Identification of hub genes involved in cisplatin resistance in head and neck cancer

• Published in: Journal of Genetic Engineering and Biotechnology Vol. 21; no. 1; pp. 9 - 17
• Main Authors: Chaudhary, Raushan Kumar, Khanal, Pukar, Mateti, Uday Venkat, Shastry, C. S., Shetty, Jayarama
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.12.2023; Springer; Springer Nature B.V; Elsevier
• Subjects: 5-Fluorouracil; Analysis; Anopheles; Antimitotic agents; Antineoplastic agents; Axl protein; bioinformatics; Biological activity; Biomedical Engineering and Bioengineering; biotechnology; Bortezomib; Cancer; Cancer therapies; Carboplatin; Chemotherapy; Cisplatin; Cisplatin-resistance; DNA repair; Doxorubicin; Drug discovery; Drug dosages; Drug resistance; drug therapy; Drug–gene interaction; Engineering; fluorouracil; Gemcitabine; Gene expression; Genes; Genetic aspects; genetic databases; Genomes; Head & neck cancer; Head and neck cancer; head and neck neoplasms; HNSCC; Hub genes; Human papillomavirus; humans; Imatinib; Methotrexate; Ontology; Overall survival; Paclitaxel; Pathogenesis; protein synthesis; Protein-protein interactions; Proteins; Survival; Survival analysis; survival rate; Uplift resistance; India; Hub genes; Protein–protein interactions; Cisplatin-resistance; HNSCC; Drug–gene interaction; Gene expression; Overall survival
• ISSN: 1687-157X; 2090-5920
• DOI: 10.1186/s43141-023-00468-y

Background Cisplatin resistance is one of the major contributors to the poor survival rate among head and neck cancer (HNC) patients. Focusing on the protein–protein interaction rather than a single protein could provide a better understanding of drug resistance. Thus, this study aimed to identify hub genes in a complex network of cisplatin resistance associated genes in HNC chemotherapy via a series of bioinformatic tools. Methods The genes involved in cisplatin resistance were retrieved from the NCBI gene database using “head and neck cancer” and “cisplatin resistance” as key words. The human genes retrieved were analyzed for their interactions and enriched using the STRING database. The interaction between KEGG pathways and genes was visualized in Cytoscape 3.7.2. Further, the hub gene was identified using the Cytohubba plugin of Cytoscape and validated using UALCAN and Human Protein Atlas database. Validated genes were investigated for the drug–gene interaction using the DGIbd database. Results Out of 137 genes obtained using key words, 133 were associated with cisplatin resistance in the human species. A total of 150 KEGG pathways, 82 cellular components, 123 molecular functions, and 1752 biological processes were modulated on enrichment analysis. Out of 37 hub genes, CCND1, AXL, CDKN2A, TERT, and EXH2 genes were found to have significant ( p  < 0.05) mRNA expression and effect on overall survival whereas protein expression was found to be positive for all the significant genes except TERT. Thus, they can be targeted with palbociclib, methotrexate, bortezomib and fluorouracil, sorafenib, dasatinib, carboplatin, paclitaxel, gemcitabine, imatinib, doxorubicin, and vorinostat. Conclusion As the pathogenesis of head and neck cancer is complex, targeting hub genes and associated pathways involved in cisplatin resistance could bring a milestone change in the drug discovery and management of drug resistance which might uplift overall survival among HNC patients.