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.