WO2023109876A1 - Biomarqueurs pour le traitement du cancer colorectal - Google Patents

Biomarqueurs pour le traitement du cancer colorectal Download PDF

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WO2023109876A1
WO2023109876A1 PCT/CN2022/139152 CN2022139152W WO2023109876A1 WO 2023109876 A1 WO2023109876 A1 WO 2023109876A1 CN 2022139152 W CN2022139152 W CN 2022139152W WO 2023109876 A1 WO2023109876 A1 WO 2023109876A1
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drug
aberrations
individual
drug sensitive
drug resistant
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PCT/CN2022/139152
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Pengfei YUAN
Ming Jin
Yongjian Zhang
Hongyan Shen
Ling Yang
Na LIU
Meihua SU
Yaru Zheng
Yulan Li
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Edigene Therapeutics (Beijing) Inc.
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Publication of WO2023109876A1 publication Critical patent/WO2023109876A1/fr

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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present disclosure relates to biomarkers associated with colorectal cancers, as well as to methods of diagnosis, assessment, and treatment of colorectal cancers.
  • Colorectal cancer is the third most common cancer in the world, the second leading cause of cancer-related deaths, and the leading cause of death from gastrointestinal cancer. According to the traditional pathological staging, colorectal cancer is divided into stage 0, stage I, stage II, stage III and stage IV according to the depth of tumor infiltration, lymph node metastasis and distant metastasis.
  • the treatment of early-stage colorectal cancer is usually carried out by surgery or radiotherapy. In addition to surgery and radiotherapy, middle-and late-stage patients are usually treated systematically in combination with chemotherapy and targeted drug therapies. With current treatments, the five-year survival rate for early-stage colorectal cancer exceeds 90%, while the five-year survival rate for advanced metastatic colorectal cancer is only 14%.
  • CDKs Cyclin dependent kinases
  • Cyclin-dependent kinase 7 plays important roles in the regulation of the cell cycle. Together with cyclin H and MAT1, CDK7 forms a trimeric complex functioning as a CDK-activating kinase (CAK) , which activates other CDKs, including CDKs 1, 2, 4, and 6 through T-loop phosphorylation. Phosphorylation of these CDKs is important in progressing the cell cycle.
  • CAK CDK-activating kinase
  • CAK Abnormal regulation of transcription is also prevalent in many cancers.
  • CAK is also a general transcription factor (essential component of TFIIH) .
  • CDK7 plays important roles in activating transcription.
  • CDK7 phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (Pol II) at Ser5 facilitates initiation of transcription.
  • CDK7 phosphorylates CDK9, which then phosphorylates Pol II CTD at Ser2 to promote transcription elongation.
  • CDK7 Elevated levels of CDK7 have been observed in certain cancer types. Due to its role in regulating both the cell cycle and transcription, CDK7 is an attractive target for cancer treatments.
  • the present application in one aspect provide a method of treating a colorectal cancer in an individual (e.g., human) , comprising administering to the individual an effective amount of an inhibitor of CDK7 (hereinafter also referred to as “CDK7 inhibitor” or “CDK7i” ) , wherein the individual is selected for treatment on the basis of having one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11,
  • a method of treating a colorectal cancer in an individual comprising administering to the individual an effective amount of a CDK7 inhibitor, wherein the individual is selected for treatment on the basis of having a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) above a threshold level in a sample from the individual; wherein the drug sensitive aberration (e.g., mutation) is one or more drug sensitive aberrations (e.g., mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CD
  • a method of treating a colorectal cancer in an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B
  • a method of treating a colorectal cancer in an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the individual is above a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of treating a colorectal cancer in an individual comprising responsive to acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC
  • a method of treating a colorectal cancer in an individual comprising responsive to acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the individual is above a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • the acquiring knowledge of one or more drug sensitive aberrations in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPDYA, SMAD2, JUN, DNTTIP1, RBM10, TSC2, TSC1,
  • drug sensitive aberrations e.g., drug sensitive
  • a method of treating a colorectal cancer in an individual comprising detecting one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B,
  • a method of treating a colorectal cancer in an individual comprising administering to the individual an effective amount of a CDK7 inhibitor, wherein the individual comprises one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of treating a colorectal cancer in an individual comprising administering to the individual an effective amount of a CDK7 inhibitor, wherein the individual comprises one or more drug sensitive aberrations (e.g., drug sensitive mutations) in in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX
  • a method of identifying an individual (e.g., human) having a colorectal cancer who may benefit from a treatment comprising administration of a CDK7 inhibitor comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, T
  • a method of identifying an individual (e.g., human) having a colorectal cancer who may not benefit from a treatment comprising administration of a CDK7 inhibitor comprising detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, ILK, KAT2A, KAT6A, KDM5C, KIAA1109,
  • a method of identifying an individual (e.g., human) having a colorectal cancer who may benefit from a treatment comprising administration of a CDK7 inhibitor comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, T
  • a method of selecting a treatment for an individual comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND
  • a method of selecting treatment for an individual comprising detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, ILK, KAT2A, KAT6A, KDM5C, KIAA1109, KIDINS220, LZTS3, MAML3, MAP2K
  • a method of selecting a treatment for an individual comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND
  • a method of identifying one or more treatment options for an individual comprising: (a) detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of identifying one or more treatment options for an individual comprising: (a) detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, ILK, KAT2A, KAT6A, KDM5C, KIAA1109, KIDINS220, LZ
  • a method of identifying one or more treatment options for an individual comprising: (a) detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7
  • drug sensitive aberrations e.g., drug sensitive mutations
  • the method further comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of selecting a treatment for an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FN
  • a method of excluding a treatment for an individual (e.g., human) having a colorectal cancer comprising acquiring knowledge of one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, ILK, KAT2A, KAT6A, KDM5C, KIAA1109, KIDINS220, LZTS3, MAML3, MAP2K4, MAP3
  • drug resistant aberrations e
  • a method of selecting a treatment for an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FN
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of predicting survival of an individual e.g., human having a colorectal cancer treated with a treatment comprising administration of a CDK7 inhibitor
  • the method comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RF
  • a method of predicting survival of an individual e.g., human having a colorectal cancer treated with a treatment comprising administration of a CDK7 inhibitor
  • the method comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RF
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of evaluating an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising: acquiring information that identifies one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FB
  • drug sensitive aberrations e
  • a method of evaluating an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising: acquiring information that identifies one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, H
  • a method of evaluating an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising: acquiring information that identifies one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FB
  • drug sensitive aberrations e
  • a method of screening an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, S
  • a method of screening an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising acquiring knowledge of one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, I
  • a method of screening an individual e.g., human having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer, comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, S
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • the colorectal cancer is any of advanced colon cancer, malignant colon cancer, metastatic colon cancer, stage I, II, III, or IV colon cancer, a colon cancer characterized with a genomic instability, a colon cancer characterized with an alteration of a pathway, a colon cancer classified under the colon cancer subtype (CCS) system as CCS1, CCS2, or CCS3, a colon cancer classified under colorectal cancer assigner (CRCA system) as stem-like, goblet-like, inflammatory, transit-amplifying, or enterocyte subtype, a colon cancer classified under the colon cancer molecular subtype (CCMS) system as C1, C2, C3, C4, C5, or C6 subtype, a colon cancer classified under the CRC intrinsic subtype (CRCIS) system as Type A, Type B, or Type C subtype, or a colon cancer classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS1, CMS2, CMS3, or CMS4.
  • CCS colon cancer subtype
  • CCS1 colon cancer subtype
  • the colon cancer has a microsatellite instability (MSI) status of MSI-high or MSI-low.
  • the individual has previously undergone a therapy (e.g., chemotherapy, radiation, surgery or immunomodulatory therapy) .
  • a therapy e.g., chemotherapy, radiation, surgery or immunomodulatory therapy
  • the individual does not respond to a previous therapy (e.g., chemotherapy, radiation, surgery or immunomodulatory therapy) .
  • the treatment or the one or more treatment options further comprise an additional anti-cancer treatment.
  • the additional anti-cancer treatment comprises one or more of a small molecule inhibitor, an antibody, a cellular therapy, or a nucleic acid.
  • the cellular therapy is an adoptive therapy, a T cell-based therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR) -T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, or a dendritic cell (DC) -based therapy.
  • NK natural killer
  • CAR chimeric antigen receptor
  • TCR recombinant T cell receptor
  • DC dendritic cell
  • the nucleic acid comprises a double-stranded RNA (dsRNA) , a small interfering RNA (siRNA) , or a small hairpin RNA (shRNA) .
  • the additional anti-cancer treatment comprises one or more of a surgery, radiotherapy, chemotherapy, anti-angiogenic therapy, anti-DNA repair therapy, anti-inflammatory therapy, an anti-neoplastic agent, a chemotherapeutic agent, a growth inhibitory agent, an anti-angiogenic agent, or a cytotoxic agent.
  • the additional anti-cancer treatment comprises another CDK inhibitor, e.g., a CDK4 and/or CDK6 (CDK4/6) inhibitor.
  • the additional anti-cancer treatment comprises a Raf kinase inhibitor (e.g., a BRAF inhibitor) .
  • the additional anti-cancer treatment comprises a mitogen-activated protein kinase kinase (MEK) inhibitor.
  • MEK mitogen-activated protein kinase kinase
  • the sample from the individual comprises fluid, cells, or tissue. In some embodiments, the sample from the individual comprises a tumor biopsy or a circulating tumor cell. In some embodiments, the sample from the individual comprises one or more nucleic acids. In some embodiments, the sample from the individual comprises RNA (e.g., mRNA) , genomic DNA, circulating tumor DNA, cell-free DNA, or cell-free RNA. In some embodiments, the sample from the individual comprises chromatin. In some embodiments, the sample from the individual comprises one or more polypeptides. In some embodiments, the sample is a formalin-fixed paraffin-embedded (FFPE) sample.
  • FFPE formalin-fixed paraffin-embedded
  • the sample comprises one or more nucleic acids (e.g., DNA, RNA) and/or one or more polypeptides obtained from an FFPE sample from the individual.
  • the one or more nucleic acids comprise mRNA and/or genomic DNA.
  • the sample is derived from a colorectal cancer tissue in the individual.
  • the sample is selectively enriched for the certain types of polypeptides (e.g., polypeptides or portion thereof encoded by one or a plurality of drug sensitive genes and/or one or a plurality of drug resistant genes) prior to the aberration (e.g., mutation or expression or activity or modification) analysis.
  • the selectively enriching comprises: (a) combining a bait with the sample, thereby allowing the bait to bind to the one or more polypeptides in the sample and producing bait-polypeptide complexes; and (b) isolating the bait-polypeptide complexes to produce the enriched sample.
  • the bait comprises a capture polypeptide molecule configured to bind to the polypeptides (or portion thereof) encoded by the one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPDYA, SMAD2, JUN, DNTTIP1, RBM10, T
  • the capture polypeptide molecule is a polypeptide. In some embodiments, the capture polypeptide molecule is an antibody an antibody fragment. In some embodiments, the bait is conjugated to an affinity reagent or to a detection reagent. In some embodiments, the affinity reagent is biotin. In some embodiments, the detection reagent is a fluorescent marker. In some embodiments, the methods further comprise performing protein-sequencing or mass spectrometry on the one or more polypeptides in the enriched sample.
  • the sample is selectively enriched for the certain types of nucleic acids (e.g., nucleic acids comprising or encoded by one or a plurality of drug sensitive genes and/or one or a plurality of drug resistant genes) prior to the aberration (e.g., mutation or expression or activity) analysis.
  • the selectively enriching comprises: (a) combining a bait with the sample, thereby hybridizing the bait to the one or more nucleic acids in the sample and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the bait comprises a capture nucleic acid molecule configured to hybridize to the one or a plurality of drug sensitive genes (or RNAs encoded thereof) selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPDYA, SMAD2, JUN, DNTTIP1, RBM10, TSC2, TGFBR2,
  • the capture nucleic acid molecule comprises between about 10 and about 30 nucleotides, between about 50 and about 1000 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, or between about 100 and 200 nucleotides.
  • the bait is conjugated to an affinity reagent or to a detection reagent.
  • the affinity reagent is an antibody, an antibody fragment, or biotin, or wherein the detection reagent is a fluorescent marker.
  • the capture nucleic acid molecule comprises a DNA, RNA, or mixed DNA/RNA molecule.
  • the selectively enriching comprises amplifying the one or more nucleic acids in the sample using a polymerase chain reaction (PCR) to produce the enriched sample.
  • the methods further comprise sequencing the one or more nucleic acid molecules, or a relevant portion thereof (e.g., a nucleic acid fragment known to contain a mutation) , in the enriched sample.
  • a plurality of capture nucleic acid molecules configured to hybridize to a plurality of drug sensitive genes (or RNAs encoded thereof) selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPD
  • kits comprising a plurality of capture nucleic acid molecules (or a plurality of baits each comprising a capture nucleic acid molecule) configured to hybridize to a plurality of drug sensitive genes (or RNAs encoded thereof) selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B,
  • the capture nucleic acid molecule comprises between about 10 and about 30 nucleotides, between about 50 and about 1000 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, or between about 100 and 200 nucleotides.
  • the bait is conjugated to an affinity reagent or to a detection reagent.
  • the affinity reagent is an antibody, an antibody fragment, or biotin, or wherein the detection reagent is a fluorescent marker.
  • the capture nucleic acid molecule comprises a DNA, RNA, or mixed DNA/RNA molecule.
  • the selectively enriching comprises amplifying the one or more nucleic acids in the sample using a PCR to produce the enriched sample.
  • the methods further comprise sequencing the one or more nucleic acid molecules, or a relevant portion thereof (e.g., a nucleic acid fragment known to contain a mutation) , in the enriched sample.
  • a system comprising: a memory configured to store one or more program instructions; and one or more processors configured to execute the one or more program instructions, wherein the one or more program instructions when executed by the one or more processors are configured to: (a) obtain a plurality of sequence reads of one or more nucleic acids (e.g., DNA or RNA) or peptides, wherein the one or more nucleic acids or peptides are derived from a sample obtained from an individual (e.g., human) having a colorectal cancer; (b) analyze the plurality of sequence reads for the presence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1,
  • FBXW7
  • the sequence reads are obtained from DNA-seq. In some embodiments, the sequence reads are obtained from RNA-seq. In some embodiments, the sequence reads are obtained from protein-seq (e.g., mass spectrometry) .
  • a non-transitory computer readable storage medium comprising one or more programs executable by one or more computer processors for performing a method, wherein the method comprises: (a) obtaining a plurality of sequence reads of one or more nucleic acids (e.g., DNA or RNA) or peptides, wherein the one or more nucleic acids or peptides are derived from a sample obtained from an individual having a colorectal cancer; (b) analyzing the plurality of sequence reads for the presence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT
  • the sequence reads are obtained from DNA-seq. In some embodiments, the sequence reads are obtained from RNA-seq. In some embodiments, the sequence reads are obtained from protein-seq (e.g., mass spectrometry) .
  • the one or more mutations comprise one or more of an insertion, deletion or substitution of one or more nucleotides, a genomic rearrangement, an alteration in a promoter, a gene fusion, or a copy number alteration. In some embodiments, the one or more mutations result in one or more of an insertion, deletion or substitution of one or more amino acid residues in a polypeptide encoded by a drug sensitive gene or a drug resistant gene.
  • the plurality of sequence reads is obtained by sequencing, whole exome sequencing, RNA-sequencing, whole genome sequencing, gene-targeted sequencing, or next-generation sequencing.
  • the sequence reads are obtained from protein-sequencing (e.g., mass spectrometry) .
  • the entire gene or gene product e.g., RNA, polypeptide
  • a relevant portion of a gene or gene product e.g., RNA, polypeptide
  • is sequenced such as a nucleic acid or polypeptide fragment known to contain a mutation or modification.
  • a CDK7 inhibitor for use in a method of treating a colorectal cancer, wherein the method comprises administering the CDK7 inhibitor to an individual (e.g., human) having a colorectal cancer, wherein one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4,
  • drug sensitive aberrations
  • a CDK7 inhibitor for use in a method of treating a colorectal cancer, wherein the method comprises administering the CDK7 inhibitor to an individual (e.g., human) having a colorectal cancer, wherein one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4,
  • drug sensitive aberrations
  • FIG. 1 shows an exemplary procedure for screening drug sensitive and/or drug resistant genes to anti-cancer drug.
  • FIG. 2 shows exemplary screening workflow for Cas9 + sgRNA iBAR cancer cell library.
  • FIG. 3 shows an exemplary target gene identification workflow for Cas9 + sgRNA iBAR cancer cell library.
  • the present disclosure is based, at least in part, on the discovery of certain biomarkers and their association with drug sensitivity or drug resistance to the treatment of an inhibitor of CDK7 (CDK7 inhibitor) .
  • CDK7 inhibitor an inhibitor of CDK7
  • the inventors have identified a group of genes (referred to as “drug sensitive genes” ) which, when mutated (e.g., inactivated) or repressed for expression in a colorectal cancer cell, render the colorectal cancer cell more sensitive to treatment with a CDK7 inhibitor as compared to a colorectal cancer cell not having such mutation (s) or repression.
  • the inventors have also identified a group of genes (referred to as “drug resistant genes” ) which, when mutated (e.g., inactivated) or repressed for expression in a colorectal cancer cells, render the colorectal cancer cell more resistant to treatment with a CDK7 inhibitor as compared to a colorectal cancer cell not having such mutations or repression.
  • CDK7 inhibitor e.g., a CDK7 inhibitor
  • Aberrations e.g., mutations, aberrant expression, aberrant activity, and/or aberrant modification (e.g., post-translational modification) in these genes can be useful biomarkers for treating (or not treating) an individual having colorectal cancer with a CDK7 inhibitor.
  • patients carrying a mutation (e.g., inactivation) in a drug sensitive gene described herein, and/or with reduced or absent expression (e.g., mRNA or protein) of the drug sensitive gene compared to a healthy individual, and/or with reduced or abolished activity of the drug sensitive gene (e.g., RNA or protein activity, such as due to epigenetic or post-translational modification) compared to a healthy individual, are particularly suitable for treatment with the corresponding anti-cancer drug.
  • the present invention in some embodiments provides a method of treating a colorectal cancer by a CDK7 inhibitor, wherein the treatment is based on the presence or absence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) described herein.
  • the treatment options comprises a treatment comprising administration of a CDK7 inhibitor.
  • provided herein are methods of selecting treatment for an individual having a colorectal cancer based on the presence or absence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) described herein.
  • methods of predicting survival of an individual having a colorectal cancer treated with a CDK7 inhibitor based on the presence or absence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) described herein.
  • kits for identifying an individual having a colorectal cancer who may benefit from a treatment comprising administration of a CDK7 inhibitor based on the presence or absence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) described herein.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • systems comprising one or more processors; and a non-transitory computer readable storage medium comprising one or more programs executable by the one or more processors for performing any one of the methods described herein.
  • the term “configured to hybridize to” indicates that a nucleic acid molecule has a nucleotide sequence with sufficient length and sequence complementarity to the nucleotide sequence of a target nucleic acid to allow the nucleic acid molecule to hybridize to the target nucleic acid, e.g., with a T m of at least 65°C in an aqueous solution of 1 ⁇ SCC (150 mM sodium chloride and 15 mM trisodium citrate) and 0.1%SDS.
  • Other hybridization conditions may be used when hybridizing a nucleic acid molecule to a target nucleic acid molecule, for example in the context of a described method.
  • Percent (%) sequence identity with respect to a reference polypeptide or polynucleotide sequence is defined as the percentage of amino acid residues or nucleotides in a sequence that are identical to the amino acid residues or nucleotides in the reference polypeptide or polynucleotide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • mammals include, but are not limited to, domesticated animals (e.g., cows, sheep, cats, dogs, and horses) , primates (e.g., humans and non-human primates such as monkeys) , rabbits, and rodents (e.g., mice and rats) .
  • the individual or subject is a human.
  • the individual is human patient, e.g., a human patient having a cancer described herein.
  • treatment is an approach for obtaining beneficial or desired results including clinical results.
  • beneficial or desired clinical results include, but are not limited to, one or more of the following: alleviating one or more symptoms resulting from the disease, diminishing the extent of the disease, stabilizing the disease (e.g., preventing or delaying the worsening of the disease) , preventing or delaying the spread (e.g., metastasis) of the disease, preventing or delaying the recurrence of the disease, delay or slowing the progression of the disease, ameliorating the disease state, providing a remission (partial or total) of the disease, decreasing the dose of one or more other medications required to treat the disease, delaying the progression of the disease, increasing the quality of life, and/or prolonging survival.
  • treatment is a reduction of a pathological consequence of a cancer. The methods of the invention contemplate any one or more of these aspects of treatment.
  • “delaying” the development of a cancer means to defer, hinder, slow, retard, stabilize, and/or postpone development of the disease. This delay can be of varying lengths of time, depending on the history of the disease and/or individual being treated. As is evident to one skilled in the art, a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease.
  • a method that “delays” development of a cancer is a method that reduces probability of disease development in a given time frame and/or reduces the extent of the disease in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a statistically significant number of subjects.
  • Cancer development can be detectable using standard methods, including, but not limited to, computerized axial tomography (CAT Scan) , Magnetic Resonance Imaging (MRI) , abdominal ultrasound, clotting tests, arteriography, or biopsy. Development may also refer to cancer progression that may be initially undetectable and includes occurrence, recurrence, and onset.
  • CAT Scan computerized axial tomography
  • MRI Magnetic Resonance Imaging
  • abdominal ultrasound clotting tests
  • arteriography arteriography
  • biopsy biopsy.
  • cancer progression may be initially undetectable and includes occurrence, recurrence, and onset.
  • an amount of a compound or composition sufficient to treat a specified disorder, condition or disease such as ameliorate, palliate, lessen, and/or delay one or more of its symptoms.
  • beneficial or desired results include, e.g., decreasing one or more symptoms resulting from the disease (biochemical, histologic and/or behavioral) , including its complications and intermediate pathological phenotypes presenting during development of the disease, increasing the quality of life of those suffering from the disease, decreasing the dose of other medications required to treat the disease, enhancing effect of another medication, delaying the progression of the disease, and/or prolonging survival of patients.
  • an effective amount comprises an amount sufficient to cause a tumor tissue to shrink and/or to decrease the growth rate of the tumor tissue or to prevent or delay other unwanted cell proliferation in the tumor. In some embodiments, an effective amount is an amount sufficient to delay development of a cancer. In some embodiments, an effective amount is an amount sufficient to prevent or delay recurrence. An effective amount can be administered in one or more administrations.
  • the effective amount of the drug or composition may: (i) reduce the number of tumor cells; (ii) reduce the tumor size; (iii) inhibit, retard, slow to some extent and preferably stop a tumor cell infiltration into peripheral organs; (iv) inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; (v) inhibit tumor growth; (vi) prevent or delay occurrence and/or recurrence of tumor; and/or (vii) relieve to some extent one or more of the symptoms associated with the cancer.
  • “Likely to respond” or “responsiveness” as used herein refers to any kind of improvement or positive response either clinical or non-clinical selected from, but not limited to, measurable reduction in tumor size or evidence of disease or disease progression, complete response, partial response, stable disease, increase or elongation of progression free survival, or increase or elongation of overall survival.
  • an individual that is likely to respond to treatment with an anti-cancer therapy e.g., an anti-cancer therapy provided herein, alone or in combination, has an increased probability of responding to treatment with the anti-cancer therapy alone or in combination, relative to a reference individual or group of individuals.
  • “Unlikely to” refers to a decreased probability that an event, item, object, thing or person will occur relative to a reference individual or group of individuals.
  • an individual that is unlikely to respond to treatment with an anti-cancer therapy e.g., an anti-cancer therapy provided herein, alone or in combination, has a decreased probability of responding to treatment with the anti-cancer therapy, alone or in combination, relative to a reference individual or group of individuals.
  • Doubling time” or “population doubling time” (PDT) herein refers to the time it takes for a cell population to double in size.
  • Cell doubling time ln (2) / (growth rate) .
  • Growth rate (gr) refers to the amount of doubling in one unit of time. in which N (t) is the number of cells at time t, N (0) is the number of cells at time 0, t is time (usually in hours) .
  • sample refers to a biological sample obtained or derived from a source of interest, as described herein.
  • the present application in some embodiments provides a method of identifying an individual having a colorectal cancer who may benefit from a treatment comprising administration of a CDK7 inhibitor, the method comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes, wherein the presence of the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in the sample identifies the individual as one who may benefit from the treatment.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of identifying an individual having a colorectal cancer who may not benefit from a treatment comprising administration of a CDK7 inhibitor comprising detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, wherein the presence of the one or more drug resistant aberrations (e.g., drug resistant mutations) in the sample identifies the individual as one who may not benefit from a treatment.
  • a method of identifying an individual having a colorectal cancer who may benefit from a treatment comprising administration of a CDK7 inhibitor comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, wherein a composite score of the drug sensitive aberrations (e.g., drug sensitive mutations) and the drug resistant aberrations (e.g., drug resistant mutations) above a threshold level identifies the individual as one who may benefit from the treatment.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of selecting a treatment for an individual having a colorectal cancer comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes, wherein the presence of the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in the sample identifies a treatment comprising administration of a CDK7 inhibitor as a suitable treatment for the individual.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of selecting treatment for an individual having a colorectal cancer comprising detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, wherein the presence of the one or more drug resistant aberrations (e.g., drug resistant mutations) in the sample identifies a treatment comprising administration of a CDK7 inhibitor as an unsuitable treatment for the individual.
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of selecting a treatment for an individual having a colorectal cancer comprising detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, wherein a composite score of the drug sensitive aberrations (e.g., drug sensitive mutations) and the drug resistant aberrations (e.g., drug resistant mutations) above a threshold level identifies a treatment comprising administration of a CDK7 inhibitor as a suitable treatment for the individual.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of identifying one or more treatment options for an individual having a colorectal cancer comprising: (a) detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes; and (b) generating a report, wherein the report comprises one or more treatment options identified for the individual based at least in part on the presence of the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in the sample, wherein the one or more treatment options comprise a treatment comprising administration of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of identifying one or more treatment options for an individual having a colorectal cancer comprising: (a) detecting in a sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes; and (b) generating a report, wherein the report comprises one or more treatment options identified for the individual based at least in part on the presence of the one or more drug resistant aberrations (e.g., drug resistant mutations) in the sample, wherein the one or more treatment options do not comprise a treatment comprising administration of a CDK7 inhibitor.
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of identifying one or more treatment options for an individual having a colorectal cancer comprising: (a) detecting in a sample from the individual one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes; (b) detecting in the sample from the individual one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes; and (c) generating a report, wherein the report comprises one or more treatment options identified for the individual based at least in part on the presence of the one or more drug sensitive aberrations (e.g., drug sensitive mutations) and the one or more drug resistant aberrations (e.g., drug resistant mutations) in the sample, wherein the one or more treatment options comprise a treatment comprising administration of a CDK7 inhibitor.
  • the one or more treatment options comprise a treatment comprising administration of a CDK7 inhibitor.
  • the method further comprises obtaining a composite score of the drug sensitive aberrations (e.g., drug sensitive mutations) and the drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of selecting a treatment for an individual having a colorectal cancer comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample from the individual, wherein responsive to the acquisition of knowledge: (i) the individual is classified as a candidate to receive a treatment comprising administration of a CDK7 inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment comprising administration of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of excluding a treatment for an individual having a colorectal cancer comprising acquiring knowledge of one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, wherein responsive to the acquisition of knowledge: (i) the individual is classified as a candidate not to receive a treatment comprising administration of a CDK7 inhibitor; and/or (ii) the individual is identified as unlikely to respond to a treatment comprising administration of a CDK7 inhibitor.
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of selecting a treatment for an individual having a colorectal cancer comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, wherein responsive to the acquisition of knowledge: (i) the individual is classified as a candidate to receive a treatment comprising administration of a CDK7 inhibitor; and/or (ii) the individual is identified as likely to respond to a treatment comprising administration of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of predicting survival of an individual having a colorectal cancer treated with a treatment comprising administration of a CDK7 inhibitor comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample from the individual, , wherein responsive to the acquisition of said knowledge, the individual is predicted to have longer survival after treatment with the CDK7 inhibitor, as compared to an individual who does not have the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in an equivalent sample.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of predicting survival of an individual having a colorectal cancer treated with a treatment comprising administration of a CDK7 inhibitor comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, wherein responsive to the acquisition of said knowledge, the individual is predicted to have longer survival after treatment with the CDK7 inhibitor, as compared to an individual who does not have the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in an equivalent sample.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of evaluating an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising: acquiring information that identifies one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in the individual, wherein said information identifies the individual as being suitable for a treatment comprising administration of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of evaluating an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising: acquiring information that identifies one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in the individual, wherein said information identifies the individual as being unsuitable for a treatment comprising administration of a CDK7 inhibitor.
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of evaluating an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising: acquiring information that identifies one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in the individual and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in the individual, wherein said information (e.g., a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) above a threshold level) identifies the individual as being suitable for a treatment comprising administration of a CDK7 inhibitor.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of screening an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample from the individual, wherein responsive to the acquisition of said knowledge, the individual is predicted to have decreased risk of colorectal cancer recurrence, aggressive colorectal cancer, anti-cancer therapy resistance, or poor prognosis, as compared to an individual not having the one or more drug sensitive aberrations (e.g., drug sensitive mutations) .
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of screening an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising acquiring knowledge of one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, wherein responsive to the acquisition of said knowledge, the individual is predicted to have increased risk of colorectal cancer recurrence, aggressive colorectal cancer, anti-cancer therapy resistance, or poor prognosis, as compared to an individual not having the one or more drug resistant aberrations (e.g., drug resistant mutations) .
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of screening an individual having a colorectal cancer, suspected of having a colorectal cancer, being tested for a colorectal cancer, being treated for a colorectal cancer, or being tested for a susceptibility for colorectal cancer comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, wherein responsive to the acquisition of said knowledge, the individual is predicted to have decreased risk of colorectal cancer recurrence, aggressive colorectal cancer, anti-cancer therapy resistance, or poor prognosis, as compared to an individual not having the one or more drug sensitive aberrations (e.g., drug sensitive mutations) .
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the method further comprises comparing the composite score with a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • the anti-cancer therapy comprises administration of a CDK7 inhibitor.
  • a method of treating a colorectal cancer in an individual comprising administering to the individual an effective amount of a CDK7 inhibitor, wherein the individual is selected for treatment on the basis of having one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample from the individual.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of treating a colorectal cancer in an individual comprising administering to the individual an effective amount of a CDK7 inhibitor, wherein the individual is selected for treatment on the basis of having a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) above a threshold level in a sample from the individual, wherein the drug sensitive aberrations (e.g., drug sensitive mutations) is one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and wherein the drug resistant aberrations (e.g., drug resistant mutations) is one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of treating a colorectal cancer in an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample from the individual, and responsive to said knowledge, administering to the individual an effective amount of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of treating a colorectal cancer in an individual comprising acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, and responsive to said knowledge, administering to the individual an effective amount of a CDK7 inhibitor.
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the individual is above a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • a method of treating a colorectal cancer in an individual comprising responsive to acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes in a sample of the individual, administering to the individual an effective amount of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • a method of treating a colorectal cancer in an individual comprising responsive to acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample of the individual, administering to the individual an effective amount of a CDK7 inhibitor.
  • the acquisition of knowledge comprises obtaining a composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the sample of the individual.
  • the composite score of drug sensitive aberrations (e.g., drug sensitive mutations) and drug resistant aberrations (e.g., drug resistant mutations) in the individual is above a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • the acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample of the individual comprises detecting the one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in the sample.
  • a method of treating a colorectal cancer in an individual comprising detecting one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample from the individual, and administering to the individual an effective amount of a CDK7 inhibitor.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • a method of treating a colorectal cancer in an individual comprising administering to an individual an effective amount of a CDK7 inhibitor, wherein the individual comprises one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes.
  • a CDK7 inhibitor comprising administering to an individual an effective amount of a CDK7 inhibitor, wherein the individual comprises one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes.
  • a method of treating a colorectal cancer in an individual comprising administering to an individual an effective amount of a CDK7 inhibitor, wherein the individual comprises one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, and wherein a composite score of the drug sensitive aberrations (e.g., drug sensitive mutations) and the drug resistant aberrations (e.g., drug resistant mutations) is above a threshold level.
  • the composite score is determined by Formula I.
  • the threshold level is zero.
  • the one or a plurality of drug sensitive genes is selected from the group consisting of drug sensitive genes provided in Table 1. In some embodiments, the one or a plurality of drug sensitive genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all genes provided in Table 1.
  • the one or a plurality of drug sensitive genes is selected from the group consisting of ANK3, ARNT, BAMBI, CCND1, CDC25B, CDC42, CDH23, CDK12, CDK6, CENPF, CHD2, CHD7, CREBBP, CRK, CRKL, CTNNB1, CTNNBIP1, DDIT4, DKK1, DLG5, DLL4, DOCK1, E2F4, EGFR, EP300, FAM21C, FBXW11, FBXW7, FGF8, FZD8, HOXB13, HPRT1, HUWE1, ID1, ID2, ITGB1, JUN, KMT2D, KMT2E, MAPK1, MAPK11, MYCBP2, MYH9, NBEAL2, NCSTN, NF2, NLE1, NODAL, NPHS1, NRAP, OSM, PARP1, PIK3CB, PRKDC, PTPN11
  • the one or a plurality of drug sensitive genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, or all genes provided in Table 1a) .
  • the one or a plurality of drug sensitive gene is selected from the group consisting of ARID2, ARNT, BAMBI, CCND1, CCND3, CDC25A, CDC25B, CDC42, CDK4, CDK6, CRKL, CSNK2A1, CTNNB1, CTNNBIP1, DLG5, DLL4, DOT1L, E2F3, E2F4, EGFR, FBXW7, FGF8, HPRT1, ID1, ID2, ITGB1, JUN, KMT2D, LARP4B , MAPK1, MAPK11, NCSTN, NF2, NODAL, NPM1, OSM, PBRM1, PRKAA1, PRKDC, RAPGEF1, RBM10, RHOA, RICTOR, RIPK1, SAV1,
  • the one or a plurality of drug sensitive genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or all genes provided in Table 1b) .
  • the one or plurality of drug sensitive gene is selected from the group consisting of BUB1B, CDC42, CDK4, CHEK2, CREBBP, CRKL, CSNK2A1, CTNNB1, DAXX, DDIT4, DIDO1, DKK1, DLG5, DOCK1, E2F3, EGFR, EIF2S1, EP300, ESPL1, FBXW7, FGF8, ID1, ITGB1, JUN, LATS2, MAPK1, MAPK8, NCSTN, NF2, NLE1, NPM1, PARP1, PIK3CB, PLA2G6, PLK1, PRKAA1, PRKDC, RBM10, RET, RHOA, RIPK1, RPS6KB1, SAV1, SMAD4, SNW1, SRC, TCF7L2, TGFBR
  • the one or a plurality of drug sensitive genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, or all genes provided in Table 1c) .
  • the one or plurality of drug sensitive gene is selected from the group consisting of ANK3, BUB1B, CCND1, CCND3, CDC25A, CDC25B, CDC42, CDK12, CDK4, CDK6, CDK7, CENPF, CHEK2, CNOT1, CSNK2A1, CTNNB1, CUL9, DOT1L, E2F3, E2F4, EGFR, EP300, ESPL1, FBXW11, FBXW7, FGF8, ID2, ITGB1, JUN, KMT2E, LATS2, MAPK1, MYH9, NF2, NLE1, NPM1, PBRM1, PLK1, PRKAA1, PRKDC, PTPN11, RHOA, RIPK1, RPS6KB1, SPDYA, SRC, SVIL,
  • the one or a plurality of drug resistant genes is selected from the group consisting of drug resistant genes provided in Table 2. In some embodiments, the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or all genes provided in Table 2.
  • the one or a plurality of drug resistant genes is selected from the group consisting of ACVR1, CDKN1A, CKS2, CTBP1, EIF4G1, HSP90AA1, HSP90AB1, ILK, KAT2A, MAPK14, MLST8, NCOR1, PPP2R1A, PRKAR1A, PTEN, RBL1, RHEB, ROCK2, RPS6KA2, RPS6KA3, RPTOR, STK11, TP53, TP53BP1, TP73, and USP28.
  • the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, or all genes provided in Table 2a) .
  • the one or a plurality of drug resistant gene is selected from the group consisting of ADRA2A, BMPR1A, BMPR2, CDKN1A, CKS2, CTBP1, CTBP2, HDAC1, HDAC2, HES5, ILK, KAT2A, MAPK14, PRKAR1A, PTEN, RAC1, RAF1, RBPJ, RPS6KA2, RPTOR, STK11, TEAD3, TP53, TP73, and USP28.
  • the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 5, 10, 15, 20, or all genes provided in Table 2b) .
  • the one or plurality of drug resistant gene is selected from the group consisting of ACVR1, ANKRD1, BMPR2, CDKN1A, EIF4G1, HDAC1, HDAC2, HSP90AB1, ILK, MAP2K4, MAPK14, PPP2R1A, PPP2R1B, PTEN, RAF1, RPS6KA2, RPS6KA3, STK11, TNFRSF10B, TP53, TP73, USP28, ARID1A, KIDINS220, MED12, and ZMYND8.
  • the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 5, 10, 15, 20, or all genes provided in Table 2c) .
  • the one or plurality of drug resistant gene is selected from the group consisting of ACVR1, HES5, ILK, MAPK14, PPP2R1A, PRKAR1A, PTEN, RAC1, ROCK2, and SIGLEC8.
  • the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or all genes provided in Table 2d) .
  • the one or a plurality of drug sensitive genes is selected from the group consisting of drug sensitive genes provide in Table 1
  • the one or a plurality of drug resistant genes is selected from the group consisting of drug resistant genes provided in Table 2.
  • the one or a plurality of drug sensitive genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all genes provided in Table 1
  • the one or a plurality of drug resistant genes comprise at least about any of 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, or all genes provided in Table 2.
  • an “aberration” at a gene refers to a genetic and/or epigenetic aberration of a gene, an aberrant expression level, and/or an aberrant activity level, and/or an aberrant modification level of the gene (or gene product, such as RNA or protein) that may lead to abnormal loss of function or reduced function and/or abnormal expression (e.g., reduced or absent) of the RNA and/or protein encoded by the gene.
  • a genetic aberration comprises a change to the nucleic acid (such as DNA or RNA) or protein sequence (i.e.
  • an aberration at a gene comprises a mutation of the gene, includes, but not limited to, deletion, frameshift, insertion, indel, missense mutation, nonsense mutation, point mutation, silent mutation, splice site mutation, splice variant, and translocation.
  • the mutation may be a loss or deletion of the gene.
  • the mutation is a deleterious mutation.
  • an aberration at a gene comprises aberrant (e.g., reduced or absent) expression (e.g., mRNA or protein) of a gene compared to a control level.
  • an aberration at a gene comprises aberrant (e.g., reduced or abolished) activity of a gene product (e.g., RNA or protein) compared to a control level, such as activation or inhibition of downstream targets.
  • an aberration at a gene comprises aberrant modification (e.g., increased, decreased, or mis-modification) of a gene (e.g., at DNA level or histone level) or gene product (e.g., RNA or protein) compared to a control level, such as post-translational modification (e.g., phosphorylation, ubiquitination) .
  • an aberration at a gene comprises a copy number variation of the gene.
  • the copy number variation of the gene is caused by structural rearrangement of the genome, including deletions, duplications, inversion, and translocations.
  • an aberration at a gene comprises an aberrant epigenetic feature of the gene, including, but not limited to, DNA methylation, hydroxymethylation, increased or decreased histone binding, histone methylation, histone acetylation, chromatin remodeling, and the like.
  • the aberration is determined in comparison to a control or reference, such as a reference sequence (such as a nucleic acid sequence or a protein sequence) , a control expression (such as RNA or protein expression) level, a control activity (such as activation or inhibition of downstream targets) level, or a control modification (e.g., post-translational modification or epigenetic modification) level.
  • the aberrant expression level or the aberrant activity level in a gene may be below the control level (such as about any of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%or more below the control level) .
  • the aberrant modification level in a gene e.g., modification of DNA, nucleosome, RNA, or protein
  • the control level such as about any of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%or more below the control level
  • the control level such as about any of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%or more below the control level
  • above the control level such as about any of 10%, 20%, 30%, 40%, 60%, 70%, 80%, 90%or more above the control level
  • the aberrant modification in a gene is a mis-modification, e.g., ubiquitination instead of phosphorylation.
  • the control level e.g. expression level or activity level or modification level
  • the control population is the median level (e.g. expression level or activity level or modification level) of a control population.
  • the control population is a population having the same cancer as the individual being/to be treated.
  • the control population is a healthy population that does not have the cancer, and optionally with comparable demographic characteristics (e.g. gender, age, ethnicity, etc. ) as the individual being/to be treated.
  • the control level e.g.
  • expression level or activity level or modification level is a level (e.g. expression level or activity level or modification level) of a healthy tissue from the same individual.
  • An aberration at a gene may be determined by comparing to a reference sequence, including epigenetic patterns of the reference sequence in a control sample.
  • the reference sequence is the sequence (DNA, RNA or protein sequence) corresponding to a fully functional allele of the corresponding gene, such as an allele (e.g. the prevalent allele) of the corresponding gene present in a healthy population of individuals that do not have the cancer, but may optionally have similar demographic characteristics (such as gender, age, ethnicity etc. ) as the individual being/to be treated.
  • An aberration at a target gene is herein also referred to as “target gene aberration, ” including but not limited to target gene mutation.
  • An aberration at a drug sensitive gene is herein also referred to as “drug sensitive aberration, ” including but not limited to drug sensitive mutation, which makes the cancer cells sensitive to an anti-cancer drug (e.g., CDK7 inhibitor) .
  • An aberration at a drug resistant gene is herein also referred to as “drug resistant aberration, ” including but not limited to drug resistant mutation, which makes the cancer cells resistant to an anti-cancer drug (e.g., CDK7 inhibitor) .
  • An aberration at a patient gene is herein also referred to as “patient gene aberration, ” including but not limited to patient gene mutation.
  • An aberration at a patient target gene is herein also referred to as “patient target gene aberration, ” including but not limited to patient target gene mutation.
  • the “status” of an aberration at a gene may refer to the presence or absence of the aberration at the gene, or the aberrant level (expression or activity or modification level) of the gene.
  • the presence of an aberration (such as a mutation) in one or more drug sensitive genes as compared to a control indicates that (a) the individual is more likely to respond to an anti-cancer drug (e.g., CDK7 inhibitor) treatment or (b) the individual is selected for an anti-cancer drug treatment.
  • an anti-cancer drug e.g., CDK7 inhibitor
  • the absence of an aberration (such as a mutation) in one or more drug sensitive genes compared to a control indicates that (a) the individual is less likely to respond to an anti-cancer drug (e.g., CDK7 inhibitor) treatment or (b) the individual is not selected for an anti-cancer drug treatment.
  • an aberrant level such as expression level or activity level or modification level
  • a larger deviation of the level e.g.
  • a prediction model e.g., composite score
  • the level (s) e.g. expression level or activity level or modification level
  • the prediction model including, for example, coefficient for each level, may be obtained by statistical analysis, such as regression analysis, using clinical trial data.
  • detecting the one or more drug sensitive aberrations and/or drug resistant aberrations comprises detecting mutation (s) in the one or more drug sensitive genes and/or the one or more drug resistant genes (or gene product) , such as by DNA-seq, RNA-seq, mass spectrometry, or any other nucleic acid/peptide sequence detection methods.
  • detecting the one or more drug sensitive aberrations and/or drug resistant aberrations comprises detecting aberrant (e.g., reduced or absent) expression (e.g., RNA or protein) of the one or more drug sensitive genes and/or the one or more drug resistant genes compared to a control level, such as by qPCR, RNA-seq, mass spectrometry, western blot, or any other RNA or protein expression level detection methods.
  • aberrant expression e.g., RNA or protein
  • detecting the one or more drug sensitive aberrations and/or drug resistant aberrations comprises detecting aberrant modification at the one or more drug sensitive genes and/or the one or more drug resistant genes compared to a control level (e.g., healthy individual) , such as epigenetic modification (e.g., DNA methylation, histone methylation, histone acetylation) or post-translational modification (e.g., ubiquitination, phosphorylation) .
  • epigenetic modification e.g., DNA methylation, histone methylation, histone acetylation
  • post-translational modification e.g., ubiquitination, phosphorylation
  • detecting the one or more drug sensitive aberrations and/or drug resistant aberrations comprises detecting aberrant (e.g., reduced or absent) activity of expression product (e.g., RNA or protein) (or portion thereof) of the one or more drug sensitive genes and/or the one or more drug resistant genes compared to a control level (e.g., healthy individual) .
  • aberrant e.g., reduced or absent activity of expression product (e.g., RNA or protein) (or portion thereof) of the one or more drug sensitive genes and/or the one or more drug resistant genes compared to a control level (e.g., healthy individual) .
  • Any suitable gene function/activity testing methods can be used herein, such as detecting signal transduction, activation status (e.g., phosphorylation status) of downstream pathway molecules, protein-protein binding affinity and/or specificity, metabolism, cell behavior (e.g., cell proliferation, death, cell cycle) , cytokine release, etc.
  • the composite score can be calculated, and/or the composite score threshold level can be selected, using any methods known in the art. For example, see response score or recombination proficiency score (RPS) in US20160369353, also see US20200254259, US20180068083, the contents of each of which are incorporated herein by reference in their entirety.
  • RPS response score or recombination proficiency score
  • the composite score is based on one or more of drug sensitive aberrations and/or drug resistant aberrations, such as one or more of drug sensitive mutations, drug resistant mutations, aberrant expression of the drug sensitive genes, aberrant expression of the drug resistant genes, aberrant activity of expression products of the drug sensitive genes, aberrant activity of expression products of the drug resistant genes, aberrant modification of the drug sensitive genes (or gene product) , and aberrant modification of the drug resistant genes (or gene product) , etc.
  • the composite score is obtained by subtracting (the number of drug resistant genes with drug resistant aberrations carried by the patient) from (the number of drug sensitive genes with drug sensitive aberrations carried by the patient) , wherein the individual is selected for treatment if the composite score is above zero.
  • the severity of the drug sensitive mutation or drug resistant mutation in the patient adds weight to the composite score, for example, a drug sensitive mutation that affects the expression and/or activity of a drug sensitive gene more adds more weight to the composite score compared to another drug sensitive mutation that affects less of the expression and/or activity of the same drug sensitive gene.
  • the degree of the aberrant expression of a drug sensitive gene or a drug resistant gene in the patient compared to a control level adds weight to the composite score, for example, loss of expression of a drug sensitive gene adds more weight to the composite score compared to reduced expression of the same drug sensitive gene.
  • the degree of the aberrant activity (e.g., RNA or protein activity) of a drug sensitive gene or a drug resistant gene in the patient compared to a control level adds weight to the composite score, for example, loss of protein activity (e.g., abolished binding) of a drug sensitive gene adds more weight to the composite score compared to reduced protein activity (e.g., reduced binding) of the same drug sensitive gene.
  • the degree of the aberrant modification e.g., modification of DNA, nucleosome, RNA, or protein
  • a control level e.g., healthy individual
  • each drug resistant gene has a resistance score
  • each drug sensitive gene has a sensitivity score (e.g., based on experiments, publications or databases) .
  • the composite score is obtained by subtracting (the absolute value of the sum of the resistance scores of the drug resistant genes) from (the absolute value of the sum of the sensitivity scores of the drug sensitive genes) , wherein the individual is selected for treatment if the composite score is above zero.
  • parameter “m” is the total number of drug resistant genes and drug sensitive genes described herein (hereinafter also referred to as “gene panel described herein” ) .
  • parameter “m” is the total number of drug sensitive genes provided in Table 1 and drug resistant genes provided in Table 2 ( “full gene panel” ) , or a selected subgroup of drug sensitive genes provided in Table 1 and a selected subgroup of drug resistant genes provided in Table 2 ( “subgroup gene panel” , such as drug sensitive genes and drug resistant genes with function (s) in “cell cycle” from Tables 1 and 2) .
  • one or more patient aberrations e.g., mutation, or aberrant expression/activity/modification
  • one or more patient mutations e.g., nonsynonymous, nonsense, missense, frameshift, insertion, deletion, stop-loss, stop-gain, mutation that results in mis-splicing, gene fusion, etc.
  • patient mutations e.g., nonsynonymous, nonsense, missense, frameshift, insertion, deletion, stop-loss, stop-gain, mutation that results in mis-splicing, gene fusion, etc.
  • no patient aberration e.g., patient mutation
  • Patient gene (s) or patient aberrations e.g., mutation, or aberrant expression/activity/modification
  • a patient e.g., patient sample, such as by NGS
  • patient target gene (s) or patient target aberration (s) ” (such as “patient target mutation (s) ” )
  • Parameter “m” is an integer of at least 1, and is a constant for specific cancer type and specific anti-cancer drug.
  • the composite score is calculated based on one or more patient-related parameters, such as i) the number of deleterious mutation (s) (e.g., nonsynonymous, nonsense, missense, frameshift, insertion, deletion, stop-loss, stop-gain, mutation that results in mis-splicing, gene fusion, etc.
  • s deleterious mutation
  • s nonsynonymous, nonsense, missense, frameshift, insertion, deletion, stop-loss, stop-gain, mutation that results in mis-splicing, gene fusion, etc.
  • the one or more patient-related parameters are derived based on data/information from patient sample, such as sequencing read counts. Parameter denotes estimated fraction of cells carrying j th mutation in i th patient target gene identified from the patient.
  • n is an integer of at least 1, and is the total number of detected deleterious patient target mutations of the corresponding identified patient target gene.
  • j is an integer, and 1 ⁇ j ⁇ n.
  • the fraction of cells carrying j th mutation in i th patient target gene is estimated based on the fraction of sequences comprising the j th mutation among all sequences comprising a mutation in the i th patient target gene identified from the patient sample.
  • LFC i denotes the log-scale (e.g., log2) fold change of expression level of i th patient target gene in patient disease tissue vs. normal tissue.
  • Expression level of a patient target gene can be measured using any known methods, such as RNA-seq, qPCR, mass spectrometry, western blot, FISH, immunofluorescence staining, etc.
  • the composite score is calculated based on one or more gene-related parameters, such as i) the correlation (positive correlation or negative correlation) between a patient target gene and an anti-cancer drug (e.g., CDK7 inhibitor) treatment (e.g., at IC50) (parameter “r” ) , which is derived from machine learning (e.g., based on training models from public data on cell lines) , ii) the normalized weight of a patient target gene in response to an anti-cancer drug treatment (parameter ) , which is derived from machine learning (e.g., based on training models from public data on cell lines) , iii) the predicted impact of a deleterious mutation of a patient target gene (parameter “ ⁇ ” ; e.g., based on harmfulness prediction with public databases, such as aberrant gene or gene product activity) , iv) the ratio of net survival contribution of a patient target gene to total survival at a given time point according to the Kaplan-M
  • the one or more gene-related parameters are derived based on data in public or patient database (s) , for training the composite score model.
  • Parameter “r i ” denotes the correlation (positive correlation or negative correlation) between i th patient target gene identified from the patient and an anti-cancer drug treatment (e.g., at IC50) , which is derived from machine learning.
  • Parameter denotes the normalized weight of i th patient target gene in response to an anti-cancer drug treatment (i.e., the contribution of the loss-of-function of i th patient target gene to the anti-cancer drug treatment) , which is derived from machine learning.
  • Parameter “ ⁇ ij ” denotes the predicted impact of the j th deleterious mutation of i th patient target gene (e.g., based on harmfulness prediction with public databases, or is a manually assigned constant) .
  • Parameter denotes the ratio of net survival contribution of i th patient target gene to total survival at a given time point according to the Kaplan-Meier survival curve (e.g., based on TCGA and/or cBioPortal databases) .
  • LFC i denotes the log-scale (e.g., log2) fold change of expression level of i th patient target gene in disease tissue vs. normal tissue (e.g., based on patient database (s) , i.e., information collected from patients having the same cancer) .
  • i is an integer
  • j is an integer
  • the composite score is calculated based on one or more pathway-related parameters, such as i) the estimated weight of a patient target gene in pathway (s) and/or regulatory network (s) involving the patient target gene (parameter e.g., based on public database (s) such as KEGG and InterProScan) , ii) the normalized weight of a patient target gene in anti-cancer drug-related pathway (s) (parameter “ ⁇ ” ; e.g., based on public database (s) ) , etc.
  • the one or more pathway-related parameters are derived based on data in public database (s) , for training the composite score model.
  • Parameter denotes the estimated weight of i th patient target gene in pathway (s) and/or regulatory network (s) involving i th patient target gene (e.g., based on public database (s) such as KEGG and InterProScan) .
  • Parameter “ ⁇ i ” denotes the normalized weight of i th patient target gene in anti-cancer drug-related pathway (s) , e.g., based on public database (s) .
  • “i” is an integer, and 0 ⁇ i ⁇ m.
  • the composite score is calculated based on one or more parameters selected from one or more of patient-related parameters, gene-related parameters, and pathway-related parameters described herein.
  • the composite score is calculated using Formula I:
  • a, b, and c are constants for model tuning (e.g., constants derived from trained model for corresponding anti-cancer drug, such as a CDK7 inhibitor) , wherein -1 ⁇ a ⁇ 1, -1 ⁇ b ⁇ 1, and -1 ⁇ c ⁇ 1;
  • m is the total number of drug resistant genes and drug sensitive genes in the gene panel described herein (e.g., full gene panel or subgroup gene panel) ;
  • n is the number of deleterious mutation (s) detected on i th patient target gene in the patient
  • r i is the correlation (positive correlation or negative correlation) between i th patient target gene and the anti-cancer drug treatment (e.g., at IC50) ;
  • ⁇ ij is the predicted impact of the j th deleterious mutation of i th patient target gene
  • LFC i is the log-scale (e.g., log2) fold change of expression level of i th patient target gene in disease tissue vs. normal tissue;
  • ⁇ i is the normalized weight of i th patient target gene in the anti-cancer drug-related pathway (s) ; wherein i and j are both integers, 0 ⁇ i ⁇ m, and 1 ⁇ j ⁇ n; and
  • Z (LFC i ) is the standard score ( “Z-score” ) of LFC i :
  • ⁇ i is the standard deviation of log-scale (e.g., log2) fold change of expression level of i th patient target gene in disease tissue vs. normal tissue (e.g., based on patient databases, i.e., information collected from patients having the same cancer) .
  • the composite score threshold level is 0. In some embodiments, if the composite score of the patient according to Formula I is above 0, the patient is suitable for (i.e., may benefit from) the anti-cancer drug (e.g., CDK7 inhibitor) treatment. In some embodiments, if the composite score of the patient according to Formula I is above or equal to at least 0.1 (e.g., 0.3) , the patient is selected for or is recommended for the anti-cancer drug treatment.
  • the composite score threshold level is 0. In some embodiments, if the composite score of the patient according to Formula I is above 0, the patient is suitable for (i.e., may benefit from) the anti-cancer drug (e.g., CDK7 inhibitor) treatment. In some embodiments, if the composite score of the patient according to Formula I is above or equal to at least 0.1 (e.g., 0.3) , the patient is selected for or is recommended for the anti-cancer drug treatment.
  • the patient is suitable for the anti-cancer drug treatment, but should be further evaluated using other method (s) (e.g., drug dosage test, cancer genetic testing (e.g., look for additional synergistic mutations that may contribute to the anti-cancer drug treatment, or verify the primary cancer type) , etc. ) or based on other information (e.g., patient’s clinical record or known drug resistance, etc. ) to determine whether the patient should be selected or recommended for the anti-cancer drug treatment.
  • other method e.g., drug dosage test, cancer genetic testing (e.g., look for additional synergistic mutations that may contribute to the anti-cancer drug treatment, or verify the primary cancer type) , etc.
  • other information e.g., patient’s clinical record or known drug resistance, etc.
  • the patient is not suitable for (i.e., may not benefit from) or is excluded from the anti-cancer drug treatment.
  • further evaluation using other method (s) e.g., drug dosage test, cancer genetic testing (e.g., look for additional synergistic mutations that may contribute to the anti-cancer drug treatment, or verify the primary cancer type) , etc. ) or based on other information (e.g., patient’s clinical record or known drug resistance, etc. ) should be conducted if the composite score of the patient according to Formula I is equal to 0, or very close to 0 (e.g., -0.1 to 0) , before completely ruling out the patient from receiving the anti-cancer drug treatment.
  • the methods further comprise selectively enriching in a sample in the individual one or more nucleic acids or polypeptides comprising or encoded by one or a plurality of drug sensitive genes (or portion thereof) , such as a drug sensitive gene selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPDYA,
  • the methods further comprise selectively enriching in a sample in the individual one or more nucleic acids or polypeptides comprising or encoded by one or a plurality of drug resistant genes (or portion thereof) , such as a drug resistant gene selected from the group consisting of ACVR1, ADRA2A, AMOTL2, ANKDD1A, ANKRD1, ARID1A, BAZ1A, BMPR1A, BMPR2, CACNG2, CDKN1A, CHP1, CKS2, CTBP1, CTBP2, DIP2B, EIF1, EIF3A, EIF4B, EIF4G1, FCGBP, FRAT1, FRYL, GCN1L1, GNA11, HDAC1, HDAC2, HES1, HES5, HSP90AA1, HSP90AB1, ILK, KAT2A, KAT6A, KDM5C, KIAA1109, KIDINS220, LZTS3, MAML3, MAP2K4, MAP3K1, MAP3K4, MAPK14,
  • the methods further comprise selectively enriching in a sample in the individual one or more nucleic acids or polypeptides comprising or encoded by one or a plurality of drug sensitive genes (or portion thereof) , such as a drug sensitive gene selected from the group consisting of FBXW7, E2F3, PBRM1, NFAT5, CHD7, CDK6, ABCC1, EIF4E2, UBR5, DUSP4, ELAVL1, PRKAA1, RHOA, ARNT, DIDO1, PARP1, HPRT1, CDC25B, ARID2, RPS6KB1, CNOT1, CDC25A, CDK12, TDP2, ZGRF1, NPM1, NCSTN, RBM12B, KMT2E, SF3B1, MAPK8, FBXW11, SRF, CSNK2A1, SCAF4, CCND3, CTNND1, E2F4, TGFBR2, RFX7, RIF1, CCND1, PRKDC, FNDC3B, RIPK1, SPDYA,
  • the selectively enriching comprises: (a) combining a bait with the sample, thereby hybridizing the bait to the one or more nucleic acids in the sample and producing nucleic acid hybrids; and (b) isolating the nucleic acid hybrids to produce the enriched sample.
  • the selectively enriching comprises amplifying the one or more nucleic acids in the sample using a PCR to produce the enriched sample.
  • the methods further comprise sequencing the one or more nucleic acid molecules, or a relevant portion thereof (e.g., a nucleic acid fragment known to contain a mutation) , in the enriched sample.
  • the selectively enriching comprises: (a) combining a bait (e.g., antibody) with the sample, thereby binding the bait to the one or more polypeptides in the sample and producing bait-polypeptide complexes; and (b) isolating the bait-polypeptide complexes to produce the enriched sample.
  • a bait e.g., antibody
  • the methods described herein in some embodiments comprise treatment of colorectal cancer, also referred to as colon cancer, which include, but is not limited to, advanced colon cancer, malignant colon cancer, metastatic colon cancer, stage I, II, III, or IV colon cancer, a colon cancer characterized with a genomic instability, a colon cancer characterized with an alteration of a pathway, a colon cancer classified under the colon cancer subtype (CCS) system as CCS1, CCS2, or CCS3, a colon cancer classified under colorectal cancer assigner (CRCA system) as stem-like, goblet-like, inflammatory, transit-amplifying, or enterocyte subtype, a colon cancer classified under the colon cancer molecular subtype (CCMS) system as C1, C2, C3, C4, C5, or C6 subtype, a colon cancer classified under the CRC intrinsic subtype (CRCIS) system as Type A, Type B, or Type C subtype, or a colon cancer classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS1, CMS2,
  • the colon cancer has a microsatellite instability (MSI) status of MSI-high or MSI-low.
  • the individual has previously undergone a therapy (e.g., chemotherapy, radiation, surgery or immunomodulatory therapy) .
  • a therapy e.g., chemotherapy, radiation, surgery or immunomodulatory therapy
  • the individual does not respond to a previous therapy (e.g., chemotherapy, radiation, surgery or immunomodulatory therapy) .
  • the method described herein is used to treat colon cancer at different stages.
  • the method is used to treat stage I colon cancer.
  • the method is used to treat stage II (for example, stage IIA, IIB, or IIC) colon cancer.
  • the method is used to treat stage III (for example, stage IIIA, IIIB, or IIIC) colon cancer.
  • the method is used to treat stage IV (for example, stage IVA, IVB, or IVC) colon cancer.
  • the method is used to treat stage 0 colon cancer (i.e., carcinoma in situ) .
  • the colon cancer is characterized with a genomic instability.
  • the genomic instability comprises at least one modification of genomic DNA.
  • the modification is a chromosomal instability (CIN) .
  • the modification is a loss of heterozygosity (e.g., a massive loss of chromosomal DNA) .
  • the modification is a microsatellite instability (MSI) .
  • the modification of genomic DNA comprises a modification of DNA methylation or histone modification.
  • the colon cancer is characterized with at least 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, or 18%lower total DNA methylation than normal tissue.
  • the modification of genomic DNA comprises a CpG island methylator phenotype (CIMP) .
  • the colon cancer is characterized with a modified CpG island methylation.
  • the modified CpG island methylation comprises hypermethylation of a CpG-rich promoter.
  • the colon cancer can be classified under different system as different subtype.
  • classification systems are described in for example, Rodriguez-Salas et al., Crit Rev Oncol Hematol. 2017 Jan; 109: 9-19; De Sousa E Melo et al., Nat Med. 2013 May; 19 (5) : 614-8; Sadanandam et al., Nat Med. 2013 May; 19 (5) : 619-25; Marisa et al., PloS Med. 2013; 10 (5) ; Roepman et al., Int J Cancer. 2014 Feb 1; 134 (3) : 552-62; Salazar et al., J Clin Oncol. 2011 Jan 1; 29 (1) : 17-24.
  • the colon cancer is classified under the colon cancer subtype (CCS) system as CCS1. In some embodiments, the colon cancer is classified under the colon cancer subtype (CCS) system as CCS2. In some embodiments, the colon cancer is classified under the colon cancer subtype (CCS) system as CCS3.
  • the colon cancer is classified under colorectal cancer assigner (CRCA system) as stem-like subtype. In some embodiments, the colon cancer is classified under colorectal cancer assigner (CRCA system) as inflammatory subtype. In some embodiments, the colon cancer is classified under colorectal cancer assigner (CRCA system) as transit-amplifying subtype. In some embodiments, the colon cancer is classified under colorectal cancer assigner (CRCA system) as enterocyte subtype.
  • the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C1 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C2 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C3 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C4 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C5 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as C6 subtype. In some embodiments, the colon cancer is classified under the colon cancer molecular subtype (CCMS) system as both C1 and C5 subtype.
  • the colon cancer is classified under the CRC intrinsic subtype (CRCIS) system as Type A subtype (i.e., MMR-deficient epithelial subtype) . In some embodiments, the colon cancer is classified under the CRC intrinsic subtype (CRCIS) system as Type B subtype (i.e., epithelial proliferative subtype) . In some embodiments, the colon cancer is classified under the CRC intrinsic subtype (CRCIS) system as Type C subtype. In some embodiments, the colon cancer is classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS1. In some embodiments, the colon cancer is classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS2. In some embodiments, the colon cancer is classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS3. In some embodiments, the colon cancer is classified under the colorectal cancer subtyping consortium (CRCSC) classification system as CMS4.
  • CRCSC colorectal cancer subtyping consortium
  • methods disclosed herein comprise administering an effective amount of a CDK7 inhibitor.
  • CDK7 inhibitors encompassed by the present disclosure include pharmaceutically acceptable compositions that inhibit CDK7.
  • the CDK7 inhibitor binds within the ATP-binding site of CDK7.
  • the CDK7 inhibitor binds reversibly to the ATP-biding site of CDK7.
  • the CDK7 inhibitor is an ATP-competitive covalent inhibitor of CDK7.
  • the CDK7 inhibitor reduces or abolishes the interaction between CDK7 and cyclin H, and/or the interaction between CDK7 and MAT1.
  • the CDK7 inhibitor reduces or abolishes the formation of the CDK7-cycH-MAT1 complex. In some embodiments, the CDK7 inhibitor forms a covalent bond with one or more components of the CDK7-cycH-MAT1 complex. In some embodiments, the CDK7 inhibitor reduces or abolishes phosphorylation at Thr170 and/or Ser164 of CDK7 T-loop. In some embodiments, the CDK7 inhibitor i) prevents CDK2 activation and delays S phase; and/or ii) prevents CDK1 activation and mitotic entry. In some embodiments, the CDK7 inhibitor inhibits or abolishes transcription initiation and/or elongation.
  • the CDK7 inhibitor is a pyrazolopyrimidine derivative. In some embodiments, the CDK7 inhibitor is a pyrazolotriazine derivative. In some embodiments, the CDK7 inhibitor is pyrimidine based. In some embodiments, the CDK7 inhibitor is pyrrolidinopyrazole based. In some embodiments, the CDK7 inhibitor is selected from the group consisting of BS-181, CT7001 (samuraciclib or ICE0942) , LDC4297, QS1189, THZ1, THZ2, LY3405105, SY-5609, SY-1365, YKL-5-124, and an analog or derivative or salt thereof.
  • the CDK7 inhibitor is a pan-CDK inhibitor, e.g. an inhibitor for two or more CDKs, including at least CDK7.
  • the CDK7 inhibitor also inhibits one or more of CDK1, 2, 4, 5, 6, and 9.
  • the pan-CDK inhibitor can inhibit CDK7 and CDK4.
  • the CDK7 inhibitor is selected from the group consisting of alvocidib (also known as flavopiridol, HMR 1275, L-868275) , seliciclib (a. k. a.
  • the CDK7 inhibitor is specific for CDK7.
  • the CDK7 inhibitor is selected from the group consisting of BS-181, CT7001 (samuraciclib or ICEC0942) , LY3405105, LDC4297, SY-1365, THZ1 (SY-079) , YKL-5-124, THZ2, SY-5609, QS1189, and an analog or derivative or salt thereof.
  • the CDK7 inhibitor is THZ1, or analog or derivative or salt thereof.
  • the effective amount of the CDK7 inhibitor is about 1 mg to about 1000 mg, such as about 10 mg to about 800 mg, about 100 mg to about 600 mg, or about 200 mg to about 500 mg. In some embodiments, the effective amount of a CDK7 inhibitor is at least about 1 mg, such as at least about any of 5 mg, 10 mg, 15 mg, 20 mg, 25 mg, 50 mg, 75 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg, 800 mg, 850 mg, 900 mg, 950 mg, or 1000 mg.
  • the effective amount of the CDK7 inhibitor is no greater than about 1000 mg, such as no greater than about any of 950 mg, 900 mg, 850 mg, 800 mg, 750 mg, 700 mg, 650 mg, 600 mg, 550 mg, 500 mg, 450 mg, 400 mg, 350 mg, 300 mg, 250 mg, 200 mg, 150 mg, 100 mg, 75 mg, 50 mg, 25 mg, 20 mg, 15 mg, 10 mg, 5 mg, or 1 mg.
  • the CDK7 inhibitor is administered to the individual parenterally, including intravenous, intra-arterial, intraperitoneal, intrapulmonary, oral, inhalation, intravesicular, intramuscular, intra-tracheal, subcutaneous, intraocular, intrathecal, or transdermal administration. In some embodiments, the CDK7 inhibitor is administered to the individual orally.
  • the CDK7 inhibitor is administered in combination with a second anti-cancer therapy or agent.
  • the second anti-cancer therapy is a different CDK7 inhibitor (e.g., pan-CDK inhibitor or CDK7 specific inhibitor) .
  • the second anti-cancer therapy comprises administration of an inhibitor of another CDK, such as a CDK6 inhibitor, a CDK4 inhibitor, or a CDK4/6 inhibitor.
  • the second anti-cancer therapy or agent is another cell cycle regulator or transcription regulator that is not a CDK7 inhibitor.
  • the second anti-cancer therapy or agent is a small molecule inhibitor, an antibody, a cellular therapy (i.e., a cell-based therapy) , or a nucleic acid.
  • the cellular therapy is an adoptive therapy, a T cell-based therapy, a natural killer (NK) cell-based therapy, a chimeric antigen receptor (CAR) -T cell therapy, a recombinant T cell receptor (TCR) T cell therapy, or a dendritic cell (DC) -based therapy.
  • the nucleic acid comprises a double-stranded RNA (dsRNA) , a small interfering RNA (siRNA) , or a small hairpin RNA (shRNA) .
  • the second anti-cancer therapy is or comprises administration of a chemotherapeutic agent, an anti-hormonal agent, an antimetabolite chemotherapeutic agent, a kinase inhibitor, a peptide, a gene therapy, a vaccine, a platinum-based chemotherapeutic agent, an immunotherapy, an antibody, or a checkpoint inhibitor.
  • the anti-cancer therapy is an FGFR-targeted therapy.
  • the second anti-cancer therapy is a PTEN-targeted therapy. In some embodiments, the second anti-cancer therapy is an RB1-targeted therapy. In some embodiments, the second anti-cancer therapy is an EGFR-targeted therapy. In some embodiments, the second anti-cancer therapy is a SMARCA4-targeted therapy. In some embodiments, the second anti-cancer therapy is a TP53-targeted therapy. In some embodiments, the second anti-cancer therapy is a KRAS-targeted therapy. In some embodiments, the second anti-cancer therapy is a KRAS (G12C) -targeted therapy.
  • the second anti-cancer therapy is an NF2-targeted therapy. In some embodiments, the second anti-cancer therapy is a VHL-targeted therapy. In some embodiments, the second anti-cancer therapy is a PBRM1-targeted therapy. In some embodiments, the second anti-cancer therapy is an immunotherapy.
  • the methods provided herein comprise generating a report, and/or providing a report to party.
  • a report according to the present disclosure comprises information about the presence or absence of a drug sensitive aberration, such as a drug sensitive mutation in any of the drug sensitive genes described herein. In some embodiments, a report according to the present disclosure comprises information about the presence or absence of a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein.
  • a report according to the present disclosure indicates that a drug sensitive aberration, such as a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein) is present in a sample obtained from the individual. In one embodiment, a report according to the present disclosure indicates that a drug sensitive aberration, such as a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein) is not present in a sample obtained from the individual.
  • a report according to the present disclosure indicates that a drug sensitive aberration such as a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein) has been detected in a sample obtained from the individual.
  • a report according to the present disclosure indicates that a drug sensitive aberration, such as a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein) has not been detected in a sample obtained from the individual.
  • the report comprises an identifier for the individual from which the sample was obtained.
  • the report includes information on the role of a drug sensitive aberration (e.g., a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein) in colorectal cancer.
  • a drug sensitive aberration e.g., a drug sensitive mutation in any of the drug sensitive genes described herein (and/or a drug resistant aberration, such as a drug resistant mutation in any of the drug resistant genes described herein
  • Such information can include one or more of: information on prognosis of a colorectal cancer, information on resistance of a cancer to a CDK7 inhibitor treatment; information on potential or suggested therapeutic options (e.g., such as treatment with a CDK7 inhibitor, or combination therapy) ; or information on therapeutic options that should be avoided.
  • the report includes information on the likely effectiveness, acceptability, and/or advisability of applying a therapeutic option (e.g., a treatment comprising a CDK7 inhibitor) to an individual having a colorectal cancer.
  • a therapeutic option e.g., a treatment comprising a CDK7 inhibitor
  • the report includes information or a recommendation on the administration of a treatment (e.g., a treatment comprising a CDK7 inhibitor) .
  • the information or recommendation includes the dosage of the treatment and/or a treatment regimen (e.g., in combination with other treatments) .
  • the report comprises information or a recommendation for at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more treatments.
  • the report comprises information or a recommendation of not using at least one, at least two, at least three, at least four, at least five, at least six, at least seven, at least eight, at least nine, at least ten, or more treatments.
  • a report according to the present disclosure is generated by a method comprising one or more of the following steps: obtaining a sample, such as a sample described herein, from an individual having colorectal cancer; detecting one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes, or acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes; and generating a report.
  • the report generated is a personalized cancer report.
  • a report according to the present disclosure may be in an electronic, web-based, or paper form.
  • the report may be provided to an individual or a patient, or to an individual or entity other than the individual or patient (e.g., other than the individual or patient with the cancer) , such as one or more of a caregiver, a physician, an oncologist, a hospital, a clinic, a third party payer, an insurance company, or a government entity.
  • the report is provided or delivered to the individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from obtaining a sample from the individual (e.g., an individual having a cancer) .
  • the report is provided or delivered to an individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from detecting one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample obtained from the individual (e.g., an individual having a colorectal cancer) .
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the report is provided or delivered to an individual or entity within any of about 1 day or more, about 7 days or more, about 14 days or more, about 21 days or more, about 30 days or more, about 45 days or more, or about 60 days or more from acquiring knowledge of one or more drug sensitive aberrations (e.g., drug sensitive mutations) in one or a plurality of drug sensitive genes and/or one or more drug resistant aberrations (e.g., drug resistant mutations) in one or a plurality of drug resistant genes in a sample obtained from the individual (e.g., an individual having a colorectal cancer) .
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the drug sensitive mutation or drug resistant mutation is selected from the group consisting of splice site mutation, nonsense mutation, frameshift mutation, and missense mutation.
  • the drug sensitive mutation or drug resistant mutation is a deleterious or pathogenic (i.e., inactivating) mutation. Pathogenic inactivating mutations (loss-of-function) of certain genes can be determined by review of experimental evidence within the published scientific literature and review of critical regions that may be disrupted, including but not limited to frameshift, missense mutations, truncating mutations, deletions, copy number variations, nonsense mutations, and loss or deletion of the gene.
  • Pathogenic or inactivating mutation includes but not limited to homozygous deletions, bi-allelic (double hit) mutations, splice site mutations (e.g., a 2nd or an additional splice site mutation) , frameshift mutations, and nonsense mutations in coding region, missense mutations with confirmed impact.
  • Drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • a nucleic acid hybridization assay such as a nucleic acid hybridization assay, immunofluorescence staining, western blot, an amplification-based assay (e.g., PCR) , a PCR-RFLP assay, real-time PCR, sequencing (e.g., Sanger sequencing or next-generation sequencing) , a screening analysis (e.g., using karyotype methods) , such as DNA sequencing, RNA-seq, ChIP-seq, DNase-seq, micrococcal nuclease (MNase) -seq (e.g., for detecting nucleosomal arrangement at gene regulatory region) , fluorescence in situ hybridization (FISH) , break away FISH, spectral karyotyping, multiplex-FISH, comparative genomic hybridization, in situ hybrid
  • one or more drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • an in situ hybridization method such as a fluorescence in situ hybridization (FISH) method.
  • FISH fluorescence in situ hybridization
  • FISH analysis is used to identify the chromosomal rearrangement resulting in the mutations as described herein. In some embodiments, FISH analysis is used to identify an RNA molecule or protein comprising one or more drug sensitive mutations or/or drug resistant mutations described herein. In some embodiments, FISH analysis is used to identify aberrant expression of an RNA or protein. In some embodiments, FISH analysis is used to identify aberrant modification of a DNA, an RNA, or a protein. Methods for performing FISH are known in the art and can be used in nearly any type of tissue.
  • protein probes are labeled (e.g., fluorescently or radiolabeled) and incubated with tissues that contain target proteins or receptors, and the interaction sites can be localized (e.g., via microscope) through detection of the labeled protein probe.
  • nucleic acid probes which are detectably labeled e.g. fluorescently labeled
  • FISH analysis nucleic acid probes which are detectably labeled, e.g. fluorescently labeled, are allowed to bind to specific regions of DNA, e.g., a chromosome, or an RNA, e.g., an mRNA, and then examined, e.g., through a microscope.
  • DNA or RNA molecules are first fixed onto a slide, the labeled probe is then hybridized to the DNA or RNA molecules, and then visualization is achieved, e.g., using enzyme-linked label-based detection methods known in the art.
  • the resolution of FISH analysis is on the order of detection of 60 to 100000 nucleotides, e.g., 60 base pairs (bp) up to 100 kilobase pairs of DNA.
  • Nucleic acid probes used in FISH analysis comprise single stranded nucleic acids. Such probes are typically at least about 50 nucleotides in length. In some embodiments, probes comprise about 100 to about 500 nucleotides.
  • Probes that hybridize with centromeric DNA and locus-specific DNA or RNA are available commercially, for example, from Vysis, Inc. (Downers Grove, Ill. ) , Molecular Probes, Inc. (Eugene, Oreg. ) or from Cytocell (Oxfordshire, UK) .
  • probes can be made non-commercially from chromosomal or genomic DNA or other sources of nucleic acids (or polypeptides) through standard techniques. Examples of probes, labeling and hybridization methods are known in the art.
  • FISH FISH
  • Fiber FISH Fiber FISH
  • Q-FISH Q-FISH
  • Flow-FISH MA-FISH
  • break-away FISH hybrid fusion-FISH
  • multi-fluor FISH or mFISH proteins can be detected via immunofluorescence staining, e.g., using antibodies or antigen-binding fragments thereof.
  • one or more drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • an array-based method such as array-based comparative genomic hybridization (CGH) methods.
  • CGH comparative genomic hybridization
  • a first sample of nucleic acids e.g., from a sample, such as from a tumor
  • a second sample of nucleic acids e.g., a control, such as from a healthy cell/tissue
  • equal quantities of the two samples are mixed and co-hybridized to a DNA microarray of several thousand evenly spaced cloned DNA fragments or oligonucleotides, which have been spotted in triplicate on the array.
  • digital imaging systems are used to capture and quantify the relative fluorescence intensities of each of the hybridized fluorophores.
  • the resulting ratio of the fluorescence intensities is proportional to the ratio of the copy numbers of DNA sequences in the two samples.
  • differences in the ratio of the signals from the two labels are detected and the ratio provides a measure of the copy number.
  • Array-based CGH can also be performed with single-color labeling.
  • a control e.g., control nucleic acid sample, such as from a healthy cell/tissue
  • a test sample e.g., a nucleic acid sample obtained from an individual or from a tumor
  • a second array with identical content
  • Copy number differences are calculated based on absolute signals from the two arrays.
  • the array is use for detecting RNAs in the sample.
  • the resulting ratio of the fluorescence intensities is proportional to the ratio of the amount of RNA in the two samples, e.g., to reflect aberrant expression level.
  • the array is a protein array or protein chip.
  • one or more drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • an amplification-based method a sample of nucleic acids, such as a sample obtained from an individual or from a tumor, is used as a template in an amplification reaction (e.g., PCR) using one or more oligonucleotides or primers, e.g., such as one or more oligonucleotides or primers provided herein.
  • the presence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure in the sample can be determined based on the presence or absence of an amplification product.
  • Quantitative amplification methods are also known in the art and may be used according to the methods provided herein.
  • the known nucleotide sequence for genes is sufficient to enable one of skill in the art to routinely select primers to amplify any portion of the gene.
  • Fluorogenic quantitative PCR can also be used. In fluorogenic quantitative PCR, quantitation is based on the amount of fluorescence signals, e.g., TaqMan and Sybr green.
  • amplification methods suitable for use according to the methods provided herein include, e.g., ligase chain reaction (LCR) , transcription amplification, self-sustained sequence replication, dot PCR, and linker adapter PCR.
  • LCR ligase chain reaction
  • one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure are detected using a sequencing method.
  • Any method of sequencing known in the art can be used to detect one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure.
  • Exemplary sequencing methods that may be used include those based on techniques developed by Maxam and Gilbert or Sanger.
  • the sequencing method is DNA sequencing.
  • the sequencing method is RNA sequencing. Automated sequencing procedures may also be used, e.g., including sequencing by mass spectrometry.
  • the entire gene or gene product e.g., RNA, polypeptide
  • a relevant portion of a gene or gene product e.g., RNA, polypeptide
  • the aberration comprises aberrant expression.
  • the aberration comprises aberrant modification (e.g., on DNA, RNA, or polypeptide level) .
  • one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure are detected using hybrid capture-based sequencing (hybrid capture-based next-generation sequencing (NGS) ) , e.g., using adaptor ligation-based libraries. See, e.g., Frampton, G.M. et al. (2013) Nat. Biotech. 31: 1023-1031.
  • one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure are detected using next-generation sequencing (NGS) .
  • NGS next-generation sequencing
  • Next-generation sequencing includes any sequencing method that determines the nucleotide sequence of either individual nucleic acid molecules or clonally expanded proxies for individual nucleic acid molecules in a highly parallel fashion (e.g., greater than 10 5 molecules may be sequenced simultaneously) .
  • Next generation sequencing methods suitable for use according to the methods provided herein are known in the art and include, without limitation, massively parallel short-read sequencing, template-based sequencing, pyrosequencing, real-time sequencing comprising imaging the continuous incorporation of dye-labeling nucleotides during DNA synthesis, nanopore sequencing, sequencing by hybridization, nano-transistor array based sequencing, polony sequencing, scanning tunneling microscopy (STM) -based sequencing, or nanowire- molecule sensor based sequencing.
  • STM scanning tunneling microscopy
  • Exemplary NGS methods and platforms that may be used to detect one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure include, without limitation, the HeliScope Gene Sequencing system from Helicos BioSciences (Cambridge, MA., USA) , the PacBio RS system from Pacific Biosciences (Menlo Park, CA, USA) , massively parallel short-read sequencing such as the Solexa sequencer and other methods and platforms from Illumina Inc.
  • Additional exemplary methods and platforms that may be used to detect one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure include, without limitation, the Genome Sequencer (GS) FLX System from Roche (Basel, CHE) , the G.
  • GS Genome Sequencer
  • the methods comprise providing a sample from an individual having a colorectal cancer, wherein the sample comprises one or more polypeptides.
  • the methods further comprise preparing a protein or polypeptide library (e.g., for mass-spec) from the one or more polypeptides in the sample.
  • Sample or library preparation methods for protein sequencing or mass spectrometry are well known. E. g., see Laura Restrepo-Pérez et al (2016) Nat Nanotechnol, 13: 786–796) .
  • the methods comprise providing a sample from an individual having a colorectal cancer, wherein the sample comprises one or more nucleic acids.
  • the methods further comprise preparing a nucleic acid sequencing library from the one or more nucleic acids in the sample.
  • Methods for the preparation of nucleic acid sequencing libraries e.g., suitable for any of the sequencing methods described herein (e.g., next generation sequencing) , are known in the art.
  • the sequencing library is prepared as described in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031.
  • the library is amplified.
  • the sequencing library is amplified using a PCR.
  • the sequencing library is amplified as described in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031.
  • the methods further comprise selectively enriching for one or more nucleic acids (e.g., one or more nucleic acids comprising one or more gene alterations described herein) to produce an enriched sample.
  • the selectively enriching comprises combining a bait, such as a bait described herein, with a sample (e.g., the library) , thereby hybridizing the bait to the one or more nucleic acids in the sample (e.g., in the library) , and producing nucleic acid hybrids; and isolating the nucleic acid hybrids to produce an enriched sample.
  • the selectively enriching is performed as described in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031.
  • the methods further comprise amplifying, e.g. using PCR, the nucleic acids in the enriched sample.
  • the methods further comprise sequencing the enriched sample, thereby producing a plurality of sequencing reads.
  • the sequencing is performed using any method for sequencing known in the art or provided herein.
  • the sequencing is performed using an Illumina sequencer.
  • the sequencing is performed as described in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031.
  • the methods further comprise analyzing the plurality of sequencing reads, e.g., for the presence of one or more gene alterations described herein.
  • the analyzing step comprises aligning the plurality of sequencing reads to the human genome, e.g., to human genome version hg19, e.g., using any suitable methods, such as a BWA aligner.
  • the analyzing step further comprises removing PCR duplicate reads, and/or collecting sequence metrics (e.g., using Picard 1.47 and/or Samtools) .
  • the analyzing step comprises performing local alignment optimization, e.g., using GATK.
  • the analyzing step further comprises variant calling.
  • the analyzing step comprises detecting base substitutions, e.g., using a Bayesian methodology.
  • the analyzing step comprises detecting indels, e.g., using the Bruijn approach. In some embodiments, the analyzing step comprises detecting copy number alterations, e.g., using comparative genomic hybridization-like methods. In some embodiments, the analyzing step comprises detecting genomic rearrangements and/or gene fusions, e.g., by analyzing chimeric read pairs. In some embodiments, the analyzing step is performed as described in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031. In some embodiments, the methods further comprise detecting, based on the analyzing step, one or more gene alterations described herein.
  • Baits capturing polypeptide, capturing nucleic acid, probes, primers, and oligonucleotide
  • a plurality of capture nucleic acid molecules configured to hybridize to a plurality of drug sensitive genes and/or a plurality of drug resistant genes, or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • an expression products e.g., polypeptide
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to a plurality of drug sensitive genes and/or a plurality of drug resistant genes, or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to expression products (e.g., polypeptide) of a plurality of drug sensitive genes and/or a plurality of drug resistant genes.
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1, or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • the polypeptide or portion thereof
  • the polypeptide or portion thereof
  • kits comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1, or RNAs encoded thereof.
  • kits comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1.
  • capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, or all drug sensitive genes provided in Table 1a) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, or all drug sensitive genes provided in Table 1a) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • kits comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, or all drug sensitive genes provided in Table 1a) , or RNAs encoded thereof.
  • kits comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, or all drug sensitive genes provided in Table 1a) .
  • capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 55, or all drug sensitive genes provided in Table 1b) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 55, or all drug sensitive genes provided in Table 1b) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • kits comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 55, or all drug sensitive genes provided in Table 1b) , or RNAs encoded thereof.
  • kits comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 55, or all drug sensitive genes provided in Table 1b) .
  • capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1c) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1c) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1c) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1c) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1d) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1d) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1d) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, or all drug sensitive genes provided in Table 1d) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2, or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • kits comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2, or RNAs encoded thereof.
  • kits comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2.
  • capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 25, or all drug resistant genes provided in Table 2a) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 25, or all drug resistant genes provided in Table 2a) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 25, or all drug resistant genes provided in Table 2a) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 25, or all drug resistant genes provided in Table 2a) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2b) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2b) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2b) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2b) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2c) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2c) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2c) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, or all drug resistant genes provided in Table 2c) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or all drug resistant genes provided in Table 2d) , or RNAs encoded thereof.
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • bind to the polypeptide (or portion thereof) encoded by at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or all drug resistant genes provided in Table 2d) e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • a kit comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or all drug resistant genes provided in Table 2d) , or RNAs encoded thereof.
  • a kit comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, or all drug resistant genes provided in Table 2d) .
  • a plurality of capture nucleic acid molecules configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1 (or RNAs encoded thereof) and at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2 (or RNAs encoded thereof) .
  • a plurality of capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • the polypeptide or portion thereof
  • the polypeptide or portion thereof
  • kits comprising a plurality of capture nucleic acid molecules (or probes, primers, oligonucleotides, or baits each comprising a capture nucleic acid molecule) configured to hybridize to at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1 (or RNAs encoded thereof) and at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2 (or RNAs encoded thereof) .
  • kits comprising a plurality of capture polypeptide molecules (e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule) configured to bind to the polypeptide (or portion thereof) encoded by at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, or all drug sensitive genes provided in Table 1 and at least any of 1, 5, 10, 20, 30, 40, 50, 60, 70, 75, or all drug resistant genes provided in Table 2.
  • capture polypeptide molecules e.g., polypeptide, antibody or fragment thereof, or baits each comprising a capture polypeptide molecule
  • baits suitable for the detection of one or more drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the bait comprises a capture polypeptide molecule configured to bind to a target polypeptide or a fragment or portion thereof.
  • the fragment comprises (or is) at least about 5 aa in length.
  • the capture polypeptide molecule is a polypeptide (e.g., a ligand of a receptor encoded by a drug sensitive gene/drug resistant gene) .
  • the capture polypeptide molecule is an antibody or antigen-binding fragment thereof.
  • the capture polypeptide molecule is at least about 10 aa in length, such as at least about any of 15 aa, 20 aa, 30 aa, 40 aa, 50 aa, 100 aa, 1000 aa, or longer.
  • the bait comprises a capture nucleic acid molecule configured to hybridize to a target nucleic acid molecule or a fragment or portion thereof.
  • the fragment comprises (or is) between about 5 and about 25 nucleotides, between about 5 and about 300 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the capture nucleic acid molecule is between about 5 and about 25 nucleotides, between about 5 and about 300 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the fragment comprises (or is) about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 225 nucleotides, about 250 nucleotides, about 275 nucleotides, or about 300 nucleotides in length.
  • the capture nucleic acid molecule comprises (or is) about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 225 nucleotides, about 250 nucleotides, about 275 nucleotides, or about 300 nucleotides in length. In some embodiments, the capture nucleic acid molecule is about 100 nucleotides, about 125 nucleotides, about 150 nucleotides, about 175 nucleotides, about 200 nucleotides, about 225 nucleotides, about 250 nucleotides, about 275 nucleotides, or about 300 nucleotides in length.
  • the capture nucleic acid molecule is between about 5 and about 25 nucleotides in length, between about 5 and about 300 nucleotides in length, between about 100 and about 300 nucleotides in length, between about 130 and about 230 nucleotides in length, or between about 150 and about 200 nucleotides in length.
  • the capture nucleic acid molecule is a DNA, RNA, or a DNA/RNA molecule.
  • a bait provided herein comprises a DNA, RNA, or a DNA/RNA molecule. In some embodiments, a bait provided herein comprises a polypeptide, or antibody or antigen-binding fragment thereof. In some embodiments, a bait provided herein includes a label or a tag. In some embodiments, the label or tag is a radiolabel, a fluorescent label, an enzymatic label, a sequence tag, biotin, or another ligand. In some embodiments, a bait provided herein includes a detection reagent such as a fluorescent marker.
  • a bait provided herein includes (e.g., is conjugated to) an affinity tag, e.g., that allows capture and isolation of a hybrid formed by a bait and a nucleic acid hybridized to the bait.
  • the affinity tag is an antibody, an antibody fragment, biotin, or any other suitable affinity tag or reagent known in the art.
  • a bait is suitable for solution phase hybridization.
  • Baits can be produced and used according to methods known in the art, e.g., as described in WO2012092426A1 and/or or in Frampton et al (2013) Nat Biotechnol, 31: 1023-1031, incorporated herein by reference.
  • biotinylated baits e.g., RNA baits
  • RNA baits can be produced by obtaining a pool of synthetic long oligonucleotides, originally synthesized on a microarray, and amplifying the oligonucleotides to produce the bait sequences.
  • the baits are produced by adding an RNA polymerase promoter sequence at one end of the bait sequences, and synthesizing RNA sequences using RNA polymerase.
  • libraries of synthetic oligodeoxynucleotides can be obtained from commercial suppliers, such as Agilent Technologies, Inc., and amplified using known nucleic acid amplification methods. Any suitable protein (e.g., antibody) synthesis methods can be used herein to make baits.
  • a bait provided herein is at least about 10 aa in length.
  • a bait provided herein comprises a target-specific bait sequence (e.g., a capture polypeptide molecule described herein) and universal tails on each end.
  • the target-specific sequence e.g., a capture polypeptide molecule described herein, is at least about 10 aa in length, such as at least about any of 15 aa, 20 aa, 30 aa, 40 aa, 50 aa, 100 aa, 1000 aa, or longer.
  • a bait provided herein is between about 100 nucleotides and about 300 nucleotides. In some embodiments, a bait provided herein is between about 130 nucleotides and about 230 nucleotides. In some embodiments, a bait provided herein is between about 150 nucleotides and about 200 nucleotides. In some embodiments, a bait provided herein comprises a target-specific bait sequence (e.g., a capture nucleic acid molecule described herein) and universal tails on each end. In some embodiments, the target-specific sequence, e.g., a capture nucleic acid molecule described herein, is between about 10 nucleotides and about 300 nucleotides.
  • a target-specific bait sequence e.g., a capture nucleic acid molecule described herein
  • the target-specific sequence e.g., a capture nucleic acid molecule described herein
  • the target-specific sequence is between about 100 nucleotides and about 200 nucleotides. In some embodiments, the target-specific sequence, e.g., a capture nucleic acid molecule described herein, is between about 120 nucleotides and about 170 nucleotides. In some embodiments, the target-specific sequence, e.g., a capture nucleic acid molecule described herein, is about 150 nucleotides or about 170 nucleotides.
  • a bait provided herein comprises an oligonucleotide comprising about 200 nucleotides, of which about 150 nucleotides or about 170 nucleotides are target-specific (e.g., a capture nucleic acid molecule described herein) , and the other 50 nucleotides or 30 nucleotides (e.g., 25 or 15 nucleotides on each end of the bait) are universal arbitrary tails, e.g., suitable for PCR amplification.
  • target-specific e.g., a capture nucleic acid molecule described herein
  • probes e.g., nucleic acid molecules, suitable for the detection of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure.
  • a probe provided herein comprises a nucleic acid sequence configured to hybridize to a target nucleic acid molecule comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure or a fragment or portion thereof.
  • the probe comprises a nucleic acid molecule which is a DNA, RNA, or a DNA/RNA molecule.
  • the probe comprises a nucleic acid molecule comprising any of between about 10 and about 20 nucleotides, between about 12 and about 20 nucleotides, between about 10 and about 1000 nucleotides, between about 50 and about 500 nucleotides, between about 100 and about 500 nucleotides, between about 100 and about 300 nucleotides, between about 130 and about 230 nucleotides, or between about 150 and about 200 nucleotides.
  • the probe comprises a nucleic acid molecule comprising any of 10 nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14 nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, 20 nucleotides, 21 nucleotides, 22 nucleotides, 23 nucleotides, 24 nucleotides, 25 nucleotides, 26 nucleotides, 27 nucleotides, 28 nucleotides, 29 nucleotides, or 30 nucleotides.
  • the probe comprises a nucleic acid molecule comprising any of between about 40 nucleotides and about 50 nucleotides, about 50 nucleotides and about 100 nucleotides, about 100 nucleotides and about 150 nucleotides, about 150 nucleotides and about 200 nucleotides, about 200 nucleotides and about 250 nucleotides, about 250 nucleotides and about 300 nucleotides, about 300 nucleotides and about 350 nucleotides, about 350 nucleotides and about 400 nucleotides, about 400 nucleotides and about 450 nucleotides, about 450 nucleotides and about 500 nucleotides, about 500 nucleotides and about 550 nucleotides, about 550 nucleotides and about 600 nucleotides, about 600 nucleotides and about 650 nucleotides, about 650 nucleotides and about 700 nucleotides, about 700 nucle
  • a probe provided herein includes a label or a tag.
  • the label or tag is a radiolabel (e.g., a radioisotope) , a fluorescent label (e.g., a fluorescent compound) , an enzymatic label, an enzyme co-factor, a sequence tag, biotin, or another ligand.
  • a probe provided herein includes a detection reagent such as a fluorescent marker.
  • a probe provided herein includes (e.g., is conjugated to) an affinity tag, e.g., that allows capture and isolation of a hybrid formed by a probe and a nucleic acid hybridized to the probe.
  • the affinity tag is an antibody, an antibody fragment, biotin, or any other suitable affinity tag or reagent known in the art.
  • a probe is suitable for solution phase hybridization.
  • one or more probes provided herein are suitable for use in in situ hybridization methods, e.g., as described above, such as FISH.
  • Chromosomal probes are typically about 50 to about 10 5 nucleotides in length. Longer probes typically comprise smaller fragments of about 100 to about 500 nucleotides. Probes that hybridize with centromeric DNA and locus-specific DNA are available commercially, for example, from Vysis, Inc. (Downers Grove, Ill. ) , Molecular Probes, Inc. (Eugene, Oreg. ) or from Cytocell (Oxfordshire, UK) . Alternatively, probes can be made non-commercially from chromosomal or genomic DNA through standard techniques.
  • sources of DNA that can be used include genomic DNA, cloned DNA sequences, somatic cell hybrids that contain one, or a part of one, chromosome (e.g., human chromosome) along with the normal chromosome complement of the host, and chromosomes purified by flow cytometry or microdissection.
  • chromosome e.g., human chromosome
  • the region of interest can be isolated through cloning, or by site-specific amplification via PCR.
  • Probes of the disclosure may also hybridize to RNA molecules, e.g., mRNA.
  • probes such as probes for use in the FISH methods described herein, are labeled such that a chromosomal region or a region on an RNA to which the probes hybridize can be detected.
  • Probes typically are directly labeled with a fluorophore, allowing the probe to be visualized without a secondary detection molecule.
  • Probes can also be labeled by nick translation, random primer labeling or PCR labeling. Labeling may be accomplished using fluorescent (direct) -or haptene (indirect) -labeled nucleotides.
  • labels include: AMCA-6-dUTP, CascadeBlue-4-dUTP, Fluorescein-12-dUTP, Rhodamine-6-dUTP, TexasRed-6-dUTP, Cy3-6-dUTP, Cy5-dUTP, Biotin (BIO) -11-dUTP, Digoxygenin (DIG) -11-dUTP and Dinitrophenyl (DNP) -11-dUTP.
  • Probes can also be indirectly labeled with biotin or digoxygenin, or labeled with radioactive isotopes such as 32 P and 3 H, and secondary detection molecules are used, or further processing is performed, to visualize the probes.
  • a probe labeled with biotin can be detected by avidin conjugated to a detectable marker, e.g., avidin can be conjugated to an enzymatic marker such as alkaline phosphatase or horseradish peroxidase.
  • Enzymatic markers can be detected in standard colorimetric reactions using a substrate and/or a catalyst for the enzyme.
  • Catalysts for alkaline phosphatase include 5-bromo-4-chloro-3-indolylphosphate and nitro blue tetrazolium.
  • Diaminobenzoate can be used as a catalyst for horseradish peroxidase.
  • Probes can also be prepared such that a fluorescent or other label is added after hybridization of the probe to its target to detect that the probe hybridized to the target.
  • probes can be used that have antigenic molecules incorporated into the nucleotide sequence. After hybridization, these antigenic molecules are detected, for example, using specific antibodies reactive with the antigenic molecules. Such antibodies can, for example, themselves incorporate a fluorochrome, or can be detected using a second antibody with a bound fluorochrome.
  • fluorescent probes e.g., used in FISH techniques, fluorescence can be viewed with a fluorescence microscope equipped with an appropriate filter for each fluorophore, or by using dual or triple band-pass filter sets to observe multiple fluorophores.
  • techniques such as flow cytometry can be used to examine the hybridization pattern of the chromosomal probes.
  • an oligonucleotide e.g., useful as primers.
  • an oligonucleotide, e.g., a primer provided herein comprises a nucleotide sequence configured to hybridize to a target nucleic acid molecule comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure or a fragment or portion thereof.
  • the aberration comprises aberrant expression level.
  • the aberration comprises aberrant modification.
  • an oligonucleotide e.g., a primer, provided herein may be useful for initiating DNA synthesis via PCR or a sequencing method.
  • the oligonucleotide may be used to amplify a nucleic acid molecule comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure, or a fragment thereof (e.g., known to contain a mutation) , e.g., using PCR.
  • the oligonucleotide may be used to sequence a nucleic acid molecule comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure, or a fragment thereof.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • pairs of oligonucleotides e.g., pairs of primers, are provided herein, which are configured to hybridize to a nucleic acid molecule comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure, or a fragment thereof.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • a pair of oligonucleotides of the disclosure may be used for directing amplification of a nucleic acid molecule or fragment thereof comprising one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure, e.g., using a PCR reaction.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • an oligonucleotide e.g., a primer, provided herein is a single stranded nucleic acid molecule, e.g., for use in sequencing or amplification methods.
  • an oligonucleotide provided herein is a double stranded nucleic acid molecule.
  • a double stranded oligonucleotide is treated, e.g., denatured, to separate its two strands prior to use, e.g., in sequencing or amplification methods.
  • Oligonucleotides provided herein comprise a nucleotide sequence of sufficient length to hybridize to their target and to prime the synthesis of extension products, e.g., during PCR or sequencing.
  • an oligonucleotide e.g., a primer
  • a primer comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more deoxyribonucleotides or ribonucleotides.
  • an oligonucleotide provided herein comprises at least about any of 8, 10, 15, 20, or 30 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 10 and about 30 deoxyribonucleotides or ribonucleotides. In some embodiments, an oligonucleotide provided herein comprises between about 10 and about 25 deoxyribonucleotides or ribonucleotides, including for example about 10 and about 20, about 10 and about 15, about 12 and about 20, or about 17 and about 20 deoxyribonucleotides or ribonucleotides.
  • the length and nucleotide sequence of an oligonucleotide provided herein is determined according to methods known in the art, e.g., based on factors such as the specific application (e.g., PCR, sequencing library preparation, sequencing) , reaction conditions (e.g., buffers, temperature) , and the nucleotide composition of the nucleotide sequence of the oligonucleotide or of its target complementary sequence.
  • the source of the sample can be solid tissue as from a fresh, frozen and/or preserved organ, tissue sample, biopsy, resection, smear, or aspirate; blood or any blood constituents; bodily fluids such as cerebrospinal fluid, amniotic fluid, urine, saliva, sputum, peritoneal fluid or interstitial fluid; or cells from any time in gestation or development of an individual.
  • the source of the sample is blood or blood constituents.
  • the source of the sample is a tumor sample, e.g., a colon cancer sample.
  • the sample is or comprises biological tissue or fluid.
  • the sample can contain compounds that are not naturally intermixed with the tissue in nature, such as preservatives, anticoagulants, buffers, fixatives, nutrients, antibiotics or the like.
  • the sample comprises genomic or subgenomic DNA fragments, or RNA, such as mRNA isolated from a sample, e.g., a tumor sample, a normal adjacent tissue (NAT) sample, a tissue sample, or a blood sample obtained from an individual.
  • NAT normal adjacent tissue
  • the sample comprises cDNA derived from an mRNA sample or from a sample comprising mRNA.
  • the sample comprises polypeptide (s) , such as post-translational modified polypeptides.
  • the tissue is preserved as a frozen sample or as a formaldehyde-or paraformaldehyde-fixed paraffin-embedded (FFPE) tissue preparation.
  • FFPE formaldehyde-or paraformaldehyde-fixed paraffin-embedded
  • the sample can be embedded in a matrix, e.g., an FFPE block or a frozen sample.
  • the sample comprises cell-free DNA (cfDNA) . In some embodiments, the sample comprises cell-free RNA (cfRNA) . In some embodiments, the sample comprises circulating nucleic acids. In some embodiments, the sample comprises circulating tumor DNA (ctDNA) .
  • a sample may be or comprise bone marrow; a bone marrow aspirate; blood; blood cells; ascites; tissue or fine needle biopsy samples; cell-containing body fluids; free floating nucleic acids; sputum; saliva; urine; cerebrospinal fluid, peritoneal fluid; pleural fluid; feces; lymph; gynecological fluids; skin swabs; vaginal swabs; oral swabs; nasal swabs; washings or lavages such as ductal lavages or bronchoalveolar lavages; aspirates; scrapings; bone marrow specimens; tissue biopsy specimens; surgical specimens; other body fluids, secretions, and/or excretions; and/or cells therefrom.
  • a biological sample is or comprises cells obtained from an individual.
  • a sample is a primary sample obtained directly from a source of interest by any appropriate means.
  • a primary biological sample is obtained by a method chosen from biopsy (e.g., fine needle aspiration or tissue biopsy) , surgery, or collection of body fluid (e.g., blood, lymph, or feces) .
  • body fluid e.g., blood, lymph, or feces
  • sample refers to a preparation that is obtained by processing (e.g., by removing one or more components of and/or by adding one or more agents to) a primary sample.
  • Such a processed sample may comprise, for example nucleic acids or proteins extracted from a sample or obtained by subjecting a primary sample to techniques such as amplification or reverse transcription of mRNA, or isolation and/or purification of certain components.
  • the sample comprises tumor nucleic acids, such as nucleic acids from a tumor or a cancer sample, e.g., genomic DNA, RNA, or cDNA derived from RNA, from a tumor or cancer sample.
  • the sample comprises tumor polypeptides, such as polypeptides from a tumor or a cancer sample.
  • a tumor nucleic acid or polypeptide sample is purified or isolated (e.g., it is removed from its natural state) .
  • the sample is a control nucleic acid sample or a reference nucleic acid sample, e.g., genomic DNA, RNA, or cDNA derived from RNA, not containing an aberration (e.g., mutation, or aberrant expression/activity/modification) described herein.
  • the sample is a control polypeptide sample or a reference polypeptide sample, not containing an aberration (e.g., mutation, or aberrant expression/activity/modification) described herein.
  • the reference or control nucleic acid or polypeptide sample comprises a wild type or a non-mutated sequence.
  • the reference nucleic acid or polypeptide sample is purified or isolated (e.g., it is removed from its natural state) .
  • the reference nucleic acid or polypeptide sample is from a non-tumor sample, e.g., a blood control, a normal adjacent tumor (NAT) , or any other non-cancerous sample from the same or a different subject.
  • a non-tumor sample e.g., a blood control, a normal adjacent tumor (NAT) , or any other non-cancerous sample from the same or a different subject.
  • non-transitory computer-readable storage media comprise one or more programs for execution by one or more processors of a device, the one or more programs including instructions which, when executed by the one or more processors, cause the device to perform a method according to any of the embodiments described herein.
  • systems comprising one or more processors and a non-transitory computer-readable storage media.
  • a system of the disclosure comprises one or more processors; and a non-transitory computer readable storage medium comprising one or more programs executable by the one or more processors for performing a method.
  • the method comprises one or more of: (a) sequencing one or more nucleic acids or polypeptides, thereby producing a plurality of sequencing reads, wherein the one or more nucleic acids or polypeptides are derived from a sample obtained from an individual having a colorectal cancer; (b) analyzing the plurality of sequencing reads for the presence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure; and (c) detecting, based on the analyzing step, one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure in the sample.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • a system of the disclosure comprises a memory configured to store one or more program instructions; and one or more processors configured to execute the one or more program instructions.
  • the one or more program instructions when executed by the one or more processors are configured to: (a) obtain a plurality of sequence reads of one or more nucleic acids or polypeptides, wherein the one or more nucleic acids or polypeptides are derived from a sample obtained from an individual having a colorectal cancer; (b) analyze the plurality of sequence reads for the presence of one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure; and (c) detect, based on the analyzing, one or more drug sensitive aberrations (e.g., drug sensitive mutations) and/or drug resistant aberrations (e.g., drug resistant mutations) of the disclosure.
  • drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • a system of the disclosure comprises a memory configured to store one or more program instructions; and one or more processors configured to execute the one or more program instructions.
  • the one or more processors, and the non-transitory computer readable storage medium comprising one or more programs executable by the one or more processors are within a device.
  • the non-transitory computer-readable storage media comprise one or more programs for execution by one or more processors of the device, the one or more programs including instructions which, when executed by the one or more processors, cause the device to perform the method according to any of the embodiments described herein.
  • kits for detecting one or more drug sensitive aberrations e.g., drug sensitive mutations
  • drug resistant aberrations e.g., drug resistant mutations
  • the kit comprises a reagent (e.g., one or more oligonucleotides, primers, probes or baits of the present disclosure) for detecting a wild-type counterpart of the drug sensitive genes and/or drug resistant genes.
  • the reagent comprises one or more oligonucleotides, primers, probes or baits of the present disclosure capable of hybridizing to a nucleic acid molecule comprising one or more drug sensitive mutations and/or drug resistant mutations (or with aberrant expression/activity/modification) of the disclosure, or to a wild-type counterpart.
  • the reagent comprises one or more baits (e.g., polypeptide, antibody or fragment thereof) of the present disclosure capable of bind to one or more polypeptides (e.g., wild-type, or with mutation or aberrant expression/activity/modification) encoded by one or more drug sensitive genes and/or drug resistant genes described herein.
  • the kit is for use according to any protein or polypeptide detection assay known in the art or described herein, such as mass spectrometry (e.g., tandem mass spectrometry) , a reporter assay (e.g., a fluorescence-based assay) , immunoblots such as a Western blot, immunoassays such as enzyme-linked immunosorbent assays (ELISA) , immunohistochemistry, other immunological assays (e.g., fluid or gel precipitin reactions, immunodiffusion, immunoelectrophoresis, radioimmunoassay (RIA) , immunofluorescent assays) , and analytic biochemical methods (e.g., electrophoresis, capillary electrophoresis, high performance liquid chromatography (HPLC) , thin layer chromatography (TLC) , or hyperdiffusion chromatography) .
  • the kit further comprises instructions for detecting a polypeptide encoded by a gene
  • This example provides exemplary methods for identifying drug sensitive genes and/or drug resistant genes of a CDK7 inhibitor (such as THZ1 or salt thereof) .
  • a CDK7 inhibitor such as THZ1 or salt thereof.
  • a cancer cell library carrying sgRNA iBAR targeting cancer-related genes was constructed for Cas9-mediated gene knock-out (KO) .
  • KO Cas9-mediated gene knock-out
  • FIGs. 1-2 show the exemplary workflow.
  • genes with DNA mutation frequency ⁇ 5%and RNA expression level up-or down-regulated by more than 2-fold from patients with stage III and IV colorectal cancer (expressed in cell, or on cell surface) were selected as library genes for further sgRNA iBAR design (total 1323 genes) .
  • sgRNA iBAR library was designed and constructed similarly as described in WO2020125762 and Zhu et al. ( “Guide RNAs with embedded barcodes boost CRISPR-pooled screens, ” Genome Biol. 2019; 20: 20) , the contents of each of which are incorporated herein by reference in their entirety. Briefly, 1323 genes selected above were retrieved from UCSC human genome. sgRNAs targeting each gene were designed using the DeepRank algorithm (see Zhu et al. ) , each gene had three different targeting sgRNAs, and four 6-bp iBARs (iBAR 6 s) were randomly assigned to each sgRNA ( “sgRNA iBAR ” ) .
  • the internal barcode sequence was designed to be placed in the tetra loop of the gRNA scaffold outside of the Cas9-sgRNA ribonucleoprotein complex, which did not affect the activity of its upstream guide sequence.
  • 500 control sgRNAs not targeting any human genes were designed as negative control, and four iBAR 6 s were randomly assigned to each control sgRNA ( “control sgRNA iBAR ” ) .
  • the designed CRISPR sgRNA iBAR library therefore included a total of 17876 sgRNAs iBAR (target and control) .
  • DNA oligonucleotides encoding the sgRNAs iBAR were designed and synthesized (by Twist Bioscience) , then PCR amplified. PCR products were purified with PCR purification kit, then cloned via Golden Gate cloning into lentiviral sgRNA iBAR -expressing backbone modified in house based on pLenti-sgRNA-Lib (addgene #53121) to obtain sgRNA iBAR plasmids, which encodes 15876 sgRNAs iBAR covering 1323 human genes (3 sets of sgRNA iBAR for each gene targeting 3 different target sites, each set of sgRNA iBAR contains 4 sgRNAs iBAR ) , and 2000 control sgRNAs iBAR targeting 500 non-gene regions (1 set of sgRNA iBAR for each non-gene region, each set of sgRNA iBAR contains 4 sgRNAs i
  • sgRNA iBAR plasmids obtained above.
  • 1 ⁇ L sgRNA iBAR plasmids were added into a sterile 1.5 mL Eppendorf tube, 50 ⁇ L competent cells (E. coli) were further added to the tube and swirled, then electroporation was conducted.
  • sgRNA iBAR library lentiviruses were obtained using standard protocol. Briefly, 1 ⁇ 10 7 293T cells were placed in a 150 mm cell culture dish, 20 mL cell culture medium was added, then 293T cells were cultured overnight in a 37°C, 5%CO 2 incubator. The next day, culture medium was discarded, 10 mL fresh serum-free medium was added to the 293T cell.
  • the transfection complex was prepared using serum-free medium (4 mL) , sgRNA iBAR library plasmids obtained above (20 ⁇ g) , pCMVR8.74 plasmid (20 ⁇ g) , and pCMV-VSV-G plasmid (2 ⁇ g) ; after mixing, 105 ⁇ L PEI was added; after mixing, the transfection complex was let stand for 15 minutes in room temperature. The transfection complex was then added to 293T cells in 10 mL fresh serum-free medium, incubated in an incubator at 37°C, 5%CO 2 for 6 hours. Cell medium was discarded.
  • HCT116 human colon cancer cell line
  • Caco2 human colorectal adenocarcinoma cell line
  • sgRNA iBAR library lentivirus obtained above were added to 2 ⁇ 10 7 Cas9 + cancer cells in medium (no antibiotics) at an MOI of 3 and gently mixed.
  • Cas9 + cancer cells were cultured for 24 hours in a 37°C, 5%CO 2 incubator for infection. The next day, the medium was discarded, fresh complete medium was added to the Cas9 + cancer cells, then cultured in a 37°C, 5%CO 2 incubator.
  • Cas9 + cancer cells were passaged every 3 days, in fresh complete medium supplemented with Puromycin.
  • Cas9 + cancer cells not successfully transfected with sgRNA iBAR plasmids would die.
  • sgRNA iBAR cancer cell library was obtained (hereinafter also referred to as “Cas9 + sgRNA iBAR HCT116 library, ” and “Cas9 + sgRNA iBAR Caco2 library” , respectively) .
  • CDK7 inhibitor such as THZ1 or salt thereof
  • the final CDK7 inhibitor concentrations for HCT116 cells were 0.33 ⁇ M, 0.11 ⁇ M, 0.04 ⁇ M, 0.01 ⁇ M, 0.004 ⁇ M, 0.001 ⁇ M, 0.46 nM, 0.15 nM, and 0.05 nM.
  • the final CDK7 inhibitor concentrations for Caco2 cells were 10 ⁇ M, 3.33 ⁇ M, 1.11 ⁇ M, 0.37 ⁇ M, 0.12 ⁇ M, 0.04 ⁇ M, 0.01 ⁇ M, 0.005 ⁇ M, 0.002 ⁇ M, 0.51 nM, 0.17 nM, and 0.06 nM.
  • Luminescent Cell Viability Assay ATP assay
  • Cas9 + sgRNA iBAR cancer cell library screening Based on the obtained drug toxicity curve for each cancer cell line, drug concentrations corresponding to cell growth inhibition of IC 50 -IC 70 were chosen for Cas9 + sgRNA iBAR cancer cell library screening.
  • the concentration of CDK7 inhibitor THZ1 was 15nM for HCT116 and 0.25uM for Caco2.1 ⁇ 10 6
  • Cas9 + sgRNA iBAR cancer cells were placed in a 150 mm cell culture dish and cultured in a 37°C, 5%CO 2 cell incubator. The next day, Cas9 + sgRNA iBAR cancer cells were treated with CDK7 inhibitor (test group) or DMSO (control group) . Two biological replicates were set up for each group.
  • Fresh cell medium (added with drug or DMSO) was changed every three days. The drug or control treatment continued, and cells were collected after treating for 9-10 doubling time or after treating for 16-17 doubling time (see FIG. 2) .
  • adherent cells dead cells would be floating in the culture medium, hence adherent cells harvested by trypsinization were alive (or mostly alive) cells.
  • the cell number was always at least about 1000-fold of the size of the sgRNA iBAR library for each replicate, i.e., at least about 1000 cells for each sgRNA iBAR .
  • Genomic DNA was extracted from post-treatment cancer cells collected above (mostly alive Cas9 + sgRNA iBAR cancer cells) .
  • For each cancer cell type there was a “9-10 PDT test group, ” a “16-17 PDT test group, ” a “9-10 PDT control group, ” and a “16-17 PDT control group” ; with two biological replicates for each group.
  • CDK7 inhibitor was also tested on two different cell line libraries. sgRNA iBAR encoding fragments were PCR amplified from the extracted genome, purified, and prepared for NGS sequencing.
  • MAGeCK iBAR algorithm was used for sequencing data analysis (see Zhu et al., “Guide RNAs with embedded barcodes boost CRISPR-pooled screens, ” Genome Biol. 2019; 20: 20; the content of which is incorporated herein by reference in its entirety) , which contains three main parts: analysis preparation, statistical tests, and rank aggregation. Briefly, each sgRNA iBAR targeted gene was scored and ranked based on the enrichment or depletion degree of each gene between the test group and the control group, in order to determine if such gene was a candidate gene with high confidence. See FIG. 3 for target gene identification workflow.
  • sgRNA iBAR encoding fragments would be depleted compared to control (negative screen) for candidate genes whose inactivation result in sensitive phenotype to anti-cancer drug killing; while sgRNA iBAR encoding fragments would be enriched compared to control (positive screen) for candidate genes whose inactivation result in resistant phenotype to anti-cancer drug killing.
  • These top ranking candidates were found to be involved in cell proliferation, cell death, cell cycle regulation, cell differentiation, or cell adhesion.
  • candidate genes whose sgRNA iBAR encoding fragments are depleted in the harvested alive cells in either “9-10 PDT test group” or “16-17 PDT test group” and in either cell line library (e.g., either Cas9 + sgRNA iBAR HCT116 library or Cas9 + sgRNA iBAR Caco2 library) with FDR ⁇ 0.1 were categorized as drug sensitive genes whose inactivation makes the cancer cells sensitive to the anti-cancer drug.
  • Exemplary drug sensitive genes of CDK7 inhibitor (such as THZ1 or salt thereof) are shown in Table 1.
  • candidate genes whose sgRNA iBAR encoding fragments are enriched in the harvested alive cells in either “9-10 PDT test group” or “16-17 PDT test group” and in either cell line library with FDR ⁇ 0.1 were categorized as drug resistant genes whose inactivation makes the cancer cells resistant to the anti-cancer drug.
  • Exemplary drug resistant genes of CDK7 inhibitor (such as THZ1 or salt thereof) are shown in Table 2.
  • Results obtained here particularly genes whose inactivation were found to confer cancer cell sensitivity to anti-cancer drug (e.g., CDK7 inhibitor) killing, demonstrate valuable targets in cancer therapy as well as biomarkers for patient selection.
  • Drug resistant genes whose inactivation make cancer cells resistant to anti-cancer drug (s) would serve as biomarkers for not selecting such patients, and/or that alternative cancer therapeutic agent (s) should be used.
  • nucleic acids encoding the sgRNAs targeting these genes were designed and synthesized. The forward strand and the reverse strand were allowed to anneal to form double-stranded nucleic acid with over-hangs on both ends.
  • the lentiviral sgRNA-expressing backbone modified in house based on pLenti-sgRNA-Lib (addgene #53121) was enzymatically cleaved, the double-stranded nucleic acid was ligated into the cleavage site, to obtain sgRNA plasmids. This sgRNA plasmid carries puromycin and ampicillin antibiotic genes.
  • sgRNA plasmids were extracted with kit, then sequenced to verify sequences.
  • sgRNA lentiviruses were then obtained using standard protocol. Briefly, 5 ⁇ 10 6 293T cells were placed in a 10 cm cell culture dish and cultured overnight in a 37°C, 5%CO 2 incubator. The next day, culture medium was discarded, fresh serum-free medium was added to the 293T cells.
  • the transfection complex was prepared using serum-free medium (1 mL) , sgRNA plasmid purified above (10 ⁇ g) , pCMVR8.74 plasmid (10 ⁇ g) , and pCMV-VSV-G plasmid (1 ⁇ g) ; after mixing, 52.5 ⁇ L PEI was added. After mixing, the transfection complex was let stand for 15 minutes in room temperature.
  • the transfection complex was then added to 293T cells in fresh serum-free medium, incubated in an incubator at 37°C, 5%CO 2 for 6-8 hours.
  • Cell medium was discarded, fresh complete medium was added to 293T cells, then incubated in an incubator at 37°C, 5%CO 2 .72 hours later, the cell culture was collected and centrifuged at 200 g, 5 minutes.
  • the supernatant containing sgRNA lentiviruses was collected, filtered with a 0.45 ⁇ m filter, then stored at -80°C for later use.
  • cancer cell line with target gene KO 2 ⁇ 10 5 SW620 cancer cells were seeded in 6-well plate and cultured in 37°C, 5%CO 2 incubator. After 24 hours, 100 ⁇ L Cas9 packaged lentivirus was added into the cell medium, and cancer cells were cultured in 37°C, 5%CO 2 incubator. After 24 hours, the medium was discarded, and fresh complete medium was added to the cancer cells. The cancer cells were allowed to grow for 7 days in 37°C, 5%CO 2 incubator, then sorted with FACS using mCherry marker (carried on the Cas9-lentiviral vector) .
  • the sorted cancer cells with mCherry fluorescence were Cas9 expressing (Cas9 + ) cells, and were expanded for Cas9 + sgRNA construction.
  • 500 ⁇ L non-concentrated sgRNA lentiviruses obtained above were added to 2 ⁇ 10 7 Cas9 + cancer cells in medium (no antibiotics) at an MOI of 3 and gently mixed.
  • Cas9 + cancer cells were cultured overnight in a 37°C, 5%CO 2 incubator for infection. The next day, the medium was discarded, fresh complete medium was added to the Cas9 + cancer cells, then cultured in a 37°C, 5%CO 2 incubator for 48 hours. Then 1 ⁇ L puromycin was added to the culture medium for selection. Cas9 + cancer cells not successfully transfected with sgRNA plasmids would die.
  • KO efficiency a subset of cancer cells treated with puromycin from above were collected. Genomic DNA was extracted, and target gene sequence was amplified and sequenced. KO efficiency was calculated by Tracking of Indels by Decomposition (TIDE) web tool, which can accurately reconstructs the spectrum of indels from the sequence traces, and reporting the detected indels and their frequencies as KO efficiency. Results are summarized in Table 3.
  • the screening identified drug sensitive genes after KO indeed conferred sensitivity to CDK7i killing in cancer cells
  • the screening identified drug resistant genes after KO conferred resistance to CDK7i killing in cancer cells.
  • the IC50 fold change between target gene KO and WT cancer cells largely followed screening results: highly enriched or depleted target genes from the screen (e.g., with higher screen score) also showed greater difference in IC50.
  • the above method can be used in drug sensitive gene and/or drug resistant gene screening for any anti-cancer drugs (such as drugs targeting different pathways or the same pathway) and any cancer types.
  • the obtained drug sensitive genes and/or drug resistant genes have significant implications in cancer therapy, patient selection, and new drug screening or design.
  • the diagnosis of a cancer patient indicates that for a single pathway (e.g., targeted by CDK7 inhibitor, etc. ) : 1) the patient only has inactivate mutation in target gene (s) whose inactivation confers sensitivity to pathway-targeting drug (s) , then this patient is a perfect candidate for treatment with such drug (s) ; 2) the patient only has inactivate mutation in target gene (s) whose inactivation confers resistance to pathway-targeting drug (s) , then this patient may not be suitable for treatment with drug (s) targeting such pathway, and alternative treatment methods should be sought; 3) the patient has inactivate mutation in both target gene (s) whose inactivation confers resistance to pathway-targeting drug (s) , and target gene (s) whose inactivation confers sensitivity to pathway-targeting drug (s) , then more analysis needs to be conducted, e.g., if the drug sensitivity is sufficient to help kill cancer cells before drug resistance occurs, if genes conferring drug resistance are of less significance
  • Target genes obtained for multiple anti-cancer drugs can be combined or overlapped to find common target genes.
  • Gene functions and/or mechanisms of action can be further analyzed to make treatment decision, and/or for drug design/development. For example, if a patient carries inactivate mutation in a gene whose inactivation confers sensitivity to drugs X, Y, and Z, then a combination therapy with drugs X, Y, and Z might confer synergistic anti-cancer activity.
  • a patient carries inactivate mutations in different genes (of the same pathway or different pathways) whose inactivation confers sensitivity to drugs X, Y, and Z
  • a combination therapy with drugs X, Y, and Z might confer synergistic anti-cancer activity.
  • a new drug can be designed to target various pathways involving target genes whose deletion confer sensitivity to known drugs, then the obtained new drug might have superior therapeutic effect compared to known drugs.
  • drug X that will experience drug resistance from the target gene mutation later during treatment can be used first, and a drug Y that will experience drug resistance from the target gene mutation early on but may be sufficiently effective can be used only at the beginning or throughout the process, in combination with drug X.
  • Example 2 Composite score reflects cancer killing efficacy by anti-cancer drug
  • a collection of colorectal cancer cell lines and/or patient-derived xenografts (PDXs) is tested for response to CDK7i treatment, by measuring cell viability rate (reflected as IC50) or PDX growth inhibition rate following standard methods (also see Example 1) .
  • Cancer samples are selected based on various response against CDK7i treatment, for use in composite score calculation. Their corresponding cell viability response or PDX growth inhibition response is reflected as “drug response. ”
  • Cancer samples are individually sequenced by NGS. For each sample, mutations are detected from the sequencing data. The raw mutation sites are further filtered according to mutation quality to remove low confidence mutation sites. The remaining high-quality mutation sites are mapped to corresponding genes, and annotated for the impact of the mutation on the corresponding gene function based on database. Only mutation sites with deleterious impact to corresponding genes are retained for subsequent analysis.
  • the remaining mutation sites from above are annotated based on prevalence, clinical significance, curated impact, gene ontology, and pathway information etc. from both external and internal database sources. Low-clinical impact mutations are further filtered out. Then overall loss-of-function (LOF) probability is calculated for each gene mapped to the remaining mutations for each sample.
  • LEF loss-of-function
  • CDK7i sensitive genes and CDK7i resistant genes obtained from and/or verified in Example 1 and with at least one high confidence deleterious mutation in any of the cancer samples after filtering, are selected ( “test gene panel” ) .
  • the gene-level LOF probability across the selected CDK7i sensitive/resistant genes is used to calculate the portion in Formula I.
  • Gene-level contribution and pathway- level contribution of mutations detected in the “test gene panel” to CDK7i treatment are quantified by integrating the corresponding weight coefficient of correlation of each gene (r i ) , and pre-calculated weight for the related pathways in CDK7i response to calculate the raw composite score.
  • the raw composite score is further adjusted and scaled accordingly to the sample types (i.e., cell line, PDX, patient) to generate the final composite score for each cancer sample.
  • Cancer samples sensitive to CDK7i killing should have composite score according to Formula I of above 0; while cancer samples resistant to CDK7i killing should have composite score according to Formula I of below 0.
  • CDK7i sensitive genes and CDK7i resistant genes identified using screening methods described herein, and composite scores obtained based on them using methods described herein, should correctly reflect/predict cancer killing efficacy by CDK7i, and can serve as tools for cancer diagnosis, treatment selection, and/or patient selection.
  • the composite score of the patient according to Formula I is above 0, the patient may be suitable for (i.e., may benefit from) CDK7i treatment. If the composite score of the patient according to Formula I is above or equal to at least 0.1 (e.g., 0.3) , the patient can be selected or recommended for CDK7i treatment.
  • the patient may be suitable for CDK7i treatment, but should be further evaluated using other method (s) (e.g., drug dosage test, cancer genetic testing (e.g., look for additional synergistic mutations that may contribute to CDK7i treatment, or verify the primary cancer type) , etc. ) or based on other information (e.g., patient’s clinical record or known drug resistance, etc. ) to determine whether the patient should be selected or recommended for CDK7i treatment. If the composite score of the patient according to Formula I is below or equal to 0, the patient may not be suitable for (i.e., may not benefit from) or should be excluded from CDK7i treatment.
  • other method e.g., drug dosage test, cancer genetic testing (e.g., look for additional synergistic mutations that may contribute to CDK7i treatment, or verify the primary cancer type) , etc. ) or based on other information (e.g., patient’s clinical record or known drug resistance, etc. ) to determine whether the patient should be selected or recommended

Abstract

L'invention concerne : une méthode de traitement d'un cancer colorectal chez un individu, comprenant l'administration à l'individu d'une quantité efficace d'un inhibiteur de CDK7, l'individu étant sélectionné pour un traitement en fonction d'une ou de plusieurs aberrations sensibles aux médicaments dans un ou plusieurs gènes sensibles aux médicaments; et un procédé d'identification d'un individu souffrant d'un cancer colorectal qui peut tirer profit d'un traitement comprenant l'administration d'un inhibiteur de CDK7, le procédé comprenant la détection dans un échantillon prélevé chez l'individu d'une ou plusieurs aberrations sensibles aux médicaments dans un ou plusieurs gènes sensibles aux médicaments. La présente invention concerne également une pluralité de molécules d'acide nucléique de capture, un système et un support de stockage lisible par ordinateur non transitoire.
PCT/CN2022/139152 2021-12-16 2022-12-14 Biomarqueurs pour le traitement du cancer colorectal WO2023109876A1 (fr)

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