Abstract
BackgroundGenome-wide DNA hypomethylation plays a role in genomic instability and carcinogenesis. LINE-1 (L1 retrotransposon) constitutes a substantial portion of the human genome, and LINE-1 methylation correlates with global DNA methylation status. LINE-1 hypomethylation in colon cancer has been strongly associated with poor prognosis. However, whether LINE-1 hypomethylators constitute a distinct cancer subtype remains uncertain. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. Thus, it is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features.DesignUtilizing a database of 869 colorectal cancers in two prospective cohort studies, we constructed multivariate linear and logistic regression models for LINE-1 methylation (quantified by Pyrosequencing). Variables included age, sex, body mass index, family history of colorectal cancer, smoking status, tumor location, stage, grade, mucinous component, signet ring cells, tumor infiltrating lymphocytes, CpG island methylator phenotype (CIMP), microsatellite instability, expression of TP53 (p53), CDKN1A (p21), CTNNB1 (β-catenin), PTGS2 (cyclooxygenase-2), and FASN, and mutations in KRAS, BRAF, and PIK3CA.ResultsTumoral LINE-1 methylation ranged from 23.1 to 90.3 of 0-100 scale (mean 61.4; median 62.3; standard deviation 9.6), and distributed approximately normally except for extreme hypomethylators [LINE-1 methylation < 40; N = 22 (2.5%), which were far more than what could be expected by normal distribution]. LINE-1 extreme hypomethylators were significantly associated with younger patients (p = 0.0058). Residual plot by multivariate linear regression showed that LINE-1 extreme hypomethylators clustered as one distinct group, separate from the main tumor group. The multivariate linear regression model could explain 8.4% of the total variability of LINE-1 methylation (R-square = 0.084). Multivariate logistic regression models for binary LINE-1 hypomethylation outcomes (cutoffs of 40, 50 and 60) showed at most fair predictive ability (area under receiver operator characteristics curve < 0.63).ConclusionsLINE-1 extreme hypomethylators appear to constitute a previously-unrecognized, distinct subtype of colorectal cancers, which needs to be confirmed by additional studies. Our tumor LINE-1 methylation data indicate enormous epigenomic diversity of individual colorectal cancers.
Highlights
DNA methylation is a major epigenetic mechanism in Xchromosome inactivation, imprinting and repression of transposable elements and endogenous retroviral sequences [1]
In our previous studies which focused on different hypotheses, we examined the relationship between LINE1 methylation and CpG island methylator phenotype (CIMP) to test the hypothesis whether there is any relationship between global DNA methylation level and CIMP [19]; the relation between LINE-1 methylation and patient survival [20]; the relationship between LINE-1 methylation levels within synchronous colorectal cancer pairs [21]; and the relationship between LINE-1 hypomethylation and 18 q loss of heterozygosity (LOH) as a part of analysis on prognostic significance of 18 q LOH [23]
LINE-1 methylation levels in 869 colorectal cancers Utilizing 869 colorectal cancers identified in the two independent prospective cohort studies, we quantified LINE-1 methylation by bisulfite-PCR and Pyrosequencing technology (Figure 1)
Summary
DNA methylation is a major epigenetic mechanism in Xchromosome inactivation, imprinting and repression of transposable elements and endogenous retroviral sequences [1]. Global DNA hypomethylation appears to play an important role in genomic instability [2,3], lead-. LINE-1 methylation has been shown to be highly variable among colon cancers [18,19], and LINE-1 hypomethylation is strongly associated with poor prognosis in colon cancer [20]. Whether LINE-1 hypomethylators constitute a distinct tumor subtype remains uncertain. Our recent study has shown a significant correlation of LINE-1 methylation levels within synchronous colorectal cancer pairs (i.e., two or more primary tumors in one patient), which suggests the presence of genetic and/or environmental factors influencing LINE-1 methylation levels that are unlikely the result of a purely stochastic phenomenon [21]. Recent evidence for concordant LINE-1 hypomethylation within synchronous colorectal cancer pairs suggests the presence of a non-stochastic mechanism influencing tumor LINE-1 methylation level. It is of particular interest to examine whether its wide variation can be attributed to clinical, pathologic or molecular features
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