Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways

Sanchari Bhattacharyya, Kith Pradhan, Nathaniel Campbell, Jozef Mazdo, Aparna Vasantkumar, Shahina Maqbool, Tushar D. Bhagat, Sonal Gupta, Masako Suzuki, Yiting Yu, John M. Greally, Ulrich Steidl, James Bradner, Meelad Dawlaty, Lucy Godley, Anirban Maitra, Amit Verma

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of cytosine methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq and gene expression by RNA-seq in pancreatic cancer and control samples. 5-hmC was specifically enriched at open regions of chromatin, and gain of 5-hmC was correlated with up-regulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as MYC, KRAS, VEGFA, and BRD4. Specifically, BRD4 was overexpressed and acquired 5-hmC at enhancer regions in the majority of neoplastic samples. Functionally, acquisition of 5-hmC at BRD4 promoter was associated with increase in transcript expression in reporter assays and primary samples. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human pancreatic cancer.

Original languageEnglish (US)
Pages (from-to)1830-1842
Number of pages13
JournalGenome Research
Volume27
Issue number11
DOIs
StatePublished - Nov 1 2017

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Nucleic Acid Regulatory Sequences
Pancreatic Neoplasms
Epigenomics
Chromatin
Genome
Cytosine
5-hydroxymethylcytosine
Heterografts
Base Pairing
Methylation
Neoplasms
Up-Regulation
RNA
Gene Expression
Cell Line
Growth

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Altered hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways. / Bhattacharyya, Sanchari; Pradhan, Kith; Campbell, Nathaniel; Mazdo, Jozef; Vasantkumar, Aparna; Maqbool, Shahina; Bhagat, Tushar D.; Gupta, Sonal; Suzuki, Masako; Yu, Yiting; Greally, John M.; Steidl, Ulrich; Bradner, James; Dawlaty, Meelad; Godley, Lucy; Maitra, Anirban; Verma, Amit.

In: Genome Research, Vol. 27, No. 11, 01.11.2017, p. 1830-1842.

Research output: Contribution to journalArticle

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abstract = "Transcriptional deregulation of oncogenic pathways is a hallmark of cancer and can be due to epigenetic alterations. 5-Hydroxymethylcytosine (5-hmC) is an epigenetic modification that has not been studied in pancreatic cancer. Genome-wide analysis of 5-hmC-enriched loci with hmC-seal was conducted in a cohort of low-passage pancreatic cancer cell lines, primary patient-derived xenografts, and pancreatic controls and revealed strikingly altered patterns in neoplastic tissues. Differentially hydroxymethylated regions preferentially affected known regulatory regions of the genome, specifically overlapping with known H3K4me1 enhancers. Furthermore, base pair resolution analysis of cytosine methylation and hydroxymethylation with oxidative bisulfite sequencing was conducted and correlated with chromatin accessibility by ATAC-seq and gene expression by RNA-seq in pancreatic cancer and control samples. 5-hmC was specifically enriched at open regions of chromatin, and gain of 5-hmC was correlated with up-regulation of the cognate transcripts, including many oncogenic pathways implicated in pancreatic neoplasia, such as MYC, KRAS, VEGFA, and BRD4. Specifically, BRD4 was overexpressed and acquired 5-hmC at enhancer regions in the majority of neoplastic samples. Functionally, acquisition of 5-hmC at BRD4 promoter was associated with increase in transcript expression in reporter assays and primary samples. Furthermore, blockade of BRD4 inhibited pancreatic cancer growth in vivo. In summary, redistribution of 5-hmC and preferential enrichment at oncogenic enhancers is a novel regulatory mechanism in human pancreatic cancer.",
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AU - Suzuki, Masako

AU - Yu, Yiting

AU - Greally, John M.

AU - Steidl, Ulrich

AU - Bradner, James

AU - Dawlaty, Meelad

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AU - Verma, Amit

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