Bioinformatics Analysis of Oral Squamous Cell Carcinomas and Their Interaction to Identify Molecular Signatures

• Published in: Artificial Intelligence pp. 155 - 169
• Main Authors: Sarker, Bandhan, Rahaman, Md. Matiur, Khan, Suman, Sinha, Jayashri Deb, Barman, Subhabrata
• Format: Book Chapter
• Language: English
• Published: Cham Springer Nature Switzerland
• Series: Communications in Computer and Information Science
• Subjects: Differentially expressed genes (DEGs); Drug discovery; Hub-genes; miRNA; Oral squamous cell carcinomas (OSCC); Transcription factors (TFs)
• ISBN: 9783031224843; 3031224841
• ISSN: 1865-0929; 1865-0937
• DOI: 10.1007/978-3-031-22485-0_15

Squamous epithelium is the origin of solid tumor oral squamous cell carcinoma (OSCC). Every year, nearly 400,000 OSCC patients are added to the cancer database. Presently, chemo-radiotherapy is the main important adjuvant treatment for OSCC; nevertheless, clinical resistance (drug resistance) to chemotherapy still leads to a poor prognosis of OSCC patients. Identification of potential genes and drugs might be a significant lead for the analyses of OSCC research. We aimed to identify molecular signatures for the diagnosis of OSCC patients. Statistical methods (ANOVA, limma and SAM) were used to identify differentially expressed genes (DEGs) from two datasets GSE111585 and GSE115119. Considering the cutoff values less than 0.05 and |log FC| greater than 1, we obtained 27 up-regulated and 25 down-regulated common DEGs. Protein-protein interaction (PPI) network determined hub genes (AR, ETS1, MET, PDGFB and VAV3) using STRING database. Other biomolecules: Reporter transcription factors (HIF1A, MYC, FOXP3, E2F4, WT1, PURA, ZEB1 and USF2), microRNAs (hsa-miR-589-3p, hsa-miR-155-5p and hsa-miR-301b-3p) associated with hub-genes were determined. For the hub genes, we also performed GO and KEGG enrichment analysis. We constructed gene-drug interaction using the DGIdb database and identify targeted drugs (IMATINIB, BROMOCRIPTINE, NIFEDIPINE, PIRETANIDE and TRIAMTERENE) for OSCC. Our study suggested that the biomarkers (hub-genes, TFs and miRNAs) and the discovered drugs might be a therapeutic target of OSCC.