Differential Gene Expression Analysis and Biomarker Identification for Colorectal Cancer

Abstract

Background: Colorectal cancer is a multifaceted disease with complex molecular mechanisms influencing its onset and progression. CRC has been observed to exhibit familial clustering patterns since the early 1900s. Like the majority of cancers, colorectal cancer can develop as a result of mutations in specific genes. Aim: The study aims to identify target biomarkers for colorectal cancer. Methodology: In this study, an integrated approach was undertaken to elucidate the gene expression patterns and molecular interactions associated with colorectal cancer (CRC) progression. The study was conducted at the Department of Bioinformatics, Stella Maris College, Chennai, Tamil Nadu, India. Between November 2023 and March 2024. Differential Gene expression analysis was carried out across different stages of colon adenocarcinoma. This was followed by Gene ontology analysis, Pathway enrichment analysis, Protein interaction network analysis, Biomarker screening and Molecular Docking. Results: Gene expression profiling revealed differential expression of key genes (CXCL1, CXCL2, CXCL3, COL1A1, COL1A2) across different stages of colon adenocarcinoma. Notably, early-stage samples exhibited elevated expression of CXCL genes, while MMP1 and MMP3 were upregulated in advanced stages. Gene Ontology analysis highlighted enrichment in processes related to extracellular matrix organization and proteolysis. Prognostic biomarkers, neurotransmitters, neuropeptides, and intracellular signaling pathways were identified for the CRC survival prediction. Protein-protein interaction network analysis identified key modules, unveiling protein clusters for further investigation. Molecular docking analysis targeting CRC-associated proteins CXCL2 and CXCL3 identified potential therapeutic compounds with high affinity, including Isorhamnetin, Kaempferol, Jaranol, Curcumin, Epigallocatechin gallate, Hesperidin, Resveratrol, Liquiritin, and Baicalin. Conclusion: This comprehensive analysis provided valuable insights into the molecular landscape of CRC, identifying potential therapeutic targets and prognostic markers for precision medicine strategies in CRC management.