Periodic Reporting for period 1 - MicroT (Microbiota-T cell interactions - antigen-specificity and regulation in health and disease)
Reporting period: 2022-07-01 to 2024-12-31
The composition of the microorganisms that live in and on our bodies – the so-called microbiome – has an enormous influence on human health. Antigen-specific CD4+ T helper cells are central orchestrators of immune reactions against microbial species. Microbiota-reactive CD4+ T cells acquire diverse functional profiles to adapt the immune response for a balanced host interaction with individual microbes. Imbalanced host immunity and/or microbiota composition may contribute to inflammatory diseases. Thus, the combination of both, the specificity for a distinct microbial antigen and the functional properties of the respective T cells, are key factors for protective vs. pathologic immune reactions. Moreover, CD4+ T cells have the capacity to memorize previous antigen-encounters and provide the same effector functions upon re-exposure. This ability to form (long-term) memory may also be a major reason for chronicity and treatment resistance of microbiota-associated diseases once pathologic T cell responses have formed.
Despite its major impact on human health, current data on the T cell-microbiota interactions are limited, especially in humans. Currently, we do not know which microbes are targets of specific T cell reactivity in humans, how the (chronic) interaction with the huge number of different microbial species is regulated by T cell specificity and function, and how changes in these factors contribute to microbiota-associated diseases. We hypothesize, that the exposure to a huge number of different microbial species has a profound influence on shaping the human T cell repertoire and that chronic T cell activation by microbial species must be tightly regulated on the cellular level. These mechanisms may be particularly impaired in the elderly, whose T cells have been repeatedly exposed to microbial antigens over decades, and in patients with chronic inflammatory diseases, where alterations in microbe-specific CD4+ T cells may contribute to pathogenicity. Therefore, we aim to characterize microbe-specific CD4+ T cell responses directly in human samples to define microbial species and specific antigens that drive CD4+ T cell responses in humans and the cellular and molecular players of protective and pathologic T cell-microbiota interactions.
Despite its major impact on human health, current data on the T cell-microbiota interactions are limited, especially in humans. Currently, we do not know which microbes are targets of specific T cell reactivity in humans, how the (chronic) interaction with the huge number of different microbial species is regulated by T cell specificity and function, and how changes in these factors contribute to microbiota-associated diseases. We hypothesize, that the exposure to a huge number of different microbial species has a profound influence on shaping the human T cell repertoire and that chronic T cell activation by microbial species must be tightly regulated on the cellular level. These mechanisms may be particularly impaired in the elderly, whose T cells have been repeatedly exposed to microbial antigens over decades, and in patients with chronic inflammatory diseases, where alterations in microbe-specific CD4+ T cells may contribute to pathogenicity. Therefore, we aim to characterize microbe-specific CD4+ T cell responses directly in human samples to define microbial species and specific antigens that drive CD4+ T cell responses in humans and the cellular and molecular players of protective and pathologic T cell-microbiota interactions.
1. Identification of CD4+ T cell target microbes in humans
The microbial species that are major targets of human CD4+ T cell responses remain currently poorly defined. Therefore, our first goal was to identify microbes that induce CD4+ T cell responses in healthy donors. Since the microbiota is extraordinary divers, a global analysis of microbe-specific T cell responses is not possible. Therefore, we analyzed an extensive list of >50 candidate microbial species that are (i) frequently identified and abundant in humans, (ii) covering the most prominent phyla, (iii) are selected based on a reported association with pathology or protection in CIDs and/or (iv) are associated with the induction of a certain CD4+ T cell subset in mice. Our data show that microbe-reactive CD4+ T cells can be detected in healthy humans and, despite individual differences in microbiome composition, reveal consistent patterns of strong T cell target microbes across multiple donors. Furthermore, we observe that functional CD4+ T cell subsets that are specifically focused on certain microbial species. Thus, this broad screening framework has identified microbial species that commonly induce T cell reactivity in humans and defined different microbe-specific reactivity patterns.
2. Altered CD4+ T cell reactivity against microbes in patients with chronic inflammatory diseases
A major translational aspect of MicroT is to determine whether microbe-reactive T cells are altered in patients with chronic inflammatory diseases, potentially revealing novel therapeutic targets. We started analyzing the CD4+ T cell responses to 13 common bacterial and fungal species in patients with inflammatory bowel disease (IBD) and healthy donors. Surprisingly, we could show that intestinal and dietary yeasts, such as Candida species, but also typically harmless Saccharomyces cerevisiae drive strongly increased inflammatory CD4+ T cell reactions in patients with Crohn’s disease. These yeast-responsive CD4+ T cells produce IFN-g and cytotoxic molecules, are enriched in the inflamed mucosa of patients and occur specifically in a subgroup of 50-60% of Crohn’s disease patients who are positive for anti-Saccharomyces cerevisiae antibodies (ASCAs). By using scRNA and T cell receptor sequencing approaches, we could further show, that the cytotoxic yeast-reactive CD4+ T cells are highly cross-reactive to different yeast species. Together these data indicate that repetitive exposure to similar epitopes present in different yeast species drives strong clonal expansion of cross-reactive clonotypes and imprints a cytotoxic functional profile that could contribute to disease pathogenesis in this subgroup of patients. These data have been published in Nature Medicine in 2023 and reveal novel concepts for potential treatment strategies in Crohn’s disease, which are now being explored in several subprojects.
3. Microbial target antigens of human Th17 cells
Th17 cells are a specialized CD4+ T cell subset crucial for interactions with the microbiota, while pathogenic Th17 responses are thought to contribute to immune pathology in various inflammatory conditions. To date, the specific mechanisms driving protective versus pathogenic Th17 responses in humans remain largely unknown. Previous studies, including our own, have shown that the fungus C. albicans is a strong driver of Th17 responses in humans. Interestingly, initial data indicate that these homeostatic C. albicans-specific Th17 cells are predominantly located in the oral mucosa rather than the intestine but migrate to the gut in inflammatory bowel disease. These results may support the role of the oral-gut axis in chronic intestinal inflammation, which is currently being further investigated by tracking C. albicans-specific T cells via T cell receptor sequencing across different human tissue compartments.
The microbial species that are major targets of human CD4+ T cell responses remain currently poorly defined. Therefore, our first goal was to identify microbes that induce CD4+ T cell responses in healthy donors. Since the microbiota is extraordinary divers, a global analysis of microbe-specific T cell responses is not possible. Therefore, we analyzed an extensive list of >50 candidate microbial species that are (i) frequently identified and abundant in humans, (ii) covering the most prominent phyla, (iii) are selected based on a reported association with pathology or protection in CIDs and/or (iv) are associated with the induction of a certain CD4+ T cell subset in mice. Our data show that microbe-reactive CD4+ T cells can be detected in healthy humans and, despite individual differences in microbiome composition, reveal consistent patterns of strong T cell target microbes across multiple donors. Furthermore, we observe that functional CD4+ T cell subsets that are specifically focused on certain microbial species. Thus, this broad screening framework has identified microbial species that commonly induce T cell reactivity in humans and defined different microbe-specific reactivity patterns.
2. Altered CD4+ T cell reactivity against microbes in patients with chronic inflammatory diseases
A major translational aspect of MicroT is to determine whether microbe-reactive T cells are altered in patients with chronic inflammatory diseases, potentially revealing novel therapeutic targets. We started analyzing the CD4+ T cell responses to 13 common bacterial and fungal species in patients with inflammatory bowel disease (IBD) and healthy donors. Surprisingly, we could show that intestinal and dietary yeasts, such as Candida species, but also typically harmless Saccharomyces cerevisiae drive strongly increased inflammatory CD4+ T cell reactions in patients with Crohn’s disease. These yeast-responsive CD4+ T cells produce IFN-g and cytotoxic molecules, are enriched in the inflamed mucosa of patients and occur specifically in a subgroup of 50-60% of Crohn’s disease patients who are positive for anti-Saccharomyces cerevisiae antibodies (ASCAs). By using scRNA and T cell receptor sequencing approaches, we could further show, that the cytotoxic yeast-reactive CD4+ T cells are highly cross-reactive to different yeast species. Together these data indicate that repetitive exposure to similar epitopes present in different yeast species drives strong clonal expansion of cross-reactive clonotypes and imprints a cytotoxic functional profile that could contribute to disease pathogenesis in this subgroup of patients. These data have been published in Nature Medicine in 2023 and reveal novel concepts for potential treatment strategies in Crohn’s disease, which are now being explored in several subprojects.
3. Microbial target antigens of human Th17 cells
Th17 cells are a specialized CD4+ T cell subset crucial for interactions with the microbiota, while pathogenic Th17 responses are thought to contribute to immune pathology in various inflammatory conditions. To date, the specific mechanisms driving protective versus pathogenic Th17 responses in humans remain largely unknown. Previous studies, including our own, have shown that the fungus C. albicans is a strong driver of Th17 responses in humans. Interestingly, initial data indicate that these homeostatic C. albicans-specific Th17 cells are predominantly located in the oral mucosa rather than the intestine but migrate to the gut in inflammatory bowel disease. These results may support the role of the oral-gut axis in chronic intestinal inflammation, which is currently being further investigated by tracking C. albicans-specific T cells via T cell receptor sequencing across different human tissue compartments.
We are investigating fundamental mechanisms of T cell-microbiota interactions in humans which has the potential to identify novel therapeutic targets or diagnostic markers for microbiota-mediated diseases. Our identification of intestinal and dietary yeasts as drivers of inflammatory CD4+ T cell reactions in IBD has already revealed novel treatment concepts, which we currently investigate, such as yeast-free diet and antifungal treatments. Additionally, we are evaluating strategies to specifically eliminate or silence disease-relevant T cell specificities, which, if successful, could be a proof-of-principle approach applicable to many T cell-mediated diseases.