Han Yoo-Jeong, Zhang Jing, Zheng Yonglan, Huo Dezheng, Olopade Olufunmilayo I
Center for Clinical Cancer Genetics and Global Health; and Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, United States of America.
Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, United States of America.
PLoS One. 2016 Nov 2;11(11):e0165559. doi: 10.1371/journal.pone.0165559. eCollection 2016.
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.
全基因组关联研究（GWAS）已经鉴定出了低外显率和高频单核苷酸多态性（SNP），这些多态性与乳腺癌的遗传易感性有关。位于16q12，靠近TOX3和CASC16基因的SNP，是GWAS鉴定出的易感位点之一，在不同人群中均显示出与乳腺癌相关的有力证据。为了研究乳腺癌中TOX3调控的分子机制，我们使用细胞系以及通过癌症基因组图谱（TCGA）获得的原发性乳腺肿瘤数据集，对遗传和表观遗传因素进行了研究。与正常乳腺组织或基底样肿瘤相比，TOX3在管腔亚型肿瘤中的表达高度上调。表达数量性状基因座（eQTL）分析显示，rs3803662和rs4784227基因型与乳腺肿瘤中TOX3的表达存在显著关联。对TOX3启动子中四个CpG岛进行亚硫酸氢盐测序，结果显示管腔样和基底样癌细胞系之间存在明显差异。用5-氮杂-2'-脱氧胞苷处理基底样癌细胞系可增加TOX3的表达。TCGA数据集证实，管腔型乳腺肿瘤启动子的甲基化水平显著降低，且甲基化与TOX3表达呈负相关。甲基化数量性状基因座（mQTL）分析显示，rs3803662或rs4784227与乳腺肿瘤中TOX3启动子甲基化之间的相关性较弱或无相关性，这表明遗传和表观遗传事件之间存在独立关系。这些数据表明，在乳腺癌中存在一个由种系变异和体细胞表观遗传修饰以亚型特异性方式驱动的复杂的TOX3调控系统。
