Lightning Talk & Poster Presentation CD1-MR1 Workshop 2025

From accessibility to identity: Epigenetic regulation of murine MAIT cell thymic development (#47)

Anne-laure Le Gac 1 , Linda Bilonda Mutala 1 , Aurélie Delahousse 1 , Laetitia Perrin 1 , Rafael De Almeida Paiva 1 , Marion Salou 1 , Olivier Lantz 1 2 3
  1. Inserm U932, Immunity and Cancer, Institut Curie, PSL University, Paris, FRANCE
  2. Laboratoire d'immunologie clinique, Institut Curie, Paris, FRANCE
  3. Gustave-Roussy Institut Curie (CIC-BT1428), Centre d'investigation Clinique en Biothérapie, Paris, France

Mucosal-associated invariant T (MAIT) are selected by MR1-expressing double positive thymocytes inducing the expression of the transcription factor PLZF and ensuing memory phenotype in the thymus. In mice, subsequent maturation results into two effector subsets: MAIT1 (T-bet⁺) and MAIT17 (RORγt+)1,2. The molecular mechanisms guiding this commitment remain poorly understood, but our previous scRNA-seq analysis revealed that it occurs within a transcriptionally homogeneous intermediary cluster of cells1. Our prior work also indicated that TCR features were not involved in this process3. Since gene expression reflects transient states, we hypothesized that chromatin accessibility captures early fate commitment and upstream regulatory mechanisms, driven either by specific signals or stochastic events. To determine the mechanisms driving type 1 or 17 commitment, we performed paired single-nucleus (sn)RNA and ATAC sequencing on thymic MAIT cells. snATAC-seq accurately recapitulated developmental trajectories previously inferred from scRNA-seq, and reduced cell cycle–related biases in the pseudotime analysis. This trajectory analysis reveals distinct chromatin landscapes and associated transcription factors driving either MAIT1 or MAIT17 fate. Moreover, we identified precommitted cells harboring a chromatin state characterizing mature MAIT1 or MAIT17 cells but expressing a transcriptome resembling immature precursor cells. These cells are likely to have received an early epigenetic priming towards the MAIT1 or MAIT17 lineage. Analysis of differentially accessible motifs between the MAIT1 or MAIT17 precommitted cells, together with the expression of the associated transcription factors identified FOXP1/MEF2A and NRD1/NRD2 important for MAIT1 and MAIT17 commitment, respectively. Finally, chromatin profiling of mature subsets revealed epigenetic plasticity associated to MAIT17 but not MAIT1 cells, as Tbx21 remained epigenetically accessible in MAIT17 cells, while Rorc was not accessible in MAIT1 cells.  This first multi-omics analysis of murine thymic MAIT cell development identified novel targets involved in MAIT cell subset commitment that will be tested using Crispr/cas9 mediated genetic manipulations.

  1. Legoux,F.,et al. Immunity.,53, 710–723(2020).
  2. Bugaut,H.,et al. JExpMed.;221(2):e20231487(2024).
  3. Karnaukhov,V*,Le Gac,A-L*,Bilonda-Mutala,L.*et al. PNAS.,121(14):e2311348121(2024).