Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling

Katia Nones, Nic Waddell, Sarah Song, Ann Marie Patch, David Miller, Amber Johns, Jianmin Wu, Karin S. Kassahn, David Wood, Peter Bailey, Lynn Fink, Suzanne Manning, Angelika N. Christ, Craig Nourse, Stephen Kazakoff, Darrin Taylor, Conrad Leonard, David K. Chang, Marc D. Jones, Michelle ThomasClare Watson, Mark Pinese, Mark Cowley, Ilse Rooman, Marina Pajic, Giovanni Butturini, Anna Malpaga, Vincenzo Corbo, Stefano Crippa, Massimo Falconi, Giuseppe Zamboni, Paola Castelli, Rita T. Lawlor, Anthony J. Gill, Aldo Scarpa, John V. Pearson, Andrew V. Biankin, Sean M. Grimmond

Research output: Contribution to journalArticle

Abstract

The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5 region of genes (including the proximal promoter, 5UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy. What's new? Based on a large genome-wide scan of DNA methylation, this study reports that global DNA methylation patterns can robustly segregate tumor and non-malignant pancreata. Cancer methylation also affects key pathways in pancreatic carcinogenesis, including TGF-β, WNT, and axon guidance signaling. This study confirms that methylation plays an important role in the development and progression of pancreatic cancer, with implications for both ongoing research and therapeutic development.

Original languageEnglish
Pages (from-to)1110-1118
Number of pages9
JournalInternational Journal of Cancer
Volume135
Issue number5
DOIs
Publication statusPublished - Sep 1 2014

Fingerprint

DNA Methylation
Epigenomics
Adenocarcinoma
Genome
Methylation
Pancreas
Carcinogenesis
Genes
High-Throughput Nucleotide Sequencing
Neoplasms
CpG Islands
Pancreatic Neoplasms
Cell Adhesion
Integrins
Up-Regulation
Gene Expression
Polymerase Chain Reaction
Messenger RNA
Mutation
Axon Guidance

Keywords

  • axon-guidance
  • methylation
  • pancreatic cancer
  • SLIT-ROBO pathway
  • stellate cell activation

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. / Nones, Katia; Waddell, Nic; Song, Sarah; Patch, Ann Marie; Miller, David; Johns, Amber; Wu, Jianmin; Kassahn, Karin S.; Wood, David; Bailey, Peter; Fink, Lynn; Manning, Suzanne; Christ, Angelika N.; Nourse, Craig; Kazakoff, Stephen; Taylor, Darrin; Leonard, Conrad; Chang, David K.; Jones, Marc D.; Thomas, Michelle; Watson, Clare; Pinese, Mark; Cowley, Mark; Rooman, Ilse; Pajic, Marina; Butturini, Giovanni; Malpaga, Anna; Corbo, Vincenzo; Crippa, Stefano; Falconi, Massimo; Zamboni, Giuseppe; Castelli, Paola; Lawlor, Rita T.; Gill, Anthony J.; Scarpa, Aldo; Pearson, John V.; Biankin, Andrew V.; Grimmond, Sean M.

In: International Journal of Cancer, Vol. 135, No. 5, 01.09.2014, p. 1110-1118.

Research output: Contribution to journalArticle

Nones, K, Waddell, N, Song, S, Patch, AM, Miller, D, Johns, A, Wu, J, Kassahn, KS, Wood, D, Bailey, P, Fink, L, Manning, S, Christ, AN, Nourse, C, Kazakoff, S, Taylor, D, Leonard, C, Chang, DK, Jones, MD, Thomas, M, Watson, C, Pinese, M, Cowley, M, Rooman, I, Pajic, M, Butturini, G, Malpaga, A, Corbo, V, Crippa, S, Falconi, M, Zamboni, G, Castelli, P, Lawlor, RT, Gill, AJ, Scarpa, A, Pearson, JV, Biankin, AV & Grimmond, SM 2014, 'Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling', International Journal of Cancer, vol. 135, no. 5, pp. 1110-1118. https://doi.org/10.1002/ijc.28765
Nones, Katia ; Waddell, Nic ; Song, Sarah ; Patch, Ann Marie ; Miller, David ; Johns, Amber ; Wu, Jianmin ; Kassahn, Karin S. ; Wood, David ; Bailey, Peter ; Fink, Lynn ; Manning, Suzanne ; Christ, Angelika N. ; Nourse, Craig ; Kazakoff, Stephen ; Taylor, Darrin ; Leonard, Conrad ; Chang, David K. ; Jones, Marc D. ; Thomas, Michelle ; Watson, Clare ; Pinese, Mark ; Cowley, Mark ; Rooman, Ilse ; Pajic, Marina ; Butturini, Giovanni ; Malpaga, Anna ; Corbo, Vincenzo ; Crippa, Stefano ; Falconi, Massimo ; Zamboni, Giuseppe ; Castelli, Paola ; Lawlor, Rita T. ; Gill, Anthony J. ; Scarpa, Aldo ; Pearson, John V. ; Biankin, Andrew V. ; Grimmond, Sean M. / Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. In: International Journal of Cancer. 2014 ; Vol. 135, No. 5. pp. 1110-1118.
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abstract = "The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5 region of genes (including the proximal promoter, 5UTR and CpG islands). Approximately 33{\%} DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy. What's new? Based on a large genome-wide scan of DNA methylation, this study reports that global DNA methylation patterns can robustly segregate tumor and non-malignant pancreata. Cancer methylation also affects key pathways in pancreatic carcinogenesis, including TGF-β, WNT, and axon guidance signaling. This study confirms that methylation plays an important role in the development and progression of pancreatic cancer, with implications for both ongoing research and therapeutic development.",
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T1 - Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling

AU - Nones, Katia

AU - Waddell, Nic

AU - Song, Sarah

AU - Patch, Ann Marie

AU - Miller, David

AU - Johns, Amber

AU - Wu, Jianmin

AU - Kassahn, Karin S.

AU - Wood, David

AU - Bailey, Peter

AU - Fink, Lynn

AU - Manning, Suzanne

AU - Christ, Angelika N.

AU - Nourse, Craig

AU - Kazakoff, Stephen

AU - Taylor, Darrin

AU - Leonard, Conrad

AU - Chang, David K.

AU - Jones, Marc D.

AU - Thomas, Michelle

AU - Watson, Clare

AU - Pinese, Mark

AU - Cowley, Mark

AU - Rooman, Ilse

AU - Pajic, Marina

AU - Butturini, Giovanni

AU - Malpaga, Anna

AU - Corbo, Vincenzo

AU - Crippa, Stefano

AU - Falconi, Massimo

AU - Zamboni, Giuseppe

AU - Castelli, Paola

AU - Lawlor, Rita T.

AU - Gill, Anthony J.

AU - Scarpa, Aldo

AU - Pearson, John V.

AU - Biankin, Andrew V.

AU - Grimmond, Sean M.

PY - 2014/9/1

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N2 - The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5 region of genes (including the proximal promoter, 5UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy. What's new? Based on a large genome-wide scan of DNA methylation, this study reports that global DNA methylation patterns can robustly segregate tumor and non-malignant pancreata. Cancer methylation also affects key pathways in pancreatic carcinogenesis, including TGF-β, WNT, and axon guidance signaling. This study confirms that methylation plays an important role in the development and progression of pancreatic cancer, with implications for both ongoing research and therapeutic development.

AB - The importance of epigenetic modifications such as DNA methylation in tumorigenesis is increasingly being appreciated. To define the genome-wide pattern of DNA methylation in pancreatic ductal adenocarcinomas (PDAC), we captured the methylation profiles of 167 untreated resected PDACs and compared them to a panel of 29 adjacent nontransformed pancreata using high-density arrays. A total of 11,634 CpG sites associated with 3,522 genes were significantly differentially methylated (DM) in PDAC and were capable of segregating PDAC from non-malignant pancreas, regardless of tumor cellularity. As expected, PDAC hypermethylation was most prevalent in the 5 region of genes (including the proximal promoter, 5UTR and CpG islands). Approximately 33% DM genes showed significant inverse correlation with mRNA expression levels. Pathway analysis revealed an enrichment of aberrantly methylated genes involved in key molecular mechanisms important to PDAC: TGF-β, WNT, integrin signaling, cell adhesion, stellate cell activation and axon guidance. Given the recent discovery that SLIT-ROBO mutations play a clinically important role in PDAC, the role of epigenetic perturbation of axon guidance was pursued in more detail. Bisulfite amplicon deep sequencing and qRT-PCR expression analyses confirmed recurrent perturbation of axon guidance pathway genes SLIT2, SLIT3, ROBO1, ROBO3, ITGA2 and MET and suggests epigenetic suppression of SLIT-ROBO signaling and up-regulation of MET and ITGA2 expression. Hypomethylation of MET and ITGA2 correlated with high gene expression, which was associated with poor survival. These data suggest that aberrant methylation plays an important role in pancreatic carcinogenesis affecting core signaling pathways with potential implications for the disease pathophysiology and therapy. What's new? Based on a large genome-wide scan of DNA methylation, this study reports that global DNA methylation patterns can robustly segregate tumor and non-malignant pancreata. Cancer methylation also affects key pathways in pancreatic carcinogenesis, including TGF-β, WNT, and axon guidance signaling. This study confirms that methylation plays an important role in the development and progression of pancreatic cancer, with implications for both ongoing research and therapeutic development.

KW - axon-guidance

KW - methylation

KW - pancreatic cancer

KW - SLIT-ROBO pathway

KW - stellate cell activation

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