Abstract A37: Mapping super-enhancer signatures in pancreatic ductal adenocarcinoma, cancer-associated fibroblasts and their targeting by epigenetic inhibitors
Authors: Noel Pawan , Hussein Shaimaa , Chen Kenian , Hoff Daniel D. Von , Lin Yin , Han Haiyong 
Published: March 2020

Background: Super-enhancers (SEs) are implicated in regulating genes that establish cell identity, state, and fate. Thus, therapeutic targeting of SEs has emerged as a promising approach for cancer treatment. To understand SE-regulation of gene expression in the tumor microenvironment (TME), we mapped the SE landscape in pancreatic ductal adenocarcinoma (PDAC) cell lines and cancer-associated fibroblasts (CAF) derived from different PDAC patients. Given the dismal 5-year survival rate of just 9% for patients with PDAC, novel treatments are desperately needed. Agents that can inhibit oncogenic SE networks may have potential in the treatment of PDAC.

Methods: SE landscapes in 9 PDAC and 9 CAF cell lines were mapped using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for genome-wide binding of H3K27ac. SE ranking and calling were performed using ROSE. RNAseq was carried out to establish gene expression profiles. The effect of epigenetic modulators on SE-associated gene expression was evaluated using Nanostring technology. CRISPR interference (CRISPRi) was used to functionally validate the effect of SE disruption on the expression of a critical SE-associated oncogene.

Results: While total enhancers and SEs mapped were higher in CAFs versus PDAC cells, the fraction of enhancers constituting SEs was similar (~5% of all enhancers) in both cell types. PDAC and CAF cells had distinct SE landscapes. Among the 4,192 SEs identified in both cell types, 31% of SEs were shared by at least one or more PDAC or CAF cells, while 20 SEs were recurrent in all eighteen samples. More than 150 SEs were common in most CAFs, while around 100 SEs were present in majority of PDAC cell lines. Strikingly, the presence of SE was almost always associated with upregulation of the gene closest to the SE element. Gene ontology analysis of SE-associated genes highlighted significant enrichment in biologic pathways of tissue morphogenesis, vasculature development, and epithelial cell differentiation in both PDAC and CAFs. Epigenetic inhibitors that target either the bromo-domain proteins or those that inhibit the transcription factor complex II had the most prominent effects on transcriptional repression of SE-associated genes. CRISPRi mediated disruption of an SE element regulating the MYC oncogene resulted in its transcriptional repression, suggesting that SEs positively exert transcriptional pressure on its associated target gene(s).

Conclusions: Overall, potentially critical biologic pathways that may be under SE control in PDAC and CAF cells were elucidated. The cell-type specific distinct nature of SE landscape suggests that SEs may be evolutionarily conserved and may be exploited for therapeutic potential. These results offer a means to identify agents that disrupt SEs and further study the consequences of perturbing SE networks in PDAC and its TME. (This work was supported partly by a BSWRI/TGen Collaborative Grant in Oncology Research and the SU2C-CRUK-Lustgarten Foundation Pancreatic Cancer Dream Team grant.)

Citation Format: Pawan Noel, Shaimaa Hussein, Kenian Chen, Daniel D. Von Hoff, Yin Lin, Haiyong Han. Mapping super-enhancer signatures in pancreatic ductal adenocarcinoma, cancer-associated fibroblasts and their targeting by epigenetic inhibitors [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr A37.