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Identification of candidate target genes of oral squamous cell carcinoma using high-throughput RNA-Seq data and in
Unnati Soni1, Anirudh Singh1, Ramendra Soni2
1Department of Applied Sciences, Indian Institute of Information Technology, Prayagraj, India.
Abstract:
Oral Squamous Cell Carcinoma (OSCC) accounts for more than 90% of all kinds of oral neoplasms that develop in the oral cavity. It is a type of malignancy that shows high morbidity and recurrence rate, but data on the disease's target genes and biomarkers is still insufficient. In this study, in silico studies have been performed to find out the novel target genes and their potential therapeutic inhibitors for the effective and efficient treatment of OSCC. The DESeq2 package of RStudio was used in the current investigation to screen and identify differentially expressed genes for OSCC. As a result of gene expression analysis, the top 10 novel genes were identified using the Cytohubba plugin of Cytoscape, and among them, the ubiquitin-conjugating enzyme (UBE2D1) was found to be upregulated and playing a significant role in the progression of human oral cancers. Following this, naturally occurring compounds were virtually evaluated and simulated against the discovered novel target as prospective drugs utilizing the Maestro, Schrodinger, and Gromacs software. In a simulated screening of naturally occurring potential inhibitors against the novel target UBE2D1, Epigallocatechin 3-gallate, Quercetin, Luteoline, Curcumin, and Baicalein were identified as potent inhibitors. Novel identified gene UBE2D1 has a significant role in the proliferation of human cancers through suppression of 'guardian of genome' p53 via ubiquitination dependent pathway. Therefore, the treatment of OSCC may benefit significantly from targeting this gene and its discovered naturally occurring inhibitors.Communicated by Ramaswamy H. Sarma.
Insights
Researchers identified UBE2D1 as a key gene in oral squamous cell carcinoma (OSCC) progression. Naturally occurring compounds like EGCG and Quercetin show promise as inhibitors for potential OSCC treatment.
Area of Science:
- Oncology
- Bioinformatics
- Drug Discovery
Background:
- Oral Squamous Cell Carcinoma (OSCC) is a prevalent malignancy with high recurrence rates.
- Insufficient data exists on OSCC's specific target genes and biomarkers.
- Novel therapeutic strategies are needed for effective OSCC treatment.
Purpose of the Study:
- To identify novel target genes and potential therapeutic inhibitors for OSCC using *in silico* methods.
- To investigate the role of identified genes in oral cancer progression.
- To screen natural compounds as potential inhibitors for therapeutic targets.
Main Methods:
- Differential gene expression analysis using DESeq2 in RStudio.
- Identification of key genes using Cytohubba plugin in Cytoscape.
- Virtual screening and molecular simulation of natural compounds against UBE2D1 using Maestro, Schrodinger, and Gromacs software.
Main Results:
- UBE2D1 was identified as a significantly upregulated gene in OSCC.
- UBE2D1 promotes oral cancer proliferation by suppressing p53 via ubiquitination.
- Epigallocatechin 3-gallate, Quercetin, Luteoline, Curcumin, and Baicalein were identified as potent inhibitors of UBE2D1.
Conclusions:
- Targeting the UBE2D1 gene presents a promising therapeutic strategy for OSCC.
- Naturally occurring compounds identified show potential as novel drugs for OSCC treatment.
- Further research into UBE2D1 and its inhibitors could lead to improved OSCC therapies.
