Methods for determining cancer resistance to histone deacetylase inhibitors

Abstract

Described herein are methods and compositions for determining whether a particular cancer is resistant to or susceptible to a histone deacetylase inhibitor or to histone deacetylase inhibitors. The methods include analysis of the expression levels of at least four biomarker genes associated with response to a histone deacetylase inhibitor. Also described herein are methods and compositions for increasing the likelihood of a therapeutically effective treatment in a patient, comprising an analysis of the expression levels of at least four biomarker genes associated with response to a histone deacetylase inhibitor. Also described herein are isolated populations of nucleic acids derived from a cancer sensitive to or resistant to a histone deacetylase inhibitor. Further described are kits and indications that are optionally used in conjunction with the aforementioned methods and compositions.

1 .- 19 . (canceled) 
     
     
         20 . A kit comprising an isolated population of nucleic acids, wherein the isolated population of nucleic acids comprises a plurality of nucleic acids derived from a cancer cell, wherein the cancer cell is a type of cancer cell that is sensitive to an HDAC inhibitor compound. 
     
     
         21 . A kit comprising an isolated population of nucleic acids, wherein the isolated population of nucleic acids comprises a plurality of nucleic acids derived from a cancer cell, wherein the cancer cell is the type of cancer cell that is resistant to an HDAC inhibitor compound. 
     
     
         22 . The kit of  claim 20  or  21 , wherein the nucleic acid sequences of at least four of DEFA6, ITGB4, TM4SF4, SYK, PPAP2C, RAB25, HEPH, NOXO1, TM4SF4, PTPN3, EPHA2, FGFBP1, ABCC3, TPMT, IL18, or DPEP1 are represented in the isolated population of nucleic acids. 
     
     
         23 . The kit of  claim 21 , wherein the isolated population of nucleic acids is    
     
     
         24 . The kit of  claim 20  or  21 , wherein the isolated population contains RNAs. 
     
     
         25 . The kit of  claim 20  or  21 , wherein the isolated population contains cDNAs. 
     
     
         26 . The kit of  claim 20  or  21  further comprising an insert indicating the ratio of a biomarker gene nucleic acid level in the population to an internal expression control gene acid nucleic level in the population. 
     
     
         27 . The kit of  claim 20  or  21 , wherein the HDAC inhibitor compound is PCI-24781. 
     
     
         28 . The kit of  claim 20  or  21 , wherein the cancer cell is a colon carcinoma cell.