Genomic profiling of H3K27ac and transcription factor binding in ERG-overexpressing prostate cancer. Homo sapiens

Structural rearrangements leading to the TMPRSS2:ERG (T2E) fusion typify ~50% of prostate tumors and result in overexpression of the ERG transcription factor. Using T2E and non-T2E primary prostate tumors, we assessed the impact of ERG overexpression on chromatin by integrating ChIP-seq against H3K27ac, a chromatin modification found at active cis-regulatory elements, with paired genomic and expression data. We show that T2E tumors have a consistent and distinct cis-regulatory landscape to non-T2E tumors which drives their unique transcriptional profile. The T2E-specific cis-regulatory landscape is driven by ERG-mediated co-option of prostate master transcription factors HOXB13 and FOXA1 and is typified by Cluster Of Regulatory Elements (COREs) including one spreading into the ERG locus of the structurally rearranged allele. This gives rise to a cis-regulatory element within the rearranged ERG gene that contributes to ERG overexpression. The unique cis-regulatory landscape in T2E primary prostate tumors also reveals the activation of the NOTCH signalling pathway. Accordingly, chemical NOTCH pathway inhibition limited the invasive nature of T2E prostate cancer cells, revealing an actionable vulnerability against T2E prostate tumors. Taken together, our work delineates the role of ERG over-expression in co-opting master transcription factors to deploy a unique cis-regulatory landscape inducing a dependency on NOTCH signaling in T2E prostate tumors. Overall design: Genomic profiles of H3K27ac in ERG overexpressing prostate cancer and prostate cancer without ERG overexpression. Genomic binding of AR, FOXA1, HOXB13 in 22Rv1 prostate cells and of HOXB13 in LNCaP prostate cells. Genomic binding of FOXA1 and HOXB13, as well as H3K27ac profiles, upon knockdown of ERG in VCaP prostate cells.

导致TMPRSS2:ERG（T2E）融合的染色体结构重排，约占前列腺肿瘤病例的50%，并会引发ERG转录因子的过表达。本研究借助T2E型与非T2E型原发性前列腺肿瘤样本，通过整合针对H3K27ac（活性顺式调控元件标志性组蛋白修饰）的染色质免疫共沉淀测序（ChIP-seq）数据与配对的基因组及表达谱数据，评估了ERG过表达对染色质调控的影响。研究结果显示，T2E型肿瘤拥有与非T2E型肿瘤既保守又独特的顺式调控图谱，该图谱驱动了其特有的转录特征。T2E型特异性顺式调控图谱由ERG介导的前列腺核心转录因子HOXB13与FOXA1的共招募所塑造，并以调控元件簇（Cluster Of Regulatory Elements，COREs）为典型特征，其中一个调控元件簇延伸至发生结构重排的等位基因的ERG基因座内。这一重排事件在ERG基因内部形成了全新的顺式调控元件，进而促进了ERG的过表达。此外，T2E型原发性前列腺肿瘤的独特顺式调控图谱还揭示了NOTCH信号通路的激活。据此，化学抑制NOTCH通路可显著削弱T2E型前列腺癌细胞的侵袭能力，为T2E型前列腺肿瘤找到了可靶向的治疗脆弱位点。综上，本研究阐明了ERG过表达通过招募核心转录因子构建独特顺式调控图谱，进而使T2E型前列腺肿瘤产生NOTCH信号通路依赖性的核心机制。

实验设计概述：
1. 检测ERG过表达型与非ERG过表达型前列腺癌样本中H3K27ac的基因组结合图谱；
2. 检测22Rv1前列腺细胞中雄激素受体（AR）、FOXA1、HOXB13的基因组结合位点，以及LNCaP前列腺细胞中HOXB13的基因组结合位点；
3. 检测VCaP前列腺细胞中敲低ERG后，FOXA1与HOXB13的基因组结合位点以及H3K27ac的基因组结合图谱。