Integration of proteomic data obtained from the saliva of children with caries through bioinformatic analysis

Abstract

Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and experiment; bioinformatics is essential to analyze proteomic data. Objective: This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors. Dental caries can affect the expression of salivary proteins. Proteomics allows us to analyze and identify many proteins in a single sample and a single experiment; bioinformatics is essential to analyze proteomic data. We extracted proteins from a bibliographic search in the Scopus and PubMed databases. We analyzed these proteins with the web application ShinyGO v0.76, ToppGene and NetworkAnalyst 3.0, and the Cytoscape platform. This research aims to identify and integrate the main differentially expressed proteins in the saliva of children with caries, infer their Gene Ontology and interactions, and identify regulatory factors. In the literature search, we extracted 26 differentially expressed proteins. These proteins show enrichment in antioxidant activity, antimicrobial response, immune response, and vitamin and mineral metabolism. We found three transcription factors that regulate most of the genes of these proteins: TFDP1, SOX13, and BCL6. We also identified three microRNAs that highly restrict the expression of these proteins: hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p. On the other hand, the main drugs associated with these proteins are potassium persulfate, aluminum, and cadmium. The differentially expressed proteins in the saliva of children with dental caries are involved in metabolic pathways related to folate, selenium, and vitamin B12 metabolism. In addition, some transcription factors (TFDP1, SOX13, and BCL6) miRNAs (hsa-mir-124-3p, hsa-mir-27a-3p, and hsa-mir-26b-5p) and chemical compounds (potassium persulfate, aluminum, and cadmium) can regulate the genes, mRNAs or proteins studied. The differentially expressed proteins in the saliva of children with dental caries reflect the cariogenic state of the patients and the immune system's response to combat this condition. These proteins participate in numerous important interactions, and transcription factors, microRNAs, and drugs can regulate their expression. None