Background: Pancreatic cancer (PC) is the 3rd leading cause of adult cancer death in the USA. Pancreatic ductal adenocarcinoma (PDAC) accounts for >90% of all PC cases and has a dismal 5-year survival rate of < 6%, mostly due to lack of reliable methods for early detection, and limited treatment options. A unique, highly fibrotic and hypo-vascularized tumor stroma or “desmoplastic reaction” (DR) forms the major barrier to currently available therapeutics. Activated cancer associated fibroblasts (CAFs) play an important role in driving and maintaining the DR in PDAC. Thus therapeutic regimens that reprogram pancreatic CAFs can potentially enhance sensitivity to anti-tumor agents and may improve patient outcomes. Recent studies implicate the role of super-enhancers (SE) in maintaining cell specific gene expression networks in both normal and diseased cells. Here we aim to define SE networks in pancreatic CAFs and epithelial tumor cells and explore the role of triptolide in modulating SE signatures.
Methods: Using genomic techniques on control vs triptolide treated pancreatic tumor and CAF cells, we measured occupancy of BRD4 and acetylated histone 3 at lysine27 (H3K27ac), marks of active SEs, using ChIP-seq. RNA-seq revealed differentially regulated genes via SE modulation by triptolide. Immunoblotting was performed to validate the effect of triptolide on the protein signature associated with dysregulated SEs.
Results: Top ranked SEs between BRD4 and H3K27ac marks showed extensive overlap, but were highly distinct between cancer cells and CAFs. The SEs in tumor cells associated with genes related to transcription (e.g.POLR2E, PARK7, MYC), whereas those in CAFs associated with genes involved in desmoplasia/fibrosis (e.g. COL1A1, COL1A2, TGFBI). Triptolide significantly altered SE activation at diverse and discrete genomic loci in both cell types. Specifically, SE regions associated with COL1A2 and TGFBI showed reduced H3K27ac binding in CAFs exposed to triptolide but not in tumor cells, which showed reduced histone signal at RNA Pol II region. Transcriptional deregulation by triptolide exceeded in CAFs vs tumor cells (1282 vs 23 genes upregulated, 1496 vs 321 genes downregulated). Finally, triptolide resulted in reduced expression of BRD4 and RNA Pol II in both tumor and CAFs, while c-MYC and Collagen I were specifically and significantly downregulated in tumor and CAFs, respectively.
Conclusions: Our results suggest that pancreatic CAFs and tumor cells harbor distinct SE networks that are characteristic of their different cell types and states. Triptolide might exert its antitumor activity by potentially targeting distinct SEs in different cells. Epigenetic reprogramming of transcription by exploiting SE modulating compounds like triptolide alone or in combination with current standard of care may provide more effective treatment options for PC patients.
Citation Format: Pawan Noel, Serina Ng, Ruben Muñoz, Daniel Von Hoff, Haiyong Han. Discrete super-enhancer networks in pancreatic cancer cells and cancer associated fibroblasts are targeted and modulated by triptolide [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2978. doi:10.1158/1538-7445.AM2017-2978