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

Nones, K. et al. (2014) Genome-wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT-ROBO, ITGA2 and MET signaling. International Journal of Cancer, 135(5), pp. 1110-1118. (doi:10.1002/ijc.28765) (PMID:24500968)

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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, 5′UTR 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.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Biankin, Professor Andrew and Grimmond, Professor Sean and Chang, Dr David
Authors: Nones, K., Waddell, N., Song, S., Patch, A.-M., Miller, D., Johns, A., Wu, J., Kassahn, K. S., Wood, D., Bailey, P., Fink, L., Manning, S., Christ, A. N., Nourse, C., Kazakoff, S., Taylor, D., Leonard, C., Chang, D. K., Jones, M. D., 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, R. T., Gill, A. J., Scarpa, A., Pearson, J. V., Biankin, A. V., and Grimmond, S. M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Cancer Sciences
Journal Name:International Journal of Cancer
Publisher:John Wiley and Sons
ISSN:0020-7136
ISSN (Online):1097-0215
Copyright Holders:Copyright © 2014 The Authors
First Published:First published in International Journal of Cancer 135(5):1110-1118
Publisher Policy:Reproduced under a Creative Commons License

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