DNMT1 inhibition reprograms pancreatic cancer stem cells via upregulation of the miR-17-92 cluster

Pancreatic ductal adenocarcinoma (PDAC) and other carcinomas are hierarchically organized, with cancer stem cells (CSC) residing at the top of the hierarchy, where they drive tumor progression, metastasis, and chemoresistance. As CSC and non-CSC share an identical genetic background, we hypothesize that differences in epigenetics account for the striking functional differences between these two cell populations. Epigenetic mechanisms, such as DNA methylation, play an important role in maintaining pluripotency and regulating the differentiation of stem cells, but the role of DNA methylation in pancreatic CSC is obscure. In this study, we investigated the genome-wide DNA methylation profile of PDAC CSC, and we determined the importance of DNA methyltransferases for CSC maintenance and tumorigenicity. Using high-throughput methylation analysis, we discovered that sorted CSCs have a higher level of DNA methylation, regardless of the heterogeneity or polyclonality of the CSC populations present in the tumors analyzed. Mechanistically, CSC expressed higher DNMT1 levels than non-CSC. Pharmacologic or genetic targeting of DNMT1 in CSCs reduced their self-renewal and in vivo tumorigenic potential, defining DNMT1 as a candidate CSC therapeutic target. The inhibitory effect we observed was mediated in part through epigenetic reactivation of previously silenced miRNAs, in particular the miR-17-92 cluster. Together, our findings indicate that DNA methylation plays an important role in CSC biology and also provide a rationale to develop epigenetic modulators to target CSC plasticity and improve the poor outcome of PDAC patientsResearch was supported by the ERC Advanced Investigator Grant (Pa-CSC 233460 to C. Heeschen) and the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 256974 (EPC-TM-NET to C. Heeschen) and n° 602783 (CAM-PaC to C. Heeschen), the 2015 SU2C Lustgarten CRUK Pancreatic Cancer Dream Team Award (to C. Heeschen), Pancreatic Cancer UK RIF2014_04 and RIF2015_03 (both to C. Heeschen), a Rámon y Cajal Merit Award from the Ministerio de Economía y Competitividad, Spain (to B. Sainz), a Clinic and Laboratory Integration Program (CLIP) grant from the Cancer Research Institute, NY, NY USA (to. B. Sainz) and a Proyecto de Investigación de Salud, ISCIII, Spain (n° PI15/01507 to B. Sainz