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  • Bioinformatics analysis of potential core genes for Esophageal squamous cell carcinoma

  • Sahar Shabani Panbeh Choleh,1,*
    1. Department of Cell and Molecular Biology, Shahid Beheshti University, Tehran, Iran


  • Introduction: Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy with a 5 year survival rate below 20%, underscoring an urgent need for robust molecular biomarkers and therapeutic targets. This study aimed to identify potential core genes and molecular signatures in ESCC through an integrative bioinformatics approach.
  • Methods: Four independent GEO microarray datasets (GSE23400, GSE29001, GSE44021, and GSE20347) were analyzed to identify differentially expressed genes (DEGs) between ESCC and normal esophageal tissues using GEO2R (adjusted P < 0.05, |logFC| ≥ 2). Overlapping DEGs were subjected to functional enrichment analysis via Enrichr (GO, KEGG, Reactome). A protein protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape, followed by hub gene identification using the CytoHubba MCC algorithm. Prognostic significance was evaluated through survival analysis using GEPIA2 based on the TCGA ESCA cohort.
  • Results: A total of 41 overlapping DEGs (11 up regulated, 30 down regulated) were consistently identified across all four datasets. Enrichment analysis revealed a striking functional dichotomy: up regulated genes were predominantly involved in extracellular matrix (ECM) remodeling and proteolysis (MMP1, MMP10, POSTN, COL1A2, COL11A1), while down regulated genes were primarily associated with epithelial differentiation and cornified envelope formation (FLG, KRT4, TGM3, SPINK5, SCEL, CRNN). The PPI network comprised 30 nodes and 150 edges, from which 10 hub genes were selected (KRT4, FLG, CRNN, POSTN, COL1A2, SPINK5, TGM3, SCEL, MMP1, COL11A1). Survival analysis revealed that none of the hub genes showed significant correlation with overall survival (Logrank P > 0.05 for all), suggesting their primary role in early tumorigenesis and local invasion rather than late stage progression.
  • Conclusion: Our integrative analysis uncovered a robust 10‑gene signature capturing a fundamental biological dichotomy in ESCC, specifically ECM remodeling versus loss of epithelial differentiation. Despite the lack of prognostic value, these hub genes represent compelling candidates for early diagnostic biomarkers and therapeutic targets. The discordance between network centrality and survival outcome highlights the critical distinction between "drivers" and "prognosticators" in cancer biology. This provides a strong rationale for future functional and translational studies.
  • Keywords: Esophageal squamous cell carcinoma; bioinformatics; differentially expressed genes; protein protein

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