Diagnostic utility of MS-MLPA in DNA methylation profiling of adenocarcinomas and neuroendocrine carcinomas of the colon-rectum

Virchows Arch. 2013 Jan;462(1):47-56. doi: 10.1007/s00428-012-1348-2. Epub 2012 Dec 9.

Abstract

Methylation-specific multiple ligation-dependent probe amplification (MS-MLPA) is a fast, new, inexpensive method that has rarely been exploited in DNA methylation profiling of colorectal cancers (CRCs). The aim of this study was to test the diagnostic utility of MS-MLPA to evaluate the methylation status of 34 genes in normal colonic mucosa samples and in a well-characterized series of 83 adenocarcinomas and 21 neuroendocrine carcinomas of colon-rectum. Two commercial MS-MLPA kits (SALSA MS-MLPA ME001-C1 Tumor suppressor-1 Kit and SALSA MS-MLPA ME002-B1 Tumor suppressor-2 Kit) were used to perform promoter methylation analysis on formalin-fixed and paraffin-embedded tissues. MS-MLPA analysis was validated by bisulfite pyrosequencing, bisulfite cycle sequencing, and methylation-specific PCR. MS-MLPA analysis identified a subset of 27 CRCs (26 % of cases) showing high levels of gene methylation involving a mean percentage of 34 % of the promoters examined. These tumors exhibited all the main clinicopathological and genetic features described for CRCs with CpG island Methylator Phenotype-High. High levels of methylation were observed with similar frequency in adenocarcinomas and in neuroendocrine carcinomas (25 % versus 29 %, respectively), but different methylation profiles were observed in the two tumor types. In both groups, tumors with microsatellite instability and widespread methylation represented a homogeneous clinicopathological entity. MS-MLPA assay is an easy and reliable system for epigenetic characterization of tumor tissues and leads to a rapid identification of CRCs with the highest levels of gene methylation. Aberrant gene methylation is a common abnormality in CRC initiation and may be observed in tumors with very different genetic and clinicopathological profiles.

MeSH terms

  • Adenocarcinoma / diagnosis
  • Adenocarcinoma / genetics*
  • Adult
  • Aged
  • Aged, 80 and over
  • Carcinoma, Neuroendocrine / diagnosis
  • Carcinoma, Neuroendocrine / genetics*
  • Colorectal Neoplasms / diagnosis
  • Colorectal Neoplasms / genetics*
  • CpG Islands / genetics
  • DNA Methylation*
  • DNA, Neoplasm / genetics*
  • Female
  • Gene Expression Profiling*
  • Humans
  • Male
  • Middle Aged
  • Neoplasm Staging
  • Nucleic Acid Amplification Techniques
  • Oligonucleotide Array Sequence Analysis
  • Tumor Suppressor Proteins / genetics

Substances

  • DNA, Neoplasm
  • Tumor Suppressor Proteins