Deciphering the role of 3D genome organization in breast cancer susceptibility (Hi-C)

Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as a “Window of Susceptibility” (WOS). Radiation exposures poses a high breast cancer risk for women between the early childhood and young adult stage and is reduced in the mid-30s. Rats have a similar WOS for developing breast cancer. Previous studies have identified a looping interaction between a genomic region in the mammary carcinoma susceptibility Mcs5c locus and a known cancer gene, PAPPA. However, the global role of three-dimensional organization in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside WOS. We compared the temporal changes in chromosomal looping to those in expression and find that interactions that have significantly higher counts within WOS are significantly enriched for genes upregulated in WOS. To systematically identify higher-order changes in 3D genome organization, we developed an approach that combines network enhancement to smooth the Hi-C matrices followed by multitask non-negative matrix factorization (NMF) to identify clusters of interacting loci. We found that large-scale topological re-organizations are enriched for differential interactions within and outside the WOS timepoints. Finally, we mapped previously published breast-cancer associated human GWAS variants to rat loci and identified the corresponding rat ortholog gene interacting with the loci. Many of the associated rat genes participate in differential interactions, recapitulate the human SNP- gene interactions and are associated with breast cancer. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may increase susceptibility to breast cancer. Overall design: Hi-C data from mammary epithelial cells for 3 6wk old rats and 3 12wk old rats

环境暴露相关的癌症风险受个体遗传因素与暴露时年龄调控。这种具有年龄特异性的易感时期被称为“易感窗口（Window of Susceptibility，WOS）”。辐射暴露对处于童年早期至青年阶段的女性具有较高的乳腺癌发病风险，该风险在35岁左右会有所降低。大鼠在罹患乳腺癌的过程中也存在类似的易感窗口。此前的研究已发现，乳腺癌易感位点Mcs5c中的基因组区域与已知癌基因PAPPA之间存在染色质环相互作用。然而，三维基因组组织在易感窗口中的全局性作用仍未明确。因此，本研究在易感窗口内与非易感窗口的大鼠乳腺上皮细胞中分别生成了Hi-C与RNA测序（RNA-seq）数据。我们将染色质环的时序变化与基因表达的时序变化进行对比后发现，在易感窗口内计数显著更高的染色质相互作用，显著富集于易感窗口内上调表达的基因中。为系统鉴定三维基因组组织的高阶变化，本研究开发了一种整合分析方法：先通过网络增强（network enhancement）对Hi-C矩阵进行平滑处理，随后结合多任务非负矩阵分解（NMF）来识别相互作用位点的聚类簇。我们发现，大规模的染色质拓扑结构重排在易感窗口时间点与非易感窗口时间点之间的差异相互作用中显著富集。最后，我们将已发表的乳腺癌相关人类全基因组关联研究（GWAS）变异位点映射至大鼠基因组位点，并鉴定出与这些位点存在相互作用的大鼠同源基因。诸多关联大鼠基因参与了差异相互作用，重现了人类单核苷酸多态性（SNP）-基因相互作用模式，且与乳腺癌发生密切相关。本研究结果表明，易感窗口特异性的三维基因组组织变化，与可能提升乳腺癌易感风险的转录调控变化存在关联。整体实验设计：从3只6周龄大鼠与3只12周龄大鼠的乳腺上皮细胞中获取Hi-C数据。