Markers of Triple-Negative Breast Cancer And Uses Thereof

Abstract

In one aspect provided herein are methods of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising determining expression of one or more genes in one or more TNBC cells of the individual; and comparing the expression of the one or more genes in the TNBC cells with the expression of the one or more genes in a control. In another aspect, the methods are directed to methods of determining a treatment protocol for the TNBC patient based on the TNBC subtype. In another aspect, the methods are directed to predicting whether an individual will benefit from a treatment for a particular TNBC subtype. In yet another aspect, the invention is directed to a method of determining whether an agent can be used to treat a TNBC subtype.

1 . A method of determining a triple negative breast cancer (TNBC) subtype in an individual in need thereof comprising
 a) determining expression of one or more genes in one or more TNBC cells of the individual; and   b) comparing the expression of the one or more genes in the TNBC cells with the expression of the one or more genes in a control,
 wherein increased expression of one or more cell cycle genes, cell division genes, proliferation genes, DNA damage response genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL1 subtype; 
 increased expression of one or more growth factor signaling genes, glycolysis genes, gluconeogenesis genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC BL2 subtype; 
 increased expression of one or more immune cell signaling genes, cytokine signaling genes, antigen processing and presentation genes, core immune signal transduction genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC IM subtype; 
 increased expression of one or more cell motility genes, extracellular matrix (ECM) receptor interaction genes, cell differentiation genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC M subtype; 
 increased expression of one or more cell motility genes, cellular differentiation genes, growth pathway genes, growth factor signaling genes, angiogenesis genes, immune signaling genes, stem cell genes, HOX genes, mesenchymal stem cell-specific marker genes or a combination thereof in the TNBC cells compared to the control indicates that the TNBC is a TNBC MSL subtype; and 
 increased expression of one or more hormone regulated genes in the TNBC cells compared to the control indicates that the TNBC is a TNBC LAR subtype. 
   
     
     
         2 . The method of  claim 1  wherein detection of the TNBC BL1 subtype comprises selectively detecting increased expression of a gene combination comprising AURKA, AURKB, CENPA, CENPF, BUB1, BUB1B, TTK, CCNA2, PLK1, PRC1, MYC, NRAS, PLK1, BIRC5, CHEK1, FANCA, FANCG, FOXM1, HNGA1, RAD54BP, RAD51, NEKS, NBN, EXO1, MSH2, MCM10, RAD21, SIX3, Z1C1, SOX4, SOX1 and MDC1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL1 subtype. 
     
     
         3 . The method of  claim 1  wherein determination that the TNBC is a TNBC BL1 subtype further comprises detecting increased expression of Ki-67 mRNA in the TNBC cells compared to the control. 
     
     
         4 . The method of  claim 1  wherein determination that the TNBC is a TNBC BL1 subtype further comprises detecting one or more mutated genes. 
     
     
         5 . The method of  claim 4  wherein the one or more mutated genes comprise mutated BRCA1, STAT4, UTX, BRCA2, TP53, CTNND1, TOP2B, CAMK1G, MAPK13, MDC1, PTEN, RB1, SMAD4, CDKN2A, ATM, ATR, CLSPN, HDAC4, NOTCH1, SMARCAL1, and TIMELESS. 
     
     
         6 . The method of  claim 1  wherein detection of the TNBC BL2 subtype comprises selectively detecting increased expression of a gene combination comprising EGFR, MET, ELF4, MAF, NUAK1, JAG1, FOSL2, 1D1, ZIC1, SOX11, 1D3, FHL2, EPHA2, TP63 and MME wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC BL2 subtype. 
     
     
         7 . The method of  claim 1  wherein determination that the TNBC is a TNBC BL2 subtype further comprises detecting one or more mutated genes. 
     
     
         8 . The method of  claim 7  wherein the one or more mutated genes comprise mutated BRCA1, RB1, TP53, PTEN, CDKN2A, UTX, BRAC2, PTCH1, PTCH2, and RET. 
     
     
         9 . The method of  claim 1  wherein detection of the TNBC M subtype comprises selectively detecting increased expression of a gene combination comprising TGFB1L1, BGN, SMAD6, SMAD7, NOTCH1, TGFB1, TGFB2, TGFB3, TGFBR1, TGFBR2, TGFBR3, MMP2, ACTA2, SNAI2, SPARC, SMAD7, PDGFRA, TAGLN, TCF4, TWIST1, ZEB1, COL3A1, JAG1, EN1, MYLK, STK38L, CDH11, ETV5, IGF1R, FGFR1, FGFR2, FGFR3, TBX3, COL5A2, GNG11, ZEB2, CTNNB1, DKK2, DKK3, SFPR4, TCF4, TCF7L2, FZD4, CAV1, CAV2, CCND1 and CCND2 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC M subtype. 
     
     
         10 . The method of  claim 1  wherein determination that the TNBC is a TNBC M subtype further comprises detecting decreased E-cadherin (CDH1) expression compared to the control. 
     
     
         11 . The method of  claim 1  wherein determination that the TNBC is a TNBC M subtype further comprises detecting one or more mutated genes. 
     
     
         12 . The method of  claim 11  wherein the one or more mutated genes comprise mutated PTEN, RB1, TP53, PIK3CA, APC, BRAF, CTNNB1, FGFR1, GLI1, HRAS, KRAS, NOTCH1, and NOTCH4. 
     
     
         13 . The method of  claim 1  wherein determination that the TNBC is a TNBC M subtype further comprises detecting chromosomal amplifications in KRAS, IGF1R or MET. 
     
     
         14 . The method of  claim 1  wherein detection of the TNBC MSL subtype comprises selectively detecting increased expression of a gene combination comprising VEGFR2 (KDR), TEK, TIE1, EPAS1, ABCA8, PROCR, ENG, ALDHA1, PER1, ABCB1, TERF21P, BCL2, BMP2, EPAS1, STAT4, PPARG, JAK1, ID1, SMAD3, TWIST1, THY1, HOXA5, HOXA10, GL13, HHEX, ZFHX4, HMBOX1, FOS, PIK3R1, MAF, MAFB, RPS6KA2, TCF4, TGFB1L1, MEIS1, MEIS2, MEOX1, MEOX2, MSX1, ITGAV, KDR, NGFR, NT5E, PDGFRA, PDGFRB, POU2F1, and VCAM1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC MSL subtype. 
     
     
         15 . The method of  claim 1  wherein determination that the TNBC is a TNBC MSL subtype further comprises detecting low expression of claudins 3, 4, 7 or a combination thereof compared to the control. 
     
     
         16 . The method of  claim 1  wherein determination that the TNBC is a MSL subtype TNBC further comprises detecting one or more mutated genes. 
     
     
         17 . The method of  claim 16  wherein the one or more mutated genes comprise mutated CDKN2A, HRAS, TP53, NF1, PIK3CA, BRCA1, BRAF, KRAS, NF2, PDGFRA, APC, CTNNB1, FGFR1, PDGFRB. 
     
     
         18 . The method of  claim 1  wherein detection of the TNBC IM subtype comprises selectively detecting increased expression of a gene combination comprising CCL19, CCL3, CCL4, CCL5, CCL8, CCR1, CCR2, CCR5, CCR7, CD2, CD37, CD38, CD3D, CD48, CD52, CD69, CD74, and CD8A wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC IM subtype. 
     
     
         19 . The method of  claim 1  wherein determination that the TNBC is a TNBC IM subtype further comprises detecting one or more mutated genes. 
     
     
         20 . The method of  claim 19  wherein the one or more mutated genes comprise TP53, CTNNA1, DDX18, HUWE1, NFKBIA, APC, BRAF, MAP2K4, RB1, STAT4, STAT1, and RET. 
     
     
         21 . The method of  claim 1  wherein detection of the TNBC LAR subtype comprises selectively detecting increased expression of a gene combination comprising AR, DHCR24, ALCAM, GATA2, GATA3, IDIH1, IDIH2, CDH11, ERBB3, CUX2, FGFR4, HOPX, FASN, FKBP5, APOD, PIP, SPDEF, CLDN8, FOXA1, KRT18, and XBP1 wherein detection of increased expression of the gene combination indicates that the TNBC is TNBC LAR subtype. 
     
     
         22 . The method of  claim 1  wherein determination that the TNBC is a LAR subtype TNBC further comprises detecting one or more mutated genes. 
     
     
         23 . The method of  claim 22  wherein the one or more mutated genes comprise PIK3CA, CDH1, PTEN, RB1, TP53, and MAP3K1. 
     
     
         24 . The method of  claim 2  wherein selective expression of the gene combination is detected using PCR, microarray analysis, next generation RNA sequencing, immunofluorescence, Western blot analysis or a combination thereof. 
     
     
         25 . The method of  claim 4  wherein the one or more mutated genes is detected using a SNaPshot assay, exome sequencing, sanger gene sequencing, resequencing array analysis, mRNA analysis/cDNA sequencing polymerase chain reaction (PCR), single-strand conformation polymorphism (sscp), heteroduplex analysis (het), allele-specific oligonucleotide (aso), restriction fragment analysis, allele-specific amplification (asa), single nucleotide primer extension, oligonucleotide ligation assay (ola), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and single strand conformation polymorphism (SSCP) or a combination thereof. 
     
     
         26 . The method of  claim 1  wherein the individual has been diagnosed with breast cancer, the individual has not been diagnosed with breast cancer, or the individual is at risk of developing breast cancer. 
     
     
         27 . The method of  claim 1  wherein the individual is a human. 
     
     
         28 . The method of  claim 1  wherein the TNBC cells are epithelial cells, mesenchymal cells, immune cells or a combination thereof. 
     
     
         29 . The method of  claim 1  wherein the control is a non-cancer cell. 
     
     
         30 . The method of  claim 29  wherein the non-cancer cell is obtained from an individual that does not have TNBC, from non-cancerous tissue from an individual with TNBC or a combination thereof. 
     
     
         31 . The method of  claim 1  further comprising determining a treatment protocol for the triple negative breast cancer (TNBC) patient based on the TNBC subtype. 
     
     
         32 . The method of  claim 31  wherein the TNBC BL1 or BL2 subtype is detected in the individual and the individual is treated with one or more drugs that damages DNA. 
     
     
         33 . The method of  claim 32  wherein the one or more drugs is an alkylating-like agent, a PARP inhibitor or a combination thereof. 
     
     
         34 . The method of  claim 33  wherein the alkylating-like drug is cisplatin and the PARP inhibitor is veliparib, olaparib or a combination thereof. 
     
     
         35 . The method of  claim 31  wherein the TNBC ML subtype is detected in the individual and the individual is treated with one or more drugs that inhibits Src, IGF1R, MET, PDGFR or a combination thereof. 
     
     
         36 . The method of  claim 35  wherein the one or more drugs is disatinib, OSI-906, BMS-754807, PF2341066, sorafinib or a combination thereof. 
     
     
         37 . The method of  claim 35  further comprising treating the individual with a P13K inhibitor, a P13K/mTOR inhibitor or a combination thereof. 
     
     
         38 . The method of 37 wherein the P13K inhibitor is BKM-120, GDC0941 or a combination thereof, and the P13K/mTOR inhibitor is NVP-BEZ235, GDC0980 or a combination thereof. 
     
     
         39 . The method of  claim 31  wherein the TNBC LAR subtype is detected in the individual and the individual is treated with one or more drugs that inhibit androgen receptor (AR). 
     
     
         40 . The method of  claim 39  wherein the one or more drugs that inhibit AR is bicalutamide, MVD3100, abiraterone or a combination thereof. 
     
     
         41 . The method of  claim 39  further comprising treating the individual with a P13K inhibitor a P13K/mTOR inhibitor or a combination thereof. 
     
     
         42 . The method of  claim 41  wherein the P13K inhibitor is BKM-120, GDC0941 or a combination thereof, and the P13K/mTOR inhibitor is NVP-BEZ235, GDC0980 or a combination thereof. 
     
     
         43 . The method of  claim 39  further comprising treating the individual with an inhibitor of HSP90. 
     
     
         44 . The method of  claim 43  wherein the inhibitor of HSP90 is DMAG. 
     
     
         45 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) subtype comprising
 a) contacting a cell line that is a model for the TNBC subtype of interest with an agent to be assessed; and   b) determining viability of the cell line in the presence of the agent, wherein if the viability of the cell line decreases in the presence of the agent, then the agent can be used to treat the TNBC subtype of interest.   
     
     
         46 . The method of  claim 45  wherein the TNBC subtype of interest is a TNBC BL-1 subtype, a TNBC BL-2 subtype, a TNBC IM subtype, a TNBC M subtype, a TNBC MSL subtype or a TNBC LAR subtype. 
     
     
         47 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-1 subtype comprising
 a) contacting one or more TNBC BL-1 subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-1 subtype.   
     
     
         48 . The method of  claim 47  wherein the one or more TNBC BL-1 subtype cell lines comprises HCC2157, HCC1599, HCC1937, HCC1143, HCC3153, MDA-MB-468, and HCC38. 
     
     
         49 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) BL-2 subtype comprising
 a) contacting one or more TNBC BL-2 subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC BL-2 subtype.   
     
     
         50 . The method of  claim 49  wherein the one or more TNBC BL-2 subtype cell lines comprises SUM149PT, CAL-851, HCC70, HCC1806 and HDQ-P1. 
     
     
         51 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) IM subtype comprising
 a) contacting one or more TNBC IM subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC IM subtype.   
     
     
         52 . The method of  claim 51  wherein the one or more TNBC IM subtype cell lines comprises HCC1187 and DU4475. 
     
     
         53 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) M subtype comprising
 a) contacting one or more TNBC M subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC M subtype.   
     
     
         54 . The method of  claim 53  wherein the one or more TNBC M subtype cell lines comprises BT-549, CAL-51 and CAL-120. 
     
     
         55 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) MSL subtype comprising
 a) contacting one or more TNBC MSL subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC MSL subtype.   
     
     
         56 . The method of  claim 55  wherein the one or more TNBC MSL subtype cell lines comprises HS578T, MDA-MB-157, SUM159PT, MDA-MB-436, and MDA-MB-231. 
     
     
         57 . A method of determining whether an agent can be used to treat a triple negative breast cancer (TNBC) LAR subtype comprising
 a) contacting one or more TNBC LAR subtype cell lines with an agent to be assessed; and   b) determining viability of the one or more cell lines in the presence of the agent, wherein if the viability of the one or more cell lines decreases in the presence of the agent, then the agent can be used to treat the TNBC LAR subtype.   
     
     
         58 . The method of  claim 57  wherein the one or more TNBC LAR subtype cell lines comprises MDA-MB, SUM185PE, HCC2185, CAL-148, and MFM-223. 
     
     
         59 . (canceled) 
     
     
         60 . (canceled) 
     
     
         61 . (canceled) 
     
     
         62 . (canceled)