Abstract A069: Hi-C analysis in patient-derived organoids reveals the impact of three-dimensional chromatin structures on pancreatic cancer transcriptional subtypes

Abstract

Abstract Three-dimensional (3D) chromatin structures connect genes to regulatory elements, thereby contributing to cell-type-specific gene regulation. However, its role in pancreatic cancer remains unclear. Inspired by our previous finding that open chromatin profiles analyzed by ATAC-seq well characterize the biological features and transcriptional status of pancreatic neoplasms, we hereby demonstrate the previously overlooked impact of 3D epigenetic regulation in pancreatic cancers. Through integrative analysis of Hi-C, ChIP-seq, and RNA-seq using patient-derived organoids, 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops were found to play important roles in characterizing pancreatic tumors. Interestingly, intraductal papillary mucinous neoplasm (IPMN) lineages tended to have unique 3D chromatin structure profiles. We further found that transcriptional subtypes in pancreatic cancer, either classical/progenitor-like or basal/squamous-like, were largely underpinned by 3D structures. Compartment was responsible for supporting many subtype-specific genes, by synchronously activating genes that were in the vicinity, as represented by CYP2C family genes. Meanwhile, enhancer-promoter loop fine-tuned some key subtype genes, such as GATA6. By exploring the driving forces behind these 3D structures, we found that HNF1B, a transcription factor implicated in the progenitor subtype, was sufficient to induce subtype switch, together with their underlying 3D genome structure alterations. We demonstrate that HNF1B overexpression in squamous-type pancreatic cancer organoids induced the upregulation and downregulation of genes associated with the progenitor and squamous subtype, respectively. Mechanistically, these dynamic transcriptional and 3D structural modulation were accompanied by HNF1B-induced long-range genomic interactions and H3K27ac modification at HNF1B bound sites, implying HNF1B as a driving force. We also provide evidence suggesting that this HNF1B-induced subtype switch was mediated through the phase-separating property of HNF1B, which was enabled by its intrinsically disordered region (IDR). Induction of mutant HNF1B, whose IDR was either deleted (HNF1B-dIDR) or substituted by transcriptional phase-separation forming IDR from another peptide AKAP95 (HNF1B-AKAP95), showed that subtype switching effects of HNF1B were diminished by HNF1B-dIDR or recapitulated by HNF1B-AKAP95. Thus, HNF1B contributes to the transcriptional subtype formation in pancreatic cancers through its phase-separating structural ability. Collectively, the mapping of 3D structural changes induced by transcription factors, such as HNF1B, is useful for further understanding the features of pancreatic cancers. Our study may imply the potential of 3D structures to effectively suppress or unwind the malignant transformation process and to discover subtype-specific therapeutic targets. Citation Format: Hiroyuki Kato, Dosuke Iwadate, Keisuke Yamamoto, Hiroaki Fujiwara, Hideaki Ijichi, Mitsuhiro Fujishiro, Keisuke Tateishi. Hi-C analysis in patient-derived organoids reveals the impact of three-dimensional chromatin structures on pancreatic cancer transcriptional subtypes [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A069.