Targeting intestinal yeasts and pathogenic yeast-responsive CD4+ T cells in Crohn’s disease

Introduction

The interaction of lifestyle and environmental factors with the well-studied predisposing genetic susceptibility is thought to trigger inflammatory bowel diseases (IBDs), including Crohn’s disease (CD) and ulcerative colitis (UC). Due to its mere size, its prominent presence at the inflamed intestinal sites, and its metabolic and immunological importance, the gut microbiome has been identified as a major disease-relevant intermediate phenotype and a potential driving factor of IBD development and its clinical course. It is assumed that dysregulated or inappropriate T cell reactions against otherwise harmless members of the microbiome play a central role for disease pathogenesis and/or chronification. However, it is still not understood which microbial species are targets of pathogenic T cell reactions in IBD. So far, microbiome studies mainly focused on bacterial changes in the gut microbiome. However, besides bacteria, alterations in the mycobiome, the fungal gut microbiome, are also associated with the pathogenesis of IBDs.

In the first funding phase of miTarget, we identified common gut commensal and food-derived yeasts as direct activators of CD4⁺ T cell responses in patients with CD and high-risk first-degree relatives (FDRs) of IBD patients from the KINDRED cohort (Martini et al. Nat Med 2023; see biobank popgen for more details on the cohort). Specifically, we detected CD4⁺ T cell reactivity to less represented fungal commensals and food-derived species in a subgroup of CD patients (ASCA⁺ patients, i.e., those with high levels of anti-Saccharomyces cerevisiae antibodies, Figure 1A). Single-cell RNA sequencing of T cell receptors (TCRs) revealed a strong expansion of clonotypes in CD patients that were shared between the T cell repertoires against C. albicans, C. tropicalis and S. cerevisiae species (Figure 1B). Our analyses suggest that increased T cell reactivity in patients with CD may also be driven by food-derived live fungi, particularly found in mold-ripened cheeses such as camembert and gorgonzola (Figure 1C).

Aims

We will perform standardized metagenomic analyses of biosamples from different time points and analyze potential disease-associated alterations of the T cell reaction against candidate microbes from members of our KINDRED (family) cohort for IBD (see Biobank Popgen for more details on the cohort).

We here aim:

• to determine disease-associated yeast-responsive public TCRs motifs,
• to resolve fungal strain variability and antibodies against fungi in healthy humans and IBD patients,
• to identify cross-recognized yeast-derived proteins and peptides,
• to discern the effect of a short-term yeast-reduction diet on yeast-responsive Th1-CTLs, and
  to define alterations of the non-bacterial microbiome in IBD patients and their first-degree relatives.
  
  

Outlook

This project holds the potential to define the exact TCRs of pathogenic CD4⁺ T cells in patients with CD, the epitopes recognized by these TCRs, the relevant fungal strains, and their origin. These findings will lay the foundation for using yeast-responsive TCRs as potential disease biomarkers or therapeutic targets, such as through T cell depletion strategies or antigen-specific Treg therapy. Additionally, we aim to present proof-of-concept data on the effect of a short-term yeast-reduction diet on pathogenic T cell responses and on its potential clinical efficacy in ASCA⁺ CD patients. Based on the results obtained, we aim to expand our research into a clinical trial assessing the effect of a yeast-free dietary intervention in larger patient cohorts and explore targeted therapeutic approaches against the pathogenic TCRs and associated microbes.