Single Cell Multi-Omics Revealing the Important Role of MR1 Mediated MAIT Cells in Maintaining Rejection for Liver Transplantation

Abstract

Mucosal-associated invariant T (MAIT) cells, representing one of the most abundant subsets of unconventional T cells, have been shown to play a significant role in regulating immune responses. However, their immunoregulatory roles in the context of liver transplantation (LT) immunity remain largely undefined. To address this, we conducted single-cell RNA/TCR sequencing, flow cytometry, and multiplex immunohistochemical (mIHC) assays to identify the proportion and characteristics of CD8+ MAIT cells in humans and mice following liver transplantation. We found that CD8+ MAIT cells were prominently represented in the single-cell CD8 profiles of human transplanted livers, demonstrating strong signalling associations with macrophages, whilst the fractional populations of MAIT1 and MAIT17 were distinctly clustered. In parallel, the proportion of CD8+ MAIT cells was significantly elevated in mouse LT models, revealing a dynamic trend where percentages increased at 1 and 2 weeks post-transplant, peaking at 3 weeks. Furthermore, using established MR1 knockout (MR1KO) LT mice, we observed that mice lacking MAIT cells exhibited milder rejection responses, indicating that MR1 mediates rejection by influencing the remodelling of the TCR repertoire after transplantation. Collectively, our study reveals that MAIT cells play a critical role in LT rejection, as MR1KO alleviated inflammatory responses and mitigated rejection via TCR repertoire remodelling. By mapping the dynamic changes of MAIT cells throughout the rejection process, these findings lay the groundwork for further investigations into the role of these cells in transplant immunity.

Keywords

graft rejection / liver transplantation / major histocompatibility complex class I related protein-1 / mucosal-associated invariant T cells

References

[1] C. Lefaucheur, K. Louis, A. B. Morris, et al., “Clinical Recommendations for Posttransplant Assessment of Anti–HLA (Human Leukocyte Antigen) Donor-Specific Antibodies: A Sensitization in Transplantation: Assessment of Risk Consensus Document,” American Journal of Transplantation 23, no. 1 (2023): 115–132, https://doi.org/10.1016/j.ajt.2022.11.013.

[2] F. Cvetkovski, J. M. Hexham, and E. Berglund, “Strategies for Liver Transplantation Tolerance,” International Journal of Molecular Sciences 22, no. 5 (2021): 2253, https://doi.org/10.3390/ijms22052253.

[3] D. Zou, Y. Dai, X. Zhang, et al., “T Cell Exhaustion Is Associated With Antigen Abundance and Promotes Transplant Acceptance,” American Journal of Transplantation 20, no. 9 (2020): 2540–2550, https://doi.org/10.1111/ajt.15870.

[4] A. J. Montano-Loza, M. L. Rodríguez-Perálvarez, G. P. Pageaux, A. Sanchez-Fueyo, and S. Feng, “Liver Transplantation Immunology: Immunosuppression, Rejection, and Immunomodulation,” Journal of Hepatology 78, no. 6 (2023): 1199–1215, https://doi.org/10.1016/j.jhep.2023.01.030.

[5] J. Fu, Z. Wang, M. Martinez, et al., “Plasticity of Intragraft Alloreactive T Cell Clones in Human Gut Correlates With Transplant Outcomes,” Journal of Experimental Medicine 221, no. 1 (2024): e20230930, https://doi.org/10.1084/jem.20230930.

[6] Y. Shan, D. Qi, L. Zhang, et al., “Single-Cell RNA-Seq Revealing the Immune Features of Donor Liver During Liver Transplantation,” Frontiers in Immunology 14 (2023): 1096733.

[7] R. Wang, X. Peng, Y. Yuan, et al., “Dynamic Immune Recovery Process After Liver Transplantation Revealed by Single-Cell Multi-Omics Analysis,” Innovation 5, no. 3 (2024): 100599, https://doi.org/10.1016/j.xinn.2024.100599.

[8] H. Huang, R. Chen, Y. Lin, et al., “Decoding Single-Cell Landscape and Intercellular Crosstalk in the Transplanted Liver,” Transplantation 107 (2022): 890–902.

[9] H. E. G. McWilliam and J. A. Villadangos, “MR1 Antigen Presentation to MAIT Cells and Other MR1-Restricted T Cells,” Nature Reviews Immunology 24, no. 3 (2024): 178–192, https://doi.org/10.1038/s41577-023-00934-1.

[10] R. Reantragoon, A. J. Corbett, I. G. Sakala, et al., “Antigen-Loaded MR1 Tetramers Define T Cell Receptor Heterogeneity in Mucosal-Associated Invariant T Cells,” Journal of Experimental Medicine 210, no. 11 (2013): 2305–2320, https://doi.org/10.1084/jem.20130958.

[11] P. Klenerman, T. S. C. Hinks, and J. E. Ussher, “Biological Functions of MAIT Cells in Tissues,” Molecular Immunology 130 (2021): 154–158, https://doi.org/10.1016/j.molimm.2020.12.017.

[12] R. Lamichhane, F. Munro, T. W. R. Harrop, et al., “Human Liver-Derived MAIT Cells Differ From Blood MAIT Cells in Their Metabolism and Response to TCR-Independent Activation,” European Journal of Immunology 51, no. 4 (2021): 879–892, https://doi.org/10.1002/eji.202048830.

[13] T. Kammann, C. Cai, T. Sekine, et al., “MAIT Cell Heterogeneity Across Paired Human Tissues Reveals Specialization of Distinct Regulatory and Enhanced Effector Profiles,” Science Immunology 9, no. 99 (2024): eadn2362, https://doi.org/10.1126/sciimmunol.adn2362.

[14] Y. Jiang, X. Wang, Q. Jiang, et al., “Restoration of IFN-γ-Producing MAIT Cell Correlates to Beneficial Allergen Immunotherapy in Allergic Rhinitis Patients,” Clinical and Experimental Allergy 55 (2025): 403–412, https://doi.org/10.1111/cea.70051.

[15] C. Boulouis, E. Mouchtaridi, T. R. Müller, et al., “Human MAIT Cell Response Profiles Biased Toward IL-17 or IL-10 Are Distinct Effector States Directed by the Cytokine Milieu,” Proceedings of the National Academy of Sciences 122, no. 6 (2025): e2414230122, https://doi.org/10.1073/pnas.2414230122.

[16] M. Mabire, P. Hegde, A. Hammoutene, et al., “MAIT Cell Inhibition Promotes Liver Fibrosis Regression via Macrophage Phenotype Reprogramming,” Nature Communications 14, no. 1 (2023): 1830, https://doi.org/10.1038/s41467-023-37453-5.

[17] P. Hegde, E. Weiss, V. Paradis, et al., “Mucosal-Associated Invariant T Cells Are a Profibrogenic Immune Cell Population in the Liver,” Nature Communications 9, no. 1 (2018): 2146, https://doi.org/10.1038/s41467-018-04450-y.

[18] M. H. Xiao, S. Wu, P. Liang, et al., “Mucosal-Associated Invariant T Cells Promote Ductular Reaction Through Amphiregulin in Biliary Atresia,” eBioMedicine 103 (2024): 105138, https://doi.org/10.1016/j.ebiom.2024.105138.

[19] S. Deschler, J. Pohl-Topcu, L. Ramsauer, et al., “Polyunsaturated Fatty Acid-Induced Metabolic Exhaustion and Ferroptosis Impair the Anti-Tumour Function of MAIT Cells in MASLD,” Journal of Hepatology 83 (2025): 1364–1378, https://doi.org/10.1016/j.jhep.2025.06.006.

[20] F. Sicheng, L. Muziying, Z. Chenwen, et al., “Regulatory Mucosa-Associated Invariant T Cells Controlled by β1 Adrenergic Receptor Signaling Contribute to Hepatocellular Carcinoma Progression,” Hepatology 78, no. 1 (2023): 72–87.

[21] D. I. Godfrey, H. F. Koay, J. McCluskey, and N. A. Gherardin, “The Biology and Functional Importance of MAIT Cells,” Nature Immunology 20, no. 9 (2019): 1110–1128, https://doi.org/10.1038/s41590-019-0444-8.

[22] X. Li, S. Li, B. Wu, et al., “Landscape of Immune Cells Heterogeneity in Liver Transplantation by Single-Cell RNA Sequencing Analysis,” Frontiers in Immunology 13 (2022): 890019, https://doi.org/10.3389/fimmu.2022.890019.

[23] X. Li, S. Li, Y. Wang, et al., “Single Cell RNA-Sequencing Delineates CD8+ Tissue Resident Memory T Cells Maintaining Rejection in Liver Transplantation,” Theranostics 14, no. 12 (2024): 4844.

[24] S. Chandra, G. Ascui, T. Riffelmacher, et al., “Transcriptomes and Metabolism Define Mouse and Human MAIT Cell Populations,” Science Immunology 89 (2023): eabn8531, https://doi.org/10.1126/sciimmunol.abn8531.

[25] Single-Cell Diversity and Functional Plasticity of Human MAIT Cells,” Nature Immunology 24, no. 9 (2023): 1409–1410, https://doi.org/10.1038/s41590-023-01600-3.

[26] A. Sattler, L. G. Thiel, A. H. Ruhm, et al., “Mucosal Associated Invariant T Cells Are Differentially Impaired in Tolerant and Immunosuppressed Liver Transplant Recipients,” American Journal of Transplantation 21, no. 1 (2021): 87–102, https://doi.org/10.1111/ajt.16122.

[27] W. Wang, C. Dai, P. Zhu, et al., “Liver Transplant-Facilitated CD161+Vα7.2+ MAIT Cell Recovery Demonstrates Clinical Benefits in Hepatic Failure Patients,” Nature Communications 16, no. 1 (2025): 4022, https://doi.org/10.1038/s41467-025-59308-x.

[28] C. Duneton, P. D. Winterberg, and M. L. Ford, “Activation and Regulation of Alloreactive T Cell Immunity in Solid Organ Transplantation,” Nature Reviews. Nephrology 18, no. 10 (2022): 663–676, https://doi.org/10.1038/s41581-022-00600-0.

[29] R. Angelico, B. Sensi, T. M. Manzia, et al., “Chronic Rejection After Liver Transplantation: Opening the Pandora's Box,” World Journal of Gastroenterology 27, no. 45 (2021): 7771–7783, https://doi.org/10.3748/wjg.v27.i45.7771.

[30] H. Robertson, H. J. Kim, J. Li, et al., “Decoding the Hallmarks of Allograft Dysfunction With a Comprehensive Pan-Organ Transcriptomic Atlas,” Nature Medicine 30 (2024): 3748–3757, https://doi.org/10.1038/s41591-024-03030-6.

[31] P. Cravedi, L. V. Riella, M. L. Ford, et al., “Advancing Mouse Models for Transplantation Research,” American Journal of Transplantation 24, no. 8 (2024): 1362–1368, https://doi.org/10.1016/j.ajt.2024.01.006.

[32] J. R. Kuchroo, D. A. Hafler, A. H. Sharpe, and L. E. Lucca, “The Double-Edged Sword: Harnessing PD-1 Blockade in Tumor and Autoimmunity,” Science Immunology 6, no. 65 (2021): eabf4034, https://doi.org/10.1126/sciimmunol.abf4034.

[33] J. Qu, B. Wu, L. Chen, et al., “CXCR6-Positive Circulating Mucosal-Associated Invariant T Cells Can Identify Patients With Non-Small Cell Lung Cancer Responding to Anti-PD-1 Immunotherapy,” Journal of Experimental & Clinical Cancer Research 43, no. 1 (2024): 134, https://doi.org/10.1186/s13046-024-03046-3.

[34] M. D. Crowther, G. Dolton, M. Legut, et al., “Genome-Wide CRISPR–Cas9 Screening Reveals Ubiquitous T Cell Cancer Targeting via the Monomorphic MHC Class I-Related Protein MR1,” Nature Immunology 21, no. 2 (2020): 178–185, https://doi.org/10.1038/s41590-019-0578-8.

[35] F. A. Buquicchio, R. Fonseca, P. K. Yan, et al., “Distinct Epigenomic Landscapes Underlie Tissue-Specific Memory T Cell Differentiation,” Immunity 57 (2024): 2202–2215, https://doi.org/10.1016/j.immuni.2024.06.014.

[36] T. Yokose, E. S. Szuter, I. Rosales, et al., “Dysfunction of Infiltrating Cytotoxic CD8+ T Cells Within the Graft Promotes Murine Kidney Allotransplant Tolerance,” Journal of Clinical Investigation 134, no. 16 (2024): e179709, https://doi.org/10.1172/JCI179709.

[37] M. A. Wood-Trageser, D. Lesniak, A. Gambella, et al., “Next-Generation Pathology Detection of T Cell–Antigen-Presenting Cell Immune Synapses in Human Liver Allografts,” Hepatology 77, no. 2 (2023): 355–366, https://doi.org/10.1002/hep.32666.

[38] J. J. P. Warunek, L. Fan, X. Zhang, et al., “Dysregulated Treg Repair Responses Lead to Chronic Rejection After Heart Transplantation,” Journal of Clinical Investigation 134, no. 23 (2024): e173593, https://doi.org/10.1172/JCI173593.

[39] S. K. Lee, J. H. Kwon, J. W. Jang, et al., “The Critical Role of Regulatory T Cells in Immune Tolerance and Rejection Following Liver Transplantation: Interactions With the Gut Microbiome,” Transplantation 109, no. 5 (2025): 784–793, https://doi.org/10.1097/TP.0000000000005220.

[40] J. Jakob, A. Kröger, F. Klawonn, D. Bruder, and L. Jänsch, “Translatome Analyses by Bio-Orthogonal Non-Canonical Amino Acid Labeling Reveal That MR1-Activated MAIT Cells Induce an M1 Phenotype and Antiviral Programming in Antigen-Presenting Monocytes,” Frontiers in Immunology 14 (2023): 1091837, https://doi.org/10.3389/fimmu.2023.1091837.

[41] B. Ruf, M. Bruhns, S. Babaei, et al., “Tumor-Associated Macrophages Trigger MAIT Cell Dysfunction at the HCC Invasive Margin,” Cell 186, no. 17 (2023): 3686–3705.e32, https://doi.org/10.1016/j.cell.2023.07.026.

[42] H. Morris, S. DeWolf, H. Robins, et al., “Tracking Donor-Reactive T Cells: Evidence for Clonal Deletion in Tolerant Kidney Transplant Patients,” Science Translational Medicine 7, no. 272 (2015): 272ra10, https://doi.org/10.1126/scitranslmed.3010760.

[43] T. Shi, A. R. Burg, J. T. Caldwell, et al., “Single-Cell Transcriptomic Analysis of Renal Allograft Rejection Reveals Insights Into Intragraft TCR Clonality,” Journal of Clinical Investigation 133, no. 14 (2023): e170191, https://doi.org/10.1172/JCI170191.

[44] Y. S. Mederacke, M. Nienen, M. Jarek, et al., “T Cell Receptor Repertoires Within Liver Allografts Are Different to Those in the Peripheral Blood,” Journal of Hepatology 74, no. 5 (2021): 1167–1175, https://doi.org/10.1016/j.jhep.2020.12.014.

[45] L. J. Howson, G. Napolitani, D. Shepherd, et al., “MAIT Cell Clonal Expansion and TCR Repertoire Shaping in Human Volunteers Challenged With Salmonella Paratyphi A,” Nature Communications 9, no. 1 (2018): 253, https://doi.org/10.1038/s41467-017-02540-x.

[46] A. Chancellor, R. Alan Simmons, R. C. Khanolkar, et al., “Promiscuous Recognition of MR1 Drives Self-Reactive Mucosal-Associated Invariant T Cell Responses,” Journal of Experimental Medicine 220, no. 9 (2023): e20221939, https://doi.org/10.1084/jem.20221939.

[47] S. P. Li, X. Q. Li, X. J. Chen, et al., “Characterization and Proteomic Analyses of Proinflammatory Cytokines in a Mouse Model of Liver Transplant Rejection,” Oxidative Medicine and Cellular Longevity 2022 (2022): 1–14, https://doi.org/10.1155/2022/5188584.

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