Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer

Abstract

Colon cancer has been viewed as the result of progressive accumulation of genetic and epigenetic abnormalities. However, this view does not fully reflect the molecular heterogeneity of the disease. We have analyzed both genetic (mutations of BRAF, KRAS, and p53 and microsatellite instability) and epigenetic alterations (DNA methylation of 27 CpG island promoter regions) in 97 primary colorectal cancer patients. Two clustering analyses on the basis of either epigenetic profiling or a combination of genetic and epigenetic profiling were performed to identify subclasses with distinct molecular signatures. Unsupervised hierarchical clustering of the DNA methylation data identified three distinct groups of colon cancers named CpG island methylator phenotype (CIMP) 1, CIMP2, and CIMP negative. Genetically, these three groups correspond to very distinct profiles. CIMP1 are characterized by MSI (80%) and BRAF mutations (53%) and rare KRAS and p53 mutations (16% and 11%, respectively). CIMP2 is associated with 92% KRAS mutations and rare MSI, BRAF, or p53 mutations (0, 4, and 31% respectively). CIMP-negative cases have a high rate of p53 mutations (71%) and lower rates of MSI (12%) or mutations of BRAF (2%) or KRAS (33%). Clustering based on both genetic and epigenetic parameters also identifies three distinct (and homogeneous) groups that largely overlap with the previous classification. The three groups are independent of age, gender, or stage, but CIMP1 and 2 are more common in proximal tumors. Together, our integrated genetic and epigenetic analysis reveals that colon cancers correspond to three molecularly distinct subclasses of disease.classification ͉ DNA methylation ͉ genetic alterations C olorectal cancer (CRC) is the second and fourth most common cancer in men and women, respectively (1). Approximately 70% of colorectal cancers are sporadic, with no inherited predisposition. A stepwise progression model involving two distinct genetic pathways has been proposed to explain the etiology of colon cancer from benign neoplasm to adenocarcinoma (2). One class of genetic alterations involves mutations of oncogenes and tumor-suppressor genes that directly control cell birth and death, such as APC, KRAS, and p53. Another involves mutations of DNA mismatch repair genes.In addition to these genetic alterations, cancer initiation and promotion can occur by epigenetic mechanisms (3). CpG methylation is the best characterized epigenetic change in the mammalian genome. Whereas CpG dinucleotides are underrepresented in the mammalian genome, approximately half of all human genes contain a CpG-rich region called a ''CpG island'' in the 5Ј area, often encompassing the promoter and transcription start site of the associated gene (4, 5). Gene silencing by hypermethylation of CpG islands (including tumor-suppressor genes) is a common event in tumors. Further, hypermethylation of specific genes such as ER␣, MYOD1, and N33 occurs in the normal colon tissue of aging individuals (6, 7), and hypermethylation of the secreted frizzled-relat...

Molecular differences in the microsatellite stable phenotype between left‐sided and right‐sided colorectal cancer

“…DNA methylation plays a major role in colorectal carcinogenesis 30, 31. DNA methylation can be classified into three types (HME, IME and LME) according to the 2‐panel method established by Yagi and Kaneda 18, 19.…”

Folate receptor-α expression in resectable hepatic colorectal cancer metastases: patterns and significance

“…These and other related markers have been extensively studied in recent years in primary colorectal cancers. 4,[22][23][24][25][26][27][28][29] The most frequent scenario, in which these markers were assessed has been stage II cancers to identify patients who might benefit from adjuvant therapy but would otherwise be denied of such an opportunity. 30 The data thus far have been inconclusive.…”

DNA methylation within the normal colorectal mucosa is associated with pathway-specific predisposition to cancer

“…There are at least two molecular pathways to sporadic colorectal cancer (CRC), the chromosomal instability (CIN) pathway and the CpG island methylator phenotype (CIMP) pathway (Shen et al, 2007b;Grady and Carethers, 2008;Issa, 2008). The CIN pathway accounts for approximately 80% of CRC, with aneuploidy providing the necessary genetic instability to drive the adenoma-carcinoma sequence (Vogelstein et al, 1988;Fearon and Vogelstein, 1990;Grady and Carethers, 2008).…”

“…In CIMP cancers, promoter methylation-induced transcriptional silencing of important tumor-suppressor genes has an important role in tumor biology (Jass et al, 2002;Jass, 2007;Grady and Carethers, 2008). BRAF or occasionally KRAS mutation-induced activation of RAS-RAF-MEK-ERK signaling is another important event in CIMP carcinogenesis (Jass et al, 2002;Kambara et al, 2004;Weisenberger et al, 2006;Shen et al, 2007b). In contrast to the CIN pathway, CIMP cancers frequently develop within the proximal colon, arise from serrated rather than adenomatous polyps, are more common in elderly females and are associated with distinct survival and treatment outcomes (Samowitz et al, 2005;Spring et al, 2006;Weisenberger et al, 2006;Jass, 2007;Shen et al, 2007a;Ogino et al, 2009).…”

“…Although methylation of certain 'type C' genes segregates very closely with, and indeed defines, CIMP CRC, there are other 'type C' genes in which methylation occurs less discriminately in both CIMP and CIN cancers. This suggests either some overlap between the CRC pathways or, perhaps, the existence of multiple CIMP pathways (Weisenberger et al, 2006;Shen et al, 2007b).…”