Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [GRO-Seq]. Homo sapiens

Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif p-values, and enrichment of H3K4me1 and H3KK27. When applied across the 13 different breast cancer cell lines, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype specific transcription factors that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes. Overall design: To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 13 different breast cancer cell lines representing the five major molecular subtypes of breast cancer.

非编码转录是活性增强子的标志性特征，可将转录因子（Transcription Factor, TF）结合与调控基因表达的分子机制相联系。为明确乳腺癌中增强子活性与生物学结局的关联，我们对代表乳腺癌5种主要分子亚型的13株不同乳腺癌细胞系的转录组（采用GRO-seq与RNA-seq技术）及表观基因组（采用ChIP-seq技术）开展了组学表征。此外，我们开发了一套稳健且无偏的计算流程，可通过整合增强子转录强度、TF mRNA表达水平、TF基序p值以及H3K4me1与H3KK27的富集情况，同时推定亚型特异性增强子及其对应的转录因子。将该流程应用于13株乳腺癌细胞系后，增强子元件总功能评分（Total Functional Score of Enhancer Elements, TFSEE）成功鉴定出关键的乳腺癌亚型特异性转录因子，这些因子通过作用于转录增强子，调控决定细胞生长结局的基因表达模式。整体实验设计：为明确乳腺癌中增强子活性与生物学结局的关联，我们对代表乳腺癌5种主要分子亚型的13株不同乳腺癌细胞系的转录组（采用GRO-seq与RNA-seq技术）及表观基因组（采用ChIP-seq技术）开展了组学表征。