三阴性乳腺癌（TNBC）是治疗上最难治疗的乳腺癌，部分原因是缺乏靶向治疗。对蛋白质编码基因之外的调控元件进行系统分析可以揭示治疗干预的途径。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。使用高通量 CRISPR 干扰测定与 RNA-seq 相结合，系统地探测了前 30 个产生 eRNA 的超级增强子的功能，从而能够在全基因组范围内对目标基因进行公正的检测。高分辨率 Hi-C 染色质相互作用图的生成能够注释每个超级增强子的直接靶基因，这突出了它们对预示 TNBC 患者临床结果较差的基因的倾向。删除控制附近 PODXL 基因的已识别超级增强子或其增强子 RNA 的特异性降解会对靶基因表达、细胞增殖和迁移产生深远的抑制作用，这说明了该数据集的实用性。此外，在 TNBC 小鼠异种移植模型中，这种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，TNBC 肿瘤样本的恶性细胞中这种超级增强子的活性增强。总的来说，这项工作探讨了几个基本问​​题，即编码到产生 eRNA 的超级增强子中的调控信息如何驱动构成三阴性乳腺癌生物学基础的基因表达网络。

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 non-coding 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-seq 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 TNBC patients. Illustrating the utility of this dataset, deletion of an identified super-enhancer controlling the nearby PODXL gene or specific degradation of its enhancer RNAs 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-seq and ATAC-seq analyses demonstrated the enhanced activity of this super-enhancer within the malignant cells of TNBC tumor specimens compared to non-malignant 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 triple-negative breast cancer.