Prognostic Significance of CLDN1, INHBA, and CXCL12 in Colon Adenocarcinoma: A Multi-Omics and Single-Cell Approach

Background/Objectives: Colon adenocarcinoma (COAD), the most prevalent form of colorectal cancer, remains a leading cause of cancer-related mortality. Advances in various treatments for COAD have significantly improved treatment outcomes. However, therapeutic limitations persist, highlighting the need for personalized strategies driven by novel biomarkers. The aim was to identify key hub genes that could be potential biomarkers of COAD using comprehensive bioinformatic analyses. Methods: Differentially expressed genes (DEGs) and co-DEGs were identified from COAD gene expression datasets. Functional enrichment analyses, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, were performed. Hub genes were extracted from protein–protein interaction (PPI) networks and validated epigenetically using microRNA (miRNA) and DNA methylation datasets. Their expression patterns were further examined via single-cell RNA sequencing (scRNA-seq) and immune cell infiltration analysis. Prognostic relevance was assessed based on tumor metastasis and survival outcomes. Results: Gene expression profiling identified 118 co-DEGs, with GO and KEGG pathway analyses revealing significant pathway enrichment. PPI network analysis pinpointed 27 key co-DEGs. Epigenetic profiling indicated that both miRNA interference and DNA methylation regulate CLDN1, INHBA, and CXCL12 expression levels. scRNA-seq analysis showed elevated CLDN1 expression in epithelial cells and INHBA in myeloid cells, and reduced CXCL12 expression in stromal cells. Prognostic analysis further demonstrated that CLDN1 and INHBA are significantly associated with poor COAD outcomes. Conclusions: We identified some potential prognostic biomarkers for patients with COAD. Further experimental validation is required to translate these findings into precision medicine for COAD.