Ang et al. BMC Cancer 2010, 10:227
Comprehensive profiling of DNA methylation in
colorectal cancer reveals subgroups with distinct
clinicopathological and molecular features
© 2010 Ang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons At-
tribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any
medium, provided the original work is properly cited.
Pei Woon Ang1,2, Marie Loh1,2, Natalia Liem3, Pei Li Lim3, Fabienne Grieu1, Aparna Vaithilingam2, Cameron Platell1,4,
Wei Peng Yong3, Barry Iacopetta1 and Richie Soong*2
Background: Most previous studies of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC) have
been conducted on a relatively small numbers of CpG sites. In the present study we performed comprehensive DNA
methylation profiling of CRC with the aim of characterizing CIMP subgroups.
Methods: DNA methylation at 1,505 CpG sites in 807 cancer-related genes was evaluated using the Illumina
GoldenGate® methylation array in 28 normal colonic mucosa and 91 consecutive CRC samples. Methylation data was
analyzed using unsupervised hierarchical clustering. CIMP subgroups were compared for various clinicopathological
and molecular features including patient age, tumor site, microsatellite instability (MSI), methylation at a consensus
panel of CpG islands and mutations in BRAF and KRAS.
Results: A total of 202 CpG sites were differentially methylated between tumor and normal tissue. Unsupervised
hierarchical clustering of methylation data from these sites revealed the existence of three CRC subgroups referred to
as CIMP-low (CIMP-L, 21% of cases), CIMP-mid (CIMP-M, 14%) and CIMP-high (CIMP-H, 65%). In comparison to CIMP-L
tumors, CIMP-H tumors were more often located in the proximal colon and showed more frequent mutation of KRAS
and BRAF (P < 0.001).
Conclusions: Comprehensive DNA methylation profiling identified three CRC subgroups with distinctive
clinicopathological and molecular features. This study suggests that both KRAS and BRAF mutations are involved with
the CIMP-H pathway of CRC rather than with distinct CIMP subgroups.
DNA hypermethylation-induced gene silencing is a com-
mon event in many malignancies and serves as an alter-
native mechanism to genetic mutation for the loss of
tumor suppressor functions [1,2]. Although the mecha-
nisms that underlie aberrant DNA methylation in cancer
cells remain to be elucidated, current evidence suggests
that it may be an early and possibly even an initiating
event in the development of colorectal cancer (CRC).
A subset of CRC has been shown to exhibit frequent
and concurrent hypermethylation at specific gene pro-
moters and is referred to as the CpG island methylator
phenotype (CIMP+) . CIMP+ CRC is associated with
distinct clinicopathological and molecular features
including proximal tumor location, preponderance in
elderly females, poorly differentiated and mucinous
tumor histology, microsatellite instability (MSI) and fre-
quent BRAF V600E mutation [3-10]. CIMP+ CRC often
lack the hallmark genetic alterations in APC, p53 and 18q
that characterize the classic
sequence. Instead, CIMP+ tumors are thought to develop
along an alternate serrated adenoma pathway in which
hypermethylation rather than mutation is used to inacti-
vate tumor suppressor genes .
* Correspondence: firstname.lastname@example.org
2 Cancer Science Institute of Singapore, National University of Singapore,
Full list of author information is available at the end of the article
Ang et al. BMC Cancer 2010, 10:227
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Cite this article as: Ang et al., Comprehensive profiling of DNA methylation
in colorectal cancer reveals subgroups with distinct clinicopathological and
molecular features BMC Cancer 2010, 10:227