Single-cell analysis of human MAIT cell transcriptional, functional and clonal diversity

Abstract

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that recognize microbial metabolites through a semi-invariant T cell receptor (TCR). Major questions remain regarding the extent of human MAIT cell functional and clonal diversity. To address these, we analyzed the single-cell transcriptome and TCR repertoire of blood and liver MAIT cells and developed functional RNA-sequencing, a method to integrate function and TCR clonotype at single-cell resolution. MAIT cell clonal diversity was comparable to conventional memory T cells, with private TCR repertoires shared across matched tissues. Baseline functional diversity was low and largely related to tissue site. MAIT cells showed stimulus-specific transcriptional responses in vitro, with cells positioned along gradients of activation. Clonal identity influenced resting and activated transcriptional profiles but intriguingly was not associated with the capacity to produce IL-17. Overall, MAIT cells show phenotypic and functional diversity according to tissue localization, stimulation environment and clonotype.

Signals that control MAIT cell function in healthy and inflamed human tissues

“…Finally, the Garner et al study also provided evidence for a link between TCR clonotype identity and transcriptional characteristics in MAIT cells. 26 This link strongly indicates a key role for the TCR signal in controlling MAIT cell function.…”

“…Finally, it is noteworthy that T cells, including MAIT cells, internalize the TCR following engagement. In the absence of the ability to use the TCR to identify MAIT cells, a recently described core gene signatures (including KLRB1, ZBTB16, and SLC4A10) 26 may prove useful to identify MAIT cells in tissues that could otherwise potentially be missed due to low TCR expression.…”

“…Importantly, a recent single-cell RNA-Seq study by Garner and colleagues provided compelling evidence that MAIT cell functional properties reflect plasticity rather than distinct lineages. 26 Typically, the mouse model is ideally suited to track cell fate decisions and differentiation over time. However, as highlighted in other reviews and studies, murine MAIT cells appear to have an inherent Th17 lineage bias and thus appear distinct from the human MAIT cell population.…”

“…These traits are vital for MAIT cells' role in combating pathogens 18,19 and their potential contribution to diseases. 109,110 The advent of single-cell RNA sequencing (scRNA-Seq) technologies has enabled researchers to delve into the transcriptomic profiles of individual MAIT cells, 26 revealing the signals that govern their interactions with the immediate environment. Additionally, the spatial organization crucial for MAIT intercellular dialogue can be deciphered by emerging highthroughput spatial transcriptomic technologies.…”

Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models

“…While studies in mice have delineated the developmental trajectories of T inn and analyses of distinct subsets of peripheral human T inn cells have shed light on the developmental stages of human Vδ2-Vγ9 (Perriman et al, 2023), and functional subtypes of human MAIT cells (Chandra et al, 2023; Garner et al, 2023), a comprehensive picture spanning development and peripheral function across T inn and T conv is lacking. In this study, we utilized the unbiased potential of single-cell genomics combined with flow cytometry to assess the range of phenotypic states T conv and T inn cells can adopt in vivo in the human thymus and blood.…”