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. 2023 Aug 14;24(9):1565–1578. doi: 10.1038/s41590-023-01575-1

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a, UMAP of blood and liver MAIT cells and conventional memory T (T_mem) cells colored by cell type. n = 89,456 cells from 12 donors. b, UMAP split by sample type, namely blood from healthy donors (nonmatched), blood from liver donors (matched) and liver. c, Pearson’s correlation between the log₂ fold change in gene expression between MAIT and T_mem cells in the blood, and MAIT and T_mem cells in the liver. d,e, UMAP of matched blood and liver MAIT cells (n = 35,407 cells from six donors) colored by the 11 identified clusters (d) or by tissue (e). f, Proportion of cells in each cluster from the blood and liver. g–i, UMAPs colored by expression of CD69 (g) and CCL3 (h) genes or CD69 protein (i). j, Gene set enrichment analysis of liver compared with blood MAIT cells using published human and mouse tissue-resident memory T cell gene signatures. NES, normalized enrichment score. k, Over-representation analysis on the genes significantly upregulated in liver MAIT cells compared with blood MAIT cells. Top 15 gene ontology terms and associated Benjamini–Hochberg adjusted P values are shown. l, Heatmap showing activity (row-scaled AUCell scores) of the 20 most differentially active regulons (largest difference in average AUCell score) between matched blood and liver MAIT cells in Exp 1. n = 3 donors.