Genome-Wide CpG Island Profiling of Intraductal Papillary Mucinous Neoplasms of the Pancreas

Abstract

Purpose Intraductal papillary mucinous neoplasms (IPMNs) are precursors to infiltrating pancreatic ductal adenocarcinomas. Widespread epigenetic alterations are characteristic of many cancers, yet few studies have systematically analyzed epigenetic alterations of neoplastic precursors. Our goal was to perform genome-wide CpG island methylation profiling to identify aberrantly methylated loci in IPMNs. Experimental Design We compared the CpG island methylation profiles of 6 IPMNs to normal primary pancreatic duct samples using methylation CpG island amplification (MCA) and Agilent CpG island microarray (MCAM) analysis. When selected 13 genes identified as differentially methylated by MCAM for methylation-specific PCR (MSP) analysis in an independent set of IPMNs and normal pancreas samples and performed expression analysis of selected genes. Results We identified 2,259 loci as differentially methylated in at least one of 6 IPMNs including 245 genes hypermethylated in IPMNs with high-grade dysplasia compared to normal pancreatic duct samples. Eleven of 13 genes evaluated by MSP were more commonly methylated in 61 IPMNs than in 43 normal pancreas samples. Several genes, (BNIP3, PTCHD2, SOX17, NXPH1, EBF3), were significantly more likely to be methylated in IPMNs with high-grade than with lower-grade dysplasia. One gene, Sox17, demonstrated loss of protein expression by immunohistochemistry in 22% (19 of 88) of IPMNs. The most specific marker, BNIP3, was not methylated in any IPMNs with low-grade dysplasia or in normal pancreas samples. Conclusions IPMNs undergo extensive aberrant CpG island hypermethylation. The detection of genes selectively methylated in high-grade IPMNs such as BNIP3 may have utility in the clinical evaluation of IPMNs.

Effect of inhibition of MEK pathway on 5-aza-deoxycytidine-suppressed pancreatic cancer cell proliferation

“…Previous studies have convincingly proven the role of aberrant methylation and histone acetylation in the initiation and progression of several tumor types, including pancreatic adenocarcinoma (Omura and Goggins, 2009;Hong et al, 2012). The MEK pathway plays an important role in the regulation of cell division, and the current study as well as others suggest that an increase of MEK pathway activity may be responsible for the increased DNA methyltransferase enzyme activity and promoter hypermethylation of tumor suppressor genes.…”

Updates and Critical Evaluation on Novel Biomarkers for the Malignant Progression of Intraductal Papillary Mucinous Neoplasms of the Pancreas

“…Significantly, the mismatch repair genes MutL homolog 1 (hMLH1) and O 6 -alkylguanine DNA alkyltransferase (MGMT) are found more frequently methylated in the higher grade IPMNs than in lower grade IPMNs (64). We should mention that, in the adenocarcinomas associated with IPMN, hypermethylation involving three or more promoter regions is found in 55% of the samples, while, in non-invasive IPMNs, 20% of the samples are found methylated in at three or more gene promoters (65). It is assumable that the pancreatic juice can be analyzed concerning the methylated DNA in order to differentiate the invasive from non-invasive IPMNs before surgery.…”

Molecular Characterization and Pathogenesis of Intraductal Papillary Mucinous Neoplasms of the Pancreas

“…In clinical routine, MRI and MRCP are the primary diagnostic options [3]. In contrast to PanINs, IPMNs can be detected by imaging techniques because of their bigger size (>1 cm) [21]. The greater difficulty in diagnosing PanINs by imaging compared to IPMNs makes PanINs more dangerous because a late diagnosis increases the risk of an association with malignancy.…”

“…Patients can greatly benefit from a diagnosis of IPMN at an early stage because precursor lesions can be treated quite well without the risk of an association with pancreatic cancer [21]. IPMNs grow slowly but can become invasive and produce metastases.…”