Somatic cell fusions reveal extensive heterogeneity in basal-like breast cancer [methylation450]

Basal-like and luminal breast tumors have distinct clinical behavior and molecular profiles, yet the underlying mechanisms are poorly defined. To interrogate processes that determine these distinct phenotypes and their inheritance pattern, we generated somatic cell fusions and performed integrated genetic and epigenetic (DNA methylation and chromatin) profiling. We found that the basal-like trait is generally dominant and it is largely defined by epigenetic repression of luminal transcription factors. Definition of super-enhancers highlighted a core program common in luminal cells but high degree of heterogeneity in basal-like breast cancers that correlates with clinical outcome. We also found that protein extracts of basal-like cells is sufficient to induce luminal-to-basal phenotypic switch implying a trigger of basal-like autoregulatory circuits. We determined that KDM6A might be required for luminal-basal fusions, and identified EN1, TBX18, and TCF4 as candidate transcriptional regulators of luminal-to-basal switch. Our findings highlight the remarkable epigenetic plasticity of breast cancer cells. Bisulphite converted DNA from 20 breast cancer cell lines were hybridized to the Illumina Infinium HumanMethylation450 BeadChip.基底样（Basal-like）与管腔型（luminal）乳腺肿瘤具有截然不同的临床行为与分子特征，但其潜在的调控机制尚未得到充分阐释。为探究决定这两类肿瘤独特表型及其遗传模式的生物学过程，本研究构建了体细胞融合（somatic cell fusion）体系，并开展了整合式遗传与表观遗传（DNA甲基化与染色质）组学分析。研究发现，基底样表型通常呈显性特征，其形成主要通过表观遗传抑制管腔型转录因子得以实现。超增强子（super-enhancer）的鉴定分析显示，管腔型细胞存在一套共有的核心调控程序，而基底样乳腺癌则表现出高度异质性，且该异质性与患者临床预后显著相关。本研究还发现，基底样细胞的蛋白提取物足以诱导管腔型向基底样的表型转换，这提示基底样细胞存在自主调控环路的激活机制。我们证实，KDM6A可能参与了管腔型-基底型体细胞融合过程，并筛选出EN1、TBX18与TCF4作为管腔型向基底型表型转换的候选转录调控因子。本研究结果凸显了乳腺癌细胞极强的表观遗传可塑性。本研究对20株乳腺癌细胞系的亚硫酸氢盐转化DNA进行了Illumina Infinium HumanMethylation450 BeadChip芯片杂交检测。