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1. RIPK3 controls MAIT cell accumulation during development but not during infection

Author: Timothy Patton, Zhe Zhao, Xin Yi Lim, Eleanor Eddy, Huimeng Wang, Adam G. Nelson, Bronte Ennis, Sidonia B. G. Eckle, Michael N. T. Souter, Troi J. Pediongco, Hui-Fern Koay, Jian-Guo Zhang, Tirta M. Djajawi, Cynthia Louis, Najoua Lalaoui, Nicolas Jacquelot, Andrew M. Lew, Daniel G. Pellicci, James McCluskey, Yifan Zhan, Zhenjun Chen, Kate E. Lawlor, and Alexandra J. Corbett
Subjects: Cytology, QH573-671
Abstract: Abstract Cell death mechanisms in T lymphocytes vary according to their developmental stage, cell subset and activation status. The cell death control mechanisms of mucosal-associated invariant T (MAIT) cells, a specialized T cell population, are largely unknown. Here we report that MAIT cells express key necroptotic machinery; receptor-interacting protein kinase 3 (RIPK3) and mixed lineage kinase domain-like (MLKL) protein, in abundance. Despite this, we discovered that the loss of RIPK3, but not necroptotic effector MLKL or apoptotic caspase-8, specifically increased MAIT cell abundance at steady-state in the thymus, spleen, liver and lungs, in a cell-intrinsic manner. In contrast, over the course of infection with Francisella tularensis, RIPK3 deficiency did not impact the magnitude of the expansion nor contraction of MAIT cell pools. These findings suggest that, distinct from conventional T cells, the accumulation of MAIT cells is restrained by RIPK3 signalling, likely prior to thymic egress, in a manner independent of canonical apoptotic and necroptotic cell death pathways.
Published: 2023
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2. Synthetic 5-amino-6-D-ribitylaminouracil paired with inflammatory stimuli facilitates MAIT cell expansion in vivo

Author: Adam G. Nelson, Huimeng Wang, Phoebe M. Dewar, Eleanor M. Eddy, Songyi Li, Xin Yi Lim, Timothy Patton, Yuchen Zhou, Troi J. Pediongco, Lucy J. Meehan, Bronwyn S. Meehan, Jeffrey Y. W. Mak, David P. Fairlie, Andrew W. Stent, Lars Kjer-Nielsen, James McCluskey, Sidonia B. G. Eckle, Alexandra J. Corbett, Michael N. T. Souter, and Zhenjun Chen
Subjects: MAIT cells, 5-amino-6-D-ribitylaminouracil (5-A-RU), MAIT cell boosting, mouse model, CpG, IL-23, Immunologic diseases. Allergy, RC581-607
Abstract: IntroductionMucosal-associated invariant T (MAIT) cells are a population of innate-like T cells, which mediate host immunity to microbial infection by recognizing metabolite antigens derived from microbial riboflavin synthesis presented by the MHC-I-related protein 1 (MR1). Namely, the potent MAIT cell antigens, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU) and 5-(2-oxoethylideneamino)-6-D-ribitylaminouracil (5-OE-RU), form via the condensation of the riboflavin precursor 5-amino-6-D-ribitylaminouracil (5-A-RU) with the reactive carbonyl species (RCS) methylglyoxal (MG) and glyoxal (G), respectively. Although MAIT cells are abundant in humans, they are rare in mice, and increasing their abundance using expansion protocols with antigen and adjuvant has been shown to facilitate their study in mouse models of infection and disease. MethodsHere, we outline three methods to increase the abundance of MAIT cells in C57BL/6 mice using a combination of inflammatory stimuli, 5-A-RU and MG.ResultsOur data demonstrate that the administration of synthetic 5-A-RU in combination with one of three different inflammatory stimuli is sufficient to increase the frequency and absolute numbers of MAIT cells in C57BL/6 mice. The resultant boosted MAIT cells are functional and can provide protection against a lethal infection of Legionella longbeachae.ConclusionThese results provide alternative methods for expanding MAIT cells with high doses of commercially available 5-A-RU (± MG) in the presence of various danger signals.
Published: 2023
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3. Differential location of NKT and MAIT cells within lymphoid tissue

Author: Darryl N. Johnson, Zheng Ruan, Emma V. Petley, Sapna Devi, Lauren E. Holz, Adam P. Uldrich, Jeffrey Y. W. Mak, Jyh Liang Hor, Scott N. Mueller, James McCluskey, David P. Fairlie, Phillip K. Darcy, Paul A. Beavis, William R. Heath, and Dale I. Godfrey
Subjects: Medicine, Science
Abstract: Abstract Natural Killer T (NKT) cells and Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells that express semi-invariant αβ T cell receptors (TCRs) through which they recognise CD1d and MR1 molecules, respectively, in complex with specific ligands. These cells play important roles in health and disease in many organs, but their precise intra-organ location is not well established. Here, using CD1d and MR1 tetramer staining techniques, we describe the precise location of NKT and MAIT cells in lymphoid and peripheral organs. Within the thymus, NKT cells were concentrated in the medullary side of the corticomedullary junction. In spleen and lymph nodes, NKT cells were mainly localised within T cell zones, although following in vivo activation with the potent NKT-cell ligand α-GalCer, they expanded throughout the spleen. MAIT cells were clearly detectable in Vα19 TCR transgenic mice and were rare but detectable in lymphoid tissue of non-transgenic mice. In contrast to NKT cells, MAIT cells were more closely associated with the B cell zone and red pulp of the spleen. Accordingly, we have provided an extensive analysis of the in situ localisation of NKT and MAIT cells and suggest differences between the intra-organ location of these two cell types.
Published: 2022
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4. Suppression of MR1 by human cytomegalovirus inhibits MAIT cell activation

Author: Caroline L. Ashley, Brian P. McSharry, Hamish E. G. McWilliam, Richard J. Stanton, Ceri A. Fielding, Rommel A. Mathias, David P. Fairlie, James McCluskey, Jose A. Villadangos, Jamie Rossjohn, Allison Abendroth, and Barry Slobedman
Subjects: human cytomegalovirus, herpesvirus, MHC class I related protein-1, MR1, mucosal-associated invariant T cells, MAIT cells, Immunologic diseases. Allergy, RC581-607
Abstract: IntroductionThe antigen presentation molecule MHC class I related protein-1 (MR1) is best characterized by its ability to present bacterially derived metabolites of vitamin B2 biosynthesis to mucosal-associated invariant T-cells (MAIT cells).MethodsThrough in vitro human cytomegalovirus (HCMV) infection in the presence of MR1 ligand we investigate the modulation of MR1 expression. Using coimmunoprecipitation, mass spectrometry, expression by recombinant adenovirus and HCMV deletion mutants we investigate HCMV gpUS9 and its family members as potential regulators of MR1 expression. The functional consequences of MR1 modulation by HCMV infection are explored in coculture activation assays with either Jurkat cells engineered to express the MAIT cell TCR or primary MAIT cells. MR1 dependence in these activation assays is established by addition of MR1 neutralizing antibody and CRISPR/Cas-9 mediated MR1 knockout.ResultsHere we demonstrate that HCMV infection efficiently suppresses MR1 surface expression and reduces total MR1 protein levels. Expression of the viral glycoprotein gpUS9 in isolation could reduce both cell surface and total MR1 levels, with analysis of a specific US9 HCMV deletion mutant suggesting that the virus can target MR1 using multiple mechanisms. Functional assays with primary MAIT cells demonstrated the ability of HCMV infection to inhibit bacterially driven, MR1-dependent activation using both neutralizing antibodies and engineered MR1 knockout cells.DiscussionThis study identifies a strategy encoded by HCMV to disrupt the MR1:MAIT cell axis. This immune axis is less well characterized in the context of viral infection. HCMV encodes hundreds of proteins, some of which regulate the expression of antigen presentation molecules. However the ability of this virus to regulate the MR1:MAIT TCR axis has not been studied in detail.
Published: 2023
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5. The establishment of a cytomegalovirus -specific CD8+ T-cell threshold by kinetic modeling for the prediction of post-hemopoietic stem cell transplant reactivation

Author: Jing Zhang, Jinpeng Cao, Runhui Zheng, Mengqiu Yu, Zhengfang Lin, Caixia Wang, James McCluskey, Ji Yang, Zhenjun Chen, Alexandra J. Corbett, Pengxing Cao, Wenjian Mo, and Zhongfang Wang
Subjects: Health sciences, Immunology, Immune system, Virology, Stem cells research, Mathematical biosciences, Science
Abstract: Summary: The dynamic interaction between the CMV virus and host immune response remains obscure, thus hindering the diagnosis and therapeutic management of patients with HSCT. The current diagnosis of CMV viremia depends on viral load estimation. Medical intervention based on viral load, can be unnecessary or poorly timed for many patients. Here we examined the clinical features and blood samples of patients with HSCT and assessed the CMV reactivation kinetics and corresponding CMV antigen-specific T-cell response in individual patients based on a peptide pool stimulation T-cell assay, which showed that CMV-specific CD8+ T cells were more suitable to be a diagnosis indicator for suppressing CMV reactivation. Using ROC analysis, we defined and verified a CMV-specific CD8+ T-cell counts threshold (925 cells/106 PBMCs) as an indicator of CMV reactivation post-HSCT, and suggested that use of this threshold would provide more accurate guidance for prompt medication and better management of CMV infection post-HSCT.
Published: 2022
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6. The role of mucosal-associated invariant T cells in visceral leishmaniasis

Author: Marcela de Lima Moreira, Luana Oliveira Borges-Fernandes, Marcelo Antônio Pascoal-Xavier, Ágata Lopes Ribeiro, Victória Hellena Silva Pereira, Troi Pediongco, Márcio Sobreira da Silva Araújo, Andréa Teixeira-Carvalho, Andrea Lucchesi de Carvalho, Maria Vitória Assumpção Mourão, Flávia Alves Campos, Marineide Borges, Mariângela Carneiro, Zhenjun Chen, Eleanor Saunders, Malcolm McConville, Moriya Tsuji, James McCluskey, Olindo Assis Martins-Filho, Sidonia Barbara Guiomar Eckle, Jordana Grazziela Alves Coelho-dos-Reis, and Vanessa Peruhype-Magalhães
Subjects: MAIT, Leishmania, anti-parasitic activity, MR1, IL-17+MAIT, IFN-γ+ MAIT, Immunologic diseases. Allergy, RC581-607
Abstract: Mucosal-associated invariant T (MAIT) cells are restricted by MR1 and are known to protect against bacterial and viral infections. Our understanding of the role of MAIT cells in parasitic infections, such as visceral leishmaniasis (VL) caused by protozoan parasites of Leishmania donovani, is limited. This study showed that in response to L. infantum, human peripheral blood MAIT cells from children with leishmaniasis produced TNF and IFN-γ in an MR1-dependent manner. The overall frequency of MAIT cells was inversely correlated with alanine aminotransferase levels, a specific marker of liver damage strongly associated with severe hepatic involvement in VL. In addition, there was a positive correlation between total protein levels and the frequency of IL-17A+ CD8+ MAIT cells, whereby reduced total protein levels are a marker of liver and kidney damage. Furthermore, the frequencies of IFN-γ+ and IL-10+ MAIT cells were inversely correlated with hemoglobin levels, a marker of severe anemia. In asymptomatic individuals and VL patients after treatment, MAIT cells also produced IL-17A, a cytokine signature associated with resistance to visceral leishmaniasis, suggesting that MAIT cells play important role in protecting against VL. In summary, these results broaden our understanding of MAIT-cell immunity to include protection against parasitic infections, with implications for MAIT-cell-based therapeutics and vaccines. At last, this study paves the way for the investigation of putative MAIT cell antigens that could exist in the context of Leishmania infection.
Published: 2022
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7. MAIT cells regulate NK cell-mediated tumor immunity

Author: Emma V. Petley, Hui-Fern Koay, Melissa A. Henderson, Kevin Sek, Kirsten L. Todd, Simon P. Keam, Junyun Lai, Imran G. House, Jasmine Li, Magnus Zethoven, Amanda X. Y. Chen, Amanda J. Oliver, Jessica Michie, Andrew J. Freeman, Lauren Giuffrida, Jack D. Chan, Angela Pizzolla, Jeffrey Y. W. Mak, Timothy R. McCulloch, Fernando Souza-Fonseca-Guimaraes, Conor J. Kearney, Rosemary Millen, Robert G. Ramsay, Nicholas D. Huntington, James McCluskey, Jane Oliaro, David P. Fairlie, Paul J. Neeson, Dale I. Godfrey, Paul A. Beavis, and Phillip K. Darcy
Subjects: Science
Abstract: Mucosal-associated invariant T (MAIT) cells facilitate anti-microbial responses, but their functions in cancer protection is unclear. Here the authors show that activated MAIT cells induce an IFN-γ transcriptome in natural killer (NK) cells and enhance NK-dependent anti-cancer immunity in mice, thereby hinting a new avenue for cancer therapy.
Published: 2021
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8. Francisella tularensis induces Th1 like MAIT cells conferring protection against systemic and local infection

Author: Zhe Zhao, Huimeng Wang, Mai Shi, Tianyuan Zhu, Troi Pediongco, Xin Yi Lim, Bronwyn S. Meehan, Adam G. Nelson, David P. Fairlie, Jeffrey Y. W. Mak, Sidonia B. G. Eckle, Marcela de Lima Moreira, Carolin Tumpach, Michael Bramhall, Cameron G. Williams, Hyun Jae Lee, Ashraful Haque, Maximilien Evrard, Jamie Rossjohn, James McCluskey, Alexandra J. Corbett, and Zhenjun Chen
Subjects: Science
Abstract: Mucosal-Associated Invariant T (MAIT) cells are associated with established functions during bacterial infection. Here the authors show inoculation with Francisella tularensis results in induction of MAIT cells associated with prototypic Th1 immunity and confer protection to systemic and local infection.
Published: 2021
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9. Exposure to SARS-CoV-2 generates T-cell memory in the absence of a detectable viral infection

Author: Zhongfang Wang, Xiaoyun Yang, Jiaying Zhong, Yumin Zhou, Zhiqiang Tang, Haibo Zhou, Jun He, Xinyue Mei, Yonghong Tang, Bijia Lin, Zhenjun Chen, James McCluskey, Ji Yang, Alexandra J. Corbett, and Pixin Ran
Subjects: Science
Abstract: T cells compose a critical component of the immune response to coronavirus infection with SARS-CoV-2. Here the authors characterise the T cell response to SARS CoV-2 in patients and their close contacts, and show the presence of SARS-CoV-2 specific T cells in the absence of detectable virus infection.
Published: 2021
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10. Mucosal-associated invariant T cells promote inflammation and intestinal dysbiosis leading to metabolic dysfunction during obesity

Author: Amine Toubal, Badr Kiaf, Lucie Beaudoin, Lucie Cagninacci, Moez Rhimi, Blandine Fruchet, Jennifer da Silva, Alexandra J. Corbett, Yannick Simoni, Olivier Lantz, Jamie Rossjohn, James McCluskey, Philippe Lesnik, Emmanuelle Maguin, and Agnès Lehuen
Subjects: Science
Abstract: Inflammation, immune cells and the host microbiota are intimately linked in the pathophysiology of obesity and diabetes. Here the authors show mucosal-associated invariant T cells fuel inflammation in the tissues and serve a function in promoting metabolic breakdown, polarising macrophage populations and inducing dysbiosis of the intestinal microbiota.
Published: 2020
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11. Diverse MR1-restricted T cells in mice and humans

Author: Hui-Fern Koay, Nicholas A. Gherardin, Calvin Xu, Rebecca Seneviratna, Zhe Zhao, Zhenjun Chen, David P. Fairlie, James McCluskey, Daniel G. Pellicci, Adam P. Uldrich, and Dale I. Godfrey
Subjects: Science
Abstract: Mucosal-associated invariant T (MAIT) cells express invariant TRAV1/TRAJ33 TCR-α gene segments and detect antigens presented by MR1. Here the authors show that atypical, MR1-restricted MAIT populations that include both Trav1+ and Trav1- cells are found in both Traj33-deficient mice and human peripheral blood.
Published: 2019
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12. Kinetics of Abacavir-Induced Remodelling of the Major Histocompatibility Complex Class I Peptide Repertoire

Author: Patricia T. Illing, Andy van Hateren, Rachel Darley, Nathan P. Croft, Nicole A. Mifsud, Samuel King, Lyudmila Kostenko, Mandvi Bharadwaj, James McCluskey, Tim Elliott, and Anthony W. Purcell
Subjects: MHC I antigen presentation, abacavir, T cells, drug hypersensitivity, immunopeptidome, tapasin, Immunologic diseases. Allergy, RC581-607
Abstract: Abacavir hypersensitivity syndrome can occur in individuals expressing the HLA-B*57:01 major histocompatibility complex class I allotype when utilising the drug abacavir as a part of their anti-retroviral regimen. The drug is known to bind within the HLA-B*57:01 antigen binding cleft, leading to the selection of novel self-peptide ligands, thus provoking life-threatening immune responses. However, the sub-cellular location of abacavir binding and the mechanics of altered peptide selection are not well understood. Here, we probed the impact of abacavir on the assembly of HLA-B*57:01 peptide complexes. We show that whilst abacavir had minimal impact on the maturation or average stability of HLA-B*57:01 molecules, abacavir was able to differentially enhance the formation, selectively decrease the dissociation, and alter tapasin loading dependency of certain HLA-B*57:01-peptide complexes. Our data reveals a spectrum of abacavir mediated effects on the immunopeptidome which reconciles the heterogeneous functional T cell data reported in the literature.
Published: 2021
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13. Virus-Mediated Suppression of the Antigen Presentation Molecule MR1

Author: Brian P. McSharry, Carolyn Samer, Hamish E.G. McWilliam, Caroline L. Ashley, Michael B. Yee, Megan Steain, Ligong Liu, David P. Fairlie, Paul R. Kinchington, James McCluskey, Allison Abendroth, Jose A. Villadangos, Jamie Rossjohn, and Barry Slobedman
Subjects: Biology (General), QH301-705.5
Abstract: Summary: The antigen-presenting molecule MR1 presents microbial metabolites related to vitamin B2 biosynthesis to mucosal-associated invariant T cells (MAIT cells). Although bacteria and fungi drive the MR1 biosynthesis pathway, viruses have not previously been implicated in MR1 expression or its antigen presentation. We demonstrate that several herpesviruses inhibit MR1 cell surface upregulation, including a potent inhibition by herpes simplex virus type 1 (HSV-1). This virus profoundly suppresses MR1 cell surface expression and targets the molecule for proteasomal degradation, whereas ligand-induced cell surface expression of MR1 prior to infection enables MR1 to escape HSV-1-dependent targeting. HSV-1 downregulation of MR1 is dependent on de novo viral gene expression, and we identify the Us3 viral gene product as functioning to target MR1. Furthermore, HSV-1 downregulation of MR1 disrupts MAIT T cell receptor (TCR) activation. Accordingly, virus-mediated targeting of MR1 defines an immunomodulatory strategy that functionally disrupts the MR1-MAIT TCR axis. : The antigen-presenting molecule MR1 presents bacterial and fungal metabolites to MAIT cells. McSharry et al. show that the herpesviruses HSV-1 and CMV disrupt MR1 expression. Downregulation of MR1 by HSV-1 inhibits bacterially driven MAIT TCR-dependent activation. This provides evidence of virus immunomodulatory control of the MR1-restricted immune response. Keywords: herpesvirus, herpes simplex virus, cytomegalovirus, MR1, MAIT cell, immune evasion, virus targeting of MHC I-like molecules
Published: 2020
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14. HLA-B57 micropolymorphism defines the sequence and conformational breadth of the immunopeptidome

Author: Patricia T. Illing, Phillip Pymm, Nathan P. Croft, Hugo G. Hilton, Vladimir Jojic, Alex S. Han, Juan L. Mendoza, Nicole A. Mifsud, Nadine L. Dudek, James McCluskey, Peter Parham, Jamie Rossjohn, Julian P. Vivian, and Anthony W. Purcell
Subjects: Science
Abstract: Human leukocyte antigens (HLA) are multi-allelic and polymorphic genes that present antigens to immune cells for inducing protective immunity. Here, using systems biology and structural approaches, the authors show that micropolymorphism of three HLA has effects beyond the modulation of antigen diversity.
Published: 2018
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15. MAIT cells contribute to protection against lethal influenza infection in vivo

Author: Bonnie van Wilgenburg, Liyen Loh, Zhenjun Chen, Troi J. Pediongco, Huimeng Wang, Mai Shi, Zhe Zhao, Marios Koutsakos, Simone Nüssing, Sneha Sant, Zhongfang Wang, Criselle D’Souza, Xiaoxiao Jia, Catarina F. Almeida, Lyudmila Kostenko, Sidonia B. G. Eckle, Bronwyn S. Meehan, Axel Kallies, Dale I. Godfrey, Patrick C. Reading, Alexandra J. Corbett, James McCluskey, Paul Klenerman, Katherine Kedzierska, and Timothy S. C. Hinks
Subjects: Science
Abstract: MAIT cells are abundant in the lungs and confer protection against bacterial pathogens. Whilst activation of these cells has been described during viral infections, here van Wilgenburg and colleagues show that in a murine model MAIT cells contribute to the protective host immune response to influenza virus infection.
Published: 2018
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16. MAIT cells protect against pulmonary Legionella longbeachae infection

Author: Huimeng Wang, Criselle D’Souza, Xin Yi Lim, Lyudmila Kostenko, Troi J. Pediongco, Sidonia B. G. Eckle, Bronwyn S. Meehan, Mai Shi, Nancy Wang, Shihan Li, Ligong Liu, Jeffrey Y. W. Mak, David P. Fairlie, Yoichiro Iwakura, Jennifer M. Gunnersen, Andrew W. Stent, Dale I. Godfrey, Jamie Rossjohn, Glen P. Westall, Lars Kjer-Nielsen, Richard A. Strugnell, James McCluskey, Alexandra J. Corbett, Timothy S. C. Hinks, and Zhenjun Chen
Subjects: Science
Abstract: Mucosal associated invariant T (MAIT) cells have been implicated in antibacterial responses. Here the authors show MAIT cells confer IFN-γ-mediated protection from lethal infection in a mouse model of Legionella infection, which can be enhanced by synthetic MR1 ligands.
Published: 2018
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17. Divergent T-cell receptor recognition modes of a HLA-I restricted extended tumour-associated peptide

Author: Kok Fei Chan, Benjamin S. Gully, Stephanie Gras, Dennis X. Beringer, Lars Kjer-Nielsen, Jonathan Cebon, James McCluskey, Weisan Chen, and Jamie Rossjohn
Subjects: Science
Abstract: Human leukocyte antigen (HLA) presents peptides to activate T cells, but many aspects in the T cell receptor (TCR)/HLA interaction remain unclear. Here the authors show, via structural data, that two TCRs differentially recognize the same tumour peptide/HLA complex and induce contrasting conformation changes of the peptide.
Published: 2018
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18. Stabilizing short-lived Schiff base derivatives of 5-aminouracils that activate mucosal-associated invariant T cells

Author: Jeffrey Y. W. Mak, Weijun Xu, Robert C. Reid, Alexandra J. Corbett, Bronwyn S. Meehan, Huimeng Wang, Zhenjun Chen, Jamie Rossjohn, James McCluskey, Ligong Liu, and David P. Fairlie
Subjects: Science
Abstract: MAIT cells are activated by MR1 restricted antigens derived from riboflavin biosynthesis. Here the authors characterize MAIT cell antigenicity and synthesize a water stable antigen that activates human MAIT cellsin vitro and mouse MAIT cells in vivo.
Published: 2017
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19. The balance of interleukin‐12 and interleukin‐23 determines the bias of MAIT1versusMAIT17 responses during bacterial infection

Author: Huimeng Wang, Adam G Nelson, Bingjie Wang, Zhe Zhao, Xin Yi Lim, Mai Shi, Lucy J Meehan, Xiaoxiao Jia, Katherine Kedzierska, Bronwyn S Meehan, Sidonia BG Eckle, Michael NT Souter, Troi J Pediongco, Jeffrey YW Mak, David P Fairlie, James McCluskey, Zhongfang Wang, Alexandra J Corbett, and Zhenjun Chen
Subjects: Mice, Histocompatibility Antigens Class I, Immunology, Animals, Cytokines, Immunology and Allergy, Bacterial Infections, Cell Biology, Interleukin-12, Interleukin-23, Mucosal-Associated Invariant T Cells
Abstract: Mucosal-associated invariant T (MAIT) cells are a major subset of innate-like T cells mediating protection against bacterial infection through recognition of microbial metabolites derived from riboflavin biosynthesis. Mouse MAIT cells egress from the thymus as two main subpopulations with distinct functions, namely, T-bet-expressing MAIT1 and RORγt-expressing MAIT17 cells. Previously, we reported that inducible T-cell costimulator and interleukin (IL)-23 provide essential signals for optimal MHC-related protein 1 (MR1)-dependent activation and expansion of MAIT17 cells in vivo. Here, in a model of tularemia, in which MAIT1 responses predominate, we demonstrate that IL-12 and IL-23 promote MAIT1 cell expansion during acute infection and that IL-12 is indispensable for MAIT1 phenotype and function. Furthermore, we showed that the bias toward MAIT1 or MAIT17 responses we observed during different bacterial infections was determined and modulated by the balance between IL-12 and IL-23 and that these responses could be recapitulated by cytokine coadministration with antigen. Our results indicate a potential for tailored immunotherapeutic interventions via MAIT cell manipulation.
Published: 2022
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20. Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality

Author: Timothy S.C. Hinks, Emanuele Marchi, Maisha Jabeen, Moshe Olshansky, Ayako Kurioka, Troi J. Pediongco, Bronwyn S. Meehan, Lyudmila Kostenko, Stephen J. Turner, Alexandra J. Corbett, Zhenjun Chen, Paul Klenerman, and James McCluskey
Subjects: Biology (General), QH301-705.5
Abstract: Summary: Mucosal-associated invariant T (MAIT) cells are MR1-restricted innate-like T cells conserved across mammalian species, including mice and humans. By sequencing RNA from sorted MR1-5-OP-RU tetramer+ cells derived from either human blood or murine lungs, we define the basic transcriptome of an activated MAIT cell in both species and demonstrate how this profile changes during the resolution of infection and during reinfection. We observe strong similarities between MAIT cells in humans and mice. In both species, activation leads to strong expression of pro-inflammatory cytokines and chemokines as well as a strong tissue repair signature, recently described in murine commensal-specific H2-M3-restricted T cells. Transcriptomes of MAIT cells and H2-M3-specific CD8+ T cells displayed the most similarities to invariant natural killer T (iNKT) cells when activated, but to γδ T cells after the resolution of infection. These data define the requirements for and consequences of MAIT cell activation, revealing a tissue repair phenotype expressed upon MAIT cell activation in both species. : Mucosal-associated invariant T (MAIT) cells are implicated in antibacterial and antiviral immunity. Using RNA sequencing of human MAIT cells stimulated with their cognate ligand and murine MAIT cells stimulated by acute Legionella infection, Hinks et al. report that activation leads to expression of a strong tissue repair signature in both species. Keywords: mucosal-associated invariant T cell, T cell, transcriptome, MHC-related protein 1, activation, lung, human, mouse, riboflavin, tissue repair
Published: 2019
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21. Human TRAV1-2-negative MR1-restricted T cells detect S. pyogenes and alternatives to MAIT riboflavin-based antigens

Author: Erin W. Meermeier, Bruno F. Laugel, Andrew K. Sewell, Alexandra J. Corbett, Jamie Rossjohn, James McCluskey, Melanie J. Harriff, Tamera Franks, Marielle C. Gold, and David M. Lewinsohn
Subjects: Science
Abstract: Mucosal-associated invariant T (MAIT) cells sense riboflavin biosynthetic intermediate antigens with a semi-invariant MR1-restricted T-cell receptor (TCR). Here the authors identify a new MR1-restricted TCR that senses cells infected with S. pyogenes, a bacteria unable to biosynthesize riboflavin.
Published: 2016
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22. Differential antigenic requirements by diverse MR1‐restricted T cells

Author: Rebecca Seneviratna, Samuel J Redmond, Hamish EG McWilliam, Rangsima Reantragoon, Jose A Villadangos, James McCluskey, Dale I Godfrey, and Nicholas A Gherardin
Subjects: Minor Histocompatibility Antigens, Receptors, Antigen, T-Cell, alpha-beta, Histocompatibility Antigens Class I, Immunology, Receptors, Antigen, T-Cell, Immunology and Allergy, Cell Biology, Mucosal-Associated Invariant T Cells
Abstract: MHC-related protein 1 (MR1) presents microbial riboflavin metabolites to mucosal-associated invariant T (MAIT) cells for surveillance of microbial presence. MAIT cells express a semi-invariant T-cell receptor (TCR), which recognizes MR1-antigen complexes in a pattern-recognition-like manner. Recently, diverse populations of MR1-restricted T cells have been described that exhibit broad recognition of tumor cells and appear to recognize MR1 in association with tumor-derived self-antigens, though the identity of these antigens remains unclear. Here, we have used TCR gene transfer and engineered MR1-expressing antigen-presenting cells to probe the MR1 restriction and antigen reactivity of a range of MR1-restricted TCRs, including model tumor-reactive TCRs. We confirm MR1 reactivity by these TCRs, show differential dependence on lysine at position 43 of MR1 (K43) and demonstrate competitive inhibition by the MR1 ligand 6-formylpterin. TCR-expressing reporter lines, however, failed to recapitulate the robust tumor specificity previously reported, suggesting an importance of accessory molecules for MR1-dependent tumor reactivity. Finally, MR1-mutant cell lines showed that distinct residues on the α1/α2 helices were required for TCR binding by different MR1-restricted T cells and suggested central but distinct docking modes by the broad family of MR1-restricted αβ TCRs. Collectively, these data are consistent with recognition of distinct antigens by diverse MR1-restricted T cells.
Published: 2022
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23. Quantitative affinity measurement of small molecule ligand binding to major histocompatibility complex class-I-related protein 1 MR1

Author: Carl J.H. Wang, Wael Awad, Ligong Liu, Jeffrey Y.W. Mak, Natacha Veerapen, Patricia T. Illing, Anthony W. Purcell, Sidonia B.G. Eckle, James McCluskey, Gurdyal S. Besra, David P. Fairlie, Jamie Rossjohn, and Jérôme Le Nours
Subjects: Minor Histocompatibility Antigens, Major Histocompatibility Complex, Antigen Presentation, Histocompatibility Antigens Class I, Cell Biology, Ligands, Lymphocyte Activation, Molecular Biology, Biochemistry
Abstract: The Major Histocompatibility Complex class I-related protein 1 (MR1) presents small molecule metabolites, drugs, and drug-like molecules that are recognized by MR1-reactive T cells. While we have an understanding of how antigens bind to MR1 and upregulate MR1 cell surface expression, a quantitative, cell-free, assessment of MR1 ligand-binding affinity was lacking. Here, we developed a fluorescence polarization-based assay in which fluorescent MR1 ligand was loaded into MR1 protein in vitro and competitively displaced by candidate ligands over a range of concentrations. Using this assay, ligand affinity for MR1 could be differentiated as strong (IC
Published: 2022

24. MAIT cells launch a rapid, robust and distinct hyperinflammatory response to bacterial superantigens and quickly acquire an anergic phenotype that impedes their cognate antimicrobial function: Defining a novel mechanism of superantigen-induced immunopathology and immunosuppression.

Author: Christopher R Shaler, Joshua Choi, Patrick T Rudak, Arash Memarnejadian, Peter A Szabo, Mauro E Tun-Abraham, Jamie Rossjohn, Alexandra J Corbett, James McCluskey, John K McCormick, Olivier Lantz, Roberto Hernandez-Alejandro, and S M Mansour Haeryfar
Subjects: Biology (General), QH301-705.5
Abstract: Superantigens (SAgs) are potent exotoxins secreted by Staphylococcus aureus and Streptococcus pyogenes. They target a large fraction of T cell pools to set in motion a "cytokine storm" with severe and sometimes life-threatening consequences typically encountered in toxic shock syndrome (TSS). Given the rapidity with which TSS develops, designing timely and truly targeted therapies for this syndrome requires identification of key mediators of the cytokine storm's initial wave. Equally important, early host responses to SAgs can be accompanied or followed by a state of immunosuppression, which in turn jeopardizes the host's ability to combat and clear infections. Unlike in mouse models, the mechanisms underlying SAg-associated immunosuppression in humans are ill-defined. In this work, we have identified a population of innate-like T cells, called mucosa-associated invariant T (MAIT) cells, as the most powerful source of pro-inflammatory cytokines after exposure to SAgs. We have utilized primary human peripheral blood and hepatic mononuclear cells, mouse MAIT hybridoma lines, HLA-DR4-transgenic mice, MAIThighHLA-DR4+ bone marrow chimeras, and humanized NOD-scid IL-2Rγnull mice to demonstrate for the first time that: i) mouse and human MAIT cells are hyperresponsive to SAgs, typified by staphylococcal enterotoxin B (SEB); ii) the human MAIT cell response to SEB is rapid and far greater in magnitude than that launched by unfractionated conventional T, invariant natural killer T (iNKT) or γδ T cells, and is characterized by production of interferon (IFN)-γ, tumor necrosis factor (TNF)-α and interleukin (IL)-2, but not IL-17A; iii) high-affinity MHC class II interaction with SAgs, but not MHC-related protein 1 (MR1) participation, is required for MAIT cell activation; iv) MAIT cell responses to SEB can occur in a T cell receptor (TCR) Vβ-specific manner but are largely contributed by IL-12 and IL-18; v) as MAIT cells are primed by SAgs, they also begin to develop a molecular signature consistent with exhaustion and failure to participate in antimicrobial defense. Accordingly, they upregulate lymphocyte-activation gene 3 (LAG-3), T cell immunoglobulin and mucin-3 (TIM-3), and/or programmed cell death-1 (PD-1), and acquire an anergic phenotype that interferes with their cognate function against Klebsiella pneumoniae and Escherichia coli; vi) MAIT cell hyperactivation and anergy co-utilize a signaling pathway that is governed by p38 and MEK1/2. Collectively, our findings demonstrate a pathogenic, rather than protective, role for MAIT cells during infection. Furthermore, we propose a novel mechanism of SAg-associated immunosuppression in humans. MAIT cells may therefore provide an attractive therapeutic target for the management of both early and late phases of severe SAg-mediated illnesses.
Published: 2017
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25. Exposure to SARS-CoV-2 generates T-cell memory in the absence of a detectable viral infection

Author: Ji Yang, Haibo Zhou, Xiaoyun Yang, James McCluskey, Zhongfang Wang, Yumin Zhou, Zhiqiang Tang, Zhenjun Chen, Alexandra J. Corbett, Jun He, Pixin Ran, Yonghong Tang, Xinyue Mei, Jiaying Zhong, and Bijia Lin
Subjects: 0301 basic medicine, CD4-Positive T-Lymphocytes, T cell, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viruses, Science, T cells, General Physics and Astronomy, Biology, CD8-Positive T-Lymphocytes, Antibodies, Viral, Viral infection, Asymptomatic, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Interferon-gamma, 0302 clinical medicine, Immunity, medicine, Humans, Interferon gamma, skin and connective tissue diseases, Asymptomatic Infections, Respiratory tract diseases, Multidisciplinary, SARS-CoV-2, fungi, COVID-19, virus diseases, General Chemistry, body regions, 030104 developmental biology, medicine.anatomical_structure, Virus Diseases, 030220 oncology & carcinogenesis, Case-Control Studies, Immunology, biology.protein, medicine.symptom, Antibody, Immunologic Memory, CD8, medicine.drug
Abstract: T-cell immunity is important for recovery from COVID-19 and provides heightened immunity for re-infection. However, little is known about the SARS-CoV-2-specific T-cell immunity in virus-exposed individuals. Here we report virus-specific CD4+ and CD8+ T-cell memory in recovered COVID-19 patients and close contacts. We also demonstrate the size and quality of the memory T-cell pool of COVID-19 patients are larger and better than those of close contacts. However, the proliferation capacity, size and quality of T-cell responses in close contacts are readily distinguishable from healthy donors, suggesting close contacts are able to gain T-cell immunity against SARS-CoV-2 despite lacking a detectable infection. Additionally, asymptomatic and symptomatic COVID-19 patients contain similar levels of SARS-CoV-2-specific T-cell memory. Overall, this study demonstrates the versatility and potential of memory T cells from COVID-19 patients and close contacts, which may be important for host protection., T cells compose a critical component of the immune response to coronavirus infection with SARS-CoV-2. Here the authors characterise the T cell response to SARS CoV-2 in patients and their close contacts, and show the presence of SARS-CoV-2 specific T cells in the absence of detectable virus infection.
Published: 2021

26. Rapid Detection of HLA-B*57:01-Expressing Cells Using a Label-Free Interdigitated Electrode Biosensor Platform for Prevention of Abacavir Hypersensitivity in HIV Treatment

Author: Jianxiong Chan, Gita V. Soraya, Lauren Craig, Shah M. Uddin, Marian Todaro, Duc H. Huynh, Chathurika D. Abeyrathne, Lyudmila Kostenko, James McCluskey, Efstratios Skafidas, and Patrick Kwan
Subjects: human leukocyte antigen, interdigitated electrodes, impedance sensor, protein sensor, point-of-care diagnostics, pharmacogenetics, Chemical technology, TP1-1185
Abstract: Pre-treatment screening of individuals for human leukocyte antigens (HLA) HLA-B*57:01 is recommended for the prevention of life-threatening hypersensitivity reactions to abacavir, a drug widely prescribed for HIV treatment. However, the implementation of screening in clinical practice is hindered by the slow turnaround time and high cost of conventional HLA genotyping methods. We have developed a biosensor platform using interdigitated electrode (IDE) functionalized with a monoclonal antibody to detect cells expressing HLA-B*57:01. This platform was evaluated using cell lines and peripheral blood mononuclear cells expressing different HLA-B alleles. The functionalized IDE sensor was able to specifically capture HLA-B*57:01 cells, resulting in a significant change in the impedance magnitude in 20 min. This IDE platform has the potential to be further developed to enable point-of-care HLA-B*57:01 screening.
Published: 2019
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27. Pegaga Development Drilling Operations with PMCD and CDIV Applications

Author: Annas Omar Mohammad, Azlee Abu Bakar, Khairil Azam Mohd Khaidzir, Donald Robert McKen, Lei Ming Yeow, and Timothy James McCluskey
Abstract: This paper describes the implementation of Pressurized Mud Cap Drilling (PMCD) and Casing Downhole Isolation Valve (CDIV) technology for the Pegaga Development Project to mitigate heavy fluid losses, allowing safe and effective drilling operations to reach well TD. The project consists of seven gas producers (deviated wells), drilled using a jack-up rig from a 10-slot wellhead deck. This paper also describes the planning and operational challenges met to ensure the smooth application of PMCD, starting with selection of the rig and supply vessels, challenges related to adverse weather conditions, long distances between the supply base and drilling location, sufficient mud tank capacity, continuous supply of Light Annular Mud (LAM) for PMCD operations and pandemic related personnel movement restrictions. A continuous learning process was applied for the drilling team where challenges experienced in drilling the first well in PMCD mode and lessons learned were captured and applied to the subsequent wells to improve drilling results. A comprehensive decision tree was established and refined to help the offshore team to make quick decisions when needed to switch to PMCD mode. The Pegaga gas field is located in Block SK320 in the Central Luconia Province, off the coast of Sarawak, offshore Malaysia. The main reservoir is a Pinnacle Carbonate reservoir, which is made up of vugular/karstified carbonates that are likely to cause severe or total losses. The top-hole sections for all seven wells were batched drilled before the PMCD system was rigged up prior to commencing the 12-1/4" intermediate and 8-1/2" reservoir hole sections. The 12-1/4" sections were drilled to above the target gas reservoir carbonate formations, with the PMCD system on standby in case the carbonate formations and severe losses were encountered shallower than prognosed. A single 9-5/8" CDIV (NACE standard) was run with the 9-5/8" × 10-3/4" casing string and permanently set (cemented) in the 12-1/4" open hole, which was the first time this had been done in Malaysia. The CDIVs were set in the open hole to reduce the potential volume of gas below the CDIV and reduce the mud volume required for tripping in PMCD conditions, while increasing the safety and efficiency of PMCD operations. Seven wells were drilled to TD, five in PMCD mode, two conventionally. The lower and upper completions were run and set on six wells, with four of the lower completions run and set in PMCD mode. The CDIV was used to isolate the open hole for tripping out the BHA and running in the lower completion on two of the PMCD wells, while the other three used the top kill method.
Published: 2022
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28. Atypical TRAV1-2− T cell receptor recognition of the antigen-presenting molecule MR1

Author: Ligong Liu, Megan D. Null, Maria L. Sandoval-Romero, David P. Fairlie, Wael Awad, Erin W. Meermeier, Jamie Rossjohn, David M. Lewinsohn, James McCluskey, Jérôme Le Nours, and Aneta H. Worley
Subjects: 0301 basic medicine, 030102 biochemistry & molecular biology, Chemistry, T cell, T-cell receptor, Antigen presentation, Cell Biology, Biochemistry, Cell biology, 03 medical and health sciences, 030104 developmental biology, medicine.anatomical_structure, Antigen, Docking (molecular), medicine, Minor histocompatibility antigen, Binding site, Receptor, Molecular Biology
Abstract: MR1 presents vitamin B-related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2+ αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2- MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2- TCRs interact with MR1-antigen complexes remains unclear. Here, we describe how a TRAV12-2+ TCR (termed D462-E4) recognizes an MR1-antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F'-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F'-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A'-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2+ and TRAV36+ TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.
Published: 2020
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29. IL-17 production by tissue-resident MAIT cells is locally induced in children with pneumonia

Author: Gen Lu, James McCluskey, Hai-Bin Luo, Shengbo Zhang, Diyuan Yang, Ming Liu, Yuxia Zhang, Alexandra J. Corbett, Andrew M. Lew, Yifan Zhan, Jun Cui, Michael J Zhan, Junli Nie, Jun Wang, Vanessa L. Bryant, Li Zhang, Xiaoqiong Gu, Bingtai Lu, Huifeng Fan, and Zhenjun Chen
Subjects: Male, 0301 basic medicine, Immunology, Inflammation, Mucosal associated invariant T cell, Lymphocyte Activation, Article, Monocytes, Mucosal-Associated Invariant T Cells, Immunophenotyping, Transcriptome, Mice, 03 medical and health sciences, 0302 clinical medicine, T-Lymphocyte Subsets, Animals, Humans, Immunology and Allergy, Medicine, Child, Receptor, business.industry, Gene Expression Profiling, Interleukin-17, Pneumonia, medicine.disease, Gene expression profiling, Disease Models, Animal, 030104 developmental biology, 030220 oncology & carcinogenesis, Cytokines, Th17 Cells, Female, Disease Susceptibility, Interleukin 17, Inflammation Mediators, medicine.symptom, business, Biomarkers, Transcription Factors
Abstract: Community-acquired pneumonia (CAP) contributes substantially to morbidity and mortality in children under the age of 5 years. In examining bronchoalveolar lavages (BALs) of children with CAP, we found that interleukin-17 (IL-17) production was significantly increased in severe CAP. Immune profiling showed that mucosal-associated invariant T (MAIT) cells from the BALs, but not blood, of CAP patients actively produced IL-17 (MAIT17). Single-cell RNA-sequencing revealed that MAIT17 resided in a BAL-resident PLZFhiCD103+ MAIT subset with high expression of hypoxia-inducible factor 1α (HIF-1α), reflecting the hypoxic state of the inflamed tissue. CAP BALs also contained a T-bet+ MAIT1 subset and a novel DDIT3+ (DNA damage-inducible transcript 3-positive) MAIT subset with low expression of HIF1A. Furthermore, MAIT17 differed from T-helper type 17 (Th17) cells in the expression of genes related to tissue location, innateness, and cytotoxicity. Finally, we showed that BAL monocytes were hyper-inflammatory and elicited differentiation of MAIT17. Thus, tissue-resident MAIT17 cells are induced at the infected respiratory mucosa, likely influenced by inflammatory monocytes, and contribute to IL-17-mediated inflammation during CAP.
Published: 2020
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30. Hypersensitivities following allergen antigen recognition by unconventional T cells

Author: Liyen Loh, Michael N. T. Souter, Zhenjun Chen, Sidonia B G Eckle, James McCluskey, Daniel G. Pellicci, and Marcela de Lima Moreira
Subjects: Antigen Presentation, biology, Histocompatibility Antigens Class I, Immunology, Antigen presentation, CD1, chemical and pharmacologic phenomena, Mucosal associated invariant T cell, Allergens, Natural killer T cell, Major histocompatibility complex, Mucosal-Associated Invariant T Cells, Minor Histocompatibility Antigens, 03 medical and health sciences, 0302 clinical medicine, 030228 respiratory system, Antigen, CD1D, MHC class I, Hypersensitivity, biology.protein, Humans, Immunology and Allergy, 030215 immunology
Abstract: Conventional T cells recognise protein-derived antigens in the context of major histocompatibility complex (MHC) class Ia and class II molecules and provide anti-microbial and anti-tumour immunity. Conventional T cells have also been implicated in type IV (also termed delayed-type or T cell-mediated) hypersensitivity reactions in response to protein-derived allergen antigens. In addition to conventional T cells, subsets of unconventional T cells exist, which recognise non-protein antigens in the context of monomorphic MHC class I-like molecules. These include T cells that are restricted to the cluster of differentiation 1 (CD1) family members, known as CD1-restricted T cells, and mucosal-associated invariant T cells (MAIT cells) that are restricted to the MHC-related protein 1 (MR1). Compared with conventional T cells, much less is known about the immune functions of unconventional T cells and their role in hypersensitivities. Here, we review allergen antigen presentation by MHC-I-like molecules, their recognition by unconventional T cells, and the potential role of unconventional T cells in hypersensitivities. We also speculate on possible scenarios of allergen antigen presentation by MHC-I-like molecules to unconventional T cells, the hallmarks of such responses, and the expected frequencies of hypersensitivities within the human population.
Published: 2020
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31. Peripheral Blood Mucosal-Associated Invariant T Cells in Tuberculosis Patients and Healthy Mycobacterium tuberculosis-Exposed Controls

Author: David M. Lewinsohn, Sarah K. Iwany, Fatoumatta Darboe, Anele Gela, James McCluskey, Zibiao Zhang, Mark Hatherill, Leonid Lecca, Thomas J. Scriba, Sidonia B G Eckle, Jamie Rossjohn, Kattya Lopez Tamara, D. Branch Moody, Megan Murray, Nicole Bilek, Alexandra J. Corbett, Segundo R. Leon, Roger Calderon, Sara Suliman, Ildiko Van Rhijn, Simon C Mendelsohn, Lars Kjer-Nielsen, Michelle Fisher, Simbarashe Mabwe, and Chuan-Chin Huang
Subjects: Adult, Male, 0301 basic medicine, Tuberculosis, Mucosal associated invariant T cell, Major histocompatibility complex, Risk Assessment, Mucosal-Associated Invariant T Cells, Immunophenotyping, Mycobacterium tuberculosis, Major Articles and Brief Reports, 03 medical and health sciences, 0302 clinical medicine, Antigen, Risk Factors, Prevalence, Humans, Immunology and Allergy, Medicine, Public Health Surveillance, biology, Cluster of differentiation, business.industry, Middle Aged, biology.organism_classification, medicine.disease, 3. Good health, 030104 developmental biology, Infectious Diseases, Case-Control Studies, Immunology, biology.protein, Female, business, Biomarkers, 030215 immunology, Mycobacterium
Abstract: Background In human blood, mucosal-associated invariant T (MAIT) cells are abundant T cells that recognize antigens presented on non-polymorphic major histocompatibility complex-related 1 (MR1) molecules. The MAIT cells are activated by mycobacteria, and prior human studies indicate that blood frequencies of MAIT cells, defined by cell surface markers, decline during tuberculosis (TB) disease, consistent with redistribution to the lungs. Methods We tested whether frequencies of blood MAIT cells were altered in patients with TB disease relative to healthy Mycobacterium tuberculosis-exposed controls from Peru and South Africa. We quantified their frequencies using MR1 tetramers loaded with 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil. Results Unlike findings from prior studies, frequencies of blood MAIT cells were similar among patients with TB disease and latent and uninfected controls. In both cohorts, frequencies of MAIT cells defined by MR1-tetramer staining and coexpression of CD161 and the T-cell receptor alpha variable gene TRAV1-2 were strongly correlated. Disease severity captured by body mass index or TB disease transcriptional signatures did not correlate with MAIT cell frequencies in patients with TB. Conclusions Major histocompatibility complex (MHC)-related 1-restrictied MAIT cells are detected at similar levels with tetramers or surface markers. Unlike MHC-restricted T cells, blood frequencies of MAIT cells are poor correlates of TB disease but may play a role in pathophysiology.
Published: 2020
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32. The molecular basis underpinning the potency and specificity of MAIT cell antigens

Author: Alexandra J. Corbett, Ligong Liu, Jamie Rossjohn, Weijun Xu, Jeffrey Y. W. Mak, James McCluskey, Wael Awad, Xin Yi Lim, Jérôme Le Nours, David P. Fairlie, Geraldine J. M. Ler, Andrew N. Keller, and Sidonia B G Eckle
Subjects: 0301 basic medicine, Cellular immunity, Receptors, Antigen, T-Cell, alpha-beta, Riboflavin, T cell, Immunology, Mucosal associated invariant T cell, Ligands, Lymphocyte Activation, Major histocompatibility complex, Mucosal-Associated Invariant T Cells, Jurkat Cells, 03 medical and health sciences, 0302 clinical medicine, Antigen, Cell Line, Tumor, medicine, Humans, Immunology and Allergy, Antigens, biology, Chemistry, Antigen processing, T-cell receptor, Cell biology, 030104 developmental biology, medicine.anatomical_structure, biology.protein, Cell activation, 030215 immunology
Abstract: Mucosal-associated invariant T (MAIT) cells are activated by microbial riboflavin-based metabolite antigens when presented by MR1. How modifications to the potent antigen 5-OP-RU affect presentation by MR1 and MAIT cell activation remains unclear. Here we design 20 derivatives, termed altered metabolite ligands (AMLs), to dissect the impact of different antigen components on the human MAIT-MR1 axis. Analysis of 11 crystal structures of MAIT T cell antigen receptor (TCR)-MR1-AML ternary complexes, along with biochemical and functional assays, shows that MR1 cell-surface upregulation is influenced by ribityl and non-ribityl components of the ligand and the hydrophobicity of the MR1-AML interface. The polar ribityl chain of the AML strongly influences MAIT cell activation potency through dynamic compensatory interactions within a MAIT TCR-MR1-AML interaction triad. We define the basis by which the MAIT TCR can differentially recognize AMLs, thereby providing insight into MAIT cell antigen specificity and potency.
Published: 2020
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33. Human Mucosal-Associated Invariant T Cells in Older Individuals Display Expanded TCRαβ Clonotypes with Potent Antimicrobial Responses

Author: Katherine Kedzierska, Dale I. Godfrey, Liyen Loh, James McCluskey, Carolien E. van de Sandt, Nicholas A Gherardin, E. Kaitlynn Allen, Paul G. Thomas, Sidonia B G Eckle, Martha Lappas, Thomas Loudovaris, Ludivine Grzelak, Jane Crowe, Kylie M. Quinn, Jeremy Chase Crawford, Hui-Fern Koay, Sneha Sant, Katie L. Flanagan, Nicola L. Bird, Marcela de Lima Moreira, Jamie Rossjohn, and Landsteiner Laboratory
Subjects: Adult, Male, Chemokine, Receptors, Antigen, T-Cell, alpha-beta, medicine.medical_treatment, T cell, Immunology, Mucosal associated invariant T cell, CD8-Positive T-Lymphocytes, Biology, CD8-Positive T-Lymphocytes/immunology, Granzymes, Mucosal-Associated Invariant T Cells, GZMB, Interferon-gamma, 03 medical and health sciences, alpha-beta/immunology, 0302 clinical medicine, Immune system, Granzymes/immunology, Antigen, Lysosomal-Associated Membrane Protein 1, Receptors, Escherichia coli, medicine, Humans, Immunology and Allergy, Lysosomal-Associated Membrane Protein 1/immunology, Aged, Escherichia coli/immunology, Tumor Necrosis Factor-alpha, Middle Aged, T-Cell, Tumor Necrosis Factor-alpha/immunology, Viruses/immunology, Cytokine, medicine.anatomical_structure, Receptors, Antigen, T-Cell, alpha-beta/immunology, Interferon-gamma/immunology, Viruses, biology.protein, Female, Mucosal-Associated Invariant T Cells/immunology, CD8, 030215 immunology
Abstract: Mucosal-associated invariant T (MAIT) cells are important for immune responses against microbial infections. Although known to undergo marked numerical changes with age in humans, our understanding of how MAIT cells are altered during different phases across the human life span is largely unknown. Although also abundant in the tissues, our study focuses on MAIT cell analyses in blood. Across the human life span, we show that naive-like MAIT cells in umbilical cord blood switch to a central/effector memory-like profile that is sustained into older age. Whereas low-grade levels of plasma cytokine/chemokine were apparent in older donors (>65 y old), surprisingly, they did not correlate with the ex vivo MAIT hyperinflammatory cytokine profile observed in older adults. Removal of MAIT cells from older individuals and an aged environment resulted in the reversal of the baseline effector molecule profile comparable with MAIT cells from younger adults. An upregulated basal inflammatory profile accounted for reducedEscherichia coli–specific responses in aged MAIT cells compared with their young adult counterparts when fold change in expression levels of GzmB, CD107a, IFN-γ, and TNF was examined. However, the magnitude of antimicrobial MR1-dependent activation remained as potent and polyfunctional as with younger adults. Paired TCRαβ analyses of MAIT cells revealed large clonal expansions in older adults and tissues that rivalled, remarkably, the TCRαβ repertoire diversity of virus-specific CD8+T cells. These data suggest that MAIT cells in older individuals, although associated with large clonal TCRαβ expansions and increased baseline inflammatory potential, demonstrate plasticity and provide potent antimicrobial immunity.
Published: 2020
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34. The Establishment of a CMV-Specific CD8 + T-Cell Threshold by Kinetic Modelling for Prediction of Post-HSCT Reactivation

Author: Jing Zhang, Jinpeng Cao, Runhui Zheng, Mengqiu Yu, Zhengfang Lin, Caixia Wang, James McCluskey, Ji Yang, Zhenjun Chen, Alexandra J. Corbett, Pengxing Cao, Wenjian Mo, and Zhongfang Wang
Subjects: History, Polymers and Plastics, Business and International Management, Industrial and Manufacturing Engineering
Published: 2022
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35. T cell receptor cross-reactivity between gliadin and bacterial peptides in celiac disease

Author: Jan Petersen, Hugh H. Reid, Laura Ciacchi, Melinda Y Hardy, Frits Koning, Robert P. Anderson, Khai Lee Loh, Yvonne Kooy-Winkelaar, Jason A. Tye-Din, Anthony W. Purcell, Zhenjun Chen, Jamie Rossjohn, James McCluskey, Mai T. Tran, and Nathan P. Croft
Subjects: 0303 health sciences, HLA-DQ Antigen, biology, Chemistry, T cell, fungi, T-cell receptor, nutritional and metabolic diseases, Human leukocyte antigen, medicine.disease_cause, digestive system diseases, Epitope, 03 medical and health sciences, Molecular mimicry, 0302 clinical medicine, medicine.anatomical_structure, Antigen, Structural Biology, Immunology, medicine, biology.protein, Gliadin, Molecular Biology, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Structural, biochemical and cellular analyses show that bacterial antigens can mimic gliadin epitopes involved in celiac disease being presented by HLA-DQ2.5 and recognized by T cells derived from patients.The human leukocyte antigen (HLA) locus is strongly associated with T cell-mediated autoimmune disorders. HLA-DQ2.5-mediated celiac disease (CeD) is triggered by the ingestion of gluten, although the relative roles of genetic and environmental risk factors in CeD is unclear. Here we identify microbially derived mimics of gliadin epitopes and a parental bacterial protein that is naturally processed by antigen-presenting cells and activated gliadin reactive HLA-DQ2.5-restricted T cells derived from CeD patients. Crystal structures of T cell receptors in complex with HLA-DQ2.5 bound to two distinct bacterial peptides demonstrate that molecular mimicry underpins cross-reactivity toward the gliadin epitopes. Accordingly, gliadin reactive T cells involved in CeD pathogenesis cross-react with ubiquitous bacterial peptides, thereby suggesting microbial exposure as a potential environmental factor in CeD.
Published: 2019
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36. MAIT cells regulate NK cell-mediated tumor immunity

Author: Phillip K. Darcy, Angela Pizzolla, Rosemary Millen, Jessica Michie, James McCluskey, Timothy McCulloch, Junyun Lai, Jeffrey Y. W. Mak, Jack D Chan, Jasmine Li, Jane Oliaro, Amanda X. Y. Chen, Emma V. Petley, Paul A. Beavis, Imran G House, Kevin Sek, Hui-Fern Koay, Simon P. Keam, Robert G. Ramsay, Nicholas D. Huntington, Paul J Neeson, Dale I. Godfrey, Lauren Giuffrida, Melissa A. Henderson, Fernando Souza-Fonseca-Guimaraes, Amanda J Oliver, Andrew J. Freeman, Conor J. Kearney, Kirsten L. Todd, Magnus Zethoven, and David P. Fairlie
Subjects: Science, Cell, T cells, General Physics and Astronomy, Innate lymphoid cells, Antineoplastic Agents, Context (language use), Mucosal associated invariant T cell, Biology, Article, Mucosal-Associated Invariant T Cells, General Biochemistry, Genetics and Molecular Biology, Minor Histocompatibility Antigens, Mice, Antigen, Immunity, Cell Line, Tumor, Neoplasms, medicine, Animals, Humans, Neoplasm Metastasis, Mice, Knockout, Immunity, Cellular, Multidisciplinary, Histocompatibility Antigens Class I, T-cell receptor, General Chemistry, Gene signature, Killer Cells, Natural, Mice, Inbred C57BL, medicine.anatomical_structure, Cell culture, Cancer research, Mucosal immunology, Tumour immunology, Cytokines
Abstract: The function of MR1-restricted mucosal-associated invariant T (MAIT) cells in tumor immunity is unclear. Here we show that MAIT cell-deficient mice have enhanced NK cell-dependent control of metastatic B16F10 tumor growth relative to control mice. Analyses of this interplay in human tumor samples reveal that high expression of a MAIT cell gene signature negatively impacts the prognostic significance of NK cells. Paradoxically, pre-pulsing tumors with MAIT cell antigens, or activating MAIT cells in vivo, enhances anti-tumor immunity in B16F10 and E0771 mouse tumor models, including in the context of established metastasis. These effects are associated with enhanced NK cell responses and increased expression of both IFN-γ-dependent and inflammatory genes in NK cells. Importantly, activated human MAIT cells also promote the function of NK cells isolated from patient tumor samples. Our results thus describe an activation-dependent, MAIT cell-mediated regulation of NK cells, and suggest a potential therapeutic avenue for cancer treatment., Mucosal-associated invariant T (MAIT) cells facilitate anti-microbial responses, but their functions in cancer protection is unclear. Here the authors show that activated MAIT cells induce an IFN-γ transcriptome in natural killer (NK) cells and enhance NK-dependent anti-cancer immunity in mice, thereby hinting a new avenue for cancer therapy.
Published: 2021
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37. Differential Location of NKT and MAIT Cells within Lymphoid Tissue

Author: Dale I. Godfrey, James McCluskey, Paul A. Beavis, Zheng Ruan, Sapna Devi, Lauren E. Holz, Darryl N. Johnson, Scott N. Mueller, Jeffrey Y. W. Mak, Jyh Liang Hor, Adam P Uldrich, William R. Heath, Emma V. Petley, Phillip K. Darcy, and David P. Fairlie
Subjects: Multidisciplinary, Lymphoid Tissue, Receptors, Antigen, T-Cell, alpha-beta, Receptors, Antigen, T-Cell, MAIT Cells, Mice, Transgenic, hemic and immune systems, chemical and pharmacologic phenomena, Biology, Mucosal-Associated Invariant T Cells, Cell biology, Mice, Lymphatic system, Animals, Natural Killer T-Cells, Differential (mathematics)
Abstract: Natural Killer T (NKT) cells and Mucosal-Associated Invariant T (MAIT) cells are innate-like T cells that express semi-invariant αβ T cell receptors (TCRs) through which they recognise CD1d and MR1 molecules, respectively, in complex with specific ligands. These cells play important roles in health and disease in many organs, but their precise intra-organ location is not well established. Here, using CD1d and MR1 tetramer staining techniques, we describe the precise location of NKT and MAIT cells in lymphoid and peripheral organs. Within the thymus, NKT cells were concentrated in the medullary side of the corticomedullary junction. In spleen and lymph nodes, NKT cells were mainly localised within T cell zones (TCZ), although following in vivo activation with the potent NKT-cell ligand α-GalCer, they expanded throughout the spleen. MAIT cells were clearly detectable in Vα19 TCR transgenic mice and were rare but detectable in lymphoid tissue of non-transgenic mice. In contrast to NKT cells, MAIT cells were more closely associated with the B cell zone (BCZ) and red pulp (RP) of the spleen. Accordingly, we have provided an extensive analysis of the in situ localisation of NKT and MAIT cells and suggest differences between the intra-organ location of these two cell types.
Published: 2021
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38. Kinetics of abacavir-induced remodelling of the major histocompatibility complex class I peptide repertoire

Author: Nicole A. Mifsud, Rachel Darley, James McCluskey, Tim Elliott, Anthony W. Purcell, Samuel King, Patricia T. Illing, Mandvi Bharadwaj, Nathan P. Croft, Lyudmila Kostenko, and Andy van Hateren
Subjects: 0301 basic medicine, immunopeptidome, Anti-HIV Agents, T-Lymphocytes, T cell, Immunology, T cells, Peptide, Lymphocyte Activation, Major histocompatibility complex, Epitope, Cell Line, 03 medical and health sciences, 0302 clinical medicine, tapasin, Tapasin, Abacavir, immune system diseases, medicine, HLA-B Antigens, Humans, Immunology and Allergy, peptide selection, Original Research, chemistry.chemical_classification, biology, Chemistry, abacavir, virus diseases, RC581-607, Dideoxynucleosides, Allotype, Cell biology, Kinetics, 030104 developmental biology, medicine.anatomical_structure, biology.protein, Immunologic diseases. Allergy, drug hypersensitivity, 030215 immunology, medicine.drug, MHC I antigen presentation
Abstract: Abacavir hypersensitivity syndrome can occur in individuals expressing the HLA-B*57:01 major histocompatibility complex class I allotype when utilising the drug abacavir as a part of their anti-retroviral regimen. The drug is known to bind within the HLA-B*57:01 antigen binding cleft, leading to the selection of novel self-peptide ligands, thus provoking life-threatening immune responses. However, the sub-cellular location of abacavir binding and the mechanics of altered peptide selection are not well understood. Here, we probed the impact of abacavir on the assembly of HLA-B*57:01 peptide complexes. We show that whilst abacavir had minimal impact on the maturation or average stability of HLA-B*57:01 molecules, abacavir was able to differentially enhance the formation, selectively decrease the dissociation, and alter tapasin loading dependency of certain HLA-B*57:01-peptide complexes. Our data reveals a spectrum of abacavir mediated effects on the immunopeptidome which reconciles the heterogeneous functional T cell data reported in the literature.
Published: 2021
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39. Anti-Leishmania activity of mucosal-associated invariant T-cells

Author: Maria Vitória Assumpção Mourão, Marcela de Lima Moreira, Marineide Borges, Malcolm J. McConville, Vanessa Peruhype-Magalhães, Sidonia B G Eckle, Flávia Alves Campos, Marcelo Antônio Pascoal-Xavier, Andrea Lucchesi de Carvalho, Mariângela Carneiro, Zhenjun Chen, Olindo Assis Martins-Filho, Victória Hellena Silva Pereira, Andréa Teixeira-Carvalho, James McCluskey, Moriya Tsuji, Ágata Lopes-Ribeiro, Jordana Grazziela Coelho-dos-Reis, Troi J. Pediongco, Luana Oliveira Borges Fernandes, Eleanor C Saunders, and Márcio da Silva Araújo
Subjects: parasitic diseases, Mucosal associated invariant T cell, Biology, Leishmania, biology.organism_classification, Molecular biology
Abstract: Mucosal-associated invariant T (MAIT)-cells are restricted by MR1 and are known to contribute to protection from bacterial and viral infections. Here we show that MAIT-cells also play an important role in protection from visceral leishmaniasis-VL, caused by protozoan parasites of the Leishmania donovani complex. In response to L. infantum, human peripheral blood MAIT-cells produced TNF and IFN-γ and this was MR1-dependent. Since Leishmania spp. lack riboflavin biosynthesis, this suggests that novel MAIT-cell antigen(s) exist in the context of Leishmania-infection. In asymptomatic individuals, MAIT-cells also produced IL-17A, dependent on MR1, a cytokine signature associated with resistance to visceral Leishmaniasis. In mice, MAIT-cells reduced parasite burden during peak infection and decreased pathology. In summary, these results broaden our understanding of MAIT-cell immunity to include protection from parasitic infections with implications for MAIT-cell based therapeutics and vaccines. Leishmania is an ancient and clinically important pathogen such that it may have contributed to shaping MAIT-cell biology.
Published: 2021
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40. Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

Author: Lara Gibellini, Sussan Nourshargh, Susanna Cardell, Wlodzimierz Maslinski, Mar Felipo-Benavent, Florian Mair, Hans-Martin Jäck, Lilly Lopez, Klaus Warnatz, John Trowsdale, Diana Ordonez, Marcus Eich, William Hwang, Anne Cooke, Dirk Mielenz, Alberto Orfao, Winfried F. Pickl, Vladimir Benes, Alice Yue, T. Vincent Shankey, Maria Tsoumakidou, Virginia Litwin, Gelo Victoriano Dela Cruz, Andrea Cavani, Sara De Biasi, Larissa Nogueira Almeida, Jonathan J M Landry, Claudia Haftmann, Charlotte Esser, Ana Cumano, Anneke Wilharm, Francesco Dieli, Rudi Beyaert, Alessio Mazzoni, Burkhard Ludewig, Carlo Pucillo, Dirk H. Busch, Joe Trotter, Stipan Jonjić, Marc Veldhoen, Josef Spidlen, Aja M. Rieger, Dieter Adam, Srijit Khan, Todd A. Fehniger, Giuseppe Matarese, Maximilien Evrard, Christian Maueröder, Steffen Schmitt, Kristin A. Hogquist, Barry Moran, Raghavendra Palankar, Markus Feuerer, S Schmid, Susann Rahmig, Amy E. Lovett-Racke, James V. Watson, Megan K. Levings, Susanne Melzer, Dinko Pavlinic, Christopher M. Harpur, Christina Stehle, A. Graham Pockley, Toshinori Nakayama, Attila Tárnok, Juhao Yang, Michael Lohoff, Paulo Vieira, Francisco Sala-de-Oyanguren, Christian Kurts, Anastasia Gangaev, Alfonso Blanco, Hans Scherer, Regine J. Dress, Bruno Silva-Santos, Kiyoshi Takeda, Bimba F. Hoyer, Ilenia Cammarata, Daryl Grummitt, Isabel Panse, Günnur Deniz, Bianka Baying, Friederike Ebner, Esther Schimisky, Leo Hansmann, Thomas Kamradt, Edwin van der Pol, Daniel Scott-Algara, Anna Iannone, Giorgia Alvisi, Sebastian R. Schulz, Francesco Liotta, Irmgard Förster, Beatriz Jávega, Hans-Peter Rahn, Caetano Reis e Sousa, Livius Penter, Xuetao Cao, David P. Sester, Keisuke Goda, Peter Wurst, Iain B. McInnes, Ricardo T. Gazzinelli, Federica Piancone, Gerald Willimsky, Yotam Raz, Pärt Peterson, Wolfgang Fritzsche, Yvonne Samstag, Martin Büscher, Thomas Schüler, Susanne Hartmann, Robert J. Wilkinson, Anna E. S. Brooks, Steven L. C. Ketelaars, Catherine Sautès-Fridman, Anna Rubartelli, Petra Bacher, Katja Kobow, Marco A. Cassatella, Andrea Hauser, Henrik E. Mei, Kilian Schober, Silvia Della Bella, Graham Anderson, Michael D. Ward, Garth Cameron, Sebastian Lunemann, Katharina Kriegsmann, Katarzyna M. Sitnik, Brice Gaudilliere, Chantip Dang-Heine, Marcello Pinti, Paul Klenerman, Frank A. Schildberg, Joana Barros-Martins, Laura G. Rico, Hanlin Zhang, Christian Münz, Thomas Dörner, Jakob Zimmermann, Andrea M. Cooper, Jonni S. Moore, Andreas Diefenbach, Yanling Liu, Wolfgang Bauer, Tobit Steinmetz, Katharina Pracht, Leonard Tan, Peter K. Jani, Alan M. Stall, Petra Hoffmann, Christine S. Falk, Jasmin Knopf, Simon Fillatreau, Hans-Dieter Volk, Luis E. Muñoz, David L. Haviland, William W. Agace, Jonathan Rebhahn, Ljiljana Cvetkovic, Mohamed Trebak, Jordi Petriz, Mario Clerici, Diether J. Recktenwald, Anders Ståhlberg, Tristan Holland, Helen M. McGuire, Sa A. Wang, Christian Kukat, Thomas Kroneis, Laura Cook, Wan Ting Kong, Xin M. Wang, Britta Engelhardt, Pierre Coulie, Genny Del Zotto, Sally A. Quataert, Kata Filkor, Gabriele Multhoff, Bartek Rajwa, Federica Calzetti, Hans Minderman, Cosima T. Baldari, Jens Geginat, Hervé Luche, Gert Van Isterdael, Linda Schadt, Sophia Urbanczyk, Giovanna Borsellino, Liping Yu, Dale I. Godfrey, Achille Anselmo, Rachael C. Walker, Andreas Grützkau, David W. Hedley, Birgit Sawitzki, Silvia Piconese, Maria Yazdanbakhsh, Burkhard Becher, Ramon Bellmas Sanz, Michael Delacher, Hyun-Dong Chang, Immanuel Andrä, Hans-Gustaf Ljunggren, José-Enrique O'Connor, Ahad Khalilnezhad, Sharon Sanderson, Federico Colombo, Götz R. A. Ehrhardt, Inga Sandrock, Enrico Lugli, Christian Bogdan, James B. Wing, Susann Müller, Tomohiro Kurosaki, Derek Davies, Ester B. M. Remmerswaal, Kylie M. Quinn, Christopher A. Hunter, Andreas Radbruch, Timothy P. Bushnell, Anna Erdei, Sabine Adam-Klages, Pascale Eede, Van Duc Dang, Rieke Winkelmann, Thomas Korn, Gemma A. Foulds, Dirk Baumjohann, Matthias Schiemann, Manfred Kopf, Jan Kisielow, Lisa Richter, Jochen Huehn, Gloria Martrus, Alexander Scheffold, Jessica G. Borger, Sidonia B G Eckle, John Bellamy Foster, Anna Katharina Simon, Alicia Wong, Mübeccel Akdis, Gisa Tiegs, Toralf Kaiser, James McCluskey, Anna Vittoria Mattioli, Aaron J. Marshall, Hui-Fern Koay, Eva Orlowski-Oliver, Anja E. Hauser, J. Paul Robinson, Jay K. Kolls, Luca Battistini, Mairi McGrath, Jane L. Grogan, Natalio Garbi, Timothy Tree, Kingston H. G. Mills, Stefan H. E. Kaufmann, Wolfgang Schuh, Ryan R. Brinkman, Tim R. Mosmann, Vincenzo Barnaba, Andreas Dolf, Lorenzo Cosmi, Bo Huang, Andreia C. Lino, Baerbel Keller, René A. W. van Lier, Alexandra J. Corbett, Paul S. Frenette, Pleun Hombrink, Helena Radbruch, Sofie Van Gassen, Olivier Lantz, Lorenzo Moretta, Désirée Kunkel, Kirsten A. Ward-Hartstonge, Armin Saalmüller, Leslie Y. T. Leung, Salvador Vento-Asturias, Paola Lanuti, Alicia Martínez-Romero, Sarah Warth, Zhiyong Poon, Diana Dudziak, Andrea Cossarizza, Kovit Pattanapanyasat, Konrad von Volkmann, Jessica P. Houston, Agnès Lehuen, Andrew Filby, Pratip K. Chattopadhyay, Stefano Casola, Annika Wiedemann, Hannes Stockinger, Jürgen Ruland, Arturo Zychlinsky, Claudia Waskow, Katrin Neumann, Ari Waisman, Lucienne Chatenoud, Sudipto Bari, Kamran Ghoreschi, David W. Galbraith, Yvan Saeys, Hamida Hammad, Andrea Gori, Miguel López-Botet, Gabriel Núñez, Sabine Ivison, Michael Hundemer, Dorothea Reimer, Mark C. Dessing, Günter J. Hämmerling, Rudolf A. Manz, Tomas Kalina, Jonas Hahn, Holden T. Maecker, Hendy Kristyanto, Martin S. Davey, Henning Ulrich, Michael L. Dustin, Takashi Saito, Yousuke Takahama, Milena Nasi, Johanna Huber, Jürgen Wienands, Paolo Dellabona, Andreas Schlitzer, Michael D. Leipold, Kerstin H. Mair, Christian Peth, Immo Prinz, Chiara Romagnani, José M. González-Navajas, Josephine Schlosser, Marina Saresella, Matthias Edinger, Dirk Brenner, Nicole Baumgarth, Rikard Holmdahl, Fang-Ping Huang, Guadalupe Herrera, Malte Paulsen, Gergely Toldi, Luka Cicin-Sain, Reiner Schulte, Christina E. Zielinski, Thomas Winkler, Christoph Goettlinger, Philip E. Boulais, Jennie H M Yang, Antonio Celada, Heike Kunze-Schumacher, Julia Tornack, Florian Ingelfinger, Jenny Mjösberg, Andy Riddell, Leonie Wegener, Thomas Höfer, Christoph Hess, James P. Di Santo, Anna E. Oja, J. Kühne, Willem van de Veen, Mary Bebawy, Alberto Mantovani, Bart Everts, Giovanna Lombardi, Laura Maggi, Anouk von Borstel, Pia Kvistborg, Elisabetta Traggiai, A Ochel, Nima Aghaeepour, Charles-Antoine Dutertre, Matthieu Allez, Thomas Höllt, Wenjun Ouyang, Regina Stark, Maries van den Broek, Shimon Sakaguchi, Paul K. Wallace, Silvano Sozzani, Francesca LaRosa, Annette Oxenius, Malgorzata J. Podolska, Ivana Marventano, Wilhelm Gerner, Oliver F. Wirz, Britta Frehse, Gevitha Ravichandran, Martin Herrmann, Carl S. Goodyear, Gary Warnes, Helen Ferry, Stefan Frischbutter, Tim R. Radstake, Salomé LeibundGut-Landmann, Yi Zhao, Axel Schulz, Angela Santoni, Pablo Engel, Daniela C. Hernández, Andreas Acs, Cristiano Scottà, Francesco Annunziato, Thomas Weisenburger, Wolfgang Beisker, Sue Chow, Fritz Melchers, Daniel E. Speiser, Immanuel Kwok, Florent Ginhoux, Dominic A. Boardman, Natalie Stanley, Carsten Watzl, Marie Follo, Erik Lubberts, Andreas Krueger, Susanne Ziegler, Göran K. Hansson, David Voehringer, Antonia Niedobitek, Eleni Christakou, Lai Guan Ng, Sabine Baumgart, Nicholas A Gherardin, Antonio Cosma, Orla Maguire, Jolene Bradford, Daniel Schraivogel, Linda Quatrini, Stephen D. Miller, Rheumatology, Università degli Studi di Modena e Reggio Emilia (UNIMORE), Deutsches Rheuma-ForschungsZentrum (DRFZ), Deutsches Rheuma-ForschungsZentrum, Swiss Institute of Allergy and Asthma Research (SIAF), Universität Zürich [Zürich] = University of Zurich (UZH), Institut de Recherche Saint-Louis - Hématologie Immunologie Oncologie (Département de recherche de l’UFR de médecine, ex- Institut Universitaire Hématologie-IUH) (IRSL), Université de Paris (UP), Ecotaxie, microenvironnement et développement lymphocytaire (EMily (UMR_S_1160 / U1160)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Department of Internal Medicine, Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI)-DENOTHE Center, Institute of Clinical Molecular Biology, Kiel University, Department of Life Sciences [Siena, Italy], Università degli Studi di Siena = University of Siena (UNISI), Institut Pasteur, Fondation Cenci Bolognetti - Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Réseau International des Instituts Pasteur (RIIP), Dulbecco Telethon Institute/Department of Biology, Caprotec Bioanalytics GmbH, International Occultation Timing Association European Section (IOTA ES), International Occultation Timing Association European Section, European Molecular Biology Laboratory [Heidelberg] (EMBL), VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Fondazione Santa Lucia (IRCCS), Department of Immunology, Chinese Academy of Medical Sciences, FIRC Institute of Molecular Oncology Foundation, IFOM, Istituto FIRC di Oncologia Molecolare (IFOM), Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Physiopatology and Transplantation, University of Milan (DEPT), University of Milan, Monash University [Clayton], Institut des Maladies Emergentes et des Thérapies Innovantes (IMETI), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Institute of Cellular Pathology, Université Catholique de Louvain = Catholic University of Louvain (UCL), Lymphopoïèse (Lymphopoïèse (UMR_1223 / U1223 / U-Pasteur_4)), Institut Pasteur [Paris]-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Experimental Immunology Unit, Dept. of Oncology, DIBIT San Raffaele Scientific Institute, Immunité Innée - Innate Immunity, Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris], Charité - UniversitätsMedizin = Charité - University Hospital [Berlin], Department of Biopharmacy [Bruxelles, Belgium] (Institute for Medical Immunology IMI), Université libre de Bruxelles (ULB), Charité Hospital, Humboldt-Universität zu Berlin, Agency for science, technology and research [Singapore] (A*STAR), Laboratory of Molecular Immunology and the Howard Hughes Institute, Rockefeller University [New York], Kennedy Institute of Rheumatology [Oxford, UK], Imperial College London, Theodor Kocher Institute, University of Bern, Leibniz Research Institute for Environmental Medicine [Düsseldorf, Germany] ( IUF), Université Lumière - Lyon 2 (UL2), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), University of Edinburgh, Integrative Biology Program [Milano], Istituto Nazionale Genetica Molecolare [Milano] (INGM), Singapore Immunology Network (SIgN), Biomedical Sciences Institute (BMSI), Universitat de Barcelona (UB), Rheumatologie, Cell Biology, Department of medicine [Stockholm], Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm], Department for Internal Medicine 3, Institute for Clinical Immunology, Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Delft University of Technology (TU Delft), Medical Inflammation Research, Karolinska Institutet [Stockholm], Department of Photonics Engineering [Lyngby], Technical University of Denmark [Lyngby] (DTU), Dpt of Experimental Immunology [Braunschweig], Helmholtz Centre for Infection Research (HZI), Department of Internal Medicine V, Universität Heidelberg [Heidelberg], Department of Histology and Embryology, University of Rijeka, Freiburg University Medical Center, Nuffield Dept of Clinical Medicine, University of Oxford [Oxford]-NIHR Biomedical Research Centre, Institute of Integrative Biology, Molecular Biomedicine, Berlin Institute of Health (BIH), Laboratory for Lymphocyte Differentiation, RIKEN Research Center, Institutes of Molecular Medicine and Experimental Immunology, University of Bonn, Immunité et cancer (U932), Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Department of Surgery [Vancouver, BC, Canada] (Child and Family Research Institute), University of British Columbia (UBC)-Child and Family Research Institute [Vancouver, BC, Canada], College of Food Science and Technology [Shangai], Shanghai Ocean University, Institute for Medical Microbiology and Hygiene, University of Marburg, King‘s College London, Erasmus University Medical Center [Rotterdam] (Erasmus MC), Centre d'Immunophénomique (CIPHE), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Brustzentrum Kantonsspital St. Gallen, Immunotechnology Section, Vaccine Research Center, National Institutes of Health [Bethesda] (NIH)-National Institute of Allergy and Infectious Diseases, Heinrich Pette Institute [Hamburg], Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Department of Immunology and Cell Biology, Mario Negri Institute, Laboratory of Molecular Medicine and Biotechnology, Don C. Gnocchi ONLUS Foundation, Institute of Translational Medicine, Klinik für Dermatologie, Venerologie und Allergologie, School of Biochemistry and Immunology, Department of Medicine Huddinge, Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm]-Lipid Laboratory, Università di Genova, Dipartimento di Medicina Sperimentale, Department of Environmental Microbiology, Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), Department of Radiation Oncology [Munich], Ludwig-Maximilians-Universität München (LMU), Centre de Recherche Publique- Santé, Université du Luxembourg (Uni.lu), William Harvey Research Institute, Barts and the London Medical School, University of Michigan [Ann Arbor], University of Michigan System, Centro de Investigacion del Cancer (CSIC), Universitario de Salamanca, Molecular Pathology [Tartu, Estonia], University of Tartu, Hannover Medical School [Hannover] (MHH), Centre d'Immunologie de Marseille - Luminy (CIML), Monash Biomedicine Discovery Institute, Cytometry Laboratories and School of Veterinary Medicine, Purdue University [West Lafayette], Data Mining and Modelling for Biomedicine [Ghent, Belgium], VIB Center for Inflammation Research [Ghent, Belgium], Laboratory for Cell Signaling, RIKEN Research Center for Allergy and Immunology, RIKEN Research Center for Allergy and Immunology, Osaka University [Osaka], Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome], Centre de Recherche des Cordeliers (CRC (UMR_S_1138 / U1138)), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université de Paris (UP), Institute of Medical Immunology [Berlin, Germany], FACS and Array Core Facility, Johannes Gutenberg - Universität Mainz (JGU), Otto-von-Guericke University [Magdeburg] (OVGU), SUPA School of Physics and Astronomy [University of St Andrews], University of St Andrews [Scotland]-Scottish Universities Physics Alliance (SUPA), Biologie Cellulaire des Lymphocytes - Lymphocyte Cell Biology, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), General Pathology and Immunology (GPI), University of Brescia, Université de Lausanne (UNIL), Terry Fox Laboratory, BC Cancer Agency (BCCRC)-British Columbia Cancer Agency Research Centre, Department of Molecular Immunology, Medizinische Universität Wien = Medical University of Vienna, Dept. Pediatric Cardiology, Universität Leipzig [Leipzig], Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg] (UKE), Center for Cardiovascular Sciences, Albany Medical College, Dept Pathol, Div Immunol, University of Cambridge [UK] (CAM), Department of Information Technology [Gent], Universiteit Gent, Department of Plant Systems Biology, Department of Plant Biotechnology and Genetics, Universiteit Gent = Ghent University [Belgium] (UGENT), Division of Molecular Immunology, Institute for Immunology, Department of Geological Sciences, University of Oregon [Eugene], Centers for Disease Control and Prevention [Atlanta] (CDC), Centers for Disease Control and Prevention, University of Colorado [Colorado Springs] (UCCS), FACS laboratory, Cancer Research, London, Cancer Research UK, Regeneration in Hematopoiesis and Animal Models of Hematopoiesis, Faculty of Medicine, Dresden University of Technology, Barbara Davis Center for Childhood Diabetes (BDC), University of Colorado Anschutz [Aurora], School of Computer and Electronic Information [Guangxi University], Guangxi University [Nanning], School of Materials Science and Engineering, Nanyang Technological University [Singapour], Max Planck Institute for Infection Biology (MPIIB), Max-Planck-Gesellschaft, Work in the laboratory of Dieter Adam is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)—Projektnummer 125440785 – SFB 877, Project B2.Petra Hoffmann, Andrea Hauser, and Matthias Edinger thank BD Biosciences®, San José, CA, USA, and SKAN AG, Bale, Switzerland for fruitful cooperation during the development, construction, and installation of the GMP‐compliant cell sorting equipment and the Bavarian Immune Therapy Network (BayImmuNet) for financial support.Edwin van der Pol and Paola Lanuti acknowledge Aleksandra Gąsecka M.D. for excellent experimental support and Dr. Rienk Nieuwland for textual suggestions. This work was supported by the Netherlands Organisation for Scientific Research – Domain Applied and Engineering Sciences (NWO‐TTW), research program VENI 15924.Jessica G Borger, Kylie M Quinn, Mairi McGrath, and Regina Stark thank Francesco Siracusa and Patrick Maschmeyer for providing data.Larissa Nogueira Almeida was supported by DFG research grant MA 2273/14‐1. Rudolf A. Manz was supported by the Excellence Cluster 'Inflammation at Interfaces' (EXC 306/2).Susanne Hartmann and Friederike Ebner were supported by the German Research Foundation (GRK 2046).Hans Minderman was supported by NIH R50CA211108.This work was funded by the Deutsche Forschungsgemeinschaft through the grant TRR130 (project P11 and C03) to Thomas H. Winkler.Ramon Bellmàs Sanz, Jenny Kühne, and Christine S. Falk thank Jana Keil and Kerstin Daemen for excellent technical support. The work was funded by the Germany Research Foundation CRC738/B3 (CSF).The work by the Mei laboratory was supported by German Research Foundation Grant ME 3644/5‐1 and TRR130 TP24, the German Rheumatism Research Centre Berlin, European Union Innovative Medicines Initiative ‐ Joint Undertaking ‐ RTCure Grant Agreement 777357, the Else Kröner‐Fresenius‐Foundation, German Federal Ministry of Education and Research e:Med sysINFLAME Program Grant 01ZX1306B and KMU‐innovativ 'InnoCyt', and the Leibniz Science Campus for Chronic Inflammation (http://www.chronische-entzuendung.org).Axel Ronald Schulz, Antonio Cosma, Sabine Baumgart, Brice Gaudilliere, Helen M. McGuire, and Henrik E. Mei thank Michael D. Leipold for critically reading the manuscript.Christian Kukat acknowledges support from the ISAC SRL Emerging Leaders program.John Trowsdale received funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Grant Agreement 695551)., European Project: 7728036(1978), Università degli Studi di Modena e Reggio Emilia = University of Modena and Reggio Emilia (UNIMORE), Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Università degli Studi di Firenze = University of Florence (UniFI)-DENOTHE Center, Università degli Studi di Milano = University of Milan (UNIMI), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Humboldt University Of Berlin, Leibniz Research Institute for Environmental Medicine [Düsseldorf, Germany] (IUF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), Universität Heidelberg [Heidelberg] = Heidelberg University, Universitäts Klinikum Freiburg = University Medical Center Freiburg (Uniklinik), University of Oxford-NIHR Biomedical Research Centre, Universität Bonn = University of Bonn, Università degli Studi di Firenze = University of Florence (UniFI), Università degli studi di Genova = University of Genoa (UniGe), Universidad de Salamanca, Università degli Studi di Roma 'La Sapienza' = Sapienza University [Rome] (UNIROMA), École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Université Paris Cité (UPCité), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Otto-von-Guericke-Universität Magdeburg = Otto-von-Guericke University [Magdeburg] (OVGU), Université de Lausanne = University of Lausanne (UNIL), Universität Leipzig, Universiteit Gent = Ghent University (UGENT), HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany., Cossarizza, A., Chang, H. -D., Radbruch, A., Acs, A., Adam, D., Adam-Klages, S., Agace, W. W., Aghaeepour, N., Akdis, M., Allez, M., Almeida, L. N., Alvisi, G., Anderson, G., Andra, I., Annunziato, F., Anselmo, A., Bacher, P., Baldari, C. T., Bari, S., Barnaba, V., Barros-Martins, J., Battistini, L., Bauer, W., Baumgart, S., Baumgarth, N., Baumjohann, D., Baying, B., Bebawy, M., Becher, B., Beisker, W., Benes, V., Beyaert, R., Blanco, A., Boardman, D. A., Bogdan, C., Borger, J. G., Borsellino, G., Boulais, P. E., Bradford, J. A., Brenner, D., Brinkman, R. R., Brooks, A. E. S., Busch, D. H., Buscher, M., Bushnell, T. P., Calzetti, F., Cameron, G., Cammarata, I., Cao, X., Cardell, S. L., Casola, S., Cassatella, M. A., Cavani, A., Celada, A., Chatenoud, L., Chattopadhyay, P. K., Chow, S., Christakou, E., Cicin-Sain, L., Clerici, M., Colombo, F. S., Cook, L., Cooke, A., Cooper, A. M., Corbett, A. J., Cosma, A., Cosmi, L., Coulie, P. G., Cumano, A., Cvetkovic, L., Dang, V. D., Dang-Heine, C., Davey, M. S., Davies, D., De Biasi, S., Del Zotto, G., Dela Cruz, G. V., Delacher, M., Della Bella, S., Dellabona, P., Deniz, G., Dessing, M., Di Santo, J. P., Diefenbach, A., Dieli, F., Dolf, A., Dorner, T., Dress, R. J., Dudziak, D., Dustin, M., Dutertre, C. -A., Ebner, F., Eckle, S. B. G., Edinger, M., Eede, P., Ehrhardt, G. R. A., Eich, M., Engel, P., Engelhardt, B., Erdei, A., Esser, C., Everts, B., Evrard, M., Falk, C. S., Fehniger, T. A., Felipo-Benavent, M., Ferry, H., Feuerer, M., Filby, A., Filkor, K., Fillatreau, S., Follo, M., Forster, I., Foster, J., Foulds, G. A., Frehse, B., Frenette, P. S., Frischbutter, S., Fritzsche, W., Galbraith, D. W., Gangaev, A., Garbi, N., Gaudilliere, B., Gazzinelli, R. T., Geginat, J., Gerner, W., Gherardin, N. A., Ghoreschi, K., Gibellini, L., Ginhoux, F., Goda, K., Godfrey, D. I., Goettlinger, C., Gonzalez-Navajas, J. M., Goodyear, C. S., Gori, A., Grogan, J. L., Grummitt, D., Grutzkau, A., Haftmann, C., Hahn, J., Hammad, H., Hammerling, G., Hansmann, L., Hansson, G., Harpur, C. M., Hartmann, S., Hauser, A., Hauser, A. E., Haviland, D. L., Hedley, D., Hernandez, D. C., Herrera, G., Herrmann, M., Hess, C., Hofer, T., Hoffmann, P., Hogquist, K., Holland, T., Hollt, T., Holmdahl, R., Hombrink, P., Houston, J. P., Hoyer, B. F., Huang, B., Huang, F. -P., Huber, J. E., Huehn, J., Hundemer, M., Hunter, C. A., Hwang, W. Y. K., Iannone, A., Ingelfinger, F., Ivison, S. M., Jack, H. -M., Jani, P. K., Javega, B., Jonjic, S., Kaiser, T., Kalina, T., Kamradt, T., Kaufmann, S. H. E., Keller, B., Ketelaars, S. L. C., Khalilnezhad, A., Khan, S., Kisielow, J., Klenerman, P., Knopf, J., Koay, H. -F., Kobow, K., Kolls, J. K., Kong, W. T., Kopf, M., Korn, T., Kriegsmann, K., Kristyanto, H., Kroneis, T., Krueger, A., Kuhne, J., Kukat, C., Kunkel, D., Kunze-Schumacher, H., Kurosaki, T., Kurts, C., Kvistborg, P., Kwok, I., Landry, J., Lantz, O., Lanuti, P., Larosa, F., Lehuen, A., LeibundGut-Landmann, S., Leipold, M. D., Leung, L. Y. T., Levings, M. K., Lino, A. C., Liotta, F., Litwin, V., Liu, Y., Ljunggren, H. -G., Lohoff, M., Lombardi, G., Lopez, L., Lopez-Botet, M., Lovett-Racke, A. E., Lubberts, E., Luche, H., Ludewig, B., Lugli, E., Lunemann, S., Maecker, H. T., Maggi, L., Maguire, O., Mair, F., Mair, K. H., Mantovani, A., Manz, R. A., Marshall, A. J., Martinez-Romero, A., Martrus, G., Marventano, I., Maslinski, W., Matarese, G., Mattioli, A. V., Maueroder, C., Mazzoni, A., Mccluskey, J., Mcgrath, M., Mcguire, H. M., Mcinnes, I. B., Mei, H. E., Melchers, F., Melzer, S., Mielenz, D., Miller, S. D., Mills, K. H. G., Minderman, H., Mjosberg, J., Moore, J., Moran, B., Moretta, L., Mosmann, T. R., Muller, S., Multhoff, G., Munoz, L. E., Munz, C., Nakayama, T., Nasi, M., Neumann, K., Ng, L. G., Niedobitek, A., Nourshargh, S., Nunez, G., O'Connor, J. -E., Ochel, A., Oja, A., Ordonez, D., Orfao, A., Orlowski-Oliver, E., Ouyang, W., Oxenius, A., Palankar, R., Panse, I., Pattanapanyasat, K., Paulsen, M., Pavlinic, D., Penter, L., Peterson, P., Peth, C., Petriz, J., Piancone, F., Pickl, W. F., Piconese, S., Pinti, M., Pockley, A. G., Podolska, M. J., Poon, Z., Pracht, K., Prinz, I., Pucillo, C. E. M., Quataert, S. A., Quatrini, L., Quinn, K. M., Radbruch, H., Radstake, T. R. D. J., Rahmig, S., Rahn, H. -P., Rajwa, B., Ravichandran, G., Raz, Y., Rebhahn, J. A., Recktenwald, D., Reimer, D., Reis e Sousa, C., Remmerswaal, E. B. M., Richter, L., Rico, L. G., Riddell, A., Rieger, A. M., Robinson, J. P., Romagnani, C., Rubartelli, A., Ruland, J., Saalmuller, A., Saeys, Y., Saito, T., Sakaguchi, S., Sala-de-Oyanguren, F., Samstag, Y., Sanderson, S., Sandrock, I., Santoni, A., Sanz, R. B., Saresella, M., Sautes-Fridman, C., Sawitzki, B., Schadt, L., Scheffold, A., Scherer, H. U., Schiemann, M., Schildberg, F. A., Schimisky, E., Schlitzer, A., Schlosser, J., Schmid, S., Schmitt, S., Schober, K., Schraivogel, D., Schuh, W., Schuler, T., Schulte, R., Schulz, A. R., Schulz, S. R., Scotta, C., Scott-Algara, D., Sester, D. P., Shankey, T. V., Silva-Santos, B., Simon, A. K., Sitnik, K. M., Sozzani, S., Speiser, D. E., Spidlen, J., Stahlberg, A., Stall, A. M., Stanley, N., Stark, R., Stehle, C., Steinmetz, T., Stockinger, H., Takahama, Y., Takeda, K., Tan, L., Tarnok, A., Tiegs, G., Toldi, G., Tornack, J., Traggiai, E., Trebak, M., Tree, T. I. M., Trotter, J., Trowsdale, J., Tsoumakidou, M., Ulrich, H., Urbanczyk, S., van de Veen, W., van den Broek, M., van der Pol, E., Van Gassen, S., Van Isterdael, G., van Lier, R. A. W., Veldhoen, M., Vento-Asturias, S., Vieira, P., Voehringer, D., Volk, H. -D., von Borstel, A., von Volkmann, K., Waisman, A., Walker, R. V., Wallace, P. K., Wang, S. A., Wang, X. M., Ward, M. D., Ward-Hartstonge, K. A., Warnatz, K., Warnes, G., Warth, S., Waskow, C., Watson, J. V., Watzl, C., Wegener, L., Weisenburger, T., Wiedemann, A., Wienands, J., Wilharm, A., Wilkinson, R. J., Willimsky, G., Wing, J. B., Winkelmann, R., Winkler, T. H., Wirz, O. F., Wong, A., Wurst, P., Yang, J. H. M., Yang, J., Yazdanbakhsh, M., Yu, L., Yue, A., Zhang, H., Zhao, Y., Ziegler, S. M., Zielinski, C., Zimmermann, J., Zychlinsky, A., UCL - SSS/DDUV - Institut de Duve, UCL - SSS/DDUV/GECE - Génétique cellulaire, Netherlands Organization for Scientific Research, German Research Foundation, European Commission, European Research Council, Repositório da Universidade de Lisboa, CCA - Imaging and biomarkers, Experimental Immunology, AII - Infectious diseases, AII - Inflammatory diseases, Biomedical Engineering and Physics, ACS - Atherosclerosis & ischemic syndromes, and Landsteiner Laboratory
Subjects: 0301 basic medicine, Consensus, Immunology, Consensu, Cell Separation, Biology, Article, Flow cytometry, 03 medical and health sciences, 0302 clinical medicine, Guidelines, Allergy and Immunology, medicine, Cell separation, Immunology and Allergy, Humans, guidelines, flow cytometry, immunology, medicine.diagnostic_test, BIOMEDICINE AND HEALTHCARE. Basic Medical Sciences, Cell sorting, Flow Cytometry, Cell selection, Data science, 3. Good health, 030104 developmental biology, Phenotype, [SDV.IMM]Life Sciences [q-bio]/Immunology, BIOMEDICINA I ZDRAVSTVO. Temeljne medicinske znanosti, 030215 immunology, Human
Abstract: All authors: Andrea Cossarizza Hyun‐Dong Chang Andreas Radbruch Andreas Acs Dieter Adam Sabine Adam‐Klages William W. Agace Nima Aghaeepour Mübeccel Akdis Matthieu Allez Larissa Nogueira Almeida Giorgia Alvisi Graham Anderson Immanuel Andrä Francesco Annunziato Achille Anselmo Petra Bacher Cosima T. Baldari Sudipto Bari Vincenzo Barnaba Joana Barros‐Martins Luca Battistini Wolfgang Bauer Sabine Baumgart Nicole Baumgarth Dirk Baumjohann Bianka Baying Mary Bebawy Burkhard Becher Wolfgang Beisker Vladimir Benes Rudi Beyaert Alfonso Blanco Dominic A. Boardman Christian Bogdan Jessica G. Borger Giovanna Borsellino Philip E. Boulais Jolene A. Bradford Dirk Brenner Ryan R. Brinkman Anna E. S. Brooks Dirk H. Busch Martin Büscher Timothy P. Bushnell Federica Calzetti Garth Cameron Ilenia Cammarata Xuetao Cao Susanna L. Cardell Stefano Casola Marco A. Cassatella Andrea Cavani Antonio Celada Lucienne Chatenoud Pratip K. Chattopadhyay Sue Chow Eleni Christakou Luka Čičin‐Šain Mario Clerici Federico S. Colombo Laura Cook Anne Cooke Andrea M. Cooper Alexandra J. Corbett Antonio Cosma Lorenzo Cosmi Pierre G. Coulie Ana Cumano Ljiljana Cvetkovic Van Duc Dang Chantip Dang‐Heine Martin S. Davey Derek Davies Sara De Biasi Genny Del Zotto Gelo Victoriano Dela Cruz Michael Delacher Silvia Della Bella Paolo Dellabona Günnur Deniz Mark Dessing James P. Di Santo Andreas Diefenbach Francesco Dieli Andreas Dolf Thomas Dörner Regine J. Dress Diana Dudziak Michael Dustin Charles‐Antoine Dutertre Friederike Ebner Sidonia B. G. Eckle Matthias Edinger Pascale Eede Götz R.A. Ehrhardt Marcus Eich Pablo Engel Britta Engelhardt Anna Erdei Charlotte Esser Bart Everts Maximilien Evrard Christine S. Falk Todd A. Fehniger Mar Felipo‐Benavent Helen Ferry Markus Feuerer Andrew Filby Kata Filkor Simon Fillatreau Marie Follo Irmgard Förster John Foster Gemma A. Foulds Britta Frehse Paul S. Frenette Stefan Frischbutter Wolfgang Fritzsche David W. Galbraith Anastasia Gangaev Natalio Garbi Brice Gaudilliere Ricardo T. Gazzinelli Jens Geginat Wilhelm Gerner Nicholas A. Gherardin Kamran Ghoreschi Lara Gibellini Florent Ginhoux Keisuke Goda Dale I. Godfrey Christoph Goettlinger Jose M. González‐Navajas Carl S. Goodyear Andrea Gori Jane L. Grogan Daryl Grummitt Andreas Grützkau Claudia Haftmann Jonas Hahn Hamida Hammad Günter Hämmerling Leo Hansmann Goran Hansson Christopher M. Harpur Susanne Hartmann Andrea Hauser Anja E. Hauser David L. Haviland David Hedley Daniela C. Hernández Guadalupe Herrera Martin Herrmann Christoph Hess Thomas Höfer Petra Hoffmann Kristin Hogquist Tristan Holland Thomas Höllt Rikard Holmdahl Pleun Hombrink Jessica P. Houston Bimba F. Hoyer Bo Huang Fang‐Ping Huang Johanna E. Huber Jochen Huehn Michael Hundemer Christopher A. Hunter William Y. K. Hwang Anna Iannone Florian Ingelfinger Sabine M Ivison Hans‐Martin Jäck Peter K. Jani Beatriz Jávega Stipan Jonjic Toralf Kaiser Tomas Kalina Thomas Kamradt Stefan H. E. Kaufmann Baerbel Keller Steven L. C. Ketelaars Ahad Khalilnezhad Srijit Khan Jan Kisielow Paul Klenerman Jasmin Knopf Hui‐Fern Koay Katja Kobow Jay K. Kolls Wan Ting Kong Manfred Kopf Thomas Korn Katharina Kriegsmann Hendy Kristyanto Thomas Kroneis Andreas Krueger Jenny Kühne Christian Kukat Désirée Kunkel Heike Kunze‐Schumacher Tomohiro Kurosaki Christian Kurts Pia Kvistborg Immanuel Kwok Jonathan Landry Olivier Lantz Paola Lanuti Francesca LaRosa Agnès Lehuen Salomé LeibundGut‐Landmann Michael D. Leipold Leslie Y.T. Leung Megan K. Levings Andreia C. Lino Francesco Liotta Virginia Litwin Yanling Liu Hans‐Gustaf Ljunggren Michael Lohoff Giovanna Lombardi Lilly Lopez Miguel López‐Botet Amy E. Lovett‐Racke Erik Lubberts Herve Luche Burkhard Ludewig Enrico Lugli Sebastian Lunemann Holden T. Maecker Laura Maggi Orla Maguire Florian Mair Kerstin H. Mair Alberto Mantovani Rudolf A. Manz Aaron J. Marshall Alicia Martínez‐Romero Glòria Martrus Ivana Marventano Wlodzimierz Maslinski Giuseppe Matarese Anna Vittoria Mattioli Christian Maueröder Alessio Mazzoni James McCluskey Mairi McGrath Helen M. McGuire Iain B. McInnes Henrik E. Mei Fritz Melchers Susanne Melzer Dirk Mielenz Stephen D. Miller Kingston H.G. Mills Hans Minderman Jenny Mjösberg Jonni Moore Barry Moran Lorenzo Moretta Tim R. Mosmann Susann Müller Gabriele Multhoff Luis Enrique Muñoz Christian Münz Toshinori Nakayama Milena Nasi Katrin Neumann Lai Guan Ng Antonia Niedobitek Sussan Nourshargh Gabriel Núñez José‐Enrique O'Connor Aaron Ochel Anna Oja Diana Ordonez Alberto Orfao Eva Orlowski‐Oliver Wenjun Ouyang Annette Oxenius Raghavendra Palankar Isabel Panse Kovit Pattanapanyasat Malte Paulsen Dinko Pavlinic Livius Penter Pärt Peterson Christian Peth Jordi Petriz Federica Piancone Winfried F. Pickl Silvia Piconese Marcello Pinti A. Graham Pockley Malgorzata Justyna Podolska Zhiyong Poon Katharina Pracht Immo Prinz Carlo E. M. Pucillo Sally A. Quataert Linda Quatrini Kylie M. Quinn Helena Radbruch Tim R. D. J. Radstake Susann Rahmig Hans‐Peter Rahn Bartek Rajwa Gevitha Ravichandran Yotam Raz Jonathan A. Rebhahn Diether Recktenwald Dorothea Reimer Caetano Reis e Sousa Ester B.M. Remmerswaal Lisa Richter Laura G. Rico Andy Riddell Aja M. Rieger J. Paul Robinson Chiara Romagnani Anna Rubartelli Jürgen Ruland Armin Saalmüller Yvan Saeys Takashi Saito Shimon Sakaguchi Francisco Sala‐de‐Oyanguren Yvonne Samstag Sharon Sanderson Inga Sandrock Angela Santoni Ramon Bellmàs Sanz Marina Saresella Catherine Sautes‐Fridman Birgit Sawitzki Linda Schadt Alexander Scheffold Hans U. Scherer Matthias Schiemann Frank A. Schildberg Esther Schimisky Andreas Schlitzer Josephine Schlosser Stephan Schmid Steffen Schmitt Kilian Schober Daniel Schraivogel Wolfgang Schuh Thomas Schüler Reiner Schulte Axel Ronald Schulz Sebastian R. Schulz Cristiano Scottá Daniel Scott‐Algara David P. Sester T. Vincent Shankey Bruno Silva‐Santos Anna Katharina Simon Katarzyna M. Sitnik Silvano Sozzani Daniel E. Speiser Josef Spidlen Anders Stahlberg Alan M. Stall Natalie Stanley Regina Stark Christina Stehle Tobit Steinmetz Hannes Stockinger Yousuke Takahama Kiyoshi Takeda Leonard Tan Attila Tárnok Gisa Tiegs Gergely Toldi Julia Tornack Elisabetta Traggiai Mohamed Trebak Timothy I.M. Tree Joe Trotter John Trowsdale Maria Tsoumakidou Henning Ulrich Sophia Urbanczyk Willem van de Veen Maries van den Broek Edwin van der Pol Sofie Van Gassen Gert Van Isterdael René A.W. van Lier Marc Veldhoen Salvador Vento‐Asturias Paulo Vieira David Voehringer Hans‐Dieter Volk Anouk von Borstel Konrad von Volkmann Ari Waisman Rachael V. Walker Paul K. Wallace Sa A. Wang Xin M. Wang Michael D. Ward Kirsten A Ward‐Hartstonge Klaus Warnatz Gary Warnes Sarah Warth Claudia Waskow James V. Watson Carsten Watzl Leonie Wegener Thomas Weisenburger Annika Wiedemann Jürgen Wienands Anneke Wilharm Robert John Wilkinson Gerald Willimsky James B. Wing Rieke Winkelmann Thomas H. Winkler Oliver F. Wirz Alicia Wong Peter Wurst Jennie H. M. Yang Juhao Yang Maria Yazdanbakhsh Liping Yu Alice Yue Hanlin Zhang Yi Zhao Susanne Maria Ziegler Christina Zielinski Jakob Zimmermann Arturo Zychlinsky., These guidelines are a consensus work of a considerable number of members of the immunology and flow cytometry community. They provide the theory and key practical aspects of flow cytometry enabling immunologists to avoid the common errors that often undermine immunological data. Notably, there are comprehensive sections of all major immune cell types with helpful Tables detailing phenotypes in murine and human cells. The latest flow cytometry techniques and applications are also described, featuring examples of the data that can be generated and, importantly, how the data can be analysed. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid, all written and peer‐reviewed by leading experts in the field, making this an essential research companion., This work was supported by the Netherlands Organisation for Scientific Research – Domain Applied and Engineering Sciences (NWO-TTW), research program VENI 15924. This work was funded by the Deutsche Forschungsgemeinschaft. European Union Innovative Medicines Initiative - Joint Undertaking - RTCure Grant Agreement 777357 and innovation program (Grant Agreement 695551).
Published: 2019
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41. CD8 coreceptor engagement of MR1 enhances antigen responsiveness by human MAIT and other MR1-reactive T cells

Author: Michael N.T. Souter, Wael Awad, Shihan Li, Troi J. Pediongco, Bronwyn S. Meehan, Lucy J. Meehan, Zehua Tian, Zhe Zhao, Huimeng Wang, Adam Nelson, Jérôme Le Nours, Yogesh Khandokar, T. Praveena, Jacinta Wubben, Jie Lin, Lucy C. Sullivan, George O. Lovrecz, Jeffrey Y.W. Mak, Ligong Liu, Lyudmila Kostenko, Katherine Kedzierska, Alexandra J. Corbett, David P. Fairlie, Andrew G. Brooks, Nicholas A. Gherardin, Adam P. Uldrich, Zhenjun Chen, Jamie Rossjohn, Dale I. Godfrey, James McCluskey, Daniel G. Pellicci, and Sidonia B.G. Eckle
Subjects: Minor Histocompatibility Antigens, CD8 Antigens, Receptors, Antigen, T-Cell, alpha-beta, Immunology, Histocompatibility Antigens Class I, Immunology and Allergy, Humans, Antigens, CD8-Positive T-Lymphocytes, Mucosal-Associated Invariant T Cells
Abstract: Mucosal-associated invariant T (MAIT) cells detect microbial infection via recognition of riboflavin-based antigens presented by the major histocompatibility complex class I (MHC-I)–related protein 1 (MR1). Most MAIT cells in human peripheral blood express CD8αα or CD8αβ coreceptors, and the binding site for CD8 on MHC-I molecules is relatively conserved in MR1. Yet, there is no direct evidence of CD8 interacting with MR1 or the functional consequences thereof. Similarly, the role of CD8αα in lymphocyte function remains ill-defined. Here, using newly developed MR1 tetramers, mutated at the CD8 binding site, and by determining the crystal structure of MR1–CD8αα, we show that CD8 engaged MR1, analogous to how it engages MHC-I molecules. CD8αα and CD8αβ enhanced MR1 binding and cytokine production by MAIT cells. Moreover, the CD8–MR1 interaction was critical for the recognition of folate-derived antigens by other MR1-reactive T cells. Together, our findings suggest that both CD8αα and CD8αβ act as functional coreceptors for MAIT and other MR1-reactive T cells.
Published: 2021

42. Dual TCR-alpha expression on MAIT cells as a potential confounder of TCR interpretation

Author: Segundo R León, Liyen Loh, Lars Kjer-Nielsen, James McCluskey, Ludivine Grzelak, Sarah K. Iwany, Tonatiuh A. Ocampo, Kattya Lopez Tamara, Jamie Rossjohn, Katherine Kedzierska, Leonid Lecca Garcia, Roger Calderon, Alexandra J. Corbett, Ildiko Van Rhijn, Megan Murray, Sara Suliman, and D. Branch Moody
Subjects: medicine.anatomical_structure, Antigen, Tetramer, Chemistry, T cell, T-cell receptor, Cell, medicine, Alpha (ethology), Endogeny, Transfection, Cell biology
Abstract: Mucosal-associated invariant T (MAIT) cells are innate-like T cells that are highly abundant in human blood and tissues. Most MAIT cells have an invariant T cell receptor (TCR) α chain that uses TRAV1-2 joined to TRAJ33/20/12 and recognize metabolites from bacterial riboflavin synthesis bound to the antigen-presenting molecule, MR1. Recently, our attempts to identify alternative MR1-presented antigens led to the discovery of rare MR1-restricted T cells with non-TRAV1-2 TCRs. Because altered antigen specificity is likely to lead to altered affinity for the most potent known antigen, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil (5-OP-RU), we performed bulk TCRα and β chain sequencing, and single cell-based paired TCR sequencing, on T cells that bound the MR1-5-OP-RU tetramer, but with differing intensities. Bulk sequencing showed that use of V genes other than TRAV1-2 was enriched among MR1-5-OP-RU tetramerlow cells. Whereas we initially interpreted these as diverse MR1-restricted TCRs, single cell TCR sequencing revealed that cells expressing atypical TCRα chains also co-expressed an invariant MAIT TCRα chain. Transfection of each non-TRAV1-2 TCRα chain with the TCRβ chain from the same cell demonstrated that the non-TRAV1-2 TCR did not bind the MR1-5-OP-RU tetramer. Thus, dual TCRα chain expression in human T cells and competition for the endogenous β chain explains the existence of some MR1-5-OP-RU tetramerlow T cells. The discovery of simultaneous expression of canonical and non-canonical TCRs on the same T cell means that claims of roles for non-TRAV1-2 TCR in MR1 response must be validated by TCR transfer-based confirmation of antigen specificity.
Published: 2021
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43. Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

Author: Andrea Cossarizza, Hyun‐Dong Chang, Andreas Radbruch, Sergio Abrignani, Richard Addo, Mübeccel Akdis, Immanuel Andrä, Francesco Andreata, Francesco Annunziato, Eduardo Arranz, Petra Bacher, Sudipto Bari, Vincenzo Barnaba, Joana Barros‐Martins, Dirk Baumjohann, Cristian G. Beccaria, David Bernardo, Dominic A. Boardman, Jessica Borger, Chotima Böttcher, Leonie Brockmann, Marie Burns, Dirk H. Busch, Garth Cameron, Ilenia Cammarata, Antonino Cassotta, Yinshui Chang, Fernando Gabriel Chirdo, Eleni Christakou, Luka Čičin‐Šain, Laura Cook, Alexandra J. Corbett, Rebecca Cornelis, Lorenzo Cosmi, Martin S. Davey, Sara De Biasi, Gabriele De Simone, Genny del Zotto, Michael Delacher, Francesca Di Rosa, James Di Santo, Andreas Diefenbach, Jun Dong, Thomas Dörner, Regine J. Dress, Charles‐Antoine Dutertre, Sidonia B. G. Eckle, Pascale Eede, Maximilien Evrard, Christine S. Falk, Markus Feuerer, Simon Fillatreau, Aida Fiz‐Lopez, Marie Follo, Gemma A. Foulds, Julia Fröbel, Nicola Gagliani, Giovanni Galletti, Anastasia Gangaev, Natalio Garbi, José Antonio Garrote, Jens Geginat, Nicholas A. Gherardin, Lara Gibellini, Florent Ginhoux, Dale I. Godfrey, Paola Gruarin, Claudia Haftmann, Leo Hansmann, Christopher M. Harpur, Adrian C. Hayday, Guido Heine, Daniela Carolina Hernández, Martin Herrmann, Oliver Hoelsken, Qing Huang, Samuel Huber, Johanna E. Huber, Jochen Huehn, Michael Hundemer, William Y. K. Hwang, Matteo Iannacone, Sabine M. Ivison, Hans‐Martin Jäck, Peter K. Jani, Baerbel Keller, Nina Kessler, Steven Ketelaars, Laura Knop, Jasmin Knopf, Hui‐Fern Koay, Katja Kobow, Katharina Kriegsmann, H. Kristyanto, Andreas Krueger, Jenny F. Kuehne, Heike Kunze‐Schumacher, Pia Kvistborg, Immanuel Kwok, Daniela Latorre, Daniel Lenz, Megan K. Levings, Andreia C. Lino, Francesco Liotta, Heather M. Long, Enrico Lugli, Katherine N. MacDonald, Laura Maggi, Mala K. Maini, Florian Mair, Calin Manta, Rudolf Armin Manz, Mir‐Farzin Mashreghi, Alessio Mazzoni, James McCluskey, Henrik E. Mei, Fritz Melchers, Susanne Melzer, Dirk Mielenz, Leticia Monin, Lorenzo Moretta, Gabriele Multhoff, Luis Enrique Muñoz, Miguel Muñoz‐Ruiz, Franziska Muscate, Ambra Natalini, Katrin Neumann, Lai Guan Ng, Antonia Niedobitek, Jana Niemz, Larissa Nogueira Almeida, Samuele Notarbartolo, Lennard Ostendorf, Laura J. Pallett, Amit A. Patel, Gulce Itir Percin, Giovanna Peruzzi, Marcello Pinti, A. Graham Pockley, Katharina Pracht, Immo Prinz, Irma Pujol‐Autonell, Nadia Pulvirenti, Linda Quatrini, Kylie M. Quinn, Helena Radbruch, Hefin Rhys, Maria B. Rodrigo, Chiara Romagnani, Carina Saggau, Shimon Sakaguchi, Federica Sallusto, Lieke Sanderink, Inga Sandrock, Christine Schauer, Alexander Scheffold, Hans U. Scherer, Matthias Schiemann, Frank A. Schildberg, Kilian Schober, Janina Schoen, Wolfgang Schuh, Thomas Schüler, Axel R. Schulz, Sebastian Schulz, Julia Schulze, Sonia Simonetti, Jeeshan Singh, Katarzyna M. Sitnik, Regina Stark, Sarah Starossom, Christina Stehle, Franziska Szelinski, Leonard Tan, Attila Tarnok, Julia Tornack, Timothy I. M. Tree, Jasper J. P. van Beek, Willem van de Veen, Klaas van Gisbergen, Chiara Vasco, Nikita A. Verheyden, Anouk von Borstel, Kirsten A. Ward‐Hartstonge, Klaus Warnatz, Claudia Waskow, Annika Wiedemann, Anneke Wilharm, James Wing, Oliver Wirz, Jens Wittner, Jennie H. M. Yang, Juhao Yang, Rolf M. Schwiete Foundation, Associazione Italiana per la Ricerca sul Cancro, German Research Foundation, National Institutes of Health (US), European Commission, AII - Inflammatory diseases, Cossarizza, A, Chang, H, Radbruch, A, Abrignani, S, Addo, R, Akdis, M, Andra, I, Andreata, F, Annunziato, F, Arranz, E, Bacher, P, Bari, S, Barnaba, V, Barros-Martins, J, Baumjohann, D, Beccaria, C, Bernardo, D, Boardman, D, Borger, J, Bottcher, C, Brockmann, L, Burns, M, Busch, D, Cameron, G, Cammarata, I, Cassotta, A, Chang, Y, Chirdo, F, Christakou, E, Cicin-Sain, L, Cook, L, Corbett, A, Cornelis, R, Cosmi, L, Davey, M, De Biasi, S, De Simone, G, del Zotto, G, Delacher, M, Di Rosa, F, Santo, J, Diefenbach, A, Dong, J, Dorner, T, Dress, R, Dutertre, C, Eckle, S, Eede, P, Evrard, M, Falk, C, Feuerer, M, Fillatreau, S, Fiz-Lopez, A, Follo, M, Foulds, G, Frobel, J, Gagliani, N, Galletti, G, Gangaev, A, Garbi, N, Garrote, J, Geginat, J, Gherardin, N, Gibellini, L, Ginhoux, F, Godfrey, D, Gruarin, P, Haftmann, C, Hansmann, L, Harpur, C, Hayday, A, Heine, G, Hernandez, D, Herrmann, M, Hoelsken, O, Huang, Q, Huber, S, Huber, J, Huehn, J, Hundemer, M, Hwang, W, Iannacone, M, Ivison, S, Jack, H, Jani, P, Keller, B, Kessler, N, Ketelaars, S, Knop, L, Knopf, J, Koay, H, Kobow, K, Kriegsmann, K, Kristyanto, H, Krueger, A, Kuehne, J, Kunze-Schumacher, H, Kvistborg, P, Kwok, I, Latorre, D, Lenz, D, Levings, M, Lino, A, Liotta, F, Long, H, Lugli, E, Macdonald, K, Maggi, L, Maini, M, Mair, F, Manta, C, Manz, R, Mashreghi, M, Mazzoni, A, Mccluskey, J, Mei, H, Melchers, F, Melzer, S, Mielenz, D, Monin, L, Moretta, L, Multhoff, G, Munoz, L, Munoz-Ruiz, M, Muscate, F, Natalini, A, Neumann, K, Ng, L, Niedobitek, A, Niemz, J, Almeida, L, Notarbartolo, S, Ostendorf, L, Pallett, L, Patel, A, Percin, G, Peruzzi, G, Pinti, M, Pockley, A, Pracht, K, Prinz, I, Pujol-Autonell, I, Pulvirenti, N, Quatrini, L, Quinn, K, Radbruch, H, Rhys, H, Rodrigo, M, Romagnani, C, Saggau, C, Sakaguchi, S, Sallusto, F, Sanderink, L, Sandrock, I, Schauer, C, Scheffold, A, Scherer, H, Schiemann, M, Schildberg, F, Schober, K, Schoen, J, Schuh, W, Schuler, T, Schulz, A, Schulz, S, Schulze, J, Simonetti, S, Singh, J, Sitnik, K, Stark, R, Starossom, S, Stehle, C, Szelinski, F, Tan, L, Tarnok, A, Tornack, J, Tree, T, van Beek, J, van de Veen, W, van Gisbergen, K, Vasco, C, Verheyden, N, von Borstel, A, Ward-Hartstonge, K, Warnatz, K, Waskow, C, Wiedemann, A, Wilharm, A, Wing, J, Wirz, O, Wittner, J, Yang, J, Publica, Cossarizza, A., Chang, H. -D., Radbruch, A., Abrignani, S., Addo, R., Akdis, M., Andra, I., Andreata, F., Annunziato, F., Arranz, E., Bacher, P., Bari, S., Barnaba, V., Barros-Martins, J., Baumjohann, D., Beccaria, C. G., Bernardo, D., Boardman, D. A., Borger, J., Bottcher, C., Brockmann, L., Burns, M., Busch, D. H., Cameron, G., Cammarata, I., Cassotta, A., Chang, Y., Chirdo, F. G., Christakou, E., Cicin-Sain, L., Cook, L., Corbett, A. J., Cornelis, R., Cosmi, L., Davey, M. S., De Biasi, S., De Simone, G., del Zotto, G., Delacher, M., Di Rosa, F., Santo, J. D., Diefenbach, A., Dong, J., Dorner, T., Dress, R. J., Dutertre, C. -A., Eckle, S. B. G., Eede, P., Evrard, M., Falk, C. S., Feuerer, M., Fillatreau, S., Fiz-Lopez, A., Follo, M., Foulds, G. A., Frobel, J., Gagliani, N., Galletti, G., Gangaev, A., Garbi, N., Garrote, J. A., Geginat, J., Gherardin, N. A., Gibellini, L., Ginhoux, F., Godfrey, D. I., Gruarin, P., Haftmann, C., Hansmann, L., Harpur, C. M., Hayday, A. C., Heine, G., Hernandez, D. C., Herrmann, M., Hoelsken, O., Huang, Q., Huber, S., Huber, J. E., Huehn, J., Hundemer, M., Hwang, W. Y. K., Iannacone, M., Ivison, S. M., Jack, H. -M., Jani, P. K., Keller, B., Kessler, N., Ketelaars, S., Knop, L., Knopf, J., Koay, H. -F., Kobow, K., Kriegsmann, K., Kristyanto, H., Krueger, A., Kuehne, J. F., Kunze-Schumacher, H., Kvistborg, P., Kwok, I., Latorre, D., Lenz, D., Levings, M. K., Lino, A. C., Liotta, F., Long, H. M., Lugli, E., Macdonald, K. N., Maggi, L., Maini, M. K., Mair, F., Manta, C., Manz, R. A., Mashreghi, M. -F., Mazzoni, A., Mccluskey, J., Mei, H. E., Melchers, F., Melzer, S., Mielenz, D., Monin, L., Moretta, L., Multhoff, G., Munoz, L. E., Munoz-Ruiz, M., Muscate, F., Natalini, A., Neumann, K., Ng, L. G., Niedobitek, A., Niemz, J., Almeida, L. N., Notarbartolo, S., Ostendorf, L., Pallett, L. J., Patel, A. A., Percin, G. I., Peruzzi, G., Pinti, M., Pockley, A. G., Pracht, K., Prinz, I., Pujol-Autonell, I., Pulvirenti, N., Quatrini, L., Quinn, K. M., Radbruch, H., Rhys, H., Rodrigo, M. B., Romagnani, C., Saggau, C., Sakaguchi, S., Sallusto, F., Sanderink, L., Sandrock, I., Schauer, C., Scheffold, A., Scherer, H. U., Schiemann, M., Schildberg, F. A., Schober, K., Schoen, J., Schuh, W., Schuler, T., Schulz, A. R., Schulz, S., Schulze, J., Simonetti, S., Singh, J., Sitnik, K. M., Stark, R., Starossom, S., Stehle, C., Szelinski, F., Tan, L., Tarnok, A., Tornack, J., Tree, T. I. M., van Beek, J. J. P., van de Veen, W., van Gisbergen, K., Vasco, C., Verheyden, N. A., von Borstel, A., Ward-Hartstonge, K. A., Warnatz, K., Waskow, C., Wiedemann, A., Wilharm, A., Wing, J., Wirz, O., Wittner, J., Yang, J. H. M., and Yang, J.
Subjects: Immunology, citometry, Flow Cytometry, Infections, ddc, Autoimmune Diseases, Animals, Chronic Disease, Humans, Mice, Neoplasms, Practice Guidelines as Topic, Immunology and Allergy, ddc:610, Function and Dysfunction of the Nervous System, guideline
Abstract: © 2021 The Authors., The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers., Hyun-Dong Chang is supported by the Dr. Rolf M. Schwiete Foundation. Susanne Melzer and Attila Tarnok thank De Novo Software for providing FCS Express. Enrico Lugli is supported by a grant from the Associazione Italiana per la Ricerca sul Cancro (AIRC IG20676). Gabriele De Simone and Giovanni Galletti were supported by Fellowships from the Fondazione Italiana per la Ricerca sul Cancro-Associazione Italiana per la Ricerca sul Cancro (FIRC-AIRC). Jun Dong is supported by Deutsche Forschungsgemeinschft (DFG, German Research Foundation) Projektnummer 389687267 and Chinesisch-Deutsches Zentrum für Wissenschaftsförderung [Sino-German Center for Research Promotion (SGC)] grant C-0072. Nicola Gagliani, Samuel Huber and Franziska Muscate are supported by DFG fundings: SFB841,GA 2441/3-1, HU 1714/10-1. The tetramer APC-conjugated H-2K (d) HIV-1 gag197-205 AMQMLKETI used in TDS assay for mouse blood T cells was obtained through the NIH Tetramer Facility. Larissa Nogueira Almeida was supported by DFG research grant MA 2273/14-1. Supported by the following grants: AIRC 5X1000 2018 id. 21147 (Lorenzo Moretta); AIRC IG 2017 id. 19920 (Lorenzo Moretta); RC-2020 OPBG (Lorenzo Moretta); AIRC and European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No 800924 (Linda Quatrini). Dirk Baumjohann was supported by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Emmy Noether Programme BA 5132/1-2 (252623821) and Germany's Excellence Strategy EXC2151 (390873048).
Published: 2021
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44. Mouse models illuminate MAIT cell biology

Author: Zhenjun Chen, Huimeng Wang, Alexandra J. Corbett, and James McCluskey
Subjects: 0301 basic medicine, Disease outcome, T cell, Immunology, Mucosal associated invariant T cell, Disease, Biology, Infections, Lymphocyte Activation, Mucosal-Associated Invariant T Cells, Article, Autoimmune Diseases, 03 medical and health sciences, Mice, 0302 clinical medicine, Immune system, Antigen, Neoplasms, medicine, Animals, Humans, Molecular Biology, T-cell receptor, MAIT Cells, 030104 developmental biology, medicine.anatomical_structure, Models, Animal, 030215 immunology
Abstract: The field of mucosal-associated invariant T cell (MAIT) biology has grown rapidly since the identification of the vitamin-B-based antigens recognised by these specialised T cells. Over the past few years, our understanding of the complexities of MAIT cell function has developed, as they find their place among the other better known cells of the immune system. Key questions relate to understanding when MAIT cells help, when they hinder or cause harm, and when they do not matter. Exploiting mouse strains that differ in MAIT cell numbers, leveraged by specific detection of MAIT cells using MR1-tetramers, it has now been shown that MAIT cells play important immune roles in settings that include bacterial and viral infections, autoimmune diseases and cancer. We have also learnt much about their development, modes of activation and response to commensal microbiota, and begun to try ways to manipulate MAIT cells to improve disease outcomes. Here we review recent studies that have assessed MAIT cells in models of disease.
Published: 2020

45. Endoplasmic reticulum chaperones stabilize ligand-receptive MR1 molecules for efficient presentation of metabolite antigens

Author: Hui Jing Lim, Ligong Liu, Justine D. Mintern, Sebastian Cruz-Gomez, Sam Wormald, Sidonia B G Eckle, Matthew Zorkau, David P. Fairlie, Scott J. J. Reddiex, Alexandra J. Corbett, Hamish E G McWilliam, Shihan Li, Laura F. Dagley, Yuting Yan, Jeffrey Y. W. Mak, Wael Awad, James McCluskey, Haiyin Liu, Jose A Villadangos, and Jamie Rossjohn
Subjects: 0301 basic medicine, Proteomics, Metabolite, Riboflavin, Antigen presentation, Endoplasmic Reticulum, Ligands, Lymphocyte Activation, Mucosal-Associated Invariant T Cells, Minor Histocompatibility Antigens, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Antigen, Tapasin, MHC class I, Humans, Antigens, Antigen Presentation, Multidisciplinary, biology, Chemistry, Endoplasmic reticulum, Histocompatibility Antigens Class I, Membrane Transport Proteins, Biological Sciences, Ligand (biochemistry), Cell biology, 030104 developmental biology, biology.protein, Metabolome, CRISPR-Cas Systems, Cell activation, 030215 immunology, Molecular Chaperones
Abstract: The antigen-presenting molecule MR1 (MHC class I-related protein 1) presents metabolite antigens derived from microbial vitamin B(2) synthesis to activate mucosal-associated invariant T (MAIT) cells. Key aspects of this evolutionarily conserved pathway remain uncharacterized, including where MR1 acquires ligands and what accessory proteins assist ligand binding. We answer these questions by using a fluorophore-labeled stable MR1 antigen analog, a conformation-specific MR1 mAb, proteomic analysis, and a genome-wide CRISPR/Cas9 library screen. We show that the endoplasmic reticulum (ER) contains a pool of two unliganded MR1 conformers stabilized via interactions with chaperones tapasin and tapasin-related protein. This pool is the primary source of MR1 molecules for the presentation of exogenous metabolite antigens to MAIT cells. Deletion of these chaperones reduces the ER-resident MR1 pool and hampers antigen presentation and MAIT cell activation. The MR1 antigen-presentation pathway thus co-opts ER chaperones to fulfill its unique ability to present exogenous metabolite antigens captured within the ER.
Published: 2020

46. Mucosal-Associated Invariant T Cell Effector Function Is an Intrinsic Cell Property That Can Be Augmented by the Metabolic Cofactor α-Ketoglutarate

Author: Stephen J. Turner, David P. Fairlie, Adele Barugahare, Anouk von Borstel, Martin S. Davey, Lauren J. Howson, James McCluskey, Jasmine Li, Jeffrey Y. W. Mak, and Jamie Rossjohn
Subjects: Jumonji Domain-Containing Histone Demethylases, T cell, Immunology, Population, Cell, Receptors, Antigen, T-Cell, Mucosal associated invariant T cell, Lymphocyte Activation, Mucosal-Associated Invariant T Cells, Lysine demethylase 6B, Epigenesis, Genetic, medicine, Immunology and Allergy, Humans, education, Interleukin-7 receptor, Cells, Cultured, education.field_of_study, Chemistry, Effector, T-cell receptor, Immunity, Innate, Cell biology, medicine.anatomical_structure, Cytokines, Ketoglutaric Acids
Abstract: Mucosal-associated invariant T (MAIT) cells are an innate-like population of unconventional T cells that respond rapidly to microbial metabolite Ags or cytokine stimulation. Because of this reactivity and surface expression of CD45RO+, CD45RA−, and CD127+, they are described as effector memory cells. Yet, there is heterogeneity in MAIT cell effector response. It is unclear what factors control MAIT cell effector capacity, whether it is fixed or can be modified and if this differs based on whether activation is TCR dependent or independent. To address this, we have taken a systematic approach to examine human MAIT cell effector capacity across healthy individuals in response to ligand and cytokine stimulation. We demonstrate the heterogenous nature of MAIT cell effector capacity and that the ability to produce an effector response is not directly attributable to TCR clonotype or coreceptor expression. Global gene transcription analysis revealed that the MAIT cell effector capacity produced in response to TCR stimulation is associated with increased expression of the epigenetic regulator lysine demethylase 6B (KDM6B). Addition of a KDM6B inhibitor did not alter MAIT cell effector function to Ag or cytokine stimulation. However, addition of the KDM6B cofactor α-ketoglutarate greatly enhanced MAIT cell effector capacity to TCR-dependent stimulation in a partially KDM6B-dependent manner. These results demonstrate that the TCR-dependent effector response of MAIT cells is epigenetically regulated and dependent on the availability of metabolic cofactors.
Published: 2020

47. When it's good to have MAITs

Author: Alexandra J. Corbett, James McCluskey, and Michael Nt Souter
Subjects: 0301 basic medicine, Tuberculosis, Immunology, Mucosal associated invariant T cell, Mucosal-Associated Invariant T Cells, Article, Mycobacterium tuberculosis, 03 medical and health sciences, Mice, 0302 clinical medicine, Immunology and Allergy, Medicine, Animals, Invariant (mathematics), biology, business.industry, Extramural, Vaccination, Cell Biology, biology.organism_classification, medicine.disease, 030104 developmental biology, business, 030215 immunology
Abstract: Mucosal-associated invariant T (MAIT) cells are potential targets of vaccination and host-directed therapeutics for tuberculosis, but the role of MAIT cells during Mycobacterium tuberculosis (Mtb) infection in vivo is not well understood. Here we find that following Mtb infection MAIT cells mount minimal responses, and MAIT cell-deficient MR1−/− mice display normal survival. Preinfection expansion of MAIT cells through 5-OP-RU vaccination fails to protect against subsequent Mtb challenge. In fact, 5-OP-RU vaccination delays Mtb-specific CD4 T cell priming in lung-draining lymph nodes, and conversely MR1 deficiency or blockade accelerates T cell priming. The MAIT cell-mediated delay in T cell priming is partly dependent on TGF-β. Surprisingly, 5-OP-RU treatment during chronic infection drives MAIT cell expansion and an IL-17A-dependent reduction in bacterial loads. Thus, during early infection MAIT cells directly contribute to the notoriously slow priming of CD4 T cells, but later during infection MAIT cell stimulation may be an effective host-directed therapy for tuberculosis.
Published: 2020

48. MAIT cells regulate NK cell mediated tumor immunity

Author: Emma Petley, Hui-Fern Koay, Melissa Henderson, Kevin Sek, Kirsten Todd, Simon Keam, Junyun Lai, Imran House, Magnus Zethoven, Amanda Chen, Amanda Oliver, Jessica Michie, Andrew Freeman, Lauren Giuffrida, Jack Chan, Angela Pizzolla, Jeffrey Mak, Fernando Souza-Fonseca-Guimaraes, Conor Kearney, Rosemary Millen, Rob Ramsay, Nicholas Huntington, James McCluskey, Jane Oliaro, David Fairlie, Paul Neeson, Dale Godfrey, Paul (A.) Beavis, and Phillip Darcy
Abstract: MR1-restricted mucosal-associated invariant T (MAIT) cells recognize microbial metabolites and play an important role in immunity to infection, however, the role they play in tumor immunity is unclear. Here we show that MAIT cell-deficient mice are more resistant to subcutaneous and lung metastasis B16F10 tumor growth compared to control mice, an effect that was associated with enhanced NK cell numbers and was NK cell-dependent. Analysis of this interplay in cancer patients also revealed that a high expression of a novel MAIT gene signature negatively impacted the prognostic significance of NK cells. Paradoxically, pre-pulsing tumors with MAIT cell antigens, or antigen-mediated MAIT cell activation in vivo, enhanced immunity against B16F10 and E0771 lung tumor metastasis. Furthermore, MAIT cell activation effectively reduced metastatic burden in a more stringent model of established lung metastases in mice. These effects were associated with enhanced NK cell responses and increased expression of both IFNγ-dependent and inflammatory genes in NK cells, which was neutralized by IFNγ blockade. Importantly, activated human MAIT cells also enhanced the function of NK cells isolated from patient tumor samples. These findings provide insight into the contrasting roles that MAIT cells can play in controlling anti-tumor immune responses depending on their activation status, in both mice and humans, and suggest potential therapeutic avenues for exploiting their potential anti-tumor properties for cancer treatment.
Published: 2020
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49. Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1

Author: Abdul Rezzak Hamzeh, Hui Jing Lim, T. Andrews, Lauren J. Howson, David H. McDermott, Philip M. Murphy, Jérôme Le Nours, Matthew C. Cook, Ligong Liu, Jamie Rossjohn, Martin S. Davey, Stephen J. Turner, James McCluskey, Jeffrey Y. W. Mak, Maria L. Sandoval-Romero, Shamik Majumdar, Wael Awad, Anouk von Borstel, Hamish E G McWilliam, Samar Ojaimi, David P. Fairlie, and Jose A Villadangos
Subjects: Mutation, education.field_of_study, Chemistry, T cell, Point mutation, Primary Immunodeficiency Diseases, Immunology, Cell, Population, Histocompatibility Antigens Class I, General Medicine, Mucosal associated invariant T cell, medicine.disease_cause, Ligand (biochemistry), Article, Mucosal-Associated Invariant T Cells, Cell biology, Minor Histocompatibility Antigens, medicine.anatomical_structure, Antigen, medicine, Humans, Point Mutation, education, Intraepithelial Lymphocytes
Abstract: The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a patient homozygous for a rare Arg31His (R9H in the mature protein) mutation in MR1 who has a history of difficult-to-treat viral and bacterial infections. MR1R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand. The MR1R9H crystal structure revealed that the stimulatory ligand cannot bind due to the mutation lying within, and causing structural perturbation to, the ligand-binding domain of MR1. While MR1R9H could bind and be up-regulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This shows the importance of the stimulatory ligand for MAIT cell selection in humans. The patient had an expanded γδ T cell population, indicating a compensatory interplay between these unconventional T cell subsets.
Published: 2020

50. Atypical TRAV1-2

Author: Wael, Awad, Erin W, Meermeier, Maria L, Sandoval-Romero, Jérôme, Le Nours, Aneta H, Worley, Megan D, Null, Ligong, Liu, James, McCluskey, David P, Fairlie, David M, Lewinsohn, and Jamie, Rossjohn
Subjects: Antigen Presentation, Binding Sites, Receptors, Antigen, T-Cell, alpha-beta, T-Lymphocytes, Histocompatibility Antigens Class I, Immunology, Surface Plasmon Resonance, Crystallography, X-Ray, Protein Refolding, Protein Structure, Tertiary, Minor Histocompatibility Antigens, Molecular Docking Simulation, Humans, Amino Acid Sequence, Uracil, Ribitol
Abstract: MR1 presents vitamin B–related metabolites to mucosal associated invariant T (MAIT) cells, which are characterized, in part, by the TRAV1-2(+) αβ T cell receptor (TCR). In addition, a more diverse TRAV1-2(−) MR1-restricted T cell repertoire exists that can possess altered specificity for MR1 antigens. However, the molecular basis of how such TRAV1-2(−) TCRs interact with MR1–antigen complexes remains unclear. Here, we describe how a TRAV12-2(+) TCR (termed D462-E4) recognizes an MR1–antigen complex. We report the crystal structures of the unliganded D462-E4 TCR and its complex with MR1 presenting the riboflavin-based antigen 5-OP-RU. Here, the TRBV29-1 β-chain of the D462-E4 TCR binds over the F′-pocket of MR1, whereby the complementarity-determining region (CDR) 3β loop surrounded and projected into the F′-pocket. Nevertheless, the CDR3β loop anchored proximal to the MR1 A′-pocket and mediated direct contact with the 5-OP-RU antigen. The D462-E4 TCR footprint on MR1 contrasted that of the TRAV1-2(+) and TRAV36(+) TCRs' docking topologies on MR1. Accordingly, diverse MR1-restricted T cell repertoire reveals differential docking modalities on MR1, thus providing greater scope for differing antigen specificities.
Published: 2020

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