Abstract 4922: KRAS and BRAF mutations influence correlation structure of locus-specific CpG island methylation and CIMP in colorectal cancer

Abstract

Abstract Background: The CpG island methylator phenotype (CIMP-high or CIMP1) is a distinct phenotype associated with microsatellite instability (MSI) and BRAF mutation in colon cancer. Recent investigations suggested that a separate KRAS mutation-associated CIMP subtype (CIMP-low or CIMP2) exists. However, no study has deciphered the interrelationship between KRAS, BRAF, CIMP and locus-specific CpG island methylation, utilizing causal modeling by structure equation model (SEM) analysis. Design: Utilizing the database of 861 colorectal cancers, DNA methylation at 16 CpG islands [CACNA1G, CDKN2A (p16), CHFR, CRABP1, HIC1, IGF2, IGFBP3, MGMT, MINT-1, MINT-31, MLH1, NEUROG1, p14 (CDKN2A/ARF), RUNX3, SOCS1, and WRN] was quantified by real-time PCR (MethyLight). We also examined MSI status and DNMT3B expression. To evaluate the effect of KRAS and BRAF mutation on the correlation structure of the CpG island markers and MSI, we categorized tumors into 4 groups; Group 1 (N=440) with wild-type KRAS and BRAF; Group 2 (N=308) with mutant KRAS and wild-type BRAF; Group 3 (N=107) with wild-type KRAS and mutant BRAF; and Group 4 (N=6) with mutant KRAS and BRAF, which was excluded from further analyses. We analyzed data using clustering analysis, principal component analysis (PCA) and SEM. Results: In unsupervised disjoint clustering analysis of the methylation markers, only 4 markers (CACNA1G, IGF2, RUNX3, SOCS1), were clustered with CIMP-high regardless of KRAS or BRAF mutation. In Groups 1 and 2, two latent CIMP classes, CIMP-low and CIMP-high, were assumed. However, in Group 3, CIMP-high status and CIMP-low status were clustered together so that only one latent class, “CIMP”, was assumed. PCA yielded similar findings to clustering. Based on the results of the cluster analysis and PCA and the literature data, we applied causal modeling by SEM analysis. In SEM analyses, the correlation structures between CIMP, locus-specific CpG island methylation and MSI differed according to KRAS and BRAF status, which was in agreement with results by PCA analyses. Differences between Group 1, Group 2 and Group 3 were highly significant p<0.0001). Conclusions: KRAS and BRAF mutations influence correlation structures between locus-specific CpG island methylation, and CIMP status in colorectal cancer. Our data suggest the role of KRAS and BRAF mutations in modifying propensity of CpG island methylation in a locus-specific manner. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4922.