Transcriptomic analysis of esophageal cancer reveals hub genes and networks involved in cancer progression

• Published in: Computers in biology and medicine 2023-06, Vol.159, p.106944-106944, Article 106944
• Main Authors: Chatterjee, Dipankor, Rahman, Md Mostafijur, Saha, Anik Kumar, Siam, Mohammad Kawsar Sharif, Sharif Shohan, Mohammad Umer
• Format: Article
• Language: English
• Subjects: Acetyltransferase; Algorithms; Biomarkers; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Cancer; Cancer screening; Cancer therapies; Carcinogens; Cdc25B phosphatase; Cell division; Computational Biology; Datasets; Differentially expressed genes; Epithelial cells; Epithelium; Esophageal cancer; Esophageal carcinoma; Esophageal Neoplasms - genetics; Esophagus; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Gene ontology; Gene Regulatory Networks; Genes; Genomes; Hub genes; Humans; Immune system; Infiltration; Lysine; Medical prognosis; Network analysis; Ontology; Open source software; Protein Interaction Maps - genetics; Protein-protein interaction; Proteins; Sample size; Screening; Surgery; Survival; Survival analysis; Transcriptome - genetics; Transcriptomics
• ISSN: 0010-4825; 1879-0534
• DOI: 10.1016/j.compbiomed.2023.106944

Esophageal carcinoma (ESCA) has a 5-year survival rate of fewer than 20%. The study aimed to identify new predictive biomarkers for ESCA through transcriptomics meta-analysis to address the problems of ineffective cancer therapy, lack of efficient diagnostic tools, and costly screening and contribute to developing more efficient cancer screening and treatments by identifying new marker genes. Nine GEO datasets of three kinds of esophageal carcinoma were analyzed, and 20 differentially expressed genes were detected in carcinogenic pathways. Network analysis revealed four hub genes, namely RAR Related Orphan Receptor A (RORA), lysine acetyltransferase 2B (KAT2B), Cell Division Cycle 25B (CDC25B), and Epithelial Cell Transforming 2 (ECT2). Overexpression of RORA, KAT2B, and ECT2 was identified with a bad prognosis. These hub genes modulate immune cell infiltration. These hub genes modulate immune cell infiltration. Although this research needs lab confirmation, we found interesting biomarkers in ESCA that may aid in diagnosis and treatment. •The study was conducted using computational analysis to learn more about the molecular mechanism of esophageal cancer.•A wide range of datasets, including both Microarray and RNAseq, was considered to discover potential biomarkers.•Following extensive analysis, 4 hub genes were discovered that can be studied for the proper therapeutic measure.•Involvement of the hub genes with other cancer types and their regulatory networks were observed.•This research will help determine how common medical conditions affect health and develop esophageal cancer.