Novel Application of Structural Equation Modeling to Correlation Structure Analysis of CpG Island Methylation in Colorectal Cancer

The CpG island methylator phenotype (CIMP high CIMP1) is a distinct phenotype associated with micro satellite instability (MSI) and BRAF mutation in colon cancer Recent evidence suggests the presence of KRAS mutation associated CIMP subtype (CIMP low CIMP2) We used cluster analysis principal component analysis (PCA), and structural equation modeling (SEM) a novel strategy to decipher the correlation structure of CpG island hypermethylation Using a database of 861 colon and rectal cancers DNA methylation at 16 CpG islands [CACNA1G CDKN2A (p16/ink4a) 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 Tumors were categorized into three groups Group 1 with wild type KRAS/BRAF (N = 440) Group 2 with mutant KRAS and wild type BRAF (N = 308) and Group 3 with wild type KRAS and mutant BRAF (N = 107) Tumors with mutant KRAS/BRAF (N = 6) were excluded In unsupervised hierarchical clustering analysis all but six markers (CACNA1G IGF2 RUNX3 MGMT MINT 1 and SOCS1) were differentially clustered with CIMP high and CIMP low according to KRAS and BRAF status In SEM the correlation structures between GIMP locus specific CpG island methylation and MSI differed according to KRAS and BRAF status which was consistent with PCA results In conclusion KRAS and BRAF mutations appear to differentially influence correlation structure of CpG island methylation Our novel data suggest two distinct perturbations resulting m differential locus specific propensity of CpG methylation. (Am J Pathol 2010 177 2731-2740 DOI 10 2353/ajpath 2010 100361)