Abstract LB011: Landscape of promoter centric chromatin interactions and co-regulated gene network provide insights for transcriptional regulation in prostate cancer
Authors: Khyati Raghunath Chandratre, Susmita Ramanad, Ahmed abbas Elmahdi, Yunpeng Gao, Ram Shankar Mani, Michael Zhang
Journal: Cancer Research (2024)

Abstract Eukaryotic genomes are organized into hierarchical three-dimensional (3D) structure inside the nucleus, forming topological associating domains (TADs) and providing insulated neighborhoods for the highly interacting genome regions. These regions are established by potential chromatin bridging proteins, such as the cohesin complex and CTCF, forming loops. Within the framework of these TADs lie the loops defined by the transcriptional machinery, or RNA polymerase II (RNAPol II). Changes to this 3D genome structure are associated with the development of human diseases, including cancers. Prostate cancer (PCa), associated with transcriptional dysregulation, serves as an optimal model to understand the molecular mechanism behind the formation of dynamic loops between distant regulatory elements and their target genes in 3D space to regulate gene expression and cancer progression. This study integrates two protein-centric ChIA-PET data (RNAPol II and cohesin) with multiple ChIP-Seq data (CTCF, H3K27ac, AR and FOXA1), and RNA-Seq data of PCa cell lines (LNCaP, VCaP, DU145, and RWPE1) to perform promoter (P) centered analysis. Firstly, we investigated the proportions of RNAPol II loops with co-occupancy of cohesin peaks and vice versa to quantify and understand the involvement of these proteins in transcription regulation and validate them using simulations. The results supported the hypothesis that most RNAPol II loops were significantly enriched with cohesin peaks. However, the reverse was not true since inner RNAPol II loops enriched with cohesin regulate transcription, while most of the cohesin loops form long-range interactions, TADs. Further, we compared the correlation between the promoter centric RNAPol II-associated and cohesin-mediated interactions with gene expression. In the case of RNA Pol II mediated interactions, we found a quantitative increase in the strength of interaction between loci, this trend was not observed in cohesin mediated interactions, which were relatively stable. The only exception was in the cell line VCaP, possibly due to its genetic complexity, as the strength of interactions associated with Cohesin as well as RNA Pol II increased. We next examined if the strength of interactions between cohesin loops remains unaffected in the VCaP cell line when treated with dBET inhibitor. However, there was no significant difference observed. This explained that RNAPol II loops are more dynamic, whereas cohesin loops are more stable. However, whether the cohesin loops (internal and TAD boundary) stay stable in the active and inactive regions of the genome remains unexplored. Next, the study inspects how the cluster of regulated genes is organized, preferentially forming multi-gene complexes in PCa for efficient and potential cooperative transcription. We expect a significant role of super-enhancers in identifying interactions between key oncogenes in PCa, owing to cell-type specific biology. Highly co-regulated single- and multi-valent loops will be validated in the patient cohorts to establish significant correlations. Overall, this study enhances the knowledge of promoter-centric molecular mechanisms involved in multi-gene complex formation and coregulated transcription in PCa cell lines. Citation Format: Khyati Raghunath Chandratre, Susmita Ramanad, Ahmed abbas Elmahdi, Yunpeng Gao, Ram Shankar Mani, Michael Zhang. Landscape of promoter centric chromatin interactions and co-regulated gene network provide insights for transcriptional regulation in prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB011.