Epigenetic Dysregulation of KCNK9 Imprinting and Triple-Negative Breast Cancer

Abstract

Genomic imprinting is an inherited form of parent-of-origin specific epigenetic gene regulation that is dysregulated by poor prenatal nutrition and environmental toxins. KCNK9 encodes for TASK3, a pH-regulated potassium channel membrane protein that is overexpressed in 40% of breast cancer. However, KCNK9 gene amplification accounts for increased expression in <10% of these breast cancers. Here, we showed that KCNK9 is imprinted in breast tissue and identified a differentially methylated region (DMR) controlling its imprint status. Hypomethylation at the DMR, coupled with biallelic expression of KCNK9, occurred in 63% of triple-negative breast cancers (TNBC). The association between hypomethylation and TNBC status was highly significant in African-Americans (p = 0.006), but not in Caucasians (p = 0.70). KCNK9 hypomethylation was also found in non-cancerous tissue from 77% of women at high-risk of developing breast cancer. Functional studies demonstrated that the KCNK9 gene product, TASK3, regulates mitochondrial membrane potential and apoptosis-sensitivity. In TNBC cells and non-cancerous mammary epithelial cells from high-risk women, hypomethylation of the KCNK9 DMR predicts for increased TASK3 expression and mitochondrial membrane potential (p < 0.001). This is the first identification of the KCNK9 DMR in mammary epithelial cells and demonstration that its hypomethylation in breast cancer is associated with increases in both mitochondrial membrane potential and apoptosis resistance. The high frequency of hypomethylation of the KCNK9 DMR in TNBC and non-cancerous breast tissue from high-risk women provides evidence that hypomethylation of the KNCK9 DMR/TASK3 overexpression may serve as a marker of risk and a target for prevention of TNBC, particularly in African American women.

The role of imprinting genes’ loss of imprints in cancers and their clinical implications

“…Patients with CpG85 hypermethylation have shorter overall survival (the median survival rates for hypermethylation and normal/hypomethylation are 34 and 156 weeks, respectively). KCNK9 LOI was found due to DMR hypomethylation, which leads to overexpression of its gene product, increasing mitochondrial membrane potential and anti-apoptosis in TNBC ( 11 , 12 ). Hypermethylation of the PEG3 promoter leads to LOI and decreased PEG3 mRNA expression, increasing β-catenin levels, promoting proliferation, and inhibiting p53-dependent apoptosis in human GBMLGG ( 84 ).…”

“…Moreover, higher serum IGF2 concentration is associated with metastasis in CRC, and is an indicator of poor prognosis ( 9 ). In triple-negative breast cancer (TNBC), the LOI of potassium two-pore domain channel subfamily K member 9 ( KCNK9 ) gene involving differentially methylated region (DMR) hypomethylation leads to overexpression of the gene, increasing mitochondrial membrane potential and anti-apoptotic effect ( 11 , 12 ). In human hepatocellular carcinoma (HCC), hypomethylation at CpG85 has been reported to lead to an increase in levels of an alternative RB1-E2B transcript and concomitant downregulation of the RB1 main transcript in confirmed retinoblastoma ( Rb ) LOI, resulting in the absence of the Rb pathway and the loss of its suppressor function ( 13 ).…”

The Mechanism of DNA Methylation and miRNA in Breast Cancer

“…Estrogen (17β estradiol; E2) induces DNMT3B-mediated hypomethylation in the promoter of the Yes-associated protein-1 (YAP1) and augments proliferation [43]. The overexpression of the potassium two pore domain channel subfamily K member 9 (KCNK9/TASK3) protein by the hypomethylation of KCNK9 differential methylation region (DMR) elevates mitochondrial membrane potential and inhibits apoptosis [44]. The increased expression of signal-induced proliferation-associated protein 1 (SIPA1) caused by the hypomethylation of the CpG island in the promoter-proximal element ultimately promotes epithelial-mesenchymal transformation (EMT) [27].…”