Microbiome-specific T-cell dynamics in health and disease

The host immune system is continually trained by the intestinal microbiome leading to the generation of a functionally diverse pool of long-lived CD4⁺ T cells that enforce tolerance and support integrity of the intestinal epithelial barrier. However, loss of tolerance to the microbiome is accompanied by maladaptive diversification of the CD4⁺ T cell response in patients with inflammatory bowel disease (IBD) making it important to identify the mechanisms in play. Because there has been virtually no immunodominant epitopes characterized from commensals in the human intestinal microbiome, scientists have been unable to track and characterize the associated CD4⁺ T cell responses in the human setting.

We devised a strategy to systematically identify peptide epitopes encoded by prevalent commensals in the human microbiome and validated dozens of epitopes spanning numerous individual commensals that were recognized by human T cells. In healthy donors, the T cells responses showed intra- and interindividual heterogeneity likely involving multiple distinct T cell phenotypes. Focusing on a conserved and widely recognized epitope encoded by SusC in members of Bacteroidales, we characterized how the CD4⁺ T cell response to a common commensal shifts from an IL-10 dominant response in healthy subjects to IL-17A during disease flares in IBD patients with Crohn’s disease. Building on this we elucidated the functional capacity of respective tissue resident and lymphoid CD4⁺ T cells in mice to identify considerable functional plasticity at steady state across distinct anatomical environments.

Next, we surveyed the CD4⁺ T cell landscapes at different anatomical regions of the small intestine and colon across patients with acute and chronic intestinal diseases with distinct pathophysiological modes of action, thus allowing us to capture an array of inflammation-associated CD4+ T cell states and deeply characterize the capacity for functional plasticity. This revealed an unappreciated amount of functional plasticity across clonally expanded CD4⁺ T cells encoding identical TCRs, proving that intestinal CD4⁺ T cell responses of single specificities are subject to a high degree of functional diversification. Clonally expanded CD4⁺ T cells showed increased expression of key IBD risk genes previously reported to influence diversification of pathological CD4⁺ T cells. In the case of Crohn’s disease, we found an increased diversification of TCR clones toward Th1 phenotypes, supporting a link between pathways implicated by genetics and shifts in functional phenotypes during chronic inflammation. We identified a BACH2 expressing stem-like memory phenotype in Th1 cells that was depleted during chronic inflammation and validated it to distinguish SusC-specific CD4⁺ T cells across varying inflammation states. As in mice, human tissue-resident SusC-specific CD4⁺ T cells were capable of considerable functional diversification, highlighting the need to identify gene programs, like the one enforced by BACH2, that may repress pathological diversification.

Together, the work in this PhD thesis represents considerable progress in our ability to track and characterize dynamic changes of human microbiota-specific CD4⁺ T cell phenotypes and provide valuable insight into pathological mechanisms with direct relevance for therapeutic intervention.