Salivaomics: searching for biomarkers in Crohn's disease and ulcerative colitis

• Grant number: 25/24520-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: March 01, 2026
• End date: February 28, 2030
• Field of knowledge: Health Sciences - Dentistry
• Principal Investigator: Ana Carolina Magalhães
• Grantee: Karina Oliveira Santos
• Host Institution: Faculdade de Odontologia de Bauru (FOB). Universidade de São Paulo (USP). Bauru , SP, Brazil

Abstract

Inflammatory bowel diseases (IBD), as Crohn's disease (CD) and ulcerative colitis (UC), are chronic conditions whose diagnosis and monitoring may depend on invasive and costly methods, such as colonoscopies. In this context, saliva emerges as a promising non-invasive alternative capable of reflecting inflammatory and systemic changes. This project aims to characterize the salivary molecular profile of patients with CD and UC through an integrated multi-omic approach, including proteomics, metabolomics, and oral microbiome analysis. Part 01: This step aims to develop a systematic review with meta-analysis to integrate existing evidence on biomarkers in omic analyses (proteomic, metabolomic, genomic, and microbiome) related to IBD in different types of biological samples (saliva, blood, and feces). The review will follow the PRISMA-P guidelines and will include classical and network meta-analyses, using bioinformatics tools to map interactions between molecules, genes, proteins, and metabolites. Part 02: Twenty patients with IBD (10 with CD and 10 with UC, in clinical remission) and 20 healthy controls, matched for age and gender, will be recruited. Salivary proteomic analysis will seek to identify differentially regulated proteins between groups, exploring their diagnostic potential. The results of this stage will serve as an initial screening of salivary biomarkers specific to each IBD subtype.Part 03: 160 individuals will be included (80 patients with IBD and 80 controls). In this phase, saliva and stool samples will be analyzed, measuring calprotectin, and saliva and blood for C-reactive protein (CRP), IL-1¿, IL-6, TNF-¿, IL-10 e TGF-¿ by ELISA assays. The objective is to evaluate the correlation between salivary and systemic biomarkers and their ability to reflect the different degrees of CD and UC activity (remission, mild, moderate, and severe). This analysis will validate saliva as a reliable alternative fluid for clinical monitoring.Part 04: Twelve naïve patients (six with CD and six with UC) will be followed before and after the start of advanced therapy (anti-TNF). The proteomic profile of saliva and blood, and the microbiome of saliva and feces, will be analyzed at two time points (pre- and post-treatment -12 months) using mass spectrometry and 16s rRNA sequencing. Bioinformatics analyses will integrate omic data with clinical outcomes, seeking to identify molecules and/or microorganisms associated with therapeutic response.Multi-omic integration is expected to identify specific salivary biomarkers capable of distinguishing CD and UC, reflecting inflammatory activity and predicting therapeutic responses. These findings may contribute to the development of non-invasive and personalized strategies for the diagnosis and monitoring of IBD, with a direct impact on clinical practice and patients' quality of life. (AU)