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

Dipankor Chatterjee; Md Mostafijur Rahman; Anik Kumar Saha; Mohammad Kawsar Sharif Siam; Mohammad Umer Sharif Shohan

doi:10.1016/j.compbiomed.2023.106944

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

Comput Biol Med. 2023 Jun:159:106944. doi: 10.1016/j.compbiomed.2023.106944. Epub 2023 Apr 15.

Authors

Dipankor Chatterjee¹, Md Mostafijur Rahman², Anik Kumar Saha³, Mohammad Kawsar Sharif Siam⁴, Mohammad Umer Sharif Shohan⁵

Affiliations

¹ Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh.
² Department of Microbiology, Jashore University of Science and Technology, Bangladesh.
³ Institute of Food Science and Technology, Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
⁴ Department of Pharmacy, Brac University, Dhaka, Bangladesh.
⁵ Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh. Electronic address: msharifshohan@du.ac.bd.

PMID: 37075603
DOI: 10.1016/j.compbiomed.2023.106944

Abstract

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.

Keywords: Biomarkers; Differentially expressed genes; Esophageal carcinoma; Gene ontology; Hub genes; Protein-protein interaction.

Publication types

Meta-Analysis

MeSH terms

Biomarkers, Tumor / genetics
Biomarkers, Tumor / metabolism
Computational Biology
Esophageal Neoplasms* / genetics
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Humans
Protein Interaction Maps / genetics
Transcriptome* / genetics

Substances

Biomarkers, Tumor