Genetic and Epigenetic Regulation of TOX3 Expression in Breast Cancer.

Yoo-Jeong Han,Yonglan Zheng,Olufunmilayo I. Olopade,Dezheng Huo,Jing Zhang,Hiromu Suzuki

doi:10.1371/journal.pone.0165559

Yoo-Jeong Han, Yonglan Zheng + Show 4 more

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https://doi.org/10.1371/journal.pone.0165559

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Abstract

Genome wide association studies (GWAS) have identified low penetrance and high frequency single nucleotide polymorphisms (SNPs) that contribute to genetic susceptibility of breast cancer. The SNPs at 16q12, close to the TOX3 and CASC16 genes, represent one of the susceptibility loci identified by GWAS, showing strong evidence for breast cancer association across various populations. To examine molecular mechanisms of TOX3 regulation in breast cancer, we investigated both genetic and epigenetic factors using cell lines and datasets derived from primary breast tumors available through The Cancer Genome Atlas (TCGA). TOX3 expression is highly up-regulated in luminal subtype tumors compared to normal breast tissues or basal-like tumors. Expression quantitative trait loci (eQTL) analyses revealed significant associations of rs3803662 and rs4784227 genotypes with TOX3 expression in breast tumors. Bisulfite sequencing of four CpG islands in the TOX3 promoter showed a clear difference between luminal and basal-like cancer cell lines. 5-Aza-2’-deoxycytidine treatment of a basal-like cancer cell line increased expression of TOX3. TCGA dataset verified significantly lower levels of methylation of the promoter in luminal breast tumors with an inverse correlation between methylation and expression of TOX3. Methylation QTL (mQTL) analyses showed a weak or no correlation of rs3803662 or rs4784227 with TOX3 promoter methylation in breast tumors, indicating an independent relationship between the genetic and epigenetic events. These data suggest a complex system of TOX3 regulation in breast tumors, driven by germline variants and somatic epigenetic modifications in a subtype specific manner.

Highlights

Genetic factors play important roles in the etiology of breast cancer
We investigated both genetic and epigenetic factors contributing to TOX3 expression in breast tumors and cell lines
The molecular subtype-specific expression of TOX3 in breast tumors is significantly associated with epigenetic modifications at CpG islands of the promoter

Summary

Introduction

Genetic factors play important roles in the etiology of breast cancer. Multiple breast cancer susceptibility genes such as BRCA1 and BRCA2 with high penetrant disease-associated mutations have been shown to segregate in families with breast cancer by linkage studies [1]. The SNP rs3803662 at 16q12 is one of the susceptibility loci identified by GWAS, for which the minor allele conferred increased risk of breast cancer in women of European ancestry [7]. This finding was observed in women of Asian descent [8,9] with SNP rs4784227 at 16q12 as an additional risk variant for breast cancer in Asian populations [10]. We found a significant association of TOX3 expression with rs3803662 and rs4784227, a risk variant identified in European and Asian women, respectively These results suggest that both epigenetic and genetic factors contribute to the increased expression of TOX3 in luminal cancer. Our data support a plausible molecular mechanism integrating epigenetic modifications of the TOX3 promoter and allele specific expression of SNPs in aggressive behavior of luminal breast tumors with high TOX3 expression

Results

Discussion

Materials and Methods