Abstract LB306: 3D epigenomic analysis reveals non-coding DNA regions that can reverse prostate cancer phenotypes

Abstract New evidence shows that non-coding DNA regions are recognized as cancer drivers. However, there are currently challenges to systematically identifying oncogenic non-coding DNA regions. To address these challenges, we have taken advantage of functional genomics which can identify non-coding DNA regions involved in transcriptional regulation, termed regulatory elements. By analyzing hundreds of Chromatin Immunoprecipitation coupled with sequencing (ChIP-seq) datasets generated from normal prostate and prostate tumor tissues and cells, we identified prostate cancer-specific regulatory elements that have the potential to drive carcinogenesis. Among these regulatory elements, we noted that enhancers are bound by prostate cancer-specific transcription factors such as FOXA1 and HOXB13, which have previously been identified as drivers of prostate cancer. Using genome-wide chromatin conformation capture techniques such as Hi-C and Micro-C, and integrating them with RNA-seq, we identified chromatin interaction hubs in prostate cancer that are anchored in exclusively activated enhancers and co-localized with oncogenes exhibiting elevated expression. To dissect the mechanisms of carcinogenesis, we screened the identified prostate cancer-specific enhancers using the CRISPR/Cas9 system and followed up with multi-omics analyses, including ChIP-seq, ATAC-seq, RNA-seq, and Region Capture Micro-C (RCMC) in prostate cancer cells. We found that deletion of the selected enhancers led to reduced activities of other enhancers specifically activated in prostate cancer within the hub. Moreover, we observed that enhancer deletion led to changes in FOXA1 binding and chromatin accessibility, suggesting an important pioneer role for FOXA1 in prostate cancer-specific chromatin hub formation. Furthermore, we noted that targeting these enhancers can reverse cancer phenotypes, such as cell proliferation and colony formation. We are currently interrogating changes in chromatin interactions, enhancer activities, and chromatin accessibility associated with prostate cancer-specific chromatin hub formation by altering the activity of transcription factors. Overall, our study not only provides mechanistic insights into the spatial regulation of enhancer-promoter hubs but also identifies new non-coding drivers in prostate tumorigenesis. Citation Format: Huan Cao, Zexun Wu, Baixi Ji, Seolyn Yang, Leonardo Gonzalez-Smith, Suhn K. Rhie. 3D epigenomic analysis reveals non-coding DNA regions that can reverse prostate cancer phenotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr LB306.