Illuminating the Role of Wound Healing-Related Hub Genes in Colorectal Adenocarcinoma: Molecular Mechanisms, Prognostic Implications, and Therapeutic Potential

Background: Colorectal adenocarcinoma [COAD] is a prevalent and lethal form of cancer. Understanding the molecular mechanisms underlying COAD progression is crucial for developing effective diagnostic and therapeutic strategies.

Methods: This study aims to explore wound healing-related genes in COAD and their potential roles in tumorigenesis and prognosis using in silico and in vitro methodology.

Results: A set of 70 genes associated with the "wound healing" term ere extracted from the Gene Ontology [GO] database [GO:0042060] and a protein-protein interaction [PPI] network was constructed using the STRING database. The PPI network was analyzed with the CytoHubba plugin in Cytoscape, identifying four major hub genes: MMP2, FN1, NF1, and PTK7. We then analyzed the expression of these hub genes across 16 COAD cell lines and nine normal colon cell lines using RT-qPCR, finding significant overexpression in COAD cell lines. ROC curve analysis confirmed the diagnostic potential of these genes, with MMP2, FN1, and NF1 showing high AUC values. Expression validation using the TCGA COAD cohort, OncoDB, and HPA databases corroborated these findings, highlighting the overexpression and high protein levels of these genes in COAD. Promoter methylation analysis indicated lower methylation levels in COAD samples, suggesting dysregulation through epigenetic mechanisms. Genetic alteration analysis via cBioPortal revealed a spectrum of mutations, with FN1 being the most frequently mutated. Prognostic analysis using a KM plotter showed that high expression of the hub genes is associated with poorer overall survival [OS] and disease-free survival [DFS]. Functional state correlations via CancerSEA suggested that these genes promote cell cycle, proliferation, metastasis, and stemness in COAD. Expression analysis in immune cells and drug sensitivity analyses highlighted the roles of MMP2, FN1, and NF1 in macrophages and drug resistance. A miRNA-mRNA network constructed using miRNet identified hsa-miR-200a-3p as a central regulator. Finally, functional assays in HCT116 cells demonstrated that knockdown of MMP2 and FN1 reduced proliferation, colony formation, and wound healing, suggesting these genes as potential therapeutic targets in COAD.

Conclusion: In conclusion, our study identifies MMP2, FN1, NF1, and PTK7 as key wound healing-related hub genes in COAD.