Deciphering the link between membrane signaling and hub genes: bioinformatics prediction and experimental validation in colon cancer

Abstract

Abstract Visualization of complex topological assemblies and spatiotemporal epigenetic choreography of chromatin territory is emerging for better understanding gene expression. Colon cancer is one of the leading malignant neoplasms and there is still a paucity of information regarding colon cancer. Bioinformatics prediction and analyses helps to identify essential genes and significant pathways linked to the disease and to predict alternative strategies for curative measure. Colon cancer patient sample containing gene expression profile from three independent datasets, including GSE44076, GSE20916 and GSE37364 were downloaded from Gene Expression Omnibus (GEO) and thoroughly screened using the GEO2R tool and Funrich software to find out differentially expressed genes (DEGs) common from all three datasets. Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL-17 signaling pathway, Extracellular Matrix (ECM)-receptor interaction, Focal adhesion and PI3K-Akt pathway. Down-regulated genes are involved in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. After analyzing the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential gene hub related to ECM and presumably act as master regulators in colonic cancerogenesis. Moreover, our experimental data demonstrates that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA and protein level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. These may be considered as novel biomarkers and could be targeted for therapeutic intervention. This work proofs for the first time that there is connecting link between membrane signaling hub and gene hub.