1
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López-Rodríguez JC, Barral P. Mucosal associated invariant T cells: Powerhouses of the lung. Immunol Lett 2024; 269:106910. [PMID: 39128630 DOI: 10.1016/j.imlet.2024.106910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 07/29/2024] [Accepted: 08/08/2024] [Indexed: 08/13/2024]
Abstract
The lungs face constant environmental challenges from harmless molecules, airborne pathogens and harmful agents that can damage the tissue. The lungs' immune system includes numerous tissue-resident lymphocytes that contribute to maintain tissue homeostasis and to the early initiation of immune responses. Amongst tissue-resident lymphocytes, Mucosal Associated Invariant T (MAIT) cells are present in human and murine lungs and emerging evidence supports their contribution to immune responses during infections, chronic inflammatory disorders and cancer. This review explores the mechanisms underpinning MAIT cell functions in the airways, their impact on lung immunity and the potential for targeting pulmonary MAIT cells in a therapeutic context.
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Affiliation(s)
- J C López-Rodríguez
- Centre for Inflammation Biology and Cancer Immunology, The Peter Gorer Department of Immunobiology, King's College London, London, UK; The Francis Crick Institute, London, UK.
| | - P Barral
- Centre for Inflammation Biology and Cancer Immunology, The Peter Gorer Department of Immunobiology, King's College London, London, UK; The Francis Crick Institute, London, UK.
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2
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Galaverna F, Flamini S, De Luca CD, Pili I, Boccieri E, Benini F, Quagliarella F, Rosignoli C, Rosichini M, Genah S, Catanoso M, Cardinale A, Volpe G, Coccetti M, Pitisci A, Li Pira G, Carta R, Lucarelli B, Del Bufalo F, Bertaina V, Becilli M, Pagliara D, Algeri M, Merli P, Locatelli F, Velardi E. Mucosal-associated invariant T cells are functionally impaired in pediatric and young adult patients following allogeneic hematopoietic stem cell transplantation and their recovery correlates with clinical outcomes. Haematologica 2024; 109:3222-3236. [PMID: 38813718 PMCID: PMC11443409 DOI: 10.3324/haematol.2023.284649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Mucosal-associated invariant T (MAIT) cells are innate-like T cells implicated in the response to fungal and bacterial infections. Their contribution to restoring T-cell immunity and influencing hematopoietic stem cell transplant (HSCT) outcomes remains poorly understood. We retrospectively studied MAIT-cell recovery in 145 consecutive children and young adults with hematologic malignancies undergoing allogeneic (allo)-HSCT between April 2019 and May 2022, from unrelated matched donor (MUD, N=52), with standard graft-versus-host-disease (GvHD) prophylaxis, or HLA-haploidentical (Haplo, N=93) donor after in vitro αβT/CD19-cell depletion, without post-HSCT pharmacological prophylaxis. With a median follow-up of 33 months (range, 12-49 months), overall survival (OS), disease-free survival (DFS), and non-relapse mortality (NRM) were 79.5%, 72%, and 7%, respectively; GvHD-free relapse-free survival (GRFS) was 63%, while cumulative incidence of relapse was 23%. While αβT cells were reconstituted 1-2 years post HSCT, MAIT cells showed delayed recovery and prolonged functional impairment, characterized by expression of activation (CD25, CD38), exhaustion (PD1, TIM3) and senescence (CD57) markers, and suboptimal ex vivo response. OS, DFS, and NRM were not affected by MAIT cells. Interestingly, higher MAIT cells at day +30 correlated with higher incidence of grade II-IV acute GvHD (19% vs. 7%, P=0.06). Furthermore, a greater MAIT-cell count tended to be associated with a higher incidence of chronic GvHD (cGvHD) (17% vs. 6%, P=0.07) resulting in lower GRFS (55% vs. 73%, P=0.05). Higher MAIT cells also correlated with greater cytomegalovirus (CMV) reactivation and lower late blood stream infections (BSI) (44% vs. 24%, P=0.02 and 9% vs. 18%, P=0.08, respectively). Future studies are needed to confirm the impact of early MAIT-cell recovery on cGvHD, CMV reactivation, and late BSI.
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Affiliation(s)
- Federica Galaverna
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Sara Flamini
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Carmen Dolores De Luca
- Department of Maternal and Child Health, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome
| | - Ilaria Pili
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Emilia Boccieri
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Francesca Benini
- Department of Maternal and Child Health, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome
| | - Francesco Quagliarella
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Chiara Rosignoli
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Marco Rosichini
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Molecular Medicine, Sapienza University of Rome, Viale Regina Elena 291, 00161 Rome
| | - Shirley Genah
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Marialuigia Catanoso
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Antonella Cardinale
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Gabriele Volpe
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Marianna Coccetti
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Angela Pitisci
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Giuseppina Li Pira
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Roberto Carta
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Barbarella Lucarelli
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Francesca Del Bufalo
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Valentina Bertaina
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Marco Becilli
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Daria Pagliara
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Mattia Algeri
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Health Sciences, Magna Graecia University, Catanzaro
| | - Pietro Merli
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome
| | - Franco Locatelli
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy; Department of Maternal and Child Health, Catholic University of the Sacred Heart, Largo Francesco Vito, 1, 00168 Rome.
| | - Enrico Velardi
- Research Area of Hematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome.
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3
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Raybould MIJ, Greenshields-Watson A, Agarwal P, Aguilar-Sanjuan B, Olsen TH, Turnbull OM, Quast NP, Deane CM. The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling. Cell Rep 2024; 43:114704. [PMID: 39216000 DOI: 10.1016/j.celrep.2024.114704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
T cell activation is governed through T cell receptors (TCRs), heterodimers of two sequence-variable chains (often an α and β chain) that synergistically recognize antigen fragments presented on cell surfaces. Despite this, there only exist repositories dedicated to collecting single-chain, not paired-chain, TCR sequence data. We addressed this gap by creating the Observed TCR Space (OTS) database, a source of consistently processed and annotated, full-length, paired-chain TCR sequences. Currently, OTS contains 5.35 million redundant (1.63 million non-redundant), predominantly human sequences from across 50 studies and at least 75 individuals. Using OTS, we identify pairing biases, public TCRs, and distinct chain coherence patterns relative to antibodies. We also release a paired-chain TCR language model, providing paired embedding representations and a method for residue in-filling conditional on the partner chain. OTS will be updated as a central community resource and is freely downloadable and available as a web application.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK.
| | - Alexander Greenshields-Watson
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Parth Agarwal
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Broncio Aguilar-Sanjuan
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Tobias H Olsen
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Oliver M Turnbull
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Nele P Quast
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', OX1 3LB Oxford, UK.
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4
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Loh L, Carcy S, Krovi HS, Domenico J, Spengler A, Lin Y, Torres J, Prabakar RK, Palmer W, Norman PJ, Stone M, Brunetti T, Meyer HV, Gapin L. Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models. Cell Rep 2024; 43:114705. [PMID: 39264810 DOI: 10.1016/j.celrep.2024.114705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/23/2024] [Accepted: 08/16/2024] [Indexed: 09/14/2024] Open
Abstract
The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity. We explore the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single-cell RNA sequencing (scRNA-seq) and flow cytometry. In human blood, the majority of Tinn cells share an effector program driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type 1/type 17 effector potential. Cross-species analysis uncovers species-specific distinctions, including the absence of type 2 Tinn cells in humans, which implies distinct immune regulatory mechanisms across species.
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Affiliation(s)
- Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Salomé Carcy
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Joanne Domenico
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Andrea Spengler
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yong Lin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshua Torres
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Rishvanth K Prabakar
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - William Palmer
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Paul J Norman
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Hannah V Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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5
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Hu J, Pan M, Reid B, Tworoger S, Li B. Quantifiable blood TCR repertoire components associate with immune aging. Nat Commun 2024; 15:8171. [PMID: 39289351 PMCID: PMC11408526 DOI: 10.1038/s41467-024-52522-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 09/11/2024] [Indexed: 09/19/2024] Open
Abstract
T cell senescence alters the homeostasis of distinct T cell populations and results in decayed adaptive immune protection in older individuals, but a link between aging and dynamic T cell clone changes has not been made. Here, using a newly developed computational framework, Repertoire Functional Units (RFU), we investigate over 6500 publicly available TCR repertoire sequencing samples from multiple human cohorts and identify age-associated RFUs consistently across different cohorts. Quantification of RFU reduction with aging reveals accelerated loss under immunosuppressive conditions. Systematic analysis of age-associated RFUs in clinical samples manifests a potential link between these RFUs and improved clinical outcomes, such as lower ICU admission and reduced risk of complications, during acute viral infections. Finally, patients receiving bone marrow transplantation show a secondary expansion of the age-associated clones upon stem cell transfer from younger donors. Together, our results suggest the existence of a 'TCR clock' that could reflect the immune functions in aging populations.
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Affiliation(s)
- Jing Hu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Mingyao Pan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brett Reid
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Shelley Tworoger
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
- Knight Cancer Institute and Division of Oncological Sciences, Oregon Health and Science University, Portland, OR, USA
| | - Bo Li
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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6
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Kammann T, Cai C, Sekine T, Mouchtaridi E, Boulouis C, Nilsén V, Ballesteros OR, Müller TR, Gao Y, Raineri EJM, Mily A, Adamo S, Constantz C, Niessl J, Weigel W, Kokkinou E, Stamper C, Marchalot A, Bassett J, Ferreira S, Rødahl I, Wild N, Brownlie D, Tibbitt C, Mak JYW, Fairlie DP, Leeansyah E, Michaelsson J, Marquardt N, Mjösberg J, Jorns C, Buggert M, Sandberg JK. MAIT cell heterogeneity across paired human tissues reveals specialization of distinct regulatory and enhanced effector profiles. Sci Immunol 2024; 9:eadn2362. [PMID: 39241054 DOI: 10.1126/sciimmunol.adn2362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 04/18/2024] [Accepted: 08/07/2024] [Indexed: 09/08/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells are unconventional T cells that recognize microbial riboflavin pathway metabolites presented by evolutionarily conserved MR1 molecules. We explored the human MAIT cell compartment across organ donor-matched blood, barrier, and lymphoid tissues. MAIT cell population size was donor dependent with distinct tissue compartmentalization patterns and adaptations: Intestinal CD103+ resident MAIT cells presented an immunoregulatory CD39highCD27low profile, whereas MAIT cells expressing NCAM1/CD56 dominated in the liver and exhibited enhanced effector capacity with elevated response magnitude and polyfunctionality. Both intestinal CD39high and hepatic CD56+ adaptations accumulated with donor age. CD56+ MAIT cells displayed limited T cell receptor-repertoire breadth, elevated MR1 binding, and a transcriptional profile skewed toward innate activation pathways. Furthermore, CD56 was dynamically up-regulated to a persistent steady-state equilibrium after exposure to antigen or IL-7. In summary, we demonstrate functional heterogeneity and tissue site adaptation in resident MAIT cells across human barrier tissues with distinct regulatory and effector signatures.
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Affiliation(s)
- Tobias Kammann
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Curtis Cai
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Takuya Sekine
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Elli Mouchtaridi
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Boulouis
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Vera Nilsén
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Olga Rivera Ballesteros
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Thomas R Müller
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Yu Gao
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Elisa J M Raineri
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Akhirunnesa Mily
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sarah Adamo
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Christian Constantz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Julia Niessl
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Whitney Weigel
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Christopher Stamper
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anne Marchalot
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - John Bassett
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Sabrina Ferreira
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Inga Rødahl
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Wild
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Demi Brownlie
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Chris Tibbitt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Jeffrey Y W Mak
- Centre for Chemistry and Drug Discovery, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - David P Fairlie
- Centre for Chemistry and Drug Discovery, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Edwin Leeansyah
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jakob Michaelsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Carl Jorns
- ME Transplantation, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Marcus Buggert
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Johan K Sandberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
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7
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Amini A, Klenerman P, Provine NM. Role of mucosal-associated invariant T cells in coronavirus disease 2019 vaccine immunogenicity. Curr Opin Virol 2024; 67:101412. [PMID: 38838550 DOI: 10.1016/j.coviro.2024.101412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 06/07/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells are an unconventional T cell population that are highly abundant in humans. They possess a semi-invariant T cell receptor (TCR) that recognises microbial metabolites formed during riboflavin biosynthesis, presented on a nonpolymorphic MHC-like molecule MR1. MAIT cells possess an array of effector functions, including type 1, type 17, and tissue repair activity. Deployment of these functions depends on the stimuli they receive through their TCR and/or cytokine receptors. Strong cytokine signalling, such as in response to vaccination, can bypass TCR triggering and provokes a strong proinflammatory response. Although data are still emerging, multiple aspects of MAIT cell biology are associated with modulation of immunity induced by the coronavirus disease 2019 mRNA and adenovirus vector vaccines. In this review, we will address how MAIT cells may play a role in immunogenicity of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and how these cells can be harnessed as cellular adjuvants.
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Affiliation(s)
- Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine - Experimental Medicine, University of Oxford, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine - Experimental Medicine, University of Oxford, UK; Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, UK; Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, UK.
| | - Nicholas M Provine
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, UK.
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8
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Gao M, Zhao X. Insights into the tissue repair features of MAIT cells. Front Immunol 2024; 15:1432651. [PMID: 39086492 PMCID: PMC11289772 DOI: 10.3389/fimmu.2024.1432651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/04/2024] [Indexed: 08/02/2024] Open
Abstract
Mucosa-associated invariant T (MAIT) cells are a subset of innate-like non-conventional T cells characterized by multifunctionality. In addition to their well-recognized antimicrobial activity, increasing attention is being drawn towards their roles in tissue homeostasis and repair. However, the precise mechanisms underlying these functions remain incompletely understood and are still subject to ongoing exploration. Currently, it appears that the tissue localization of MAIT cells and the nature of the diseases or stimuli, whether acute or chronic, may induce a dynamic interplay between their pro-inflammatory and anti-inflammatory, or pathogenic and reparative functions. Therefore, elucidating the conditions and mechanisms of MAIT cells' reparative functions is crucial for fully maximizing their protective effects and advancing future MAIT-related therapies. In this review, we will comprehensively discuss the establishment and potential mechanisms of their tissue repair functions as well as the translational application prospects and current challenges in this field.
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Affiliation(s)
- Mengge Gao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
| | - Xiaosu Zhao
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, China
- Research Unit of Key Technique for Diagnosis and Treatments of Hematologic Malignancies, Chinese Academy of Medical Sciences, Beijing, China
- Collaborative Innovation Center of Hematology, Peking University, Beijing, China
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9
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Yang AYP, Wistuba-Hamprecht K, Greten TF, Ruf B. Innate-like T cells in liver disease. Trends Immunol 2024; 45:535-548. [PMID: 38879436 DOI: 10.1016/j.it.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/27/2024] [Accepted: 05/27/2024] [Indexed: 07/14/2024]
Abstract
Mammalian innate-like T cells (ILTCs), including mucosal-associated invariant T (MAIT), natural killer T (NKT), and γδ T cells, are abundant tissue-resident lymphocytes that have recently emerged as orchestrators of hepatic inflammation, tissue repair, and immune homeostasis. This review explores the involvement of different ILTC subsets in liver diseases. We explore the mechanisms underlying the pro- and anti-inflammatory effector functions of ILTCs in a context-dependent manner. We highlight latest findings regarding the dynamic interplay between ILTC functional subsets and other immune and parenchymal cells which may inform candidate immunomodulatory strategies to achieve improved clinical outcomes in liver diseases. We present new insights into how distinct gene expression programs in hepatic ILTCs are induced, maintained, and reprogrammed in a context- and disease stage-dependent manner.
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Affiliation(s)
- Albert Ying-Po Yang
- Department of Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany; M3 Research Center for Malignome, Metabolome, and Microbiome, Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Kilian Wistuba-Hamprecht
- Department of Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany; M3 Research Center for Malignome, Metabolome, and Microbiome, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) - Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany; Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Dermatology, Venereology, and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany; DKFZ Hector Cancer Institute at the University Medical Center Mannheim, Mannheim, Germany
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Center for Cancer Research (CCR) Liver Cancer Program, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benjamin Ruf
- Department of Internal Medicine I, University Hospital Tübingen, Eberhard Karls University of Tübingen, Tübingen, Germany; M3 Research Center for Malignome, Metabolome, and Microbiome, Faculty of Medicine, University of Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) - Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Tübingen, Germany.
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10
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Suek N, Young T, Fu J. Immune cell profiling in intestinal transplantation. Hum Immunol 2024; 85:110808. [PMID: 38762429 PMCID: PMC11283363 DOI: 10.1016/j.humimm.2024.110808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/08/2024] [Accepted: 04/25/2024] [Indexed: 05/20/2024]
Abstract
Since the first published case study of human intestinal transplantation in 1967, there have been significant studies of intestinal transplant immunology in both animal models and humans. An improved understanding of the profiles of different immune cell subsets is critical for understanding their contributions to graft outcomes. While different studies have focused on the contribution of one or a few subsets to intestinal transplant, no study has integrated these data for a comprehensive overview of immune dynamics after intestinal transplant. Here, we provide a systematic review of the literature on different immune subsets and discuss their roles in intestinal transplant outcomes on multiple levels, focusing on chimerism and graft immune reconstitution, clonal alloreactivity, and cell phenotype. In Sections 1, 2 and 3, we lay out a shared framework for understanding intestinal transplant, focusing on the mechanisms of rejection or tolerance in the context of mucosal immunology and illustrate the unique role of the bidirectional graft-versus-host (GvH) and host-versus-graft (HvG) alloresponse. In Sections 4, 5 and 6, we further expand upon these concepts as we discuss the contribution of different cell subsets to intestinal transplant. An improved understanding of intestinal transplantation immunology will bring us closer to maximizing the potential of this important treatment.
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Affiliation(s)
- Nathan Suek
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Tyla Young
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA.
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11
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Li X, Fu S, Cheng H, Ma M, Song Z, Li J, Wu S, Zhang C, Wang X, Tang M, Pu X, Ji Q, Liang J, Zhao Z, Körner H, Li B, Shao M, Wang H. Differentiation of Type 17 Mucosal-Associated Invariant T Cells in Circulation Contributes to the Severity of Sepsis. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:1248-1261. [PMID: 38599461 DOI: 10.1016/j.ajpath.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/05/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells are essential in defending against infection. Sepsis is a systemic inflammatory response to infection and a leading cause of death. The relationship between the overall competency of the host immune response and disease severity is not fully elucidated. This study identified a higher proportion of circulating MAIT17 with expression of IL-17A and retinoic acid receptor-related orphan receptor γt in patients with sepsis. The proportion of MAIT17 was correlated with the severity of sepsis. Single-cell RNA-sequencing analysis revealed an enhanced expression of lactate dehydrogenase A (LDHA) in MAIT17 in patients with sepsis. Cell-culture experiments demonstrated that phosphoinositide 3-kinase-LDHA signaling was required for retinoic acid receptor-related orphan receptor γt expression in MAIT17. Finally, the elevated levels of plasma IL-18 promoted the differentiation of circulating MAIT17 cells in sepsis. In summary, this study reveals a new role of circulating MAIT17 in promoting sepsis severity and suggests the phosphoinositide 3-kinase-LDHA signaling as a driving force in MAIT17 responses.
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Affiliation(s)
- Xinying Li
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; School of Life Sciences, Anhui Medical University, Hefei, China
| | - Sicheng Fu
- School of Basic Medical Sciences, University of Science and Technology of China, Hefei, China
| | - Hao Cheng
- Department of Rheumatism and Immunology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Min Ma
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zijian Song
- School of Pharmacy, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Jun Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shuang Wu
- School of Pharmacy, Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China
| | - Chong Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaoxia Wang
- School of Public Health, Anhui Medical University, Hefei, China
| | - Maoyu Tang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China; Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, China
| | - Xuexue Pu
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiang Ji
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jinquan Liang
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhibin Zhao
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Heinrich Körner
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Bin Li
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Respiratory and Critical Care Medicine and Thoracic Surgery, Ruijin Hospital, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Shao
- Department of Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Hua Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Medical University, Hefei, China.
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12
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Nassiri I, Kwok AJ, Bhandari A, Bull KR, Garner LC, Klenerman P, Webber C, Parkkinen L, Lee AW, Wu Y, Fairfax B, Knight JC, Buck D, Piazza P. Demultiplexing of single-cell RNA-sequencing data using interindividual variation in gene expression. BIOINFORMATICS ADVANCES 2024; 4:vbae085. [PMID: 38911824 PMCID: PMC11193101 DOI: 10.1093/bioadv/vbae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/07/2024] [Indexed: 06/25/2024]
Abstract
Motivation Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps. Results We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells. Availability and implementation EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).
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Affiliation(s)
- Isar Nassiri
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, OX3 9DU, United Kingdom
- Department of Psychiatry, University of Oxford, Oxford, OX3 7JX, United Kingdom
| | - Andrew J Kwok
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, 999077, China
| | - Aneesha Bhandari
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Katherine R Bull
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 9DU, United Kingdom
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, OX1 3SY, United Kingdom
- NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, OX3 9DU, United Kingdom
| | - Caleb Webber
- Department of Physiology, Anatomy, Genetics, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX1 3PT, United Kingdom
- UK Dementia Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
| | - Laura Parkkinen
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Clinical Neurosciences, Oxford Parkinson’s Disease Centre, University of Oxford, Oxford, OX3 9DU, United Kingdom
| | - Angela W Lee
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Yanxia Wu
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Benjamin Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
- Department of Oncology, University of Oxford & Oxford Cancer Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7DQ, United Kingdom
| | - Julian C Knight
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Chinese Academy of Medical Science Oxford Institute, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - David Buck
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Paolo Piazza
- Nuffield Department of Medicine, Centre for Human Genetics, Oxford-GSK Institute of Molecular and Computational Medicine (IMCM), University of Oxford, Oxford, OX3 7BN, United Kingdom
- Nuffield Department of Medicine, Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
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13
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Konecny AJ, Huang Y, Setty M, Prlic M. Signals that control MAIT cell function in healthy and inflamed human tissues. Immunol Rev 2024; 323:138-149. [PMID: 38520075 DOI: 10.1111/imr.13325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Mucosal-associated invariant T (MAIT) cells have a semi-invariant T-cell receptor that allows recognition of antigen in the context of the MHC class I-related (MR1) protein. Metabolic intermediates of the riboflavin synthesis pathway have been identified as MR1-restricted antigens with agonist properties. As riboflavin synthesis occurs in many bacterial species, but not human cells, it has been proposed that the main purpose of MAIT cells is antibacterial surveillance and protection. The majority of human MAIT cells secrete interferon-gamma (IFNg) upon activation, while some MAIT cells in tissues can also express IL-17. Given that MAIT cells are present in human barrier tissues colonized by a microbiome, MAIT cells must somehow be able to distinguish colonization from infection to ensure effector functions are only elicited when necessary. Importantly, MAIT cells have additional functional properties, including the potential to contribute to restoring tissue homeostasis by expression of CTLA-4 and secretion of the cytokine IL-22. A recent study provided compelling data indicating that the range of human MAIT cell functional properties is explained by plasticity rather than distinct lineages. This further underscores the necessity to better understand how different signals regulate MAIT cell function. In this review, we highlight what is known in regards to activating and inhibitory signals for MAIT cells with a specific focus on signals relevant to healthy and inflamed tissues. We consider the quantity, quality, and the temporal order of these signals on MAIT cell function and discuss the current limitations of computational tools to extrapolate which signals are received by MAIT cells in human tissues. Using lessons learned from conventional CD8 T cells, we also discuss how TCR signals may integrate with cytokine signals in MAIT cells to elicit distinct functional states.
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Affiliation(s)
- Andrew J Konecny
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Immunology, University of Washington, Seattle, Washington, USA
| | - Yin Huang
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, USA
| | - Manu Setty
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Immunology, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
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14
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Provine NM, Al-Diwani A, Agarwal D, Dooley K, Heslington A, Murchison AG, Garner LC, Sheerin F, Klenerman P, Irani SR. Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming. Eur J Immunol 2024; 54:e2350872. [PMID: 38388988 DOI: 10.1002/eji.202350872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human LNs in vivo and has been used effectively to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies in this immunologically pivotal environment. Our data provide evidence that LN FNAs contain bone-fide LN-resident innate immune populations, with minimal contamination of blood material. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, aided by transcriptomics, identify likely receptor-ligand interactions. This represents the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
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Affiliation(s)
- Nicholas M Provine
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Adam Al-Diwani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Devika Agarwal
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Kyla Dooley
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Amelia Heslington
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Andrew G Murchison
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fintan Sheerin
- Department of Radiology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Paul Klenerman
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Sarosh R Irani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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15
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Yigit M, Basoglu OF, Unutmaz D. Mucosal-associated invariant T cells in cancer: dual roles, complex interactions and therapeutic potential. Front Immunol 2024; 15:1369236. [PMID: 38545100 PMCID: PMC10965779 DOI: 10.3389/fimmu.2024.1369236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 04/17/2024] Open
Abstract
Mucosal-associated invariant T (MAIT) cells play diverse roles in cancer, infectious diseases, and immunotherapy. This review explores their intricate involvement in cancer, from early detection to their dual functions in promoting inflammation and mediating anti-tumor responses. Within the solid tumor microenvironment (TME), MAIT cells can acquire an 'exhausted' state and secrete tumor-promoting cytokines. On the other hand, MAIT cells are highly cytotoxic, and there is evidence that they may have an anti-tumor immune response. The frequency of MAIT cells and their subsets has also been shown to have prognostic value in several cancer types. Recent innovative approaches, such as programming MAIT cells with chimeric antigen receptors (CARs), provide a novel and exciting approach to utilizing these cells in cell-based cancer immunotherapy. Because MAIT cells have a restricted T cell receptor (TCR) and recognize a common antigen, this also mitigates potential graft-versus-host disease (GVHD) and opens the possibility of using allogeneic MAIT cells as off-the-shelf cell therapies in cancer. Additionally, we outline the interactions of MAIT cells with the microbiome and their critical role in infectious diseases and how this may impact the tumor responses of these cells. Understanding these complex roles can lead to novel therapeutic strategies harnessing the targeting capabilities of MAIT cells.
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Affiliation(s)
- Mesut Yigit
- Human Immunology Laboratory, Acibadem University School of Medicine, Istanbul, Türkiye
| | - Omer Faruk Basoglu
- Human Immunology Laboratory, Acibadem University School of Medicine, Istanbul, Türkiye
| | - Derya Unutmaz
- Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
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16
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Peters AL, DePasquale EA, Begum G, Roskin KM, Woodle ES, Hildeman DA. Defining the T cell transcriptional landscape in pediatric liver transplant rejection at single cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582173. [PMID: 38464256 PMCID: PMC10925238 DOI: 10.1101/2024.02.26.582173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Acute cellular rejection (ACR) affects >80% of pediatric liver transplant recipients within 5 years, and late ACR is associated with graft failure. Traditional anti-rejection therapy for late ACR is ineffective and has remained unchanged for six decades. Although CD8+ T cells promote late ACR, little has been done to define their specificity and gene expression. Here, we used single-cell sequencing and immune repertoire profiling (10X Genomics) on 30 cryopreserved 16G liver biopsies from 14 patients (5 pre-transplant or with no ACR, 9 with ACR). We identified expanded intragraft CD8+ T cell clonotypes (CD8EXP) and their gene expression profiles in response to anti-rejection treatment. Notably, we found that expanded CD8+ clonotypes (CD8EXP) bore markers of effector and CD56hiCD161- 'NK-like' T cells, retaining their clonotype identity and phenotype in subsequent biopsies from the same patients despite histologic ACR resolution. CD8EXP clonotypes localized to portal infiltrates during active ACR, and persisted in the lobule after histologic ACR resolution. CellPhoneDB analysis revealed differential crosstalk between KC and CD8EXP during late ACR, with activation of the LTB-LTBR pathway and downregulation of TGFß signaling. Therefore, persistently-detected intragraft CD8EXP clones remain active despite ACR treatment and may contribute to long-term allograft fibrosis and failure of operational tolerance.
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Affiliation(s)
- Anna L. Peters
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Erica A.K. DePasquale
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Gousia Begum
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Krishna M. Roskin
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - E. Steve Woodle
- Division of Transplantation, Department of Surgery, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - David A. Hildeman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH, USA
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17
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Mezghiche I, Yahia-Cherbal H, Rogge L, Bianchi E. Interleukin 23 receptor: Expression and regulation in immune cells. Eur J Immunol 2024; 54:e2250348. [PMID: 37837262 DOI: 10.1002/eji.202250348] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/15/2023]
Abstract
The importance of IL-23 and its specific receptor, IL-23R, in the pathogenesis of several chronic inflammatory diseases has been established, but the underlying pathological mechanisms are not fully understood. This review focuses on IL-23R expression and regulation in immune cells.
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Affiliation(s)
| | | | - Lars Rogge
- Institut Pasteur, Université Paris Cité, Paris, France
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18
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Loh L, Carcy S, Krovi HS, Domenico J, Spengler A, Lin Y, Torres J, Palmer W, Norman PJ, Stone M, Brunetti T, Meyer HV, Gapin L. Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570707. [PMID: 38105962 PMCID: PMC10723458 DOI: 10.1101/2023.12.07.570707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity, having the ability to mount rapid responses following activation. In mice, this ability is acquired during thymic development. We explored the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single cell RNA sequencing and flow cytometry. We reveal that in human blood, the majority of Tinn cells, including iNKT, MAIT, and Vδ2+Vγ9+ T cells, share an effector program characterized by the expression of unique chemokine and cytokine receptors, and cytotoxic molecules. This program is driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type I/type III effector potential. To conduct a comprehensive cross-species analysis, we constructed a murine Tinn developmental atlas and uncovered additional species-specific distinctions, including the absence of type II Tinn cells in humans, which implies distinct immune regulatory mechanisms across species. The study provides insights into the development and functionality of Tinn cells, emphasizing their role in immune responses and their potential as targets for therapeutic interventions.
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Affiliation(s)
- Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Salomé Carcy
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Yong Lin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshua Torres
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - William Palmer
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Paul J. Norman
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Hannah V. Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, USA
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