Intangible Genetic Heterogeneity in Cancer Survival: New Insights based on DNA methylation

Colorectal cancer (CRC), the third most common cancerworldwide, is a group of diseases characterized by genetic and epigeneticchanges. Irregular gene-methylation alteration causes and advances CRC tumorgrowth. Detecting differentially methylated genes (DMGs) in CRC and patientsurvival time paves the way to early cancer detection and prognosis. However,CRC data including survival times are heterogeneous. Almost all studies tend toignore the heterogeneity of DMG effects on survival. Material & Methods: We employed a four-step data analysis process. Usingthe ۶ CRC and ۶ healthy male tissue samples, the DNA methylation read countsand read-depth for each CpG site captured by SureSelectXT Human Methyl-Seq.Approximately, ۶۸\% of the CpGs had missing data in at least one sample. ThenThe DMCHMM pipeline was utilized for identifying differentially methylatedcytosines (DMCs) in CRC vs. normal samples; results were aligned with thereference genome (hg۱۹) to obtain a list of DMGs. Candidate methylation profileswere extracted from GEO for the validation step, showcasing consistenthypo/hyper-methylation across different populations and platforms. Afterward aPPI network analysis was performed. Densely connected substructure modules weredetermined using the MCODE algorithm. Then, hub genes were selected as the DMGswith the highest correlation in the modules using cytoHubba. Finally, theeffects of DMGs and hub genes on the survival of patients were uncovered usingthe FMAFTR model to address sparsity and gene effects heterogeneity. Results: We identified ۳,۴۰۶ DMGs. Analysis of overlapped DMGswith several Gene Expression Omnibus datasets led to ۹۱۷ hypo- and ۶۵۴hyper-methylated DMGs. CRC pathways were revealed via gene ontology enrichment.Hub genes were selected based on Protein-Protein-Interaction network includingSEMA۷A, GATA۴, LHX۲, SOST, and CTLA۴, regulating the Wnt signaling pathway. Therelationship between identified DMGs/hub genes and patient survival timeuncovered a two-component mixture of AFT regression model. The genes NMNAT۲,ZFP۴۲, NPAS۲, MYLK۳, NUDT۱۳, KIRREL۳, and FKBP۶ and hub genes SOST, NFATC۱, andTLE۴ were associated with survival time in the most aggressive form of thedisease that can serve as potential diagnostic targets for early CRC detection. Conclusion: Our findings can provide insights into thedevelopment of potential therapeutic strategies for CRC.

کلیدواژه ها:

Colorectal Cancer# Human Genome ، Cancer Epigenetics ، Bisulfite Sequencing ، DNA Methylation