Methods for predicting drug responsiveness in cancer patients
The present invention features methods, devices, and kits for detecting gene expression in a patient with a cancer or determining responsive of a patient with a cancer to a treatment, such as treatment with 2X-121 or a pharmaceutically acceptable salt thereof. The invention further includes methods of treating a patient with a cancer by administering a treatment, e.g., treatment with 2X-121 or a pharmaceutically acceptable salt thereof, in particular when the patient is determined to be responsive to the treatment based on the expression of the biomarkers described herein.
1 . A method of treating a cancer in a human subject in need thereof comprising orally administering 2X-121 or a pharmaceutically acceptable salt thereof to the subject with a difference score determined from a tumor sample from the subject that is above a cutoff value of the 50th percentile or greater of the difference score in a reference population with the same diagnosis as the subject, wherein the difference score is a level of mRNA expression of HLA-E determined from the tumor sample subtracted from a level of mRNA expression of SRSF7 determined from the tumor sample.
2 . The method of claim 1 , wherein the difference score is determined by subtracting a mean score of a level of mRNA expression of biomarkers of resistance from a mean score of a level of mRNA expression of biomarkers of sensitivity, wherein:
(i) the mean score of the level of mRNA expression of the biomarkers of resistance is the mean of the level of mRNA expression of HLA-E and the level of mRNA expression of one or more biomarkers of resistance selected from the group consisting of GADD45B, CLIC1, LASP1, APOBEC3B, LGALS1, TAPBP, AHNAK, BHLHE40, S100A11, LITAF, ZBTB38, TCIRG1, S100A11P1, CTSA, FXYD5, YPEL5, HLA-C, STOM, PLIN3, IRF1, LMNA, NPC2, P4HB, KLF6, RHOC, SRGN, STAT1, PIEZO1, LGALS3, CD97, HLA-B, FNDC3B/LOC101928615, CKLF/CKLF-CMTM1, IFI35, TIPARP, TAP1, MICALL2, RRBP1, ZFP36, TNIP1, CD59, LDLRAP1, FLNB, PSG6, CBX7, RARRES3, CFLAR, SUN2, EHD2, MAP3K5, NOL12/TRIOBP, ARPC1B, TNFSF10, HLA-G, RP11-395B7.7, LEPROT, BTN3A2/BTN3A3, INPP4B, DUSP1, EVI2A, EHD1, EPAS1, IQGAP1, CLIC3, NACC2, TGFBI, IER3, MICA, CNN2, VEGFA, MBNL1, ISG15, TNFAIP8, COPG1, PSMB9, ZFP36L1, IL6ST, SHC1, GSTK1, CAV1, KRT7, TFPI, RHOG, CDH11, ABCC3, HLA-J, MYL12A, MRPS10, RRAS, TMEM2, SIDT2, RAB11FIP1, RTP4, SPTBN1, TMEM189/TMEM189-UBE2V1/UBE2V1/UBE2V2, ITGA5, CDC42EP1, OSER1, CHST15, MDFIC, CAV2, CARD10, RAC2, MLPH, F2R, ICAM3, CRIM1/LOC101929500, EVI2B, PFKFB3, MIR6513/TMBIM1, APOL3, CD55, TRAM2, S100A4, PIP4K2A, RPN2, IFIT3, PLAC8, SDF4, MVP, RNH1, EIF1, SERPINB1, ASL, CD99, USP4, TACC1, PDXK, BST2, LOC101928916/NNMT, DUSP5, COMT, LY6E, ACSL5, GBP2, TNFRSF1B, PTRF, CYR61, BTN3A1, PLEC, CTNND1/TMX2-CTNND1, TNFRSF14, ABCC10, SELPLG, GPX4, EDEM1, MIR6787/SLC16A3, DMBT1, PSMB8, COL1A1, FOS, CYLD, ADAMTS1, ALDOA, GATA6, YWHAB, CIB1, OPTN, IFI16, PTGER4, CCND1, PDLIM5, HLA-F, CYP1B1, SVIL, TAGLN2, IFI27, FLII, STAT6, WWP2, FLNC, PARP12, VPS13D, IFITM2, CTSZ, C19orf10, DAPK1, LOC101928189/RSRP1, MYOF, ATP2B4, AXL, LY96, FN1, CREB3L1, TNFSF12-TNFSF13/TNFSF13, POFUT2, WDR1, SLC7A7, MICB, GATA3, LRRFIP1, RNASET2, and ITM2A, and
the mean score of the level of mRNA expression of biomarkers of sensitivity is the mean of the level of mRNA expression of SRSF7 and the level of mRNA expression of one or more biomarkers of sensitivity selected from the group consisting of UCHL1, MLLT11, ADD2, PRMT1, SRSF3, PRMT5, COCH, RUVBL1, MARCKSL1, CHERP, MTSS1, LSM4, RAPGEF5, PRPF4, DESI2, RNPS1, SNX10, CUL3, CHD4, MSH2, HNRNPM, SRSF1, NELL2, PAICS, HOXA10, BUB1B, E2F5, MAGED4/MAGED4B/SNORA11D/SNORA11E, PRPF8, SORD, HNRNPU, PEX5, HYPK/MIR1282/SERF2/SERF2-C15ORF63, STRAP, NDUFAB1, FARSA, STOML2, ERH, HSBP1, DDX39A, ODC1, TAF5, TBC1D31, TRA2B, NUDC, DDX23, PRPF31, UBE2S, TCF4, MLF2, CCDC181, RPF1, PASK, NUP88, RNASEH2A, FBL, LOC101928747/RBMX/SNORD61, NXF1, PLEKHO1, GAR1, RPA1, ZNF24, BOP1 MIR7112, RAB3B, SLC35G2, DKC1/MIR664B/SNORA56, PSMC3IP, DNAJC7, RRP1B, NME1, SNRPA, DBN1, KIAA0020, SUPV3L1, ZNF573, FAM134B, TOX3, HSPD1, ACLY, MSANTD3-TMEFF1/TMEFF1, AKIRIN1, UBE2M, MTF2, EWSR1, SKP2, TMEM97, HNRNPD, ILKAP, NASP, SNRPD1, TIMM44, PKN1, STAU2, DNAAF2, SNRPD2, FUS, ATP6V1G2-DDX39B/DDX39B/SNORD84, PDSS1, TPGS2, SLIRP, NCL, ANP32A, SAFB, STIP1, CEP68, C8orf33, MRPL11, POLR21, MCAM/MIR6756, ECSIT, MDK, PUF60, PFN2, SYNCRIP, TSPAN3, SLC16A1, POLR2H, MAP3K7, CSRP2, BCL11A, PNKP, DNAJC6, FDFT1, FADS1/MIR1908, RPARP-AS1, DHRS7, CCNB1IP1, CCT3/LOC101927137, DDX18, AARSD1/PTGES3L/PTGES3L-AARSD1, HNRNPDL, ATXN7L3B, MRPS14, SOX4, ELOVL2, KCNJ8, TRIAP1, EIF2B1, FBXL14, MAPRE2, ORC4, MDN1, KNOP1, KBTBD11, FADS2, RANBP1, PLEKHB1, HSPE1, ITFG2/LOC100507424, SFPQ, RFC3, SDR39U1, PBK, PHB, KHDRBS1, PDAP1, SSRP1, and B3GALT2.
3 . The method of claim 2 , wherein the biomarkers of sensitivity are selected from:
(a) one or more of SEQ ID NOs: 2-25;
(b) one or more of SEQ ID NOs: 26-50;
(c) one or more of SEQ ID NOs: 51-75;
(d) one or more of SEQ ID NOs: 76-100;
(e) one or more of SEQ ID NOs: 101-125;
(f) one or more of SEQ ID NOs: 126-150; and/or
(g) one or more of SEQ ID NOs: 151-172.
4 . The method of claim 2 , wherein the biomarkers of resistance are selected from:
(a) one or more of SEQ ID NOs: 175-177 and 179-200;
(b) one or more of SEQ ID NOs: 201-225;
(c) one or more of SEQ ID NOs: 226-250;
(d) one or more of SEQ ID NOs: 251-275;
(e) one or more of SEQ ID NOs: 276-300;
(f) one or more of SEQ ID NOs: 301-325;
(g) one or more of SEQ ID NOs: 326-350;
(h) one or more of SEQ ID NOs: 351-375;
(i) one or more of SEQ ID NOs: 376-400; and/or
(j) one or more of SEQ ID NOs: 401-414.
5 . The method of claim 2 , wherein:
(i) the biomarkers of sensitivity are selected from at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 100, at least 105, at least 110, at least 115, at least 120, at least 125, at least 130, at least 135, at least 140, at least 145, at least 150, at least 155, at least 160, at least 165, at least 170, or at least 171 of SEQ ID NOs: 2-172; and/or
(ii) the biomarkers of resistance are selected from at least 5, at least 10, at least 15, at least 20, at least 25, at least 30, at least 35, at least 40, at least 45, at least 50, at least 55, at least 60, at least 65, at least 70, at least 75, at least 80, at least 85, at least 90, at least 95, at least 100, at least 105, at least 110, at least 115, at least 120, at least 125, at least 130, at least 135, at least 140, at least 145, at least 150, at least 155, at least 160, at least 165, at least 170, at least 175, at least 180, at least 185, at least 190, at least 195, at least 200, at least 205, at least 210, at least 215, at least 220, at least 225, at least 230, at least 235, or at least 240 of SEQ ID NOs: 175-177 and 179-414.
6 . The method of claim 1 , further comprising administering one or more additional therapies to the subject prior to, concurrently, or after administration of 2X-121 or the pharmaceutically acceptable salt thereof.
7 . The method of claim 6 , wherein the one or more additional therapies comprises surgery, radiation, or a therapeutic agent.
8 . The method of claim 7 , wherein the therapeutic agent is administered intravenously, intramuscularly, transdermally, intradermally, intra-arterially, intracranially, subcutaneously, intraorbitally, intraventricularly, intraspinally, intraperitoneally, or intranasally.
9 . The method of claim 1 , comprising administering 2X-121 or the pharmaceutically acceptable salt thereof to the subject two or more times.
10 . The method of claim 1 , comprising administering 2X-121 or the pharmaceutically acceptable salt thereof to the subject one or more times daily, weekly, every two weeks, every three weeks, or monthly.
11 . The method of claim 10 , comprising administering 2X-121 or the pharmaceutically acceptable salt thereof to the subject one or more times daily.
12 . The method of claim 11 , wherein about 600 mg of 2X-121 or the pharmaceutically acceptable salt thereof is administered to the subject daily.
13 . The method of claim 1 , comprising administering a second dose of 2X-121 or the pharmaceutically acceptable salt thereof to the subject two weeks, three weeks, four weeks, or five weeks after administration of a first dose of 2X-121 or the pharmaceutically acceptable salt thereof.
14 . The method of claim 1 , wherein 2X-121 or the pharmaceutically acceptable salt thereof is administered in a dosage form.
15 . The method of claim 14 , wherein 2X-121 or the pharmaceutically acceptable salt thereof is administered to the subject at a dose of about 5-5000 mg.
16 . The method of claim 15 , wherein 2X-121 or the pharmaceutically acceptable salt thereof is administered to the subject at a dose of about 10 mg, 50 mg, or 200 mg.
17 . The method of claim 15 , wherein 2X-121 or the pharmaceutically acceptable salt thereof is administered to the subject at a dose of about 50-800 mg.
18 . The method of claim 1 , wherein the cutoff value is a 60 th percentile, 70th percentile, 80 th percentile, or greater of the difference score in the reference population with the same diagnosis as the subject.
19 . The method of claim 1 , wherein:
(a) the cancer is selected from a solid tumor cancer and a hematological cancer; or
(b) the cancer is selected from the group consisting of multiple myeloma, breast cancer, acute myelogenous leukemia (AML), acute lympho-blastic leukemia (ALL), chronic lymphocytic leukemia (CLL), myelodysplastic syndrome (MDS), chronic myelogenous leukemia-chronic phase (CMLCP), diffuse large B-cell lymphoma (DLBCL), cutaneous T-cell lymphoma (CTCL), peripheral T-cell lymphoma (PTCL), Hodgkin's lymphoma, hepatocellular carcinoma (HCC), cervical cancer, prostate cancer, kidney cancer, renal cell carcinoma (RCC), esophageal cancer, melanoma, glioma, pancreatic cancer, ovarian cancer, gastrointestinal stromal tumors (GIST), sarcoma, estrogen receptor-positive (ERpos) breast cancer, lung cancer, non-small cell lung carcinoma (NSCLC), mesothelioma, intestinal cancer, colon cancer, bladder cancer, adrenal cancer, gallbladder cancer, and squamous cell carcinoma of the head and neck (SCCHN).
20 . The method of claim 19 , wherein the cancer is breast cancer.
21 . The method of claim 20 , wherein the breast cancer is estrogen receptor-positive (ER pos) breast cancer or is a metastatic form of breast cancer.
22 . The method of claim 19 , wherein the cancer is ovarian cancer.
23 . The method of claim 19 , wherein the cancer is pancreatic cancer.
24 . The method of claim 1 , wherein the subject has recurrence of cancer.
25 . A method of treating cancer in a human subject in need thereof comprising:
(a) determining a level of mRNA expression of SRSF7 and a level of mRNA expression of HLA-E in a tumor sample from the subject;
(b) calculating a difference score for the subject by subtracting the level of mRNA expression of HLA-E from the level of mRNA expression of SRSF7, wherein the difference score of the subject is above a cutoff value of a difference score in a reference population with the same diagnosis as the subject, thereby identifying the subject as responsive to 2X-121 or a pharmaceutically acceptable salt thereof, and wherein the cutoff value is a 50th percentile of the difference score in the reference population with the same diagnosis as the subject; and
(c) orally administering 2X-121 or a pharmaceutically acceptable salt thereof to the subject.
26 . The method of claim 25 , wherein the cutoff value is a 60th percentile, 70 th percentile, 80 th percentile, or greater of the difference score in a reference population with the same diagnosis as the subject.
27 . The method of claim 25 , wherein the level of mRNA expression of SRSF7 and the level of mRNA expression of HLA-E are determined using a device.
28 . The method of claim 27 , wherein the device is a microarray.
29 . The method of claim 28 , wherein the microarray is a deoxyribonucleic acid (DNA)-based platform.
30 . The method of claim 25 , wherein the level of mRNA expression of SRSF7 and the level of mRNA expression of HLA-E are determined by microarray analysis, a nucleic acid amplification method, pyrosequencing, nanopore sequencing, sequencing by synthesis, sequencing by expansion, single molecule real time technology, sequencing by ligation, microfluidics, infrared fluorescence, or a ribonucleic acid (RNA) sequencing technique (RNA-Seq).
31 . The method of claim 25 , wherein step (a) of the method further comprises:
(i) determining a level of mRNA expression of one or more biomarkers of sensitivity selected from the group consisting of UCHL1, MLLT11, ADD2, PRMT1, SRSF3, PRMT5, COCH, RUVBL1, MARCKSL1, CHERP, MTSS1, LSM4, RAPGEF5, PRPF4, DESI2, RNPS1, SNX10, CUL3, CHD4, MSH2, HNRNPM, SRSF1, NELL2, PAICS, HOXA10, BUB1B, E2F5, MAGED4/MAGED4B/SNORA11D/SNORA11E, PRPF8, SORD, HNRNPU, PEX5, HYPK/MIR1282/SERF2/SERF2-C15ORF63, STRAP, NDUFAB1, FARSA, STOML2, ERH, HSBP1, DDX39A, ODC1, TAF5, TBC1D31, TRA2B, NUDC, DDX23, PRPF31, UBE2S, TCF4, MLF2, CCDC181, RPF1, PASK, NUP88, RNASEH2A, FBL, LOC101928747/RBMX/SNORD61, NXF1, PLEKHO1, GAR1, RPA1, ZNF24, BOP1 MIR7112, RAB3B, SLC35G2, DKC1/MIR664B/SNORA56, PSMC3IP, DNAJC7, RRP1B, NME1, SNRPA, DBN1, KIAA0020, SUPV3L1, ZNF573, FAM134B, TOX3, HSPD1, ACLY, MSANTD3-TMEFF1/TMEFF1, AKIRIN1, UBE2M, MTF2, EWSR1, SKP2, TMEM97, HNRNPD, ILKAP, NASP, SNRPD1, TIMM44, PKN1, STAU2, DNAAF2, SNRPD2, FUS, ATP6V1G2-DDX39B/DDX39B/SNORD84, PDSS1, NUDG, TPGS2, SLIRP, NCL, ANP32A, SAFB, STIP1, CEP68, C8orf33, MRPL11, POLR21, MCAM/MIR6756, ECSIT, MDK, PUF60, PFN2, SYNCRIP, TSPAN3, SLC16A1, POLR2H, MAP3K7, CSRP2, BCL11A, PNKP, DNAJC6, FDFT1, FADS1/MIR1908, RPARP-AS1, DHRS7, CCNB1IP1, CCT3/LOC101927137, DDX18, AARSD1/PTGES3L/PTGES3L-AARSD1, HNRNPDL, ATXN7L3B, MRPS14, SOX4, ELOVL2, KCNJ8, TRIAP1, EIF2B1, FBXL14, MAPRE2, ORC4, MDN1, KNOP1, KBTBD11, FADS2, RANBP1, PLEKHB1, HSPE1, ITFG2/LOC100507424, SFPQ, RFC3, SDR39U1, PBK, PHB, KHDRBS1, PDAP1, SSRP1, and B3GALT2; and
(ii) determining a level of mRNA expression of one or more biomarkers of resistance selected from the group consisting of GADD45B, CLIC1, LASP1, APOBEC3B, LGALS1, TAPBP, AHNAK, BHLHE40, S100A11, LITAF, ZBTB38, TCIRG1, S100A11P1, CTSA, FXYD5, YPEL5, HLA-C, STOM, PLIN3, IRF1, LMNA, NPC2, P4HB, KLF6, RHOC, SRGN, STAT1, PIEZO1, LGALS3, CD97, HLA-B, FNDC3B/LOC101928615, CKLF/CKLF-CMTM1, IFI35, TIPARP, TAP1, MICALL2, RRBP1, ZFP36, TNIP1, CD59, LDLRAP1, FLNB, PSG6, CBX7, RARRES3, CFLAR, SUN2, EHD2, MAP3K5, NOL12/TRIOBP, CKLE, ARPC1B, TNFSF10, HLA-G, RP11-395B7.7, LEPROT, BTN3A2/BTN3A3, INPP4B, DUSP1, EVI2A, EHD1, EPAS1, IQGAP1, CLIC3, NACC2, TGFBI, IER3, MICA, CNN2, VEGFA, MBNL1, ISG15, TNFAIP8, COPG1, PSMB9, ZFP36L1, IL6ST, SHC1, GSTK1, CAV1, KRT7, TFPI, RHOG, CDH11, ABCC3, HLA-J, MYL12A, MRPS10, RRAS, TMEM2, SIDT2, RAB11FIP1, RTP4, SPTBN1, TMEM189/TMEM189-UBE2V1/UBE2V1/UBE2V2, ITGA5, CDC42EP1, OSER1, CHST15, MDFIC, CAV2, CARD10, RAC2, MLPH, F2R, ICAM3, CRIM1/LOC101929500, EVI2B, PFKFB3, MIR6513/TMBIM1, APOL3, CD55, TRAM2, S100A4, PIP4K2A, RPN2, IFIT3, PLAC8, SDF4, MVP, RNH1, EIF1, SERPINB1, ASL, CD99, USP4, TACC1, PDXK, BST2, LOC101928916/NNMT, DUSP5, COMT, LY6E, ACSL5, GBP2, TNFRSF1B, PTRF, CYR61, BTN3A1, PLEC, CTNND1/TMX2-CTNND1, TNFRSF14, ABCC10, SELPLG, GPX4, EDEM1, MIR6787/SLC16A3, DMBT1, PSMB8, COL1A1, FOS, CYLD, ADAMTS1, ALDOA, GATA6, YWHAB, CIB1, OPTN, IFI16, PTGER4, CCND1, PDLIM5, HLA-F, CYP1B1, SVIL, TAGLN2, IFI27, FLII, STAT6, WWP2, FLNC, PARP12, VPS13D, IFITM2, CTSZ, C19orf10, DAPK1, LOC101928189/RSRP1, MYOF, ATP2B4, AXL, LY96, FN1, CREB3L1, TNFSF12-TNFSF13/TNFSF13, POFUT2, WDR1, SLC7A7, MICB, GATA3, LRRFIP1, RNASET2, and ITM2A.
32 . The method of claim 31 , wherein the level of mRNA expression of SRSF7 and the level of mRNA expression of the one or more biomarkers of sensitivity and/or the level of mRNA expression of HLA-E and the level of mRNA expression of the one or more biomarkers of resistance are determined using a device.
33 . The method of claim 32 , wherein the device comprises (i) single-stranded nucleic acid molecules capable of specifically hybridizing with nucleotides of SRSF7 and single-stranded nucleic acid molecules capable of specifically hybridizing with the one or more biomarkers of sensitivity and/or (ii) single-stranded nucleic acid molecules capable of specifically hybridizing with nucleotides of HLA-E and single-stranded nucleic acid molecules capable of specifically hybridizing with the one or more biomarkers of resistance.
34 . The method of claim 33 , wherein the single-stranded nucleic acid molecules of the device have a length in the range of 10-100 nucleotides.
35 . The method of claim 34 , wherein the single-stranded nucleic acid molecules have a length in the range of 20-60 nucleotides.
36 . The method of claim 31 , wherein step (a) of the method further comprises converting the level of mRNA expression of SRSF7 and the level of mRNA expression of the one or more biomarkers of sensitivity and the level of mRNA expression of HLA-E and the level of mRNA expression of the one or more biomarkers of resistance into a mean score.
37 . The method of claim 36 , wherein step (b) of the method further comprises subtracting the mean score for the level of mRNA expression of HLA-E and the level of mRNA expression of the one or more biomarkers of resistance from the mean score for the level of mRNA expression of SRSF7 and the level of mRNA expression of the one or more biomarkers of sensitivity to obtain the difference score.
38 . The method of claim 37 , wherein the cutoff value is a 60th percentile, 70th percentile, 80th percentile, or greater of the difference score in the reference population with the same diagnosis as the subject.