Abstract 1686: Dissecting the 3D enhancer-promoter hubs in prostate tumorigenesis
Authors: Huan Cao, Zexun Wu, Leonardo Gonzalez-Smith, Seolyn Yang, Suhn K. Rhie
Journal: Cancer Research (2024)

Abstract The transcription process is controlled by regulatory elements that are often located in non-coding regions. Among regulatory elements, activities of enhancers that are bound by cell-type specific transcription factors (TFs) are tightly linked to cell identity. Enhancers loop to interact with the promoters of target genes at a distance to drive different cell fates. Evidently, transcriptional dysregulation linked to enhancers that are differentially activated in cancer is an underlying factor in tumorigenesis. To identify enhancers linked to prostate tumorigenesis, we analyzed hundreds of in-house and public H3K27ac ChIP-seq data generated from normal prostate and prostate cancer cell lines and tissues. We identified thousands of prostate cancer-specific enhancers (PSEs) that were activated exclusively in cancer conditions. To further identify the target genes of PSEs, we performed 3C-derived assays, such as Hi-C and Micro-C, and mapped genome-wide interactions. However, they were limited by the resolution to detect enhancer-promoter interactions. The recent development of Region Capture Micro-C (RCMC), a hybridization-based capture Micro-C method, allowed us to deeply map the highly nested interactions between regulatory elements. By utilizing RCMC, we generated high-resolution, focal contact maps that revealed comprehensive enhancer-promoter interactions near PSEs in prostate cancer cells. Interestingly, we found that PSEs loop to other PSEs clustered in the proximal genomic region, in addition to promoters of significantly upregulated genes in cancer compared to normal cells. We termed these regions as multi-connected "3D enhancer-promoter hubs”. To mechanistically dissect these hubs, we deleted 5+ PSEs one by one using the CRISPR/Cas9 system and performed multi-omics analyses, including RNA-seq and ChIP-seq. We found that single deletions of a subset of PSEs led to the downregulation of multiple genes looped to the deleted PSE as well as to other PSEs. Moreover, we found that deletion reduced the activity of other connected PSEs. When we further evaluated the chromatin contacts of regulatory elements in the PSE-deleted cells, we observed that many chromatin contacts remained unaffected. Finally, we identified TFs that bind to PSEs, and we are currently in the process of investigating enhancer-promoter hub connectivity by performing knockdown experiments on these TFs. Furthermore, we are using molecular assays to identify PSEs that could exert a phenotypic shift in cancer cell identity to drive prostate tumorigenesis. Overall, our study not only provides mechanistic insights into the spatial regulation of 3D enhancer-promoter hubs but also identifies new non-coding drivers in prostate tumorigenesis. Citation Format: Huan Cao, Zexun Wu, Leonardo Gonzalez-Smith, Seolyn Yang, Suhn K. Rhie. Dissecting the 3D enhancer-promoter hubs in prostate tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1686.