Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma.
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2015
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Clinical Epigenetics
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Abstract
Background: Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting
for 7.5–8.7 % of CRCs. It has been shown that SAC has a worse prognosis and different histological and molecular
features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile.
Results: The methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array was
investigated in 103 colorectal specimens, including 39 SACs and 34 matched CCs, from Spanish and Finnish patients.
Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle
transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine
deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA
and protein level using pyrosequencing, methylation-specific PCR, quantitative polymerase chain reaction (qPCR) and
immunohistochemistry. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a
novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing
SAC with CRC showing molecular and histological features of high-level microsatellite instability.
Conclusions: This methylome study demonstrates distinct epigenetic regulation patterns in SAC which are consistent
to previous expression profile studies and that DIO3 and FOXD2 might be molecular targets for a specific histologyoriented
treatment of CRC.
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Keywords
Serrated carcinoma, Colorectal cancer, Methylome, Microarray analysis, Pyrosequencing