Network analysis of differentially expressed genes involved in oral submucous fibrosis and oral squamous cell carcinoma: a comparative approach

Prerna Srivastava; Arpita Rai; Manish Kumar

doi:10.1016/j.oooo.2024.12.016

Network analysis of differentially expressed genes involved in oral submucous fibrosis and oral squamous cell carcinoma: a comparative approach

Oral Surg Oral Med Oral Pathol Oral Radiol. 2024 Dec 19:S2212-4403(24)00949-0. doi: 10.1016/j.oooo.2024.12.016. Online ahead of print.

Authors

Prerna Srivastava¹, Arpita Rai², Manish Kumar³

Affiliations

¹ Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
² Dental Institute, Rajendra Institute of Medical Sciences, Ranchi, Jharkhand, India.
³ Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India. Electronic address: manish@bitmesra.ac.in.

PMID: 39779388
DOI: 10.1016/j.oooo.2024.12.016

Abstract

Objective: Oral submucous fibrosis (OSMF) is categorized as an oral potentially malignant disorder (OPMD) with an increased risk of occurrence of oral squamous cell carcinoma (OSCC). In this study, we aimed to identify the hub genes associated with OSMF and OSCC.

Study design: Using RStudio, a set of differentially expressed genes (DEGs) were identified in (A) OSMF, (B) OSCC, and (C) comparative OSMF-OSCC category, obtained from Gene Expression Omnibus (GEO). The Protein to Protein Interaction (PPI) Network, hub genes, and functional annotation were determined using Search Tool for the Retrieval of Interacting Genes (STRING), Cytoscape, and SR-Plot, Database for Annotation, Visualization and Integrated Discovery (DAVID).

Results: A total of 2081, 2320, and 3295 DEGs were obtained from the OSMF, OSCC, and comparative categories, respectively. Hub gene and gene enrichment analysis revealed that the genes in (A) MYH6, TTN, TNNT3, MYL1, TPM2, ACTN3, NEB, MYL2, TNNT1, and TPM1; (B) CD4, SELL, CD28, CD27, PRF1, CD80, GZMB, CD40LG, ITGAX, and IL4; and (C) CD4, CD8A, CTLA4, CD28, GZMB, IL79, CD69, CD40LG, IFNG, and CD80 categories, were associated with muscle contraction, cell proliferation, and malignant transformation.

Conclusions: Hub genes and functional enrichment analysis revealed the diagnostic genes and the genes responsible for the malignant transformation in OSMF, OSCC, and the comparative category. A panel of identified genes will be of clinical significance in targeted therapy in future studies. (Oral Surg Oral Med Oral Pathol Oral Radiol YEAR;VOL:page range).