Identification of potential biomarkers and available drugs for oral squamous cell carcinoma
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ABSTRACT: Background
Oral squamous cell carcinoma (OSCC) is the most common oral tumor globally. However, optimal therapeutic targets for OSCC have not been identified. This study aimed to identify the potential gene markers and available drugs for OSCC. Methods
Two transcriptional datasets containing OSCC gene expression data (GSE30784 and GSE23558) were selected from the Gene Expression Omnibus database. The interactive web tool GEO2R was then used to analyze the differentially expressed genes (DEGs) analysis. A Venn diagram was used to integrate the DEGs screened out by the two microarrays. Subsequently, a protein-protein interaction (PPI) network analysis of DEGs was performed using the Cytoscape, Database for Annotation, Visualization and Intergrated Discovery, and STRING databases. In addition to constructing the PPI networks among these DEGs, we chose several significant gene modules to conduct further gene-drug interaction analyses. Lastly, the existing drugs that target these module genes were selected to explore their therapeutic efficacy in treating OSCC. Results
A total of 199 DEGs were screened out by the two microarrays. They were found to be associated with several processes, including the epoxygenase P450 pathway and the organelle membrane. The significant module genes in the PPI networks were CYP2E1, SCEL, KRT4, and KRT19. One existing drug, etoposide, which targets the CYP2E1 gene, was acquired. Conclusions
Four potential biomarkers (CYP2E1, SCEL, KRT4, and KRT19) and one existing drug (etoposide) were obtained for gene expression prediction through a series of bioinformatics methods.
SUBMITTER: Zhang Z
PROVIDER: S-EPMC8797665 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:IntroductionCircular RNAs (CircRNAs), an emerging non-coding RNA, have been demonstrated to be involved in tumorigenesis, metastasis, and cancer progression, and could represent novel potential biomarkers for diagnosing oral squamous cell carcinoma (OSCC). However, no meta-analysis has investigated the diagnostic role of circRNAs in OSCC. Hence, to investigate whether circRNAs could serve as specific biomarkers for OSCC, the present systematic review and meta-analysis evaluated the diagnostic efficiency of circRNAs in patients with OSCC.Materials and methodsA thorough search of online databases (Pubmed, Web of Science, Embase, and the Cochrane Library) was conducted to collect relevant studies up to March 30th, 2021. All eligible studies were case-control studies. The quality of each study was evaluated by the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool. STATA (version 15.1) and Review Manager (version 5.4) were employed to conduct the meta-analysis, and the PRISMA statement was adopted in this study.ResultsA total of 16 studies were included in the meta-analysis, with five studies on upregulated circRNAs, and 11 on downregulated circRNAs. The enrolled studies that met our eligibility criteria all derived from China. The pooled sensitivity (SEN), specificity (SPE), diagnostic odds ratio (DOR), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and the area under receiver operating characteristics curve (AUC) with the 95% confidence intervals (95% CIs) were 0.74 (0.69-0.79), 0.79 (0.73-0.84), 10.74 (7.81-14.77), 3.50 (2.78-4.45), 0.33 (0.27-0.39) and 0.83 (0.79-0.86), respectively. The subgroup analysis demonstrated that serum, plasma, and saliva specimens had a better diagnostic performance than tissue samples, with a high value of sensitivity, specificity, DOR, and AUC values. The results also showed that the subgroups of upregulated circRNAs and a sample size of ≥100 manifested higher specificity, DOR, and AUC for cancer detection than downregulated circRNAs and a sample size of < 100.ConclusionsA strong association was demonstrated between the dysregulated expression of circRNAs and the diagnosis of OSCC. Hence, circRNAs have the potential to function as promising biomarkers and therapeutic targets for OSCC.Systematic review registrationPROSPERO, number CRD42021256857.
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