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.