TET2 Drives 5hmc Marking of GATA6 and Epigenetically Defines Pancreatic Ductal Adenocarcinoma Transcriptional Subtypes.

5-Methylcytosine / analogs & derivatives Animals Antineoplastic Combined Chemotherapy Protocols / pharmacology Ascorbic Acid / pharmacology Biomarkers, Tumor / genetics Carcinoma, Pancreatic Ductal / drug therapy Cell Differentiation Cell Line, Tumor DNA Methylation / drug effects DNA-Binding Proteins / genetics Dioxygenases / genetics Epigenesis, Genetic / drug effects Epigenome Epigenomics GATA6 Transcription Factor / genetics Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Metformin / pharmacology Mice, Nude Mice, Transgenic Pancreatic Neoplasms / drug therapy Retrospective Studies Smad4 Protein / genetics Transcription, Genetic / drug effects Transcriptome Wnt Signaling Pathway / genetics Xenograft Model Antitumor Assays

Epigenetics GATA6 Pancreatic Cancer SMAD4 TET2

Journal

Gastroenterology

ISSN: 1528-0012

Titre abrégé: Gastroenterology

Pays: United States

ID NLM: 0374630

Informations de publication

Date de publication:
08 2021

Historique:

received: 27 07 2020

revised: 12 03 2021

accepted: 07 04 2021

pubmed: 30 4 2021

medline: 19 1 2022

entrez: 29 4 2021

Statut: ppublish

Résumé

Pancreatic ductal adenocarcinoma (PDAC) is characterized by advanced disease stage at presentation, aggressive disease biology, and resistance to therapy, resulting in an extremely poor 5-year survival rate of <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 is hindered by the technical limitations of analyzing clinical samples. We performed genome-wide epigenetic mapping of DNA modifications 5-methylcytosine and 5-hydroxymethylcytosine (5hmc) using oxidative bisulfite sequencing from formalin-embedded sections. We identified overlap with transcriptional signatures in formalin-fixed, paraffin-embedded tissue from resected patients, via bioinformatics using iCluster and mutational profiling and confirmed them in vivo. We found that aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci, including GATA6, which promote differentiated classical pancreatic subtypes. We showed that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5-methylcytosine hydroxylase TET2. Furthermore, we found that SMAD4 directly supports TET2 levels in classical pancreatic tumors, and loss of SMAD4 expression was associated with reduced 5hmc, GATA6, and squamous-like tumors. Importantly, enhancing TET2 stability using metformin and vitamin C/ascorbic acid restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependence in vitro and in vivo. We identified epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data showed that restoring epigenetic control increases biomarkers of classical pancreatic tumors that are associated with improved therapeutic responses and survival.

Sections du résumé

BACKGROUND & AIMS

METHODS

We performed genome-wide epigenetic mapping of DNA modifications 5-methylcytosine and 5-hydroxymethylcytosine (5hmc) using oxidative bisulfite sequencing from formalin-embedded sections. We identified overlap with transcriptional signatures in formalin-fixed, paraffin-embedded tissue from resected patients, via bioinformatics using iCluster and mutational profiling and confirmed them in vivo.

RESULTS

We found that aggressive squamous-like PDAC subtypes result from epigenetic inactivation of loci, including GATA6, which promote differentiated classical pancreatic subtypes. We showed that squamous-like PDAC transcriptional subtypes are associated with greater loss of 5hmc due to reduced expression of the 5-methylcytosine hydroxylase TET2. Furthermore, we found that SMAD4 directly supports TET2 levels in classical pancreatic tumors, and loss of SMAD4 expression was associated with reduced 5hmc, GATA6, and squamous-like tumors. Importantly, enhancing TET2 stability using metformin and vitamin C/ascorbic acid restores 5hmc and GATA6 levels, reverting squamous-like tumor phenotypes and WNT-dependence in vitro and in vivo.

CONCLUSIONS

We identified epigenetic deregulation of pancreatic differentiation as an underpinning event behind the emergence of transcriptomic subtypes in PDAC. Our data showed that restoring epigenetic control increases biomarkers of classical pancreatic tumors that are associated with improved therapeutic responses and survival.

Identifiants

DOI: 10.1053/j.gastro.2021.04.044 PMID: 33915173

pubmed: 33915173

pii: S0016-5085(21)00682-X

doi: 10.1053/j.gastro.2021.04.044

pii:

doi:

Substances chimiques

Biomarkers, Tumor 0

DNA-Binding Proteins 0

GATA6 Transcription Factor 0

GATA6 protein, human 0

SMAD4 protein, human 0

Smad4 Protein 0

5-hydroxymethylcytosine 1123-95-1

5-Methylcytosine 6R795CQT4H

Metformin 9100L32L2N

Dioxygenases EC 1.13.11.-

TET2 protein, human EC 1.13.11.-

Ascorbic Acid PQ6CK8PD0R

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

Pagination

653-668.e16

Subventions

Organisme : Pancreatic Cancer UK

ID : FLF2015_06_OXFORD

Pays : United Kingdom

Organisme : Cancer Research UK