Abstract
ABSTRACTBackgroundAberrant methylation of DNA acts epigenetically to skew the gene transcription rate up or down. In this study, we have developed a comprehensive computational framework for the stage-specific analysis of methylation patterns in colorectal cancer.MethodsCombining public-domain methylation and clinical data from TCGA, the methylation β - matrix was converted into M-value matrix, annotated with sample stages and analysed for stage-specific genes using multiple approaches involving stage-differentiated linear modelling of methylation patterns or their correlation with the phenotype and expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against control samples (adjusted p-value <0.001 and |log fold-change of M-value| >2). These results were further filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-specific DMGs. These were then subjected to a consensus analysis, followed by Kaplan–Meier survival analysis to explore the relationship between methylation and prognosis for the consensus stage-salient biomarkers.ResultsWe found significant genome-wide changes in methylation patterns in cancer samples relative to controls agnostic of stage. Our stage-differentiated analysis yielded the following stage-salient genes: one stage-I gene (“FBN1”), one stage II specific gene (“FOXG1”), one stage III specific gene (“HCN1”) and four stage IV specific genes (“NELL1”, “ZNF135”, “FAM123A”, “LAMA1”), which could be used for stage-specific diagnosis. All the biomarkers were hypermethylated, indicating down-regulation and signifying a CpG island Methylator Phenotype (CIMP) manifestation. A prognostic signature consisting of FBN1 and FOXG1was significantly associated with patient survival (p-value < 0.01) and could be used as a biomarker panel for early-stage CRC prognosis.ConclusionOur workflow for stage-differentiated consensus analysis has yielded stage-salient diagnostic biomarkers as well as an early-stage prognostic biomarker panel. In addition, our studies have affirmed a novel CIMP-like signature in colorectal cancer, urging clinical validation.Supplementary InformationSupplementary information could be found at https://doi.org/10.6084/m9.figshare.13013852
Publisher
Cold Spring Harbor Laboratory