TET2 drives 5hmc marking of GATA6 and epigenetically defines pancreatic ductal adenocarcinoma transcriptional subtypes.

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Pancreatic ductal adenocarcinoma (PDAC) is characterised by advanced disease stage at presentation, aggressive disease biology and resistance to therapy resulting in extremely poor five-year survival <10%. PDAC is classified into transcriptional subtypes with distinct survival characteristics, although how these arise is not known. Epigenetic deregulation, rather than genetics, has been proposed to underpin progression but exactly why is unclear and hindered by technical limitations of analysing clinical samples.Genome-wide epigenetic mapping of DNA modifications 5-methylcytosine (5mc) and 5-hydroxymethylcytosine (5hmc) using oxidative bisulphite sequencing (oxBS) from formalin embedded sections. Bioinformatics using iCluster and mutational profiling to identify overlap with transcriptional signatures in FFPE from resected patients and confirmation in vivo.We find that aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci including GATA6 that promote differentiated classical-pancreatic subtypes. We show that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5mc-hydroxylase TET2. Furthermore, we find that SMAD4 directly supports TET2 levels in classical-pancreatic tumors and loss of SMAD4 expression is associated reduced 5hmc, GATA6 and squamous-like tumors. Importantly, enhancing TET2 stability using Metformin and VitaminC/ascorbic acid (AA) restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependence in vitro and in vivo.We identify epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data shows that restoring epigenetic control increases biomarkers of classical-pancreatic tumors which are associated with improved therapeutic responses and survival.

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Authors: Michael Eyres, Simone Lanfredini, Haonan Xu, Adam Burns, Andrew Blake, Frances Willenbrock, Robert Goldin, Daniel Hughes, Sophie Hughes, Asmita Thapa, Dimitris Vavoulis, Aline Hubert, Zenobia D’Costa, Ahmad Sabbagh, Aswin G Abraham, Christine Blancher, Stephanie Jones, Clare Verrill, Michael Silva, Zahir Soonawalla, Timothy Maughan, Anna Schuh, Somnath Mukherjee, Eric O’Neill