Abstract B07: Two-pore domain potassium (K+) channel genes and triple-negative (TN) subtype in The Cancer Genome Atlas (TCGA) breast cancer dataset
Authors: Dookeran Keith A. , Argos Maria 
Published: March 2017

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 functionality related to expression using Spearman's correlation. Bonferroni corrected p-values were used where appropriate.

Results: Overexpression of KCNK5, KCNK9, KCNK10 and KCNK12, and underexpression of KCNK6 and KCNK15, were significantly associated with TN subtype (all p&lt;0.0033). nH black race was also associated with overexpression of KCNK5 and KCNK12, and underexpression of KCNK6 and KCNK15. With regards to survival, only KCNK9 was significantly associated with DFS (hazard ratio 1.05; 95% confidence interval, 1.01-1.09) and marginally associated with OS. Monotonicity of increased survival hazards was also observed when KCNK9 gene expression was modeled as an indicator variable categorized as tertiles. For nH black race, the most significantly associated CG loci were: 4 hypermethylated loci in the promoter region of KCNK15, 3 loci (both hyper- and hypomethylated) near KCNK4 (both body and promoter), 2 hypomethylated loci in KCNK5 gene body, and 1 hypomethylated locus in KCNK2 gene body; we did not find any race associated loci on KCNK9. In age and race adjusted models, the top K2P methylation loci associated with TN subtype were found on KCNK2, KCNK4, KCNK5, KCNK9, KCNK10, KCNK12 and KCNK15 (all p&lt;8.22*(10)-8); and loci on KCNK4, KCNK5, KCNK9, and KCNK12 were hypomethylated. In addition, specific loci on KCNK2 (cg04923840, gene body), KCNK5 (cg05255811, cg18705155, cg09130674, gene body) and KCNK9 (cg21415530, TSS1500) were significantly correlated with negative gene expression within TN subtype. Another locus (cg00981060, located between MSH2 and KCNK12) was correlated with positive gene expression. Only one CG locus among the top reported for association with TN subtype (cg01708924 near KCNK4/PRDX5) was significantly associated with DFS.

Conclusions: TN subtype is associated with specific K2P channel gene over and underexpression patterns, and similar expression patterns observed in blacks is consistent with more frequent TN disease. Our findings also suggest a link between KCNK9 overexpression and worse survival in breast cancer. Both KCNK5 and KCNK9 showed hypomethylation patterns correlated with negative expression, and overall gene overexpression related to TN subtype, and these findings appear to be consistent with prior literature.

Citation Format: Keith A. Dookeran, Maria Argos. Two-pore domain potassium (K+) channel genes and triple-negative (TN) subtype in The Cancer Genome Atlas (TCGA) breast cancer dataset. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr B07.