Socs-1 gene methylation in cancer

Abstract

Methods are provided for identifying a cell exhibiting unregulated growth associated with methylation-silenced transcription of a suppressor of cytokine signaling (SOCS)/cytokine-inducible SH2 protein (CIS) family member (SOCS/CIS) gene such as the SOCS-1 gene. In addition, methods of treating a cancer patient, wherein cancer cells in the patient exhibit methylation-silenced transcription of SOCS/CIS gene such as a SOCS-1 gene, are provided, as are reagents for practicing such methods.

1 . A method for selecting a therapeutic strategy for treating a cancer patient, the method comprising
 examining a sample comprising cancer cells from the patient for decreased expression of a suppressor of cytokine signaling (SOCS)/cytokine-inducible SH2 protein (CIS) family member (SOCS/CIS) gene product due to methylation-silenced transcription, whereby decreased expression of the SOCS/CIS gene product indicates selecting an agent that restores the SOCS/CIS gene product to the cancer cells as a component of the therapeutic strategy.   
     
     
         2 . The method of  claim 1 , wherein the agent comprises the SOCS/CIS gene product. 
     
     
         3 . The method of  claim 2 , wherein the SOCS-1 gene product is a SOCS-1 gene product. 
     
     
         4 . The method of  claim 3 , wherein the SOCS-1 gene product is encoded by SEQ ID NO:1. 
     
     
         5 . The method of  claim 1 , wherein the agent comprises a polynucleotide encoding a SOCS/CIS protein. 
     
     
         6 . The method of  claim 1 , wherein the therapeutic strategy comprises treatment with a chemotherapeutic agent. 
     
     
         7 . The method of  claim 1 , wherein the therapeutic strategy comprises radiotherapy. 
     
     
         8 . The method of  claim 1 , wherein the therapeutic strategy comprises ex vivo treatment of the cancer cells with the agent that restores the SOCS/CIS gene product and administration of the treated cancer cells to the cancer patient. 
     
     
         9 . The method of  claim 8 , wherein the treated cancer cells are expanded in culture before administration to the cancer patient. 
     
     
         10 . The method of  claim 1 , wherein the agent comprises a JAK2 kinase inhibitor. 
     
     
         11 . The method of  claim 10 , wherein the agent comprises AG490. 
     
     
         12 . The method of  claim 1 , wherein the examining step comprises detecting methylation of a cytosine residue of a CpG dinucleotide in a CpG island of a SOCS/CIS gene. 
     
     
         13 . The method of  claim 12 , wherein the SOCS/CIS gene is SOCS-1. 
     
     
         14 . The method of  claim 13 , wherein the detecting methylation comprises contacting a nucleic acid molecule comprising the SOCS-1 gene of the cancer cell with a methylation sensitive restriction endonuclease, whereby cleavage of the nucleic acid molecule is indicative of methylation of the SOCS-1 gene in the cancer cell. 
     
     
         15 . The method of  claim 13 , wherein detecting methylation comprises contacting a nucleic acid molecule comprising the SOCS-1 of the cancer cell with bisulfite ions, whereby unmethylated cytosine residues in the SOCS-1 gene sequence are converted to bisulfite modified cytosine residues,
 the method further comprising exposing the bisulfite ion treated SOCS-1 gene sequence to alkaline conditions, whereby bisulfite modified cytosine residues are converted to uracil residues, and   detecting the amount or distribution of uracil residues in the bisulfite ion treated SOCS-1 gene of the cancer cell,   wherein a decrease in the amount or distribution of uracil residues in the SOCS-1 gene from the cancer cell, as compared to the amount or distribution of uracil residues in a corresponding bisulfite ion treated unmethylated SOCS-1 gene following exposure to alkaline conditions, is indicative of methylation of cytosine residues in CpG dinucleotides in the SOCS-1 gene of the cancer cell.   
     
     
         16 . The method of  claim 15 , wherein detecting the amount or distribution of uracil residues comprises
 contacting the SOCS-1 gene sequence with an amplification primer pair comprising a forward primer and a reverse primer under conditions suitable for amplification, wherein each of the forward primer and the reverse primer selectively hybridizes to a SOCS-1 gene sequence containing cytosine residues, but not to a SOCS-1 gene sequence containing uracil residues, and   whereby generation of an amplification product is indicative of methylation of cytosine residues in CpG dinucleotides in the SOCS-1 gene of the cancer cell.   
     
     
         17 . The method of  claim 15 , wherein detecting the amount or distribution of uracil residues comprises
 contacting the SOCS-1 gene sequence with a methylation-specific amplification primer pair and an unmethylation-specific amplification primer pair under conditions suitable for amplification,   wherein the methylation-specific amplification primer pair comprises a forward primer and a reverse primer, wherein at least one of the forward primer and the reverse primer comprises an oligonucleotide that selectively hybridizes to a SOCS-1 gene sequence containing cytosine residues, and   wherein the unmethylation-specific amplification primer pair comprises a forward primer and a reverse primer, neither of which hybridizes to a SOCS-1 gene sequence containing cytosine residues; and   wherein an amplification product, if any, generated by the methylation-specific amplification primer pair has a first length, and wherein an amplification product, if any, generated by the unmethylation-specific amplification primer pair has a second length, which is different from the first length,   whereby generation of an amplification product having the first length is indicative methylation of cytosine residues in CpG dinucleotides in the SOCS-1 gene of the cancer cell.   
     
     
         18 . The method of  claim 15 , wherein detecting the amount or distribution of uracil residues comprises contacting the bisulfite ion treated SOCS-1 gene sequence, following exposure to alkaline conditions, with an oligonucleotide that selectively hybridizes to a SOCS-1 gene sequence containing cytosine residues, and
 detecting selective hybridization of the oligonucleotide.