Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression

Abstract

Background Aberrant DNA methylation acts epigenetically to skew the gene transcription rate up or down, contributing to cancer etiology. A gap in our understanding concerns the epigenomics of stagewise cancer progression. In this study, we have developed a comprehensive computational framework for the stage-differentiated modelling of DNA methylation landscapes in colorectal cancer (CRC). Methods The methylation β-matrix was derived from the public-domain TCGA data, converted into M-value matrix, annotated with AJCC stages, and analysed for stage-salient genes using an ensemble of approaches involving stage-differentiated modelling of methylation patterns and/or expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against controls (adjusted p-value <0.001 and |log fold-change of M-value| >2), and then filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-salient DMGs. These were then subjected to a consensus analysis, followed by matching with clinical data and performing Kaplan–Meier survival analysis to evaluate the impact of methylation patterns of consensus stage-salient biomarkers on disease prognosis. Results We found significant genome-wide changes in methylation patterns in cancer cases relative to controls agnostic of stage. The stage-differentiated models yielded the following consensus salient genes: one stage-I gene (FBN1), one stage-II gene (FOXG1), one stage-III gene (HCN1) and four stage-IV genes (NELL1, ZNF135, FAM123A, LAMA1). All the biomarkers were significantly hypermethylated in the promoter regions, indicating down-regulation of expression and implying a putative CpG island Methylator Phenotype (CIMP) manifestation. A prognostic signature consisting of FBN1 and FOXG1 survived all the analytical filters, and represents a novel early-stage epigenetic biomarker / target. Conclusions We have designed and executed a workflow for stage-differentiated epigenomic analysis of colorectal cancer progression, and identified several stage-salient diagnostic biomarkers, and an early-stage prognostic biomarker panel. The study has led to the discovery of an alternative CIMP-like signature in colorectal cancer, reinforcing the role of CIMP drivers in tumor pathophysiology.

Low Expression of AGPAT5 Is Associated With Clinical Stage and Poor Prognosis in Colorectal Cancer and Contributes to Tumour Progression

“…A previous study have identified that DYNC1H1, GRIN2A, and GRM1 as new driving genes for CRC stage II progression, IGF1R, CPS1, SPTA1, and DSP as new hub driving genes for CRC stage III progress, and GSK3B, GGT1, and EIF2B5 as new hub driving genes for CRC stage IV. 32 Sangeetha Muthamilselvan et al 33 found that FBN1 as a stage I-salient hyper methylated gene, FOXG1 as a stage II-salient hyper methylated gene, HCN1 as stage III-salient hyper methylated gene, and NELL1, ZNF135, FAM123A, LAMA1 as stage IV-salient hyper methylated genes, which would drive the progression of CRC. Ashok Palaniappan and Sarathi 34 reported that CRLF1, CALB2 as stage I-specific differentially expressed genes (DEGs), GREM2, ADCY5, PLAC2, and DMRT3 as stage II-specific DEGs, PIGR and SLC26A9 as stage III-specific DEGs, and GABRD, DLX3, CST6, and HOTAIR as stage IV-specific DEGs, which were identified as progression-significant biomarkers.…”

COADREADx: A comprehensive algorithmic dissection unravels salient biomarkers and actionable insights into the discrete progression of colorectal cancer

“…Comparing the transcriptomic stage-specific patterns of colorectal cancer samples identified here with their methylomic stage-specific patterns [53], we uncovered interesting connections. Some of the stage-salient genes here were also identified as stage-specific differentially methylated genes, namely: BAI3, TPM2, ZSCAN18, ZNF415 (Stage-I); PLAC2, DMRT3 (Stage-II); PIGR, TUBAL3 (Stage-III); and CST6 (Stage-IV).…”

Analyzing aberrant DNA methylation in colorectal cancer uncovered intangible heterogeneity of gene effects in the survival time of patients

“…Moreover, several studies indicate stage-specific 51 and age-specific 52 effects of DNA methylation in certain genes on the survival outcomes of CRC patients. These results clearly suggest heterogeneity in the overall survival time of patients with CRC.…”