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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - MAIT (Evolutionary conserved T cells specific for a microbial metabolite: deciphering their development in the thymus and mapping their interactions with the gut microbiota in vivo.)

Teaser

Summary

Context
The human intestine is colonized by 1012 to 1014 non-pathogenic microbes. These microbes (viruses, bacteria, parasites and fungi) constitute the intestinal microbiota. There is an increasing recognition of the role of the microbiota in human health. In particular, the occurrence of inflammatory diseases (Crohnâ€™s disease, ulcerative colitis), metabolic diseases (obesity, diabetes) and cancer has been linked to dysbiosis of the intestinal microbiota. Therefore, there is a need for a better understanding of the mechanisms of action of the microbiota on the host.

Overall objectives of the project
The overall goal of the project is to determine the effect of the microbiota on the host immune system. In particular, our research is focusing on the effect of microbial metabolites on T lymphocytes. Metabolites derived from the vitamin B2 synthesis pathway, a pathway present in most bacteria and yeasts but absent in mammals, are recognized by a population of T lymphocytes.
The specific aims of this project are:
1. To determine how T lymphocytes specific for microbial metabolites develop in the thymus.
2. To define the role of the microbiota in the function of T lymphocytes specific for microbial metabolites.

Conclusions of the action
1. We have identified the molecular pathway controlling key events of the thymic development of T lymphocytes specific for microbial metabolites.
2. We have determined how metabolite-specific T cells react and expand in response to the microbiota.

Work performed

\"Specific aim #1: To determine how T lymphocytes specific for microbial metabolites develop in the thymus.
To understand the function of metabolite-specific T cells in the intestine, it is necessary to understand how these T cells develop in the thymus. Therefore the first objective of the project was to identify and dissect the molecular pathways controlling the development of metabolite-specific T cells in the thymus.
Our understanding of the biology of metabolite-specific T cells has long been limited by the low frequency of these cells in laboratory mice. The lab has recently developed a new congenic mouse strain with a 10-fold increased frequency of polyclonal metabolite-specific T cells. Taking advantage of this mouse, I generated single-cell RNAseq data for 3,500 thymic metabolite-specific T cells. J. Gilet (bioinformatician in the lab) defined an unsupervised trajectory of developing metabolite-specific T cells. The resulting model agrees well with the current literature, and provides genome-wide information regarding modulation of gene expression along maturation. In particular, the model shows acquisition of the master transcription factor PLZF, followed by proliferation and differentiation into either RORÎ³t or Tbet+ effector T cells. This is the first unsupervised reconstruction of T cell development.
Using a genetic approach, we then identified the molecular mechanisms controlling the effector phenotype of metabolite-specific T cells in the thymus. We have shown that while TCR signals alone drive differentiation in naÃ¯ve conventional T cells, TCR signals together with SLAM-SAP signals induce PLZF expression. PLZF expression has major effects on a number of transcription factors and drives proliferation and the acquisition of effector phenotypes (Tbet or RORÎ³t) in the thymus. This mechanism highlights the significance of selection by hematopoietic cells instead of epithelial cells in the thymus.
Parts of these results have been disseminated internally through seminars, and internationally though posters at the Brazilian Mucosal Immunology Conference (Brazil, 2017) and the MR1-CD1 meeting (USA, 2017). I am now preparing a research article for publication of this work.

Specific aim #2: To define the role of the microbiota in the function of T lymphocytes specific for microbial metabolites
The antigens for metabolite-specific T cells can be detected in the feces of laboratory mice, suggesting a potential direct sensing of the microbiota by these T cells. Accordingly, blood frequency of metabolite-specific T cells is modified in several pathologies in which dysbiosis of the gut microbiota has been implicated, such as inflammatory bowel diseases (IBD), multiple sclerosis (MS), allergy, type 2 diabetes and obesity. In germ-free mice, the frequency of metabolite-specific T cells is reduced in the periphery and in the thymus. Therefore, I investigated the interplay between the microbiota and metabolite-specific T cells.
In collaboration with S. Rabot (INRA Anaxem), we monocolonized germ-free mice with various single strains of bacteria. We investigated how various strains of commensal bacteria interacted with metabolite-specific T cells. We defined the immune cells responsible for antigen-presentation to metabolite-specific T cells.
Altogether, we have shown that commensal bacteria directly control the function of metabolite-specific T cells.
The results have been disseminated internally through seminars. This work has now been submitted for publication.\"

Final results

Potential impacts of the project:
This project has lead to a better understanding of how metabolite-specific T cells develop, and what their function is in the periphery. We have identified both internal factors (signaling pathways) and external factors (microbiota-derived metabolites) controlling maturation and function of these important T cells. We expect to publish these results in high-impact journals, which will reflect favorably on the European Union scientific excellence.
Metabolic syndrome, obesity, diabetes, multiple sclerosis, allergy are among the health impairments for which alterations in the microbiota composition and modifications in the frequency of metabolite-specific T cells have been reported. This project has shed a new light on the complex interactions between T cells and the microbiota, and may provide new targets for clinical intervention in microbiota-associated diseases.