Tissue repair functions of MAIT cells: integrating thymic pre-commitment and peripheral signals

Project Information

MAIT

Grant agreement ID: 885435

DOI

10.3030/885435

Project closed

EC signature date 18 May 2020

Start date 1 October 2020

End date 30 September 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 2 499 500,00

EU contribution

€ 2 499 500,00

Coordinated by

INSTITUT CURIE
France

Periodic Reporting for period 4 - MAIT (Tissue repair functions of MAIT cells: integrating thymic pre-commitment and peripheral signals)

Reporting period: 2025-04-01 to 2025-09-30

Summary of the context and overall objectives of the project

In this project, we study the development and the functions of an innate like T cell subset called Mucosal Associated Invariant T (MAIT) cells which recognize an ubiquitous bacterial compound derived from the vitamin B2 biosynthetic pathway. Both the TCR and the restricting molecule presenting the bacterial compound are conserved in mammalian species, indicating important functions. MAIT cells display immediate effector activities.

Contrary to mainstream (i.e."conventional") T cells that are selected on epithelial cells, MAIT cells are selected on CD4+CD8+ thymocytes leading to the acquisition of a particular differentiation program linked to the expression of the PLZF transcription factor. In the murine thymus, two subsets of MAIT cells are generated: Tbet+ MAIT1 cells and RORgt+ MAIT17 cells. Both subsets are readily able to produce effector cytokines (IFN and IL-17, respectively) in the thymus. Both subsets then populate different tissues: liver and spleen for MAIT1; lung, skin and gut mucosae for MAIT17. The molecular mechanisms leading to these two outcomes have not been fully deciphered and are studied in this project.

Once in the periphery, MAIT cells are involved in antibacterial defense and in tissue homeostasis by sensing bacterial invasion or even just the metabolic status of the gut microbiota. The interplay between gut microbiota and MAIT cells is another topic studied in this project. Notably, the frequency of MAIT cells in the blood is modified in many diseases in which the microbiota is disturbed such as obesity, diabetes and inflammatory bowel diseases suggesting that MAIT cell may play a direct or indirect role in these diseases. The study of MAIT cells may allow a better understanding and treatment of the diseases seen above as MAIT triggering or inhibition may be beneficial.

MAIT cells seems also to be involved in tissue repair in the skin after wound while MAIT cells are protective during flu infection. The study of MAIT cells in experimental models will enable to decipher the involved mechanisms.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

To analyze the mechanisms of MAIT1 versus MAIT17 commitment during development, we analyzed the TCR repertoire of developing MAIT cells. The results dismissed the hypothesis that TCR avidity for the selecting ligand would be responsible for MAIT1/17 commitment as the same TCRs were found in both MAIT1 and MAIT17 subsets (PNAS, 2024) In addition, single-cell ATAC seq and scRNA seq datasets of MAIT thymocytes were generated, leading to the identification of candidate genes potentially involved in MAIT1/MAIT17 differentiation (CD1-MR1 meeting, 2024).

We completed a comprehensive study on MAIT cell development and tissue residency (Immunity, 2026, in press). We show that thymic epithelial cells select and contribute to the mature pool of MAIT but not iNKT cells, and that MAIT cells egress the thymus at several developmental stages with tropism for specific organs. We further show that increased peripheral MAIT ligands during inflammatory bowel disease (IBD) drive preferential thymic development of MAIT17 cells. We show that the MAIT17 cells specifically induced by dysbiosis during IBD in the thymus populate the intestinal mucosae thereby constituting a feedback loop to re-establish epithelial barreer integrity.

Analysis of MAIT cell relationships with the microbial environment has been completed and published (Science Immunology, 2024). We demonstrate that MAIT cells sense riboflavin derived metabolites produced by aerotolerant bacteria residing in the colon mucosa, and that colitis induces an expansion of riboflavin producing bacteria leading to increased ligand production. These ligands cross the epithelial barrier and activate MAIT cells, inducing tissue repair genes and barrier promoting mediators. Mice lacking MAIT cells are more susceptible to colitis and colitis-driven colorectal cancer.

We have analyzed the mechanisms underlying the tissue repair capacity of MAIT cells (Immunity, 2022). We show that:
1. MAIT cell repair function does not rely on cognate interaction with MR1 in the skin;
2. MAIT cells are not long-term residents in the skin;
3. repair functions are expressed at steady state;
4. MAIT cells rely on CXCR6 and CCL16 to populate the skin;
5. MAIT cells promote epithelial proliferation and angiogenesis during wound healing;
6. amphiregulin secreted by MAIT cells is necessary to accelerate skin wound healing;
7. MR1 expression on non hematopoietic cells is not necessary for MAIT mediated repair.

In parallel, we performed a comparative cross species study revealed a conserved sequence of transcriptional events underlying MAIT cell maturation across six mammalian species, with early ZBTB16 expression and co expression of TBX21 and RORC in non rodent species (Journal of Experimental Medicine, 2024). Rodents display distinct segregation of Tbet⁺ and RORγt⁺ MAIT subsets in the thymus. Integration of scRNA seq datasets highlighted a deeply conserved MAIT transcriptional program spanning 110 million years of evolution.

Finally, our results suggest that MAIT cells promote survival of influenza infected animals but are not involved in direct antiviral immunity (CD1-MR1 meeting, 2024).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

1. We showed that MAIT cells are rapidly recruited into inflamed skin and promote wound healing.
2. We evidenced a two-stage model of MAIT development: non committed intermediate-stage MAIT cells undergo a first proliferation round leading to MAIT1 or MAIT17 differentiation independently of TCR features, followed by a second proliferation phase which is higher for MAIT17.
3. We demonstrated that intestinal oxygen levels modulate MAIT ligand production. MAIT ligands produced in the colon rapidly cross the epithelial barrier, inducing MAIT dependent tissue repair pathways. Mice lacking MAIT cells showed increased susceptibility to colitis and colitis induced colorectal cancer.
4. Using scRNAseq from six mammalian species, we defined a common core gene signature characterizing MAIT development, revealing unexpectedly deep evolutionary conservation. The presence of defined MAIT1 and MAIT17 subsets in rodents is the exception but the evolutionarily conserved blended 1-17 differentiation program is acquired in the gut mucosae.
5. We dissected the developmental pathway of MAIT cells compared with iNKT cells, showing that thymic epithelial cells select MAIT but not iNKT cells, and that MAIT cells exit the thymus at several maturation stages with distinct tissue tropisms.
6. We showed that increased MAIT ligands during intestinal inflammation induce preferential thymic development of MAIT17 cells, suggesting a feedback loop favoring epithelial repair.
7. We generated single-cell epigenetic maps (ATAC seq) that pre-identified candidate regulators of MAIT1 versus MAIT17 commitment.

Our findings, published in Science Immunology, Immunity, Journal of Experimental Medicine, and PNAS, contributed substantially to the knowledge of the biology of MAIT cells.

Mechanisms of MAIT cell role during skin wound healing