Visualization of cell interactions between Tregs and other cell types in the intestine from patients with Crohn's disease

• Grant number: 25/00092-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: March 01, 2025
• End date: February 28, 2026
• Field of knowledge: Biological Sciences - Immunology - Applied Immunology
• Principal Investigator: Raphael Sanches Peres
• Grantee: Maria Eduarda Monteiro Garcia
• Host Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated research grant: 23/17817-1 - Identification of cell interactions that affect regulatory T cells function in inflammatory bowel diseases, AP.JP

Abstract

Inflammatory bowel diseases (IBD), which include Crohn's disease (CD) and ulcerative colitis (UC), are a group of chronic inflammatory conditions that affect the gastrointestinal tract. Due to the lack of a better understanding of the molecular and cellular mechanisms involved in the pathogenesis of IBD, treatment remains a challenge for clinicians. Recently, single-cell RNA sequencing (scRNA-seq) has provided valuable insights into the composition and cellular heterogeneity of the gut and circulation in patients with IBD, identifying new cellular modules and gene signatures associated with resistance to anti-TNF, the first-line biologics used in IBD treatment. However, this characterization is limited in resolution to identify cellular populations found in low numbers/frequencies in tissue and circulation, such as subsets of regulatory T cells (Tregs). Furthermore, although this approach characterizes the diversity of cells present in the tissue at the single-cell level, it does not allow the determination of the tissue's spatial organization and how interactions between cells in the gut occur. To clarify these aspects, our research group will conduct spatial transcriptomics experiments, which, in addition to providing a complete transcriptome database with single-cell resolution, will also offer a characterization of how Tregs organize and interact with other cell types in the tissue. The data obtained from the spatial transcriptomics experiments will be explored and validated in our laboratory. The goal of this project is to validate the findings from the spatial transcriptomics experiments using immunofluorescence (IF) on intestinal biopsy samples from CD patients collected prospectively (before and after anti-TNF therapy). Simultaneously, in addition to IF in human samples, we will also perform IF labeling of the identified targets in colon sections of mice with colitis, treated or not with anti-TNF, that were subjected to the colitis model induced by transfer of naive T cells in Rag1-/- animals. The demonstration that cellular interactions identified in humans also occur in the experimental model will be essential to provide evidence for the development of new therapeutic intervention strategies through testing in experimental models of intestinal inflammation.