笑对人生 (2023-03-31 23:57):
#paper doi: 10.1016/j.cell.2018.03.027.Chen H, et al. A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples. Cell. 2018 Apr 5;173(2):386-399.e12. 增强子(enhancer)通常位于结构基因的附近,是一类非编码DNA调节元件,在癌症的发展过程中起到越来越重要的作用。本研究利用TCGA数据库33癌种,总共8928肿瘤患者的RNA-seq数据,从全基因组范围识别和鉴定出大量表达的增强子。通过与正常组织进行比较,发现大多数癌种的增强子处在激活状态,且与非整倍体改变正相关,但与突变负荷无关,由此提出增强子与基因互作的染色体状态假说。为了建立因果关系的增强子-基因调控网络模型,作者通过整合eQTL分析、mRNA共表达分析以及Hi-C数据分析的结果,最终发现65个增强子-基因互作对。这些互作对经过CGC注释,总共包含22个原癌基因和8个肿瘤抑制基因。文章的最后,作者还通过CRISPR/Cas9 RNAs技术证实了存在于PD-L1基因上游140kb的一个增强子。
IF:45.500Q1 Cell, 2018-04-05. DOI: 10.1016/j.cell.2018.03.027 PMID: 29625054
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
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Abstract:
The role of enhancers, a key class of non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization of a large number of expressed enhancers in a genome-wide analysis of 8928 tumor samples across 33 cancer types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed in most cancers. Across cancer types, global enhancer activity was positively associated with aneuploidy, but not mutation load, suggesting a hypothesis centered on "chromatin-state" to explain their interplay. Integrating eQTL, mRNA co-expression, and Hi-C data analysis, we developed a computational method to infer causal enhancer-gene interactions, revealing enhancers of clinically actionable genes. Having identified an enhancer ∼140 kb downstream of PD-L1, a major immunotherapy target, we validated it experimentally. This study provides a systematic view of enhancer activity in diverse tumor contexts and suggests the clinical implications of enhancers.
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