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Abstract
Objective Pancreatic ductal adenocarcinoma (PDAC) displays a remarkable propensity towards therapy resistance. However, molecular epigenetic and transcriptional mechanisms enabling this are poorly understood. In this study, we aimed to identify novel mechanistic approaches to overcome or prevent resistance in PDAC.
Design We used in vitro and in vivo models of resistant PDAC and integrated epigenomic, transcriptomic, nascent RNA and chromatin topology data. We identified a JunD-driven subgroup of enhancers, called interactive hubs (iHUBs), which mediate transcriptional reprogramming and chemoresistance in PDAC.
Results iHUBs display characteristics typical for active enhancers (H3K27ac enrichment) in both therapy sensitive and resistant states but exhibit increased interactions and production of enhancer RNA (eRNA) in the resistant state. Notably, deletion of individual iHUBs was sufficient to decrease transcription of target genes and sensitise resistant cells to chemotherapy. Overlapping motif analysis and transcriptional profiling identified the activator protein 1 (AP1) transcription factor JunD as a master transcription factor of these enhancers. JunD depletion decreased iHUB interaction frequency and transcription of target genes. Moreover, targeting either eRNA production or signaling pathways upstream of iHUB activation using clinically tested small molecule inhibitors decreased eRNA production and interaction frequency, and restored chemotherapy responsiveness in vitro and in vivo. Representative iHUB target genes were found to be more expressed in patients with poor response to chemotherapy compared with responsive patients.
Conclusion Our findings identify an important role for a subgroup of highly connected enhancers (iHUBs) in regulating chemotherapy response and demonstrate targetability in sensitisation to chemotherapy.
- pancreatic cancer
- gene regulation
- chemotherapy
- drug resistance
- molecular oncology
Data availability statement
Data are available in a public, open access repository. All raw and processed data are available at www.ebi.ac.uk/arrayexpress under accession number E-MTAB-11730-33, E-MTAB-11737-40, E-MTAB-11744, E-MTAB-12705,7-8. All samples and their respective accession numbers are available in Tables S1-S3.Public data /referenced in text and preceded by [dataset][dataset] 29 Kutschat, A. P. et al. STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in 542 Pancreatic Cancer. Cancer Res, doi:10.1158/0008-5472.Can-20-2874 (2021).
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Data availability statement
Data are available in a public, open access repository. All raw and processed data are available at www.ebi.ac.uk/arrayexpress under accession number E-MTAB-11730-33, E-MTAB-11737-40, E-MTAB-11744, E-MTAB-12705,7-8. All samples and their respective accession numbers are available in Tables S1-S3.Public data /referenced in text and preceded by [dataset][dataset] 29 Kutschat, A. P. et al. STIM1 Mediates Calcium-dependent Epigenetic Reprogramming in 542 Pancreatic Cancer. Cancer Res, doi:10.1158/0008-5472.Can-20-2874 (2021).
Footnotes
FHH and SAJ are joint senior authors.
Twitter @3amrogram, @RobynKosinsky, @ProfJohnsen
AMA, APK and XW contributed equally.
Contributors FHH and SAJ designed experiments. FHH established resistant cells and Cas9 cells, performed ChIP-seq for H3K27ac, H3K4me3, BRD4, JunD, MED1, RNA-seq, HiChIP, ATAC-seq and 4C-seq. FHH performed bioinformatic analysis for HiChIP, ChIP-seq, and RNA-seq, 4C-Seq. XW performed leChRO-seq analysis. XW and AVB supported HiChIP analysis. APK, LT and ZN performed leChRO-seq. NJ-S, NT and RG performed IHC, AMA RA-R, WK, IL, JY, EH, SAH, RLK and MT performed experiments and established patient-derived xenografts. TLE performed Pol II ChIP-seq and lentiCas9 generation. TLE, CWW, JA-F performed proliferation assays and treatments. JA-F performed western blots. JG, JTS provided conceptual support to the manuscript. FHH and SAJ wrote the manuscript. All authors have reviewed the manuscript and provided feedback. FHH and SAJ are joint senior authors and act as guarantors for this manuscript.
Funding Research reported in this publication was supported by the Robert Bosch Stiftung (RBMF/RBCT; no grant/award number) to SAJ, the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institutes of Health under Award Number P30DK084567 (Pilot and feasibility award to FHH), CTSA Grant Number KL2 TR002379 from the National Center for Advancing Translational Science to N.J.S, Deutsche Krebshilfe (PiPAC Consortium) (70112505) to ZN, JTS, EH and SAJ, and the Deutsche Forschungsgemeinschaft (DFG) (JO 815/3-2 to SAJ, KFO5002 to EH).
Disclaimer The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
Competing interests None declared.
Patient and public involvement Patients and/or the public were not involved in the design, or conduct, or reporting, or dissemination plans of this research.
Provenance and peer review Not commissioned; externally peer reviewed.
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