, a decision tree algorithm, or a voting algorithm. The analytic process may set a threshold for determining the probability that a sample belongs to a given class. The probability preferably is at least at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or higher.

[0060] In particular embodiments, the relevant reference level for expression values of a particular gene or protein disclosed or described herein is obtained based on the expression value of a particular corresponding gene or protein in control subjects. In particular embodiments, control subjects can be those that are healthy and do not have QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC. In particular embodiments, control subjects can be those that have a non-QM- PDA PDAC, non-squamous PDAC, or SIRT6 ^h '9 ^h PDAC (i.e. classical PDAC, exocrine-like PDAC, pancreatic progenitor PDAC, immunogenic PDAC, or ADEX PDAC). As an example, the relevant reference level can be the expression value of the particular gene or protein in the control subjects.

[0061] In particular embodiments, when more than one gene or protein disclosed or described herein is assayed, expression values of the detected genes or proteins can be calculated into a score. Each expression value can be weighted evenly within an algorithm generating a score, or the expression values for particular genes or proteins disclosed or described herein can be weighted more heavily in reaching the score. For example, genes or proteins disclosed or described herein with higher sensitivity and/or specificity scores could be weighted more heavily than genes or proteins disclosed or described herein with lower sensitivity and/or specificity scores. For example, expression values of genes or proteins for diagnosing QM-PDA PDAC may be weighted as follows (from highest weight to lowest weight): KRT14; CAV1 ; LOX; HK2; NT5E; SLC4A4; MUC13; SPINK1 ; GPRC5A; FERMT1. As another example, expression values of genes or proteins for diagnosing squamous PDAC may be weighted as follows (from highest weight to lowest weight): TR63DN; EGFR; PDX1 ; GATA6; DDR2; FAP; CDCA5; KIF4A; BRIX1 ; HAT1. Genes or proteins disclosed or described herein may also be grouped into classes, and each class given a weighted score. For example, expression values of genes or proteins for diagnosing QM-PDA PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : KRT14 and CAV1 ; Class 2: LOX and HK2; Class 3: NT5E and SLC4A4; Class 4: MUC13 and SPINK1 ; and Class 5: GPRC5A and FERMT1. As another example, expression values of genes or proteins for diagnosing QM-PDA PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : KRT14; CAV1 ; LOX; HK2; Class 2: NT5E; SLC4A4; MUC13;SPINK1 ; and Class 3: GPRC5A and FERMT1. As another example, expression values of genes or proteins for diagnosing squamous PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : TR63DN and EGFR; Class 2: PDX1 and GATA6; Class 3: DDR2 and FAP; Class 4: CDCA5 and KIF4A; Class 5: BRIX1 and HAT1. As another example, expression values of genes or proteins for diagnosing squamous PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : TR63DN; EGFR; PDX1 ; and GATA6; Class 2: DDR2; FAP; CDCA5; and KIF4A; Class 3: BRIX1 and HAT1.

[0062] In particular embodiments, marker values for distinguishing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC from non-QM-PDA PDAC, non-squamous PDAC, or SIRT6 ^h '9 ^h PDAC (i.e. classical PDAC, exocrine-like PDAC, pancreatic progenitor PDAC, immunogenic PDAC, or ADEX PDAC) may be weighted as follows (from highest weight to lowest weight): SIRT6; AHNAK2; PAPPA; TWIST1 ; PHLDA1 ; AGR2; PNLIP; TFF3; CEL; S100P. Genes or proteins described or disclosed herein may also be grouped into classes, and each class given a weighted score. For example, expression values of genes or proteins described or disclosed herein for diagnosing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : SIRT6 and AHNAK2; Class 2: PAPPA and TWIST1 ; Class 3: PHLDA1 and AGR2; Class 4: PNLIP and TFF3; and Class 5: CEL and S100P. As another example, expression values of genes or proteins described or disclosed herein for diagnosing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC may be grouped into classes and weighted as follows (from highest weight to lowest weight): Class 1 : SIRT6; AHNAK2; PAPPA; and TWIST1 ; Class 2: PHLDA1 ; AGR2; PNLIP; and TFF3; and Class 3: CEL and S100P.

[0063] Any gene or protein described or disclosed herein or class of genes or proteins described or disclosed herein can be excluded from a particular value calculation. For example, in particular embodiments, Class 5 is excluded. In particular embodiments, Class 4 is excluded. In particular embodiments, Class 3 is excluded. In particular embodiments, Class 2 is excluded. In particular embodiments, Class 1 is excluded. In further embodiments, groups of classes can be excluded, for example, Classes 5 and 4; 5 and 3; 5 and 2; 4 and 3; 4 and 2; 3 and 2; etc.

[0064] Particular embodiments disclosed herein include obtaining a sample from a subject suspected of having QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC; assaying the sample for up- or down-regulation of one or more genes or proteins described or disclosed herein; determining one or more expression values of genes or proteins described or disclosed herein based on the assaying; comparing the one or more expression values of genes or proteins described or disclosed herein to a reference level; diagnosing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC in the subject according to the up- or down regulation of a gene or protein described or disclosed herein, as described elsewhere herein.

[0065] Particular embodiments also include distinguishing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC from non-QM-PDA PDAC, non-squamous PDAC, or SIRT6 ^hi9h PDAC (i.e. classical PDAC, exocrine-like PDAC, pancreatic progenitor PDAC, immunogenic PDAC, or ADEX PDAC) in a subject by obtaining a sample from a subject suspected of having QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC; assaying the sample for up- or down-regulation of one or more genes or proteins described or disclosed herein; determining one or more expression values of the genes or proteins described or disclosed herein based on the assaying; comparing the one or more expression values of the genes or proteins described or disclosed herein to a reference level; diagnosing QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC, or non-QM-PDA PDAC, non-squamous PDAC, or SIRT6 ^hi9h PDAC (i.e. classical PDAC, exocrine-like PDAC, pancreatic progenitor PDAC, immunogenic PDAC, or ADEX PDAC) in the subject according to the up- or down regulation of a gene or protein described or disclosed herein, as described elsewhere herein.

[0066] (iv) CDK7 and its inhibitors. Cyclin-dependent kinase 7 (CDK7). CDK7, in a complex with basal transcription factor TFIIH subunits cyclin H and Mat1 , has dual functions in transcription and in the cell cycle. As a component of TFIIH, CDK7 preferentially phosphorylates Serine 5 and Serine 7 of the C-terminal domain of the Rpb1 subunit of RNA polymerase II (RNAPII), regulating RNAPII occupancy on genes. CDK7 is also a CAK (CDK activating kinase) that activates cell- cycle CDKs by phosphorylating key threonine residues within target CDK activation segments (or T-loops).

[0067] Selective inhibitors of CDK7. As disclosed herein, selective CDK7 inhibitors are effective to treat PDAC tumors currently associated with the poorest prognosis. In particular embodiments, selective CDK7 inhibitors are covalent inhibitors. In particular embodiments, selective CDK7 inhibitors irreversibly inhibit CDK7. In particular embodiments, selective CDK7 inhibitors show time-dependent inhibition. In particular embodiments, selective CDK7 inhibitors do not bind the kinase domain of CDK7 (amino acids 12-295 of SEQ ID NO: 22). In particular embodiments, selective CDK7 inhibitors do not bind the ATP binding site in CDK7. In particular embodiments, selective CDK7 inhibitors bind a cysteine residue located outside of the kinase domain of CDK7. In particular embodiments, selective CDK7 inhibitors bind C312 of CDK7 (SEQ ID NO: 22). In particular embodiments, selective CDK7 inhibitors are selected from THZ1 , THZ2, SY-1365, SY- 351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001.

[0068] THZ1 is a phenylaminopyrimidine bearing a potential cysteine-reactive acrylamide moiety. THZ1 targets a remote cysteine residue located outside of the canonical kinase domain of CDK7, providing an unanticipated means of achieving selectivity for CDK7 (Kwiatkowski N et al. (2014) Nature 511 (7511): 616-620). The chemical structure of THZ1 is:

[0069] THZ2 is a modified form of THZ1 with potentially improved bioavailability. THZ2 was formed by modifying the regiochemistry of the acrylamide on THZ1 from 4-acrylamide-benzamide to 3-acrylamide-benzamide, giving rise to THZ2 (Wang Y et al. (2015) Cell 163(1): 174-186). The chemical structure of THZ2 is:

[0070] THZ1 and THZ2 are available commercially from distributors such as ApexBio (Houston, TX).

[0071] LDC3140 and LDC4297 are two additional selective CDK7 inhibitors. The chemical structure of LDC3140 is:

[0072] The chemical structure of LDC4297 is:

[0073] BS- 181 is a pyrazolo[1 ,5-a]pyrimidine-derived compound that inhibits CDK7 at nM concentrations. It may inhibit CDK2 to a small degree, but at 35-fold less potency (AN S et al. (2009) Cancer Res. 69: 6208-6215). Thus, within the current disclosure BS-181 is considered a selective CDK7 inhibitor. The chemical structure of BS-181 is:

BS-181

[0074] YKL-1-116 is a covalent and selective inhibitor of CDK7 (Kalan S et al. (2017) Cell Reports 21 : 467-481). The chemical structure of YKL-1-116:

YKL-1-116

[0075] Additional examples of selective CDK7 inhibitors include: SY-1365 (Syros Pharmaceuticals, NCT03134638); SY-351 (Ren Y et al. (2015) Blood 2015 126:1354); UD-017 (Onuma K et al. (2017) Journal of Clinical Oncology 35, no. 15_suppl, DOI: 10.1200/JC0.2017.35.15_suppl.e14086; Ogi S et al. (2017) Journal of Clinical Oncology 35, no. 15_suppl, DOI: 10.1200/JC0.2017.35.15_suppl.e14085); and CT7001 (Carrick Therapeutics, Dublin, Ireland).

[0076] In particular embodiments, SY-1365 refers to N-((l S,3R)-3-(5-chloro-4-(IH-indol-3- yl)pyrimidin-2-ylamino)-l-methylcyclohexyl)-5- -4-(dimethylamino)but-2-enamido)picolinamide. In particular embodiments, SY-1365 refers to:

In particular embodiments, SY-1365 and related compounds are described in WO 2015154039. In particular embodiments, SY-1365 refers to the compound tested under ClinicalTrials.gov Identifier: NCT03134638.

[0077] Selective inhibitors of CDK7 are also described in WO 2014063068, WO 2015058140, WO 2016105528, WO 2016160617, WO 2017044858, WO 2016142855, WO 2016193939, WO 2015058163, WO 2015154039, WO 2015154022, WO 2016058544, WO 2015124941 , WO 2016149031 , WO 2013128028, WO 2013128029, WO 2008151304 and WO 2017160797.

[0078] (v) Particular embodiments can also include administration of L-Myc inactivators. Exemplary L-Myc inactivators include CX-5461 and Actinomycin D. The chemical structure of CX- 5461 is:

[0079] Within these embodiments, L-Myc inactivation need not be complete inactivation, but must be sufficient to produce PDAC suppression.

[0080] (vi) Compositions. Compounds disclosed herein can be formulated into compositions for administration to subjects. Compositions include a selective CDK7 inhibitor and a pharmaceutically acceptable carrier. Selective CDK7 inhibitors can include those described herein as well as pharmaceutically acceptable salts, tautomers, isomers, and prodrugs thereof. Exemplary pharmaceutically acceptable salts include acetate, acid citrate, acid phosphate, ascorbate, benzenesulfonate, benzoate, besylate, bisulfate, bitartrate, bromide, chloride, citrate, ethanesulfonate, formate, fumarate, gentisinate, gluconate, glucaronate, glutamate, lactate, methanesulfonate, nitrate, iodide, isonicotinate, maleate, oleate, oxalate, p-toluenesulfonate, pamoate (i.e. , 1 ,T-methylene-bis-(2-hydroxy-3-naphthoate)), pantothenate, phosphate, saccharate, salicylate, succinate, sulfate, tannate and tartrate salts.

[0081] “Prodrugs” refer to compounds that can undergo biotransformation (e.g., either spontaneous or enzymatic) within a subject to release, or to convert (e.g., enzymatically, mechanically, electromagnetically, etc.) an active or more active form of a compound after administration. Prodrugs can be used to overcome issues associated with stability, toxicity, lack of specificity, or limited bioavailability and often offer advantages related to solubility, tissue compatibility, and/or delayed release (See e.g., Bundgard, Design of Prodrugs, pp. 7-9, 21-24, Elsevier, Amsterdam (1985); and Silverman, The Organic Chemistry of Drug Design and Drag Action, pp. 352-401 , Academic Press, San Diego, CA (1992)).

[0082] Pharmaceutically acceptable carriers which include those that do not produce significantly adverse, allergic or other untoward reactions that outweigh the benefit of administration, whether for research, prophylactic and/or therapeutic treatments. Exemplary pharmaceutically acceptable carriers and formulations are disclosed in Remington's Pharmaceutical Sciences, 18th Ed. Mack Printing Company, 1990. Moreover, compositions can be prepared to meet sterility, pyrogenicity, general safety and purity standards as required by United States FDA Office of Biological Standards and/or other relevant foreign regulatory agencies.

[0083] Exemplary generally used pharmaceutically acceptable carriers include any and all bulking agents or fillers, solvents or co-solvents, dispersion media, coatings, surfactants, antioxidants (e.g., ascorbic acid, methionine, vitamin E), preservatives, isotonic agents, absorption delaying agents, salts, stabilizers, buffering agents, chelating agents (e.g., EDTA), gels, binders, disintegration agents, and/or lubricants.

[0084] For injection, compositions can be made as aqueous solutions, such as in buffers such as Hanks' solution, Ringer's solution, or physiological saline. The solutions can contain formulatory agents such as suspending, stabilizing and/or dispersing agents. Alternatively, the composition can be in lyophilized and/or powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.

[0085] For oral administration, the compositions can be made as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions and the like.

[0086] For administration by inhalation, compositions can be made as aerosol sprays from pressurized packs or a nebulizer, with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide or other suitable gas.

[0087] Compositions can also be depot preparations. Such long acting compositions may be administered by, for example, implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Thus, for example, compounds can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as sparingly soluble salts.

[0088] (vii) Methods of Use. Methods disclosed herein include treating subjects (humans, veterinary animals (dogs, cats, reptiles, birds, etc.) livestock (horses, cattle, goats, pigs, chickens, etc.) and research animals (monkeys, rats, mice, fish, etc.) with compositions disclosed herein. Treating subjects includes delivering therapeutically effective amounts. Therapeutically effective amounts include those that provide effective amounts, prophylactic treatments and/or therapeutic treatments.

[0089] An "effective amount" is the amount of a compound necessary to result in a desired physiological change in the subject. Effective amounts are often administered for research purposes. Effective amounts disclosed herein can cause a statistically-significant effect in an animal model or in vitro assay relevant to the assessment of PDAC development or progression. Effective amounts disclosed herein can cause a statistically-significant decrease in tumor volume and/or tumor weight in a subject with QM-PDA PDAC, squamous PDAC, and/or SIRT6 ^|0W PDAC.

[0090] A "prophylactic treatment" includes a treatment administered to a subject who does not display signs or symptoms of PDAC or displays only early signs or symptoms of PDAC such that treatment is administered for the purpose of diminishing or decreasing the risk of developing PDAC further. Thus, a prophylactic treatment functions as a preventative treatment against PDAC. In particular embodiments, prophylactic treatments reduce, delay, or prevent metastasis from a primary PDAC tumor site from occurring.

[0091] A "therapeutic treatment" includes a treatment administered to a subject who displays symptoms or signs of PDAC and is administered to the subject for the purpose of diminishing or eliminating those signs or symptoms of PDAC. The therapeutic treatment can reduce, control, or eliminate the presence or activity of PDAC and/or reduce control or eliminate side effects of PDAC. In particular embodiments, therapeutic treatments reduce, delay, or prevent further metastasis from occurring.

[0092] The methods of treatment disclosed herein are effective to target and treat QM-PDA subtype of PDAC, squamous subtype of PDAC, and/or SIRT6 ^|0W PDACs but not other subtypes of PDAC (i.e. , classical, exocrine-like, pancreatic progenitor, immunogenic, or ADEX) or PDAC with SIRT6 ^h '9 ^h . Particular embodiments include suppressing PDAC in a subject by administering an L-Myc inactivator. PDAC suppression includes one or more of decreasing the number of PDAC cells in a subject, decreasing the number of metastases in as subject, decreasing tumor volume in a subject, increasing life expectancy in a subject, inducing chemo- or radiosensitivity in PDAC cells in a subject, inhibiting angiogenesis near PDAC cells in a subject, inhibiting PDAC cell proliferation in a subject, inhibiting tumor growth in a subject, preventing, reducing, or delaying metastases in a subject, prolonging a subject’s life, reducing cancer-associated pain in a subject, and/or reducing or delaying relapse or re-occurrence of PDAC following treatment in a subject.

[0093] In particular embodiments, compositions are administered as a first line treatment. In particular embodiments, compositions are administered in combination with a first line chemotherapeutic treatment. Examples of chemotherapeutic treatment agents include actinomycin, all-trans retinoic acid, azacitidine, azathioprine, bleomycin, bortezomib, carboplatin, capecitabine, cisplatin, chlorambucil, cyclophosphamide, cytarabine, daunorubicin, docetaxel, doxifluridine, doxorubicin, epirubicin, epothilone, etoposide, fluorouracil, gemcitabine, hydroxyurea, idarubicin, imatinib, irinotecan, mechlorethamine, mercaptopurine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, pemetrexed, teniposide, tioguanine, topotecan, valrubicin, vinblastine, vincristine, vindesine, and vinorelbine.

[0094] In particular embodiments, compositions are administered following the emergence of chemoresistance. Chemoresistance refers to a clinical stage when cancer cell(s) do not respond to the cell-killing effects of chemotherapeutic drugs. Cancer cells may be chemoresistant at the beginning of treatment, or may become resistant during the course of treatment.

[0095] A "tumor" is a swelling or lesion formed by an abnormal growth of cells (called neoplastic cells or tumor cells). A "tumor cell" is an abnormal cell that grows by a rapid, uncontrolled cellular proliferation and continues to grow after the stimuli that initiated the new growth cease. Tumors show partial or complete lack of structural organization and functional coordination with the normal tissue, and usually form a distinct mass of tissue, which may be benign, pre-malignant or malignant.

[0096] For administration, therapeutically effective amounts (also referred to herein as doses) can be initially estimated based on results from in vitro assays and/or animal model studies. The actual dose amount administered to a particular subject can be determined by a physician, veterinarian or researcher taking into account parameters such as physical and physiological factors including target, body weight, severity of PDAC, type of PDAC, stage of PDAC, previous or concurrent therapeutic interventions, idiopathy of the subject and route of administration.

[0097] Useful doses can range from 0.01 to 500 pg/kg or from 0.01 to 500 mg/kg. Therapeutically effective amounts can be achieved by administering single or multiple doses during the course of a treatment regimen (e.g., daily, every other day, weekly, monthly, every 6 months, or yearly).

[0098] The compositions described herein can be administered by, for example, injection, inhalation, infusion, perfusion, lavage or ingestion. Routes of administration can include intravenous, intradermal, intraarterial, intraparenteral, intranasal, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, topical, intrathecal, intratumoral, intramuscular, intravesicular, oral, subcutaneous, and/or sublingual administration and more particularly by intravenous, intradermal, intraarterial, intraparenteral, intranasal, intranodal, intralymphatic, intraperitoneal, intralesional, intraprostatic, intravaginal, intrarectal, topical, intrathecal, intratumoral, intramuscular, intravesicular, oral, subcutaneous, and/or sublingual injection.

[0099] Further, the current disclosure describes a method for determining whether a treatment is appropriate for a subject diagnosed with PDAC. As an example, a biological sample from the subject can be genetically screened and/or assayed for expression of: one or more genes associated with QM-PDA PDAC and included in the 62 gene PDAssigner panel (Table 1), one or more genes associated with squamous PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B), and/or SIRT6. In particular embodiments, a biological sample includes bodily fluids such as blood, plasma, or serum; circulating tumor cells; pancreatic juice; pancreatic tumors; PDAC tumors; and pancreatic tissue from pancreatic or PDAC tumors. In particular embodiments, a biological sample is derived from a subject or source. Particular embodiments of“derived from” refer to a biological sample being obtained from a subject or other source and including any modification to the sample, addition to the sample, or removal from the sample, as long as expression of one or more genes of the present disclosure can be measured from the sample using the systems and methods of the present disclosure.

[0100] The results of the screen and/or assay can determine whether a targeted treatment with a selective CDK7 inhibitor would be appropriate. In particular embodiments, a subject is a likely responder to a selective CDK7 inhibitor treatment regimen if the subject has a higher probability of being responsive to treatment with a selective CDK7 inhibitor compared to a subject who does not have QM-PDA PDAC, squamous PDAC, or SIRT6 ^|0W PDAC. In particular embodiments, a subject is a likely responder to a selective CDK7 inhibitor treatment regimen if a biological sample derived from the subject is determined to have one or more of the following: upregulated expression of one or more proteins or one or more corresponding genes of QM-PDA subtype in Table 1 ; normal or downregulated expression of one or more proteins or one or more corresponding genes of classical subtype in Table 1 ; and normal or downregulated expression of one or more proteins or one or more corresponding genes of exocrine-like subtype in Table 1 , relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC. In particular embodiments, a subject is a likely responder to a selective CDK7 inhibitor treatment regimen if a biological sample derived from the subject is determined to have one or more of the following: downregulated expression of one or more proteins or one or more corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and upregulated expression of one or more proteins or one or more corresponding genes of genes selected from Tables 4-7, relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-squamous PDAC. In particular embodiments, a subject is a likely responder to a selective CDK7 inhibitor treatment regimen if a biological sample derived from the subject is determined to have downregulated expression of SIRT6 relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having upregulated expression of SIRT6. Examples of biological samples from a subject include a tissue biopsy sample, a tumor biopsy sample, or a bronchoalveolar lavage sample.

[0101] Determining whether a treatment is appropriate for a subject includes performing a test to assess whether the subject is more or less likely to respond to a given therapeutic intervention, such as treatment with a compound. Actual response to the therapeutic intervention is not required.

[0102] The current disclosure also includes screening subjects for enrollment in clinical trials. In particular embodiments, screening a subject for enrollment in a clinical trial evaluating administration of selective CDK7 inhibitors includes obtaining a PDAC tumor derived from the subject; determining from the sample whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC; and enrolling the subject in the clinical trial evaluating administration of selective CDK7 inhibitors if the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, or, in particular embodiments, directing the subject to another clinical trial if the subject does not have QM-PDA, squamous, or SIRT6 ^|0W PDAC. As an example, a biological sample from the subject can be genetically screened and/or assayed for expression of: one or more genes associated with QM- PDA PDAC and included in the 62 gene PDAssigner panel (Table 1), one or more genes associated with squamous PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B), and/or SIRT6. The results of the screen and/or assay could direct the subject for inclusion or exclusion from a clinical trial administering a selective CKD7 inhibitor for QM-PDA, squamous, and/or low SIRT6 expression PDAC tumors.

[0103] Particular embodiments disclosed herein include obtaining a biological sample (e.g., blood, plasma, serum, circulating tumor cells, pancreatic juice, pancreatic tumors, PDAC tumors, pancreatic tissue from pancreatic or PDAC tumors) derived from a subject; and testing the sample for expression of one or more proteins or genes disclosed herein. In particular embodiments, the one or more proteins or one or more corresponding genes are selected from genes in Table 1. In particular embodiments, the one or more proteins or one or more corresponding genes are selected from genes associated with squamous PDAC and functioning in pancreatic endodermal cell fate determination and genes in Tables 4-7. In particular embodiments, genes associated with squamous PDAC and functioning in pancreatic endodermal cell fate determination include PDX1 , MNX1 , GATA6, and HNF1 B. In particular embodiments, the testing includes testing for expression of SIRT6. In particular embodiments, the testing includes performing one or more assays selected from RNA sequencing, gene expression microarray, quantitative real time RT-PCR, immunoassay, or a combination thereof. In particular embodiments, the one or more assays includes quantitative real time RT-PCR to measure expression of SIRT6. In particular embodiments, the one or more assays includes immunoassay to measure expression of SIRT6. In particular embodiments, the immunoassay includes immunohistochemistry using an anti- SIRT6 antibody. In particular embodiments, the testing includes contacting the sample with a molecule; and detecting binding between the molecule and a measured gene or protein within the sample.

[0104] (viii) Kits. Combinations of reagents that can be used to determine whether a treatment is appropriate for a PDAC subject or combinations of reagents that can be used to selectively treat PDAC subjects can also be provided as kits. Kits for determining whether a treatment is appropriate for a PDAC subject can include: reagents to detect expression of one or more genes in the PDAssigner 62 gene panel (Table 1); reagents to detect expression of one or more genes associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B); and/or reagents to detect expression of SIRT6. In particular embodiments, reagents to detect expression of one or more genes or their corresponding proteins disclosed herein include protein binding domains, oligonucleotides, binding ligands, aptamers, and antibodies. In particular embodiments, reagents to detect expression of one or more genes or their corresponding proteins in the PDAssigner62 gene panel (Table 1) or of one or more genes or their corresponding proteins associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B) include protein binding domains that bind one or more proteins encoded by the one or more corresponding genes in the PDAssigner 62 gene panel (Table 1) or that bind proteins encoded by the one or more corresponding genes associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B). In particular embodiments, reagents to detect expression of one or more genes in the PDAssigner 62 gene panel (Table 1) or of one or more genes associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B) include one or more oligonucleotides binding the one or more genes in the PDAssigner 62 gene panel (Table 1) or the one or more genes associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B). In particular embodiments, reagents to detect expression of SIRT6 includes a reagent selected from an anti-SIRT6 antibody and oligonucleotides binding SIRT6 polynucleotide. Kits for selectively treating PDAC subjects can include: reagents to detect expression of one or more genes or their corresponding proteins in the PDAssigner 62 gene panel (Table 1); reagents to detect expression of one or more genes or their corresponding proteins associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B); reagents to detect expression of SIRT6; and/or one or more compositions to treat PDAC subjects. In particular embodiments, the one or more compositions to treat PDAC subjects include one or more selective CDK7 inhibitors (e.g. THZ1 , THZ2, SY- 1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001) and/or one or more L-Myc inactivators (e.g., CX-5461 and Actinomycin D).

[0105] Kits can also include a notice in the form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use, or sale for human administration. The notice may state that the provided active ingredients can be administered to a subject. The kits can include further instructions for using the kit, for example, instructions regarding: assaying for expression of one or more genes in the PDAssigner 62 gene panel (Table 1); assaying for expression of one or more genes associated with the squamous subtype of PDAC (Tables 4-7, PDX1 , MNX1 , GATA6, and HNF1 B); assaying for expression of SIRT6 gene; preparation of one or more selective CDK7 inhibitors (e.g. THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001) for administration; preparation of one or more L-Myc inactivators (e.g., CX-5461 and Actinomycin D); proper disposal of related waste; and the like. The instructions can be in the form of printed instructions provided within the kit or the instructions can be printed on a portion of the kit itself. Instructions may be in the form of a sheet, pamphlet, brochure, CD-Rom, or computer-readable device, or can provide directions to instructions at a remote location, such as a website. In particular embodiments, kits can also include some or all of the necessary laboratory and/or medical supplies needed to use the kit effectively, such as syringes, ampules, tubing, facemask, an injection cap, sponges, sterile adhesive strips, Chloraprep, gloves, tubes, buffers, enzymes, and the like. Variations in contents of any of the kits described herein can be made. The instructions of the kit will direct use of the active ingredients to effectuate a new clinical use described herein.

[0106] The Exemplary Embodiments and Example below are included to demonstrate particular embodiments of the disclosure. Those of ordinary skill in the art should recognize in light of the present disclosure that many changes can be made to the specific embodiments disclosed herein and still obtain a like or similar result without departing from the spirit and scope of the disclosure.

[0107] Exemplary Embodiments.

1. A method of treating a subject diagnosed with quasimesenchymal-PDA (QM-PDA), squamous, or Sirtuin 6 (SIRT6) ^|0W pancreatic ductal adenocarcinoma (PDAC), including administering a therapeutically effective amount of one or more selective CDK7 inhibitors to the subject, thereby treating the subject diagnosed with QM-PDA, squamous, or SIRT6 ^|0W PDAC.

2. A method of embodiment 1 , wherein the one or more selective CDK7 inhibitors includes THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and CT7001 , or a combination thereof.

3. A method of embodiment 1 or 2, wherein the one or more selective CDK7 inhibitors includes THZ1 or THZ2.

4. A method of any one of embodiments 1-3, wherein the selective CDK7 inhibitor is administered with a therapeutically effective amount of a chemotherapeutic treatment agent.

5. A method of treating a subject diagnosed with QM-PDA, squamous, or SIRT6 ^|0W PDAC, including administering a therapeutically effective amount of one or more L-Myc inactivators to the subject, thereby treating the subject diagnosed with QM-PDA, squamous, or SIRT6 ^|0W PDAC.

6. A method of embodiment 5, wherein the one or more L-Myc inactivators includes CX-5461 and Actinomycin D.

7. A method of screening PDAC subjects for enrollment in a clinical trial evaluating administration of selective CDK7 inhibitors including:

obtaining a PDAC tumor sample derived from the subject;

determining from the sample whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC; and

enrolling the subject in the clinical trial evaluating administration of selective CDK7 inhibitors if the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, thereby screening the subject for enrollment in the clinical trial.

8. A method of embodiment 7, wherein the determining step further includes:

measuring the expression of one or more proteins or one or more corresponding genes selected from genes in Table 1.

9. A method of embodiment 8, wherein the subject is determined to have one or more of the following:

(a) upregulated expression of one or more proteins or one or more corresponding genes of QM-PDA subtype in Table 1 ;

(b) normal or downregulated expression of one or more proteins or one or more corresponding genes of classical subtype in Table 1 ; and

(c) normal or downregulated expression of one or more proteins or one or more corresponding genes of exocrine-like subtype in Table 1 ,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

10. A method of embodiment 7, wherein the determining step further includes:

measuring the expression of one or more proteins or one or more corresponding genes selected from genes associated with squamous PDAC and functioning in pancreatic endodermal cell fate determination and genes in Tables 4-7.

11. A method of embodiment 10, wherein the subject is determined to have one or more of the following:

(a) downregulated expression of one or more proteins or one or more corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or one or more corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-squamous PDAC.

12. A method of embodiment 7, wherein the determining step further includes measuring the expression of SIRT6.

13. A method of embodiment 12, wherein the subject is determined to have downregulated expression of SIRT6 relative to expression of SIRT6 in a non-diseased subject or in a subject having upregulated expression of SIRT6.

14. A method of any one of embodiments 8, 10, or 12, wherein the measuring step includes performing one or more assays selected from RNA sequencing, gene expression microarray, quantitative real time RT-PCR, and immunoassay.

15. A method of embodiment 14, wherein the one or more assays includes quantitative real time RT-PCR to measure expression of SIRT6.

16. A method of embodiment 14 or 15, wherein the one or more assays includes immunoassay to measure expression of SIRT6.

17. A method of embodiment 16, wherein the immunoassay includes immunohistochemistry using an anti-SIRT6 antibody.

18. A method of embodiment 7, further including directing the subject to another clinical trial if the subject does not have QM-PDA, squamous, or SIRT6 ^|0W PDAC.

19. A method of any one of embodiments 7-17, wherein the method further includes administering to the subject enrolled in the clinical trial a therapeutically effective amount of one or more selective CDK7 inhibitors selected from THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and CT7001 , or a combination thereof.

20. A method of embodiment 19, wherein the one or more selective CDK7 inhibitors includes THZ1 and THZ2.

21. A method of embodiment 19 or 20, wherein the one or more selective CDK7 inhibitors is administered with a therapeutically effective amount of a chemotherapeutic treatment agent.

22. A method of diagnosing a subject with PDAC as a likely responder to a selective CDK7 inhibitor treatment regimen, including:

obtaining a PDAC tumor sample derived from the subject;

determining in the sample whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, wherein if the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, diagnosing the subject as a likely responder to a selective CDK7 inhibitor treatment regimen.

23. A method of embodiment 22, wherein the determining step further includes:

measuring the expression of one or more proteins or one or more corresponding genes selected from genes in Table 1.

24. A method of embodiment 23, wherein the subject is determined to have one or more of the following:

(a) upregulated expression of one or more proteins or one or more corresponding genes of QM-PDA subtype in Table 1 ;

(b) normal or downregulated expression of one or more proteins or one or more corresponding genes of classical subtype in Table 1 ; and

(c) normal or downregulated expression of one or more proteins or one or more corresponding genes of exocrine-like subtype in Table 1 , relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

25. A method of embodiment 22, wherein the determining step further includes:

measuring the expression of one or more proteins or one or more corresponding genes selected from genes associated with squamous PDAC and functioning in pancreatic endodermal cell fate determination and genes in Tables 4-7.

26. A method of embodiment 25, wherein the subject is determined to have one or more of the following:

(a) downregulated expression of one or more proteins or one or more corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or one or more corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-squamous PDAC.

27. A method of embodiment 22, wherein the determining step further includes measuring the expression of SIRT6.

28. A method of embodiment 27, wherein the subject is determined to have downregulated expression of SIRT6 relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having upregulated expression of SIRT6.

29. A method of any one of embodiments 23-28, wherein the measuring step includes performing one or more assays selected from RNA sequencing, gene expression microarray, quantitative real time RT-PCR, and immunoassay.

30. A method of embodiment 29, wherein the one or more assays includes quantitative real time RT-PCR to measure expression of SIRT6.

31. A method of embodiment 29 or 30, wherein the one or more assays includes immunoassay to measure expression of SIRT6.

32. A method of embodiment 31 , wherein the immunoassay includes immunohistochemistry using an anti-SIRT6 antibody.

33. A method of embodiment 22, further including diagnosing the subject as not likely to respond to a selective CDK7 inhibitor treatment regimen if the subject does not have QM-PDA, squamous, or SIRT6 ^low PDAC.

34. A method of any one of embodiments 22-32, wherein the method further includes administering to the subject diagnosed as a likely responder a therapeutically effective amount of one or more selective CDK7 inhibitors selected from THZ1 , THZ2, SY-1365, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and CT7001 , or a combination thereof.

35. A method of embodiment 34, wherein the one or more selective CDK7 inhibitors includes THZ1 and THZ2.

36. A method of embodiment 34 or 35, wherein the one or more selective CDK7 inhibitors is administered with a therapeutically effective amount of a chemotherapeutic treatment agent.

37. A method of any one of embodiments 8, 10, 12, 23, 25, or 27, wherein the measuring includes:

contacting the sample with a molecule and detecting binding between the molecule and a measured gene or protein within the sample.

38. A method of treating a subject diagnosed with a sub-type of pancreatic ductal adenocarcinoma (PDAC) including:

determining whether the subject has been diagnosed with classical, exocrine-like, or quasi-mesenchymal-PDA (QM-PDA) PDAC; and

administering a selective CDK7 inhibitor to the subject if the subject has the QM-PDA sub- type of PDAC, but not administering a selective CDK7 inhibitor to the subject if the subject has classical or exocrine-like PDAC

thereby treating the subject diagnosed with a sub-type of PDAC.

39. The method of embodiment 38, wherein the selective CDK7 inhibitor includes SY-1365, THZ1 and/or THZ2

40. The method of embodiment 38 or 39, wherein the selective CDK7 inhibitor is administered with a chemotherapeutic treatment agent.

41. A method of treating a subject diagnosed with a sub-type of pancreatic ductal adenocarcinoma (PDAC) including:

determining whether the subject has been diagnosed with:

(i) classical, exocrine-like, or quasi-mesenchymal-PDA (QM-PDA) PDAC;

(ii) pancreatic progenitor, immunogenic, abnormally differentiated endocrine exocrine (ADEX), or squamous PDAC; and/or

(iii) Sirtuin 6 (SIRT6) ^|0W PDAC; and

administering a selective CDK7 inhibitor to the subject if the subject has the QM-PDA sub- type of PDAC, the squamous sub-type of PDAC, and/or the SI RT6 ^|0W sub-type of PDAC

but not administering a selective CDK7 inhibitor to the subject if the subject has classical or exocrine-like PDAC; pancreatic progenitor, immunogenic, or ADEX PDAC; or non- SIRT6 ^|0W PDAC,

thereby treating the subject diagnosed with a sub-type of PDAC. 42. The method of embodiment 41 , wherein the selective CDK7 inhibitor includes SY-1365, THZ1 , THZ2, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001.

43. The method of embodiment 41 or 42, wherein the selective CDK7 inhibitor includes SY-1365, THZ1 , and/or THZ2.

44. The method of any of embodiments 41-43, wherein the selective CDK7 inhibitor is administered with a chemotherapeutic treatment agent.

45. The method of any of embodiments 38-44

obtaining a PDAC tumor sample derived from the subject; and

testing the sample to determine whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC.

46. The method of embodiment 45, wherein the testing includes:

measuring the expression of the proteins or corresponding genes of Table 1.

47. The method of embodiment 45 or 46, wherein the testing reveals that the subject has one or more of:

(a) upregulated expression of one or more proteins or corresponding genes of the QM-PDA subtype of Table 1 ;

(b) normal or downregulated expression of one or more proteins or corresponding genes of classical subtype of Table 1 ; and

(c) normal or downregulated expression of one or more proteins or corresponding genes of exocrine-like subtype of Table 1 ,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

48. The method of any of embodiments 45-47, wherein the testing includes:

measuring the expression of proteins or the corresponding genes of Tables 4-7.

49. The method of any of embodiments 45-48, wherein the testing reveals that the subject has one or more of:

(a) downregulated expression of one or more proteins or corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having pancreatic progenitor, immunogenic, or ADEX PDAC.

50. The method of any of embodiments 45-49, wherein the testing includes measuring the expression of SIRT6. 51. The method of any of embodiments 45-50, wherein the testing reveals that the subject has downregulated expression of SIRT6 relative to expression of SIRT6 in a non-diseased subject or in a PDAC subject having normal or upregulated expression of SIRT6.

52. A method of treating a subject diagnosed with a sub-type of pancreatic ductal adenocarcinoma (PDAC) including determining whether the subject has been diagnosed with:

(i) classical, exocrine-like, or quasi-mesenchymal-PDA (QM-PDA) PDAC;

(ii) pancreatic progenitor, immunogenic, abnormally differentiated endocrine exocrine (ADEX), or squamous PDAC; and/or

(iii) Sirtuin 6 (SIRT6) ^|0W PDAC; and

administering an L-Myc inactivator to the subject if the subject has the QM-PDA sub-type of PDAC, the squamous sub-type of PDAC, and/or the SIRT6 ^|0W sub-type of PDAC

but not administering an L-Myc inactivator to the subject if the subject has classical or exocrine like PDAC; pancreatic progenitor, immunogenic, or ADEX PDAC; or non-SIRT6 ^low PDAC,

thereby treating the subject diagnosed with a sub-type of PDAC.

53. The method of embodiment 52, wherein the L-Myc inactivator comrprises CX-5461 or Actinomycin D.

54. The method of embodiment 52 or 53, wherein the L-Myc inactivator is administered with a chemotherapeutic treatment agent.

55. The method of any of embodiments 52-54, including

obtaining a PDAC tumor sample derived from the subject; and

testing the sample to determine whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC.

56. The method of embodiment 55, wherein the testing includes:

measuring the expression of the proteins or corresponding genes of Table 1.

57. The method of embodiment 55 or 56, wherein the testing reveals that the subject has one or more of:

(a) upregulated expression of one or more proteins or corresponding genes of the QM-PDA subtype of Table 1 ;

(b) normal or downregulated expression of one or more proteins or corresponding genes of classical subtype of Table 1 ; and

(c) normal or downregulated expression of one or more proteins or corresponding genes of exocrine-like subtype of Table 1 ,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

58. The method of any of embodiments 55-57, wherein the testing includes: measuring the expression of proteins or the corresponding genes of Tables 4-7.

59. The method of any of embodiments 55-58, wherein the testing reveals that the subject has one or more of:

(a) downregulated expression of one or more proteins or corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having pancreatic progenitor, immunogenic, or ADEX PDAC.

60. The method of any of embodiments 55-59, wherein the testing includes measuring the expression of SIRT6.

61. The method of any of embodiments 55-60, wherein the testing reveals that the subject has downregulated expression of SIRT6 relative to expression of SIRT6 in a non-diseased subject or in a PDAC subject having normal or upregulated expression of SIRT6.

62. A method of screening subjects diagnosed with pancreatic ductal adenocarcinoma (PDAC) for enrollment in a clinical trial evaluating administration of selective CDK7 inhibitors including: determining whether the subject has been diagnosed with:

(i) classical, exocrine-like, or quasi-mesenchymal-PDA (QM-PDA) PDAC;

(ii) pancreatic progenitor, immunogenic, abnormally differentiated endocrine exocrine (ADEX), or squamous PDAC; and/or

(iii) Sirtuin 6 (SIRT6) ^|0W PDAC; and

recommending the subject for enrollment in the clinical trial if the subject has QM-PDA, squamous, or SIRT6 ^low PDAC

but not recommending the subject for enrollment in the clinical trial if the subject has classical or exocrine-like PDAC; pancreatic progenitor, immunogenic, or ADEX PDAC; or non- SIRT6 ^|0W PDAC,

thereby screening subjects diagnosed with PDAC for enrollment in the clinical trial.

63. The method of embodiment 62, including

obtaining a PDAC tumor sample derived from the subject; and

testing the sample to determine whether the subject has QM-PDA, squamous, or SIRT6low PDAC.

64. The method of embodiment 63, wherein the testing includes:

measuring the expression of the proteins or corresponding genes of Table 1.

65. The method of embodiment 63 or 64, wherein the testing reveals that the subject has one or more of:

(a) upregulated expression of one or more proteins or corresponding genes of the QM-PDA subtype of Table 1 ;

(b) normal or downregulated expression of one or more proteins or corresponding genes of classical subtype of Table 1 ; and

(c) normal or downregulated expression of one or more proteins or corresponding genes of exocrine-like subtype of Table 1 ,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

66. The method of any of embodiments 63-65, wherein the testing includes:

measuring the expression of proteins or the corresponding genes of Tables 4-7.

67. The method of any of embodiments 63-66, wherein the testing reveals that the subject has one or more of:

(a) downregulated expression of one or more proteins or corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having pancreatic progenitor, immunogenic, or ADEX PDAC.

68. The method of any of embodiments 63-67, wherein the testing includes measuring the expression of SIRT6.

69. The method of any of embodiments 63-68, wherein the testing reveals that the subject has downregulated expression of SIRT6 relative to expression of SIRT6 in a non-diseased subject or in a PDAC subject having normal or upregulated expression of SIRT6.

70. The method of any of embodiments 63-69, including recommending a different clinical trial to the subject if the subject does not have QM-PDA, squamous, or SIRT6low PDAC wherein the different clinical trial does not include administering a selective CDK7 inhibitor.

71. The method of embodiment 70, wherein the subject that does not have QM-PDA, squamous, or SIRT6low PDAC has classical, exocrine- 1 ike, pancreatic progenitor, immunogenic, ADEX, or non- SIRT6low PDAC.

72. The method of any of embodiments 63-69, wherein the subject recommended for enrollment in the clinical trial is administered a selective CDK7 inhibitor including SY-1365, THZ1 , THZ2, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001.

73. The method of embodiment 72, wherein the selective CDK7 inhibitor includes SY-1365, THZ1 , and/or THZ2.

74. The method of embodiment 72 or 73, wherein the selective CDK7 inhibitor is administered with a chemotherapeutic treatment agent.

75. A method of diagnosing a subject with PDAC as a likely responder to a selective CDK7 inhibitor treatment regimen, including:

obtaining a PDAC tumor sample derived from the subject;

testing the sample to determine whether the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, wherein if the subject has QM-PDA, squamous, or SIRT6 ^|0W PDAC, diagnosing the subject as a likely responder to a selective CDK7 inhibitor treatment regimen.

76. The method of embodiment 75, wherein the testing includes:

measuring the expression of the proteins or corresponding genes of Table 1.

77. The method of embodiment 75 or 76, wherein the testing reveals that the subject has one or more of:

(a) upregulated expression of one or more proteins or corresponding genes of the QM-PDA subtype of Table 1 ;

(b) normal or downregulated expression of one or more proteins or corresponding genes of classical subtype of Table 1 ; and

(c) normal or downregulated expression of one or more proteins or corresponding genes of exocrine-like subtype of Table 1 ,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having non-QM-PDA PDAC.

78. The method of any of embodiments 75-77, wherein the testing includes:

measuring the expression of proteins or the corresponding genes of Tables 4-7.

79. The method of any of embodiments 75-78, wherein the testing reveals that the subject has one or more of:

(a) downregulated expression of one or more proteins or corresponding genes selected from PDX1 , MNX1 , GATA6, and HNF1 B; and

(b) upregulated expression of one or more proteins or corresponding genes of genes selected from Tables 4-7,

relative to expression of one or more corresponding proteins or genes in a non-diseased subject or in a subject having pancreatic progenitor, immunogenic, or ADEX PDAC.

80. The method of any of embodiments 75-79, wherein the testing includes measuring the expression of SIRT6.

81. The method of any of embodiments 75-80, wherein the testing reveals that the subject has downregulated expression of SIRT6 relative to expression of SIRT6 in a non-diseased subject or in a PDAC subject having normal or upregulated expression of SIRT6.

82. The method of any of embodiments 75-82, further including diagnosing the subject as not likely to respond to a selective CDK7 inhibitor treatment regimen if the subject does not have QM-PDA, squamous, or SIRT6low PDAC.

83. The method of embodiment 83, wherein the subject that does not have QM-PDA, squamous, or SIRT6low PDAC has classical, exocrine- 1 ike, pancreatic progenitor, immunogenic, ADEX, or non- SIRT6low PDAC.

84. The method of any of embodiments 75-82, wherein the method further includes administering to the subject diagnosed as a likely responder a selective CDK7 inhibitor including THZ1 , THZ2, SY-351 , LDC3140, LDC4297, BS-181 , UD-017, YKL-1-116, and/or CT7001.

85. The method of embodiment 84, wherein the selective CDK7 inhibitor includes SY-1365, THZ1 , and/or THZ2.

86. The method of embodiment 84 or 85, wherein the selective CDK7 inhibitor is administered with a chemotherapeutic treatment agent.

87. The method of any of the preceding embodiments, wherein measuring includes performing an assay including RNA sequencing, gene expression microarray, quantitative real time RT- PCR, and immunoassay.

88. The method of embodiment 87, wherein the assays includes quantitative real time RT-PCR to measure expression of SIRT6.

89. The method of embodiment 88, wherein the assay includes immunoassay to measure expression of SIRT6.

90. The method of embodiment 89, wherein the immunoassay is immunohistochemistry using an anti-SIRT6 antibody.

91. The method of any of the preceding embodiments, wherein the measuring includes:

contacting the sample with a molecule and detecting binding between the molecule and a measured gene or protein within the sample.

92. Use of a selective CDK7 inhibitor in treating cancer in a selected patient, wherein the patient is selected based on a diagnosis of QM-PDA PDAC, squamous PDAC, and/or SIRT6low PDAC.

[0108] Example 1. Cell Lines. Pancreatic cancer cell lines, ASPC-1 , SUIT2, HPAFII, KP4, MiaPaCa, YAPC, 8988T, PSN1 , Panc03.27, Panc-1 , BxPc3 were obtained from American Type Culture Collection (ATCC; Rockville, MD), and grown at 37 °C under 5% CO ₂ in their required growth medium per ATCC description. [0109] Gel Electrophoresis and Western Blotting. For whole cell lysate (WCL), the cell pellet was resuspended in RIPA buffer supplemented with a protease inhibitor cocktail (Complete EDTA- free, Roche Applied Science), 5mM TSA, 5mM sodium butyrate, 1mM DTT, and phosphatase inhibitors (Phosphatase Inhibitor Cocktail Sets I, II and III Calbiochem) and incubated on ice for 20 mins. The lysate was then centrifuged at 14,000 rpm for 10 mins at 4°C and the supernatant was harvested. Protein concentration was quantified by Bio-rad Protein Assay. 20 pg WCL was electrophoresed on a 10-20% gradient polyacrylamide gel with SDS (Bio-rad) and electroblotted onto polyvinylidene difluoride membranes (PVDF) (Millipore). Membranes were blocked in TBS with 5% non-fat milk and 0.1 % Tween and probed with anti-RNA Polll Ser5P (Abeam, ab5131), anti-RNA Polll Ser7P (Abeam, ab126537), anti-Cleaved Caspase 3 (CST, 9664), anti-CDK7 (SCB, sc-7344), anti-MYC (Abeam, ab32072) and anti-b actin (Sigma A5316) as a loading control. Bound proteins were detected with horseradish-peroxidase-conjugated secondary antibodies (Vector Biolaboratories) and SuperSignal West Pico Luminol/Enhancer Solution (Thermo Scientific).

[0110] Real-Time RT-PCR Analysis. Cell were treated with 100nM THZ1 or DMSO control for 6 hours and total RNA was extracted with RNAeasy Mini Kit (Qiagen) as described by the manufacturer. For cDNA synthesis, 1 pg of total RNA was reverse-transcribed by using the QuantiTect Reverse Transcription Kit (Qiagen). Real-time PCR was run in duplicate using SYBR green master mix (Bio-rad), following the manufacturer's instructions, with the exception that the final volume was 10 pi of SYBR green reaction mix. Real-time monitoring of PCR amplification was performed using the CFX384 real-time PCR detection system (Bio-rad). Data were expressed as relative mRNA levels normalized to the b-actin expression level in each sample.

[0111] Apoptosis Assay. 2.5x10 ⁵ cells/well were seeded in triplicate and treated with 100nM and 250nM THZ1. Cells were harvested after 24 hours and stained with Annexin V and Propidium Iodide using a FITC Annexin V Apoptosis Detection Kit I (BD Biosciences, #556547). Samples were analyzed immediately using a BD FACSCelesta Flow Cytometer. Analyses of apoptotic fractions was performed using FlowJo flow cytometry analysis software.

[0112] RNA Sequencing. Cell were treated with 100nM THZ1 or DMSO control for 6 hours and total RNA was extracted with RNAeasy Mini Kit (Qiagen) as described by the manufacturer. During RNA purification, samples were digested with DNase by incubating on-column for 15 minutes at room temperature, using the RNase-Free DNase Set (Qiagen, #79254). Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA). RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit v2 (lllumina, Inc., San Diego, CA, USA) and a Sciclone NGSx Workstation (PerkinElmer, Waltham, MA, USA). Library size distributions were validated using an Agilent 4200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Additional library QC, blending of pooled indexed libraries, and cluster optimization were performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-lnvitrogen, Carlsbad, CA, USA). RNA-seq libraries were pooled (18-plex) and clustered onto three flow cell lanes. Sequencing was performed using an lllumina HiSeq 2500 in rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy.

[0113] Image analysis and base calling were performed using lllumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using lllumina's bcl2fastq Conversion Software v1.8.4.

[0114] RNA-seq Data Analysis: Reads of low quality were filtered prior to alignment to the reference genome (UCSC hg38 assembly) using TopHat v2.1.0. Counts were generated from TopHat alignments for each gene using the Python package HTSeq vO.6.1. Genes which did not have at least 2 CPM in at least 3 samples were discarded, followed by TMM normalization and significance testing using the Bioconductor package edgeR v3.18.1. A false discovery rate (FDR) method was employed to correct for multiple testing. Differential expression was defined as |log ₂ (ratio) | ³ 1 (± 2-fold) with the FDR set to 5%. Using the significantly differentially expressed genes from each comparison, Venn diagrams were generated, segregating genes by logFC orientation. Genes from each comparison were ranked by logFC prior to performing GSEA Pre-ranked analysis, using the full MSigDB Collection.

[0115] Proliferation Assays. Cells were plated in 96-well plates (1000 ceils/well) in culture medium. The following day, increasing doses of either THZ1 (5232372, EMD Miliipore), Gemcitabine ((#NC0968984, Fisher-Selleck Chemical) or DMSO (BP231-100, Fisher Scientific) control was added and the cells were allowed to grow until DMSO-treated wells reached confluency (5-7 days). To quantify viable ceils, MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5- Diphenyltetrazolium Bromide (M-6494, ThermoFisher Scientific) was added to the culture media at a final concentration of 1 mg/mL and incubated for 3 h at 37°C. Formazan crystals were solubilized with 100 pL/well of DMSO and absorbance was read at 490 nm and normalized to DMSO control.

[0116] Cells were treated with lentivirus expressing CRISPR-Cas9 for sgEGFP, sgCDK7 and sgMYC and were plated in 96-well plates (1000 cells/well). At the indicated time points proliferating cells were quantified by adding MTT (M-6494, ThermoFisher Scientific) to the culture media at a final concentration of 1 mg/mL and incubated for 3 h at 37°C. Formazan crystals were solubilized with 100 pL/well of DMSO and absorbance was read at 490 nm and normalized to sgEGFP control.

[0117] Mice and Xenograft Experiments. Mice were housed in pathogen-free animal facilities. All experiments were conducted under protocol 50982 approved by the Subcommittee on Research Animal Care at Fred Hutchinson Cancer Research Center. For human BxPc3 xenografts, 5x10 ⁶ cells were injected subcutaneously into the flanks of 6-8 week old female CB17/lcr- Prkdc ^scid /lcrCr mice (JAX). Tumors were measured in two dimensions by using manual calipers. Tumor volume was calculated using the formula: V = 0.5 ^c length ^c width ^c width. Animals with tumor established (mean tumor volume of 125 mm ³ ) were divided into two groups, which were then treated with vehicle (10% DMSO in D5W, 5% dextrose in water), THZ1 (3 mg/ml, prepared in vehicle solutions) at the dose of 10 mg/kg intraperitoneally twice daily. Tumor volume was measure every 2-3 days.

[0118] As will be understood by one of ordinary skill in the art, each embodiment disclosed herein can comprise, consist essentially of or consist of its particular stated element, step, ingredient or component. Thus, the terms“include” or“including” should be interpreted to recite:“comprise, consist of, or consist essentially of.” The transition term “comprise” or“comprises” means includes, but is not limited to, and allows for the inclusion of unspecified elements, steps, ingredients, or components, even in major amounts. The transitional phrase“consisting of’ excludes any element, step, ingredient or component not specified. The transition phrase “consisting essentially of” limits the scope of the embodiment to the specified elements, steps, ingredients or components and to those that do not materially affect the embodiment. A material effect would cause a stati sti ca I ly- si gn if icant reduction in the ability of a selective CDK7 inhibitor to treat a QM-PDA, squamous, or low SIRT6 PDAC tumor according to an experimental protocol described in Example 1.

[0119] Unless otherwise indicated, all numbers expressing quantities of ingredients, properties such as molecular weight, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term“about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. When further clarity is required, the term “about” has the meaning reasonably ascribed to it by a person skilled in the art when used in conjunction with a stated numerical value or range, i.e. denoting somewhat more or somewhat less than the stated value or range, to within a range of ±20% of the stated value; ±19% of the stated value; ±18% of the stated value; ±17% of the stated value; ±16% of the stated value; ±15% of the stated value; ±14% of the stated value; ±13% of the stated value; ±12% of the stated value; ±11 % of the stated value; ±10% of the stated value; ±9% of the stated value; ±8% of the stated value; ±7% of the stated value; ±6% of the stated value; ±5% of the stated value; ±4% of the stated value; ±3% of the stated value; ±2% of the stated value; or ±1% of the stated value.

[0120] Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements.

[0121] The terms“a,”“an,”“the” and similar referents used in the context of describing the invention (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. Recitation of ranges of values herein is merely intended to serve as a shorthand method of referring individually to each separate value falling within the range. Unless otherwise indicated herein, each individual value is incorporated into the specification as if it were individually recited herein. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g.,“such as”) provided herein is intended merely to better illuminate the invention and does not pose a limitation on the scope of the invention otherwise claimed. No language in the specification should be construed as indicating any non-claimed element essential to the practice of the invention.

[0122] Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member may be referred to and claimed individually or in any combination with other members of the group or other elements found herein. It is anticipated that one or more members of a group may be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

[0123] Certain embodiments of this invention are described herein, including the best mode known to the inventors for carrying out the invention. Of course, variations on these described embodiments will become apparent to those of ordinary skill in the art upon reading the foregoing description. The inventor expects skilled artisans to employ such variations as appropriate, and the inventors intend for the invention to be practiced otherwise than specifically described herein. Accordingly, this invention includes all modifications and equivalents of the subject matter recited in the claims appended hereto as permitted by applicable law. Moreover, any combination of the above-described elements in all possible variations thereof is encompassed by the invention unless otherwise indicated herein or otherwise clearly contradicted by context.

[0124] Furthermore, numerous references have been made to patents, printed publications, journal articles and other written text throughout this specification (referenced materials herein). Each of the referenced materials are individually incorporated herein by reference in their entirety for their referenced teaching.

[0125] In closing, it is to be understood that the embodiments of the invention disclosed herein are illustrative of the principles of the present invention. Other modifications that may be employed are within the scope of the invention. Thus, by way of example, but not of limitation, alternative configurations of the present invention may be utilized in accordance with the teachings herein. Accordingly, the present invention is not limited to that precisely as shown and described.

[0126] The particulars shown herein are by way of example and for purposes of illustrative discussion of the preferred embodiments of the present invention only and are presented in the cause of providing what is believed to be the most useful and readily understood description of the principles and conceptual aspects of various embodiments of the invention. In this regard, no attempt is made to show structural details of the invention in more detail than is necessary for the fundamental understanding of the invention, the description taken with the drawings and/or examples making apparent to those skilled in the art how the several forms of the invention may be embodied in practice.

[0127] Definitions and explanations used in the present disclosure are meant and intended to be controlling in any future construction unless clearly and unambiguously modified in the following examples or when application of the meaning renders any construction meaningless or essentially meaningless. In cases where the construction of the term would render it meaningless or essentially meaningless, the definition should be taken from Webster's Dictionary, 3rd Edition or a dictionary known to those of ordinary skill in the art, such as the Oxford Dictionary of Biochemistry and Molecular Biology (Ed. Anthony Smith, Oxford University Press, Oxford, 2004).