Identification of oral cancer related candidate genes by integrating protein-protein interactions, gene ontology, pathway analysis and immunohistochemistry

Abstract

In the recent years, bioinformatics methods have been reported with a high degree of success for candidate gene identification. In this milieu, we have used an integrated bioinformatics approach assimilating information from gene ontologies (GO), protein–protein interaction (PPI) and network analysis to predict candidate genes related to oral squamous cell carcinoma (OSCC). A total of 40973 PPIs were considered for 4704 cancer-related genes to construct human cancer gene network (HCGN). The importance of each node was measured in HCGN by ten different centrality measures. We have shown that the top ranking genes are related to a significantly higher number of diseases as compared to other genes in HCGN. A total of 39 candidate oral cancer target genes were predicted by combining top ranked genes and the genes corresponding to significantly enriched oral cancer related GO terms. Initial verification using literature and available experimental data indicated that 29 genes were related with OSCC. A detailed pathway analysis led us to propose a role for the selected candidate genes in the invasion and metastasis in OSCC. We further validated our predictions using immunohistochemistry (IHC) and found that the gene FLNA was upregulated while the genes ARRB1 and HTT were downregulated in the OSCC tissue samples.

Multiclass classification of autofluorescence images of oral cavity lesions based on quantitative analysis

“…The most common histology of oral cancer is squamous cell carcinoma [1]. In males, it is the most commonly found cancer in the head and neck, accounting for 90% of the 300,000 newly diagnosed oral malignancies every year [2]. According to Stewart [3], about 60% of the new oral cancer cases and 68% of the deaths associated with oral cancer are reported in Asia.…”

miR-146a Overexpression in Oral Squamous Cell Carcinoma Potentiates Cancer Cell Migration and Invasion Possibly via Targeting HTT

“…TRAF6, IRAK1, and SOX2 had been reported as a target gene of miR-146a in OSCC (17,19,20). miR-146a has specificity to target the HTT gene, and HTT plays a vital role in oral and breast cancer biology and many other cellular activities (23)(24)(25)(26). This study hypothesized that the miR-146a might target the HTT gene to regulate OSCC progression and metastasis.…”

“…HTT expression is downregulated in breast cancer and regulates cancer cell differentiation via the maintenance of tight junctions (23). HTT gene expression is downregulated in oral cancer tissues and is one of the candidate genes involved in oral cancer biology (24). Moreover, miR-125b, miR-146a, miR-150, and miR-214 target both human and mice HTT and regulate diverse cellular processes (25,26).…”

The Biological Properties and Potential Interacting Proteins of d-Alanyl-d-alanine Ligase A from Mycobacterium tuberculosis

“…Identifying protein interaction sites and uncovering the interaction mechanism is closely relevant in the drug development industry. In addition, unveiling of protein interaction partners allows biologists to construct protein interaction networks, which in turn facilitate the understanding of many biological and clinical observations [ 19 , 20 , 21 , 22 ]. The data in this study indicated that Tb -DdlA could not maintain its activity long in vitro under the conditions tested, which might be attributable to its synergistic effect with potential interacting proteins that stabilized its activity in vivo.…”