ECCO Grant Study Synopsis: Petra Bacher

Petra Bacher, ECCO Grant Awardee

The immune repertoire of microbe-reactive T cells in blood and tissue of IBD patients


Petra Bacher
Petra Bacher

Aim of Research

Dysregulated T cell reactions against intestinal antigens are considered to be a causal or driving factor for Inflammatory Bowel Diseases (IBD). So far, technical limitations concerning the detection and characterisation of microbiota-reactive T cells have prevented determination of the exact contribution of specific T cell subsets against individual microbes to the intestinal balance and its dysregulation in IBD. Analysing the phenotype, function and T cell receptor (TCR) repertoire of microbe-specific T cells in blood and intestinal mucosa of IBD patients will therefore provide important insights to fundamental questions on the clonal expansion of pro- and anti-inflammatory microbe-reactive T cells, their clonal relation and stability and the sites (blood and/ or intestinal tissue) at which the relevant T cell subsets are located.


We have established a unique, powerful and versatile technology, antigen-reactive T cell enrichment (ARTE) that allows unbiased identification and characterisation of human antigen-specific conventional (Tcon) and regulatory (Treg) CD4+ T cell responses against microbial antigens directly ex vivo in human blood or tissues [1, 2]. Using this technology, we isolate T cells specific for defined intestinal microbes from paired human blood and intestinal tissue samples of IBD patients. QQQQWe will characterise the microbe-specific T cells using the latest high-throughput RNA sequencing technologies, which will provide transcriptomic data and TCR sequences of the different microbe-specific Tcon and Treg populations on a single cell level. The comparison with tissue from colorectal cancer control patients will allow definition of common characteristics of microbe-specific T cell responses and specific alterations in IBD patients.

Proposed timing

Since the start of the project, all relevant technologies for the isolation and analysis of the microbe-specific T cells have been established, so we expect immediate results from the single cell analyses. Overall, our project aims to provide basic and central knowledge about microbe-reactive CD4+ T cell responses, which is a prerequisite for the development of new diagnostic parameters and targeted therapeutic interventions for IBD patients.


      1. Bacher P, Hohnstein T, Beerbaum E, et al. Human Anti-fungal Th17 Immunity and Pathology Rely on Cross-Reactivity against Candida albicans. Cell. 2019; 176(6):1340-1355.

      2. Bacher P, Heinrich F, Stervbo U et al. Regulatory T Cell Specificity Directs Tolerance versus Allergy against Aeroantigens in Humans. Cell. 2016;167(4):1067-1078.

Posted in ECCO News, SciCom, Committee News, Fellowships & Grants Synopsis Reports, Volume 14, Issue 4