CRISPR 筛选转录超级增强子,发现三阴性乳腺癌进展的驱动因素。

IF 12.5 1区 医学 Q1 ONCOLOGY
Michael W Lewis, Caitlin M King, Kamila Wisniewska, Matthew J Regner, Alisha Coffey, Michael R Kelly, Raul Mendez-Giraldez, Eric S Davis, Douglas H Phanstiel, Hector L Franco
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引用次数: 0

摘要

三阴性乳腺癌(TNBC)是最难治疗的乳腺癌形式,部分原因是靶向疗法的缺乏。对蛋白质编码基因以外的调控因子进行系统分析,可以发现治疗干预的途径。为此,我们分析了 TNBC 特异性转录增强子及其非编码增强子 RNA(eRNA)转录本的调控机制。我们利用高通量 CRISPR 干扰测定和 RNA-seq 技术系统地检测了前 30 个产生 eRNA 的超级增强子的功能,从而在全基因组范围内无偏见地检测到了靶基因。通过生成高分辨率的Hi-C染色质相互作用图谱,对每个超级增强子的直接靶基因进行了注释,从而突出了它们对预示TNBC患者临床预后较差的基因的倾向性。为说明该数据集的实用性,删除控制附近 PODXL 基因的超级增强子或特异性降解其增强子 RNA 会对靶基因表达、细胞增殖和迁移产生深远的抑制作用。此外,在 TNBC 小鼠异种移植模型中,该超级增强子的缺失抑制了肿瘤的生长和转移。单细胞RNA-seq和ATAC-seq分析表明,与非恶性细胞类型相比,这种超级增强子在TNBC肿瘤标本恶性细胞中的活性增强。总之,这项研究探讨了几个基本问题,即编码到产生 eRNA 的超级增强子中的调控信息如何驱动基因表达网络,而基因表达网络是三阴性乳腺癌生物学的基础。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression.

Triple-negative breast cancer (TNBC) is the most therapeutically recalcitrant form of breast cancer, which is due in part to the paucity of targeted therapies. A systematic analysis of regulatory elements that extend beyond protein-coding genes could uncover avenues for therapeutic intervention. To this end, we analyzed the regulatory mechanisms of TNBC-specific transcriptional enhancers together with their noncoding enhancer RNA (eRNA) transcripts. The functions of the top 30 eRNA-producing super-enhancers were systematically probed using high-throughput CRISPR-interference assays coupled to RNA sequencing that enabled unbiased detection of target genes genome-wide. Generation of high-resolution Hi-C chromatin interaction maps enabled annotation of the direct target genes for each super-enhancer, which highlighted their proclivity for genes that portend worse clinical outcomes in patients with TNBC. Illustrating the utility of this dataset, deletion of an identified super-enhancer controlling the nearby PODXL gene or specific degradation of its eRNAs led to profound inhibitory effects on target gene expression, cell proliferation, and migration. Furthermore, loss of this super-enhancer suppressed tumor growth and metastasis in TNBC mouse xenograft models. Single-cell RNA sequencing and assay for transposase-accessible chromatin with high-throughput sequencing analyses demonstrated the enhanced activity of this super-enhancer within the malignant cells of TNBC tumor specimens compared with nonmalignant cell types. Collectively, this work examines several fundamental questions about how regulatory information encoded into eRNA-producing super-enhancers drives gene expression networks that underlie the biology of TNBC. Significance: Integrative analysis of eRNA-producing super-enhancers defines molecular mechanisms controlling global patterns of gene expression that regulate clinical outcomes in breast cancer, highlighting the potential of enhancers as biomarkers and therapeutic targets.

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来源期刊
Cancer research
Cancer research 医学-肿瘤学
CiteScore
16.10
自引率
0.90%
发文量
7677
审稿时长
2.5 months
期刊介绍: Cancer Research, published by the American Association for Cancer Research (AACR), is a journal that focuses on impactful original studies, reviews, and opinion pieces relevant to the broad cancer research community. Manuscripts that present conceptual or technological advances leading to insights into cancer biology are particularly sought after. The journal also places emphasis on convergence science, which involves bridging multiple distinct areas of cancer research. With primary subsections including Cancer Biology, Cancer Immunology, Cancer Metabolism and Molecular Mechanisms, Translational Cancer Biology, Cancer Landscapes, and Convergence Science, Cancer Research has a comprehensive scope. It is published twice a month and has one volume per year, with a print ISSN of 0008-5472 and an online ISSN of 1538-7445. Cancer Research is abstracted and/or indexed in various databases and platforms, including BIOSIS Previews (R) Database, MEDLINE, Current Contents/Life Sciences, Current Contents/Clinical Medicine, Science Citation Index, Scopus, and Web of Science.
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