Abstract B07: Two-pore domain potassium (K+) channel genes and triple-negative (TN) subtype in The Cancer Genome Atlas (TCGA) breast cancer dataset

Introduction: The family of 2-pore domain K+ (K2P) channel genes has 15 members, are background channels which enable the leak of K+ ions from cells, and are considered to be important for baseline activity of cells at rest including membrane potential, calcium homeostasis and volume regulation. Prior studies support the hypothesis that alterations of expression or function of K2P channels in cancer cells may play a significant role in tumor development and progression. In the vast majority of tumors, the abnormally expressed channel is wild type. The role of K2P channel genes in breast cancer is currently emerging. A recent microarray database study suggests that all but 5 K2P gene family members showed altered expression in breast cancer. Other studies suggest potential clinical utility of K2P channel genes as biomarkers associated with TN subtype. A weighted gene co-expression network analysis study showed that upregulation of KCNK5 was associated with poor outcome for TN related tumors. TN tumors are also known to occur more frequently in women of non-Hispanic (nH) black race and association between black race and unique KCNK4 and KCNK9 breast tumor methylation patterns have been suggested; KCNK9 association with TN subtype has also been observed. However, there is a paucity of studies characterizing K2P genes in clinical breast cancer, and the goal of our study was the systematic evaluation of the relationship between K2P gene DNA methylation/expression and TN breast tumor subtype, in the large publically available TCGA dataset. Methods: TCGA invasive breast cancer data was available for 1040 women of which 767 had Illumina HM450 methylation beta-values and 959 had RSEM mRNA expression z-scores (single values from level 3 data). We evaluated the direction and association of all K2P gene expression/methylation loci and TN subtype using age and race adjusted glm models. Age and race adjusted Cox models were used for analysis of disease free (DFS) and overall survival (OS). CpG methylation loci within 25kb from either end of the genes of interest were included for examination (UCSC genome browser, hg37). A total of 724 CG loci were included using this approach, but after exclusion of probes with null reads, the number of loci available for study was reduced to 608. Methylation glm model results were sorted on p-values (smallest to largest) and the top 10 associated loci were selected for reporting and further analysis. Selected loci were then checked for