Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis

Amir Shabeer; Sara Mustafa; Rimsha Sadia Bukhari; Mostafa A Abdel-Maksoud; Saeedah Musaed Almutairi; Wahidah H Al-Qahtani; Khushboo Chandio; Nazima Yousaf Khan; Jaweria Gul; Mohammed Aufy

Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis

Am J Cancer Res. 2023 Apr 15;13(4):1259-1277. eCollection 2023.

Affiliations

¹ Isra University Hyderabad Sindh, Pakistan.
² Tehsil Headquarter (THQ) Rojhan Rajanpur, Pakistan.
³ Fatima Jinnah Medical University Lahore, Pakistan.
⁴ Department of Botany and Microbiology, College of Science, King Saud University Riyadh P.O. 2455, Riyadh 11451, Saudi Arabia.
⁵ Department of Food Sciences & Nutrition, College of Food and Agricultural Sciences, King Saud University P.O. Box 270677, Riyadh 11352, Saudi Arabia.
⁶ Peoples Nursing School LUMHS Jamshoro, Pakistan.
⁷ Institute of Biochemistry, University of Balochistan Quetta, Pakistan.
⁸ Shaheed Benazir Bhutto University Sheringal, Dir Upper, Pakistan.
⁹ Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna Vienna, Austria.

PMID: 37168331
PMCID: PMC10164813

Abstract

Head and neck squamous cell carcinoma (HNSC) is one of the most lethal malignancies around the globe. Due to its complex nature, the diagnostic and prognostic signatures of HNSC remain poorly understood. This study was launched to identify signature genes and their signaling pathways related to the development of HNSC. In the current study, we retrieved the GSE53819 dataset from the Gene Expression Omnibus (GEO) database to determine the differentially expressed genes (DEGs) using the "Limma" R package. Adjusted P values P < 0.05 and |logFC| ≥ 1 were selected as the filtering conditions. To identify hub genes, the protein-protein interaction (PPI) network construction of the DEGs was performed using STRING. We further used UALCAN, GEPIA, OncoDB, GENT2, MEXPRESS, and HPA databases for the expression, validation, survival, and methylation analyses of the hub genes. The cBioPortal tool was used to investigate the genetic alterations in hub genes. CancerSEA, TIMER, DAVID, ENCORI, and DrugBank were also used to explore a few more hub gene-associated parameters. Lastly, HOK, FaDu, and SCC25 cell lines were used to validate hub gene expression via RNA sequencing (RNA-seq) technique. A total of top 250 DEGs were selected for detailed analysis in this study. From these DEGs, prognostic and diagnostic associated four hub genes, which could serve as potential molecular biomarkers and therapeutic targets in HNSC patients were identified. Four hub genes, including down-regulated DNAH1 and DNALI1, while up-regulated DNAH9 and CCDC151 were strongly implicated in HNSC. We also validated the same expression pattern of the hub genes using RNA-seq analysis in HNSC and normal cell lines. Moreover, this study also revealed some novel links between DNAH1, DNALI1, DNAH9, and CCDC151 expression and genetic alterations, promoter methylation status, immune cell infiltration, miRNAs, gene enrichment terms, and various chemotherapeutic drugs. In conclusion, we indicated four hub genes (DNAH1, DNALI1, DNAH9, and CCDC151) and their associated signaling pathways, which may improve our understanding of HNSC and could be used as new therapeutic targets.

Keywords: HNSC; biomarker; gene expression; therapeutic target.