1
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Zhang R, Trotter PB, McCaffrey J, Fitzroy R, Trivioli G, Stewart BJ, Ferdinand JR, Loudon KW, Riding A, West J, Ferro A, Clatworthy MR. Assessment of biological organ age using molecular pathology in pre-transplant kidney biopsies. Kidney Int 2024:S0085-2538(24)00311-9. [PMID: 38692408 DOI: 10.1016/j.kint.2024.03.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 01/21/2024] [Accepted: 03/18/2024] [Indexed: 05/03/2024]
Abstract
Organ shortage is a major challenge in kidney transplantation but the use of older donors, often with co-morbidities, is hampered by inconsistent outcomes. Methods of accurately stratifying marginal donor organs by clinical and histological assessment are lacking. To better understand organ variability, we profiled the transcriptomes of 271 kidneys from deceased donors at retrieval. Following correction for biopsy composition, we assessed molecular pathways that associated with delayed, and sub-optimal one-year graft function. Analysis of cortical biopsies identified an adaptive immune gene-rich module that significantly associated with increasing age and worse outcomes. Cellular deconvolution using human kidney reference single cell transcriptomes confirmed an increase in kidney-specific B and T cell signatures, as well as kidney macrophage, myofibroblast and fibroblast gene sets in this module. Surprisingly, innate immune pathway and neutrophil gene signature enrichment was associated with better outcomes. Thus, our work uncovers cellular molecular features of pathological organ ageing, identifiable at kidney retrieval, with translational potential.
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Affiliation(s)
- Roy Zhang
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Patrick B Trotter
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - James McCaffrey
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rory Fitzroy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Giorgio Trivioli
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Alexandra Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Jonathan West
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Ashley Ferro
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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2
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Talks BJ, Mather MW, Chahal M, Coates M, Clatworthy MR, Haniffa M. Mapping Human Immunity and the Education of Waldeyer's Ring. Annu Rev Genomics Hum Genet 2024. [PMID: 38594932 DOI: 10.1146/annurev-genom-120522-012938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The development and deployment of single-cell genomic technologies have driven a resolution revolution in our understanding of the immune system, providing unprecedented insight into the diversity of immune cells present throughout the body and their function in health and disease. Waldeyer's ring is the collective name for the lymphoid tissue aggregations of the upper aerodigestive tract, comprising the palatine, pharyngeal (adenoids), lingual, and tubal tonsils. These tonsils are the first immune sentinels encountered by ingested and inhaled antigens and are responsible for mounting the first wave of adaptive immune response. An effective mucosal immune response is critical to neutralizing infection in the upper airway and preventing systemic spread, and dysfunctional immune responses can result in ear, nose, and throat pathologies. This review uses Waldeyer's ring to demonstrate how single-cell technologies are being applied to advance our understanding of the immune system and highlight directions for future research.
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Affiliation(s)
- Benjamin J Talks
- 1Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
- 2Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael W Mather
- 1Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
- 2Department of Otolaryngology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Manisha Chahal
- 1Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
| | - Matthew Coates
- 3Department of Medicine, University of Cambridge, Cambridge, UK; ,
| | - Menna R Clatworthy
- 3Department of Medicine, University of Cambridge, Cambridge, UK; ,
- 4Wellcome Sanger Institute, Hinxton, UK;
| | - Muzlifah Haniffa
- 1Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK; , ,
- 4Wellcome Sanger Institute, Hinxton, UK;
- 5Department of Dermatology and National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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3
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Fitzpatrick Z, Ghabdan Zanluqui N, Rosenblum JS, Tuong ZK, Lee CYC, Chandrashekhar V, Negro-Demontel ML, Stewart AP, Posner DA, Buckley M, Allinson KSJ, Mastorakos P, Chittiboina P, Maric D, Donahue D, Helmy A, Tajsic T, Ferdinand JR, Portet A, Peñalver A, Gillman E, Zhuang Z, Clatworthy MR, McGavern DB. Venous-plexus-associated lymphoid hubs support meningeal humoral immunity. Nature 2024; 628:612-619. [PMID: 38509366 DOI: 10.1038/s41586-024-07202-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/16/2024] [Indexed: 03/22/2024]
Abstract
There is increasing interest in how immune cells in the meninges-the membranes that surround the brain and spinal cord-contribute to homeostasis and disease in the central nervous system1,2. The outer layer of the meninges, the dura mater, has recently been described to contain both innate and adaptive immune cells, and functions as a site for B cell development3-6. Here we identify organized lymphoid structures that protect fenestrated vasculature in the dura mater. The most elaborate of these dural-associated lymphoid tissues (DALT) surrounded the rostral-rhinal confluence of the sinuses and included lymphatic vessels. We termed this structure, which interfaces with the skull bone marrow and a comparable venous plexus at the skull base, the rostral-rhinal venolymphatic hub. Immune aggregates were present in DALT during homeostasis and expanded with age or after challenge with systemic or nasal antigens. DALT contain germinal centre B cells and support the generation of somatically mutated, antibody-producing cells in response to a nasal pathogen challenge. Inhibition of lymphocyte entry into the rostral-rhinal hub at the time of nasal viral challenge abrogated the generation of germinal centre B cells and class-switched plasma cells, as did perturbation of B-T cell interactions. These data demonstrate a lymphoid structure around vasculature in the dura mater that can sample antigens and rapidly support humoral immune responses after local pathogen challenge.
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Affiliation(s)
- Zachary Fitzpatrick
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nagela Ghabdan Zanluqui
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | | | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | | | - Maria Luciana Negro-Demontel
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | - Andrew P Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - David A Posner
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Monica Buckley
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
| | - Kieren S J Allinson
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Panagiotis Mastorakos
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA
- Department of Surgical Neurology, NINDS, NIH, Bethesda, MD, USA
| | | | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, NINDS, NIH, Bethesda, MD, USA
| | | | - Adel Helmy
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Tamara Tajsic
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anais Portet
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ana Peñalver
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eleanor Gillman
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Zhengping Zhuang
- Neuro-Oncology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
| | - Dorian B McGavern
- Viral Immunology and Intravital Imaging Section, National Institute of Neurological Disorders and Stroke (NINDS), National Institute of Health (NIH), Bethesda, MD, USA.
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4
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Ng-Blichfeldt JP, Stewart BJ, Clatworthy MR, Williams JM, Röper K. Identification of a core transcriptional program driving the human renal mesenchymal-to-epithelial transition. Dev Cell 2024; 59:595-612.e8. [PMID: 38340720 DOI: 10.1016/j.devcel.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/28/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024]
Abstract
During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology are poorly understood. We used human iPSC-derived renal organoids, which recapitulate nephrogenesis, to investigate mechanisms controlling renal MET. Multi-ome profiling via snRNA-seq and ATAC-seq of organoids identified dynamic changes in gene expression and chromatin accessibility driven by activators and repressors throughout MET. CRISPR interference identified that paired box 8 (PAX8) is essential for initiation of MET in human renal organoids, contrary to in vivo mouse studies, likely by activating a cell-adhesion program. While Wnt/β-catenin signaling specifies nephron fate, we find that it must be attenuated to allow hepatocyte nuclear factor 1-beta (HNF1B) and TEA-domain (TEAD) transcription factors to drive completion of MET. These results identify the interplay between fate commitment and morphogenesis in the developing human kidney, with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.
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Affiliation(s)
- John-Poul Ng-Blichfeldt
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
| | - Julie M Williams
- Bioscience Renal, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Katja Röper
- MRC-Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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5
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Stewart AP, Clatworthy MR. Single-cell genomics sheds light on kidney tissue immunity. Nat Rev Nephrol 2024; 20:71-72. [PMID: 38129546 DOI: 10.1038/s41581-023-00802-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Affiliation(s)
- Andrew P Stewart
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases and Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Menna R Clatworthy
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases and Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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6
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Dean I, Lee CYC, Tuong ZK, Li Z, Tibbitt CA, Willis C, Gaspal F, Kennedy BC, Matei-Rascu V, Fiancette R, Nordenvall C, Lindforss U, Baker SM, Stockmann C, Sexl V, Hammond SA, Dovedi SJ, Mjösberg J, Hepworth MR, Carlesso G, Clatworthy MR, Withers DR. Rapid functional impairment of natural killer cells following tumor entry limits anti-tumor immunity. Nat Commun 2024; 15:683. [PMID: 38267402 PMCID: PMC10808449 DOI: 10.1038/s41467-024-44789-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Immune cell dysfunction within the tumor microenvironment (TME) undermines the control of cancer progression. Established tumors contain phenotypically distinct, tumor-specific natural killer (NK) cells; however, the temporal dynamics, mechanistic underpinning and functional significance of the NK cell compartment remains incompletely understood. Here, we use photo-labeling, combined with longitudinal transcriptomic and cellular analyses, to interrogate the fate of intratumoral NK cells. We reveal that NK cells rapidly lose effector functions and adopt a distinct phenotypic state with features associated with tissue residency. NK cell depletion from established tumors did not alter tumor growth, indicating that intratumoral NK cells cease to actively contribute to anti-tumor responses. IL-15 administration prevented loss of function and improved tumor control, generating intratumoral NK cells with both tissue-residency characteristics and enhanced effector function. Collectively, our data reveals the fate of NK cells after recruitment into tumors and provides insight into how their function may be revived.
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Affiliation(s)
- Isaac Dean
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Colin Y C Lee
- Department of Medicine, Molecular Immunity Unit, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zewen K Tuong
- Department of Medicine, Molecular Immunity Unit, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Zhi Li
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Christopher A Tibbitt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Claire Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabrina Gaspal
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Bethany C Kennedy
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Veronika Matei-Rascu
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rémi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Caroline Nordenvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Ulrik Lindforss
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Pelvic Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Syed Murtuza Baker
- Division of Informatics, Imaging & Data Science, Faculty of Biology, Medicine and Health, the University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine, Vienna, Austria
| | | | | | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Clinical Lung and Allergy Research, Medical unit for Lung and Allergy Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Matthew R Hepworth
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, the University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | | | - Menna R Clatworthy
- Department of Medicine, Molecular Immunity Unit, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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7
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Lee CYC, Kennedy BC, Richoz N, Dean I, Tuong ZK, Gaspal F, Li Z, Willis C, Hasegawa T, Whiteside SK, Posner DA, Carlesso G, Hammond SA, Dovedi SJ, Roychoudhuri R, Withers DR, Clatworthy MR. Tumour-retained activated CCR7 + dendritic cells are heterogeneous and regulate local anti-tumour cytolytic activity. Nat Commun 2024; 15:682. [PMID: 38267413 PMCID: PMC10808534 DOI: 10.1038/s41467-024-44787-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024] Open
Abstract
Tumour dendritic cells (DCs) internalise antigen and upregulate CCR7, which directs their migration to tumour-draining lymph nodes (dLN). CCR7 expression is coupled to an activation programme enriched in regulatory molecule expression, including PD-L1. However, the spatio-temporal dynamics of CCR7+ DCs in anti-tumour immune responses remain unclear. Here, we use photoconvertible mice to precisely track DC migration. We report that CCR7+ DCs are the dominant DC population that migrate to the dLN, but a subset remains tumour-resident despite CCR7 expression. These tumour-retained CCR7+ DCs are phenotypically and transcriptionally distinct from their dLN counterparts and heterogeneous. Moreover, they progressively downregulate the expression of antigen presentation and pro-inflammatory transcripts with more prolonged tumour dwell-time. Tumour-residing CCR7+ DCs co-localise with PD-1+CD8+ T cells in human and murine solid tumours, and following anti-PD-L1 treatment, upregulate stimulatory molecules including OX40L, thereby augmenting anti-tumour cytolytic activity. Altogether, these data uncover previously unappreciated heterogeneity in CCR7+ DCs that may underpin a variable capacity to support intratumoural cytotoxic T cells.
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Affiliation(s)
- Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Bethany C Kennedy
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Isaac Dean
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Fabrina Gaspal
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zhi Li
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Claire Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tetsuo Hasegawa
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | | | - David A Posner
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - David R Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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8
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Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat Biotechnol 2024; 42:40-51. [PMID: 37055623 PMCID: PMC10791579 DOI: 10.1038/s41587-023-01734-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/07/2023] [Indexed: 04/15/2023]
Abstract
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Paediatrics, Cambridge University Hospitals, Cambridge, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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9
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Ulezko Antonova A, Lonardi S, Monti M, Missale F, Fan C, Coates ML, Bugatti M, Jaeger N, Fernandes Rodrigues P, Brioschi S, Trsan T, Fachi JL, Nguyen KM, Nunley RM, Moratto D, Zini S, Kong L, Deguine J, Peeples ME, Xavier RJ, Clatworthy MR, Wang T, Cella M, Vermi W, Colonna M. A distinct human cell type expressing MHCII and RORγt with dual characteristics of dendritic cells and type 3 innate lymphoid cells. Proc Natl Acad Sci U S A 2023; 120:e2318710120. [PMID: 38109523 PMCID: PMC10756205 DOI: 10.1073/pnas.2318710120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023] Open
Abstract
Recent studies have characterized various mouse antigen-presenting cells (APCs) expressing the lymphoid-lineage transcription factor RORγt (Retinoid-related orphan receptor gamma t), which exhibit distinct phenotypic features and are implicated in the induction of peripheral regulatory T cells (Tregs) and immune tolerance to microbiota and self-antigens. These APCs encompass Janus cells and Thetis cell subsets, some of which express the AutoImmune REgulator (AIRE). RORγt+ MHCII+ type 3 innate lymphoid cells (ILC3) have also been implicated in the instruction of microbiota-specific Tregs. While RORγt+ APCs have been actively investigated in mice, the identity and function of these cell subsets in humans remain elusive. Herein, we identify a rare subset of RORγt+ cells with dendritic cell (DC) features through integrated single-cell RNA sequencing and single-cell ATAC sequencing. These cells, which we term RORγt+ DC-like cells (R-DC-like), exhibit DC morphology, express the MHC class II machinery, and are distinct from all previously reported DC and ILC3 subsets, but share transcriptional and epigenetic similarities with DC2 and ILC3. We have developed procedures to isolate and expand them in vitro, enabling their functional characterization. R-DC-like cells proliferate in vitro, continue to express RORγt, and differentiate into CD1c+ DC2-like cells. They stimulate the proliferation of allogeneic T cells. The identification of human R-DC-like cells with proliferative potential and plasticity toward CD1c+ DC2-like cells will prompt further investigation into their impact on immune homeostasis, inflammation, and autoimmunity.
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Affiliation(s)
- Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Silvia Lonardi
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Matilde Monti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Francesco Missale
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
- Department of Head & Neck Oncology & Surgery Otorhinolaryngology, Antoni Van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam1066, The Netherlands
| | - Changxu Fan
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO63110
| | - Matthew L. Coates
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, United Kingdom
- Cambridge University Hospitals National Health Service Foundation Trust, CambridgeCB2 0QQ, United Kingdom
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | | | - Simone Brioschi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Tihana Trsan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Khai M. Nguyen
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - Ryan M. Nunley
- Washington University Orthopedics, Barnes Jewish Hospital, Saint Louis, MO63110
| | - Daniele Moratto
- Department of Lab Diagnostics, Azienda Socio Sanitaria Territoriale Spedali Civili di Brescia, Brescia25100, Italy
| | - Stefania Zini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Lingjia Kong
- Immunology Program, Broad Institute of Massachussets Institute of Technology and Harvard, Cambridge, MA02142
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
| | - Jacques Deguine
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
| | - Mark E. Peeples
- Infectious Diseases Institute, The Ohio State University, Columbus, OH43210
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH43205
- Department of Pediatrics, The Ohio State University, Columbus, OH43210
| | - Ramnik J. Xavier
- Immunology Program, Broad Institute of Massachussets Institute of Technology and Harvard, Cambridge, MA02142
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA02114
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA02114
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA02114
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, CambridgeCB2 0QH, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, CambridgeCB10 1SA, United Kingdom
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO63110
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
| | - William Vermi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
- Department of Molecular and Translational Medicine, University of Brescia, Brescia25125, Italy
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO63110
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10
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Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, Suo C, Pett JP, Wilbrey-Clark A, Dann E, Mamanova L, Richardson L, Polanski K, Pennycuick A, Allen-Hyttinen J, Herczeg IT, Arzili R, Hynds RE, Teixeira VH, Haniffa M, Lim K, Sun D, Rawlins EL, Oliver AJ, Lyons PA, Marioni JC, Ruhrberg C, Tuong ZK, Clatworthy MR, Reading JL, Janes SM, Teichmann SA, Meyer KB, Nikolić MZ. Early human lung immune cell development and its role in epithelial cell fate. Sci Immunol 2023; 8:eadf9988. [PMID: 38100545 PMCID: PMC7615868 DOI: 10.1126/sciimmunol.adf9988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 11/03/2023] [Indexed: 12/17/2023]
Abstract
Studies of human lung development have focused on epithelial and mesenchymal cell types and function, but much less is known about the developing lung immune cells, even though the airways are a major site of mucosal immunity after birth. An unanswered question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. Here, we profiled human embryonic and fetal lung immune cells using scRNA-seq, smFISH, and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including innate lymphoid cells, natural killer cells, myeloid cells, and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes expressing high levels of cytotoxicity genes and the presence of mature B lymphocytes, including B-1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the presence and diversity of immune cells during development, we also investigated their possible effect on epithelial maturation. We found that IL-1β drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1β-producing myeloid cells were found throughout the lung and adjacent to epithelial tips, suggesting that immune cells may direct human lung epithelial development.
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Affiliation(s)
- Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
- Division of Respiratory Diseases, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Rik G H Lindeboom
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Enhanc3D Genomics Ltd, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Adam Pennycuick
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Iván T Herczeg
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Romina Arzili
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Robert E Hynds
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, Great Ormond Street UCL Institute of Child Health, University College London, London, UK
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
| | - Vitor H Teixeira
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kyungtae Lim
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Dawei Sun
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Emma L Rawlins
- Wellcome Trust/CRUK Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Paul A Lyons
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James L Reading
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
- Tumour Immunodynamics and Interception Laboratory, Cancer Institute, University College London, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- CRUK Lung Cancer Centre Of Excellence, UCL Cancer Institute, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
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11
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Suchanek O, Ferdinand JR, Tuong ZK, Wijeyesinghe S, Chandra A, Clauder AK, Almeida LN, Clare S, Harcourt K, Ward CJ, Bashford-Rogers R, Lawley T, Manz RA, Okkenhaug K, Masopust D, Clatworthy MR. Tissue-resident B cells orchestrate macrophage polarisation and function. Nat Commun 2023; 14:7081. [PMID: 37925420 PMCID: PMC10625551 DOI: 10.1038/s41467-023-42625-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/17/2023] [Indexed: 11/06/2023] Open
Abstract
B cells play a central role in humoral immunity but also have antibody-independent functions. Studies to date have focused on B cells in blood and secondary lymphoid organs but whether B cells reside in non-lymphoid organs (NLO) in homeostasis is unknown. Here we identify, using intravenous labeling and parabiosis, a bona-fide tissue-resident B cell population in lung, liver, kidney and urinary bladder, a substantial proportion of which are B-1a cells. Tissue-resident B cells are present in neonatal tissues and also in germ-free mice NLOs, albeit in lower numbers than in specific pathogen-free mice and following co-housing with 'pet-store' mice. They spatially co-localise with macrophages and regulate their polarization and function, promoting an anti-inflammatory phenotype, in-part via interleukin-10 production, with effects on bacterial clearance during urinary tract infection. Thus, our data reveal a critical role for tissue-resident B cells in determining the homeostatic 'inflammatory set-point' of myeloid cells, with important consequences for tissue immunity.
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Affiliation(s)
- Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Sathi Wijeyesinghe
- Department of Microbiology and Immunology, Centre for Immunology, University of Minnesota, Minneapolis, MI, USA
| | - Anita Chandra
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Ann-Katrin Clauder
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Larissa N Almeida
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Simon Clare
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Christopher J Ward
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | | | - Trevor Lawley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rudolf A Manz
- Institute for Systemic Inflammation Research, University of Luebeck, Luebeck, Germany
| | - Klaus Okkenhaug
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - David Masopust
- Department of Microbiology and Immunology, Centre for Immunology, University of Minnesota, Minneapolis, MI, USA
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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12
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Suchanek O, Clatworthy MR. Homeostatic role of B-1 cells in tissue immunity. Front Immunol 2023; 14:1106294. [PMID: 37744333 PMCID: PMC10515722 DOI: 10.3389/fimmu.2023.1106294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 02/27/2023] [Indexed: 09/26/2023] Open
Abstract
To date, studies of tissue-resident immunity have mainly focused on innate immune cells and T cells, with limited data on B cells. B-1 B cells are a unique subset of B cells with innate-like properties, enriched in murine pleural and peritoneal cavities and distinct from conventional B-2 cells in their ontogeny, phenotype and function. Here we discuss how B-1 cells represent exemplar tissue-resident immune cells, summarizing the evidence for their long-term persistence & self-renewal within tissues, differential transcriptional programming shaped by organ-specific environmental cues, as well as their tissue-homeostatic functions. Finally, we review the emerging data supporting the presence and homeostatic role of B-1 cells across non-lymphoid organs (NLOs) both in mouse and human.
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Affiliation(s)
- Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
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13
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Ferreira IATM, Lee CYC, Foster WS, Abdullahi A, Dratva LM, Tuong ZK, Stewart BJ, Ferdinand JR, Guillaume SM, Potts MOP, Perera M, Krishna BA, Peñalver A, Cabantous M, Kemp SA, Ceron-Gutierrez L, Ebrahimi S, Lyons P, Smith KGC, Bradley J, Collier DA, McCoy LE, van der Klaauw A, Thaventhiran JED, Farooqi IS, Teichmann SA, MacAry PA, Doffinger R, Wills MR, Linterman MA, Clatworthy MR, Gupta RK. Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly. Cell Rep 2023; 42:112991. [PMID: 37590132 DOI: 10.1016/j.celrep.2023.112991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 05/15/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Suboptimal responses to a primary vaccination course have been reported in the elderly, but there is little information regarding the impact of age on responses to booster third doses. Here, we show that individuals 70 years or older (median age 73, range 70-75) who received a primary two-dose schedule with AZD1222 and booster third dose with mRNA vaccine achieve significantly lower neutralizing antibody responses against SARS-CoV-2 spike pseudotyped virus compared with those younger than 70 (median age 66, range 54-69) at 1 month post booster. Impaired neutralization potency and breadth post third dose in the elderly is associated with circulating "atypical" spike-specific B cells expressing CD11c and FCRL5. However, when considering individuals who received three doses of mRNA vaccine, we did not observe differences in neutralization or enrichment in atypical B cells. This work highlights the finding that AdV and mRNA COVID-19 vaccine formats differentially instruct the memory B cell response.
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Affiliation(s)
- Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - William S Foster
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lisa M Dratva
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Stephane M Guillaume
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Martin O P Potts
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marianne Perera
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Benjamin A Krishna
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ana Peñalver
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Mia Cabantous
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Lourdes Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Soraya Ebrahimi
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Paul Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - John Bradley
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Agatha van der Klaauw
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, Cambridge, UK
| | | | - I Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Wellcome-Medical Research Council (MRC) Institute of Metabolic Science, Cambridge, UK
| | | | - Paul A MacAry
- National University of Singapore, Singapore, Singapore
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Cambridge University Hospital NHS Trust, Cambridge, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Michelle A Linterman
- Immunology Programme, Babraham Institute, Babraham Research Campus, Cambridge, UK.
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK; Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK.
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14
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Hepkema J, Lee NK, Stewart BJ, Ruangroengkulrith S, Charoensawan V, Clatworthy MR, Hemberg M. Predicting the impact of sequence motifs on gene regulation using single-cell data. Genome Biol 2023; 24:189. [PMID: 37582793 PMCID: PMC10426127 DOI: 10.1186/s13059-023-03021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/21/2023] [Indexed: 08/17/2023] Open
Abstract
The binding of transcription factors at proximal promoters and distal enhancers is central to gene regulation. Identifying regulatory motifs and quantifying their impact on expression remains challenging. Using a convolutional neural network trained on single-cell data, we infer putative regulatory motifs and cell type-specific importance. Our model, scover, explains 29% of the variance in gene expression in multiple mouse tissues. Applying scover to distal enhancers identified using scATAC-seq from the developing human brain, we identify cell type-specific motif activities in distal enhancers. Scover can identify regulatory motifs and their importance from single-cell data where all parameters and outputs are easily interpretable.
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Affiliation(s)
- Jacob Hepkema
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Nicholas Keone Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
| | - Benjamin J Stewart
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Siwat Ruangroengkulrith
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, 7310, Thailand
- Systems Biology of Diseases Research Unit, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK.
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital, and Harvard Medical School, Boston, MA, 02115, USA.
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15
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Kanemaru K, Cranley J, Muraro D, Miranda AMA, Ho SY, Wilbrey-Clark A, Patrick Pett J, Polanski K, Richardson L, Litvinukova M, Kumasaka N, Qin Y, Jablonska Z, Semprich CI, Mach L, Dabrowska M, Richoz N, Bolt L, Mamanova L, Kapuge R, Barnett SN, Perera S, Talavera-López C, Mulas I, Mahbubani KT, Tuck L, Wang L, Huang MM, Prete M, Pritchard S, Dark J, Saeb-Parsy K, Patel M, Clatworthy MR, Hübner N, Chowdhury RA, Noseda M, Teichmann SA. Spatially resolved multiomics of human cardiac niches. Nature 2023; 619:801-810. [PMID: 37438528 PMCID: PMC10371870 DOI: 10.1038/s41586-023-06311-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.
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Affiliation(s)
- Kazumasa Kanemaru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - James Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Siew Yen Ho
- Cardiac Morphology Unit, Royal Brompton Hospital and Imperial College London, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Litvinukova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yue Qin
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Zuzanna Jablonska
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia I Semprich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rakeshlal Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carlos Talavera-López
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Würzburg Institute for Systems Immunology, Max Planck Research Group, Julius-Maximilian-Universität, Würzburg, Germany
| | - Ilaria Mulas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lu Wang
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret M Huang
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John Dark
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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16
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Stewart BJ, Fergie M, Young MD, Jones C, Sachdeva A, Blain A, Bacon CM, Rand V, Ferdinand JR, James KR, Mahbubani KT, Hook L, Jonas N, Coleman N, Saeb-Parsy K, Collin M, Clatworthy MR, Behjati S, Carey CD. Spatial and molecular profiling of the mononuclear phagocyte network in classic Hodgkin lymphoma. Blood 2023; 141:2343-2358. [PMID: 36758207 DOI: 10.1182/blood.2022015575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 12/14/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Classic Hodgkin lymphoma (cHL) has a rich immune infiltrate, which is an intrinsic component of the neoplastic process. Malignant Hodgkin Reed-Sternberg cells (HRSCs) create an immunosuppressive microenvironment by the expression of regulatory molecules, preventing T-cell activation. It has also been demonstrated that mononuclear phagocytes (MNPs) in the vicinity of HRSCs express similar regulatory mechanisms in parallel, and their presence in tissue is associated with inferior patient outcomes. MNPs in cHL have hitherto been identified by a small number of canonical markers and are usually described as tumor-associated macrophages. The organization of MNP networks and interactions with HRSCs remains unexplored at high resolution. Here, we defined the global immune-cell composition of cHL and nonlymphoma lymph nodes, integrating data across single-cell RNA sequencing, spatial transcriptomics, and multiplexed immunofluorescence. We observed that MNPs comprise multiple subsets of monocytes, macrophages, and dendritic cells (DCs). Classical monocytes, macrophages and conventional DC2s were enriched in the vicinity of HRSCs, but plasmacytoid DCs and activated DCs were excluded. Unexpectedly, cDCs and monocytes expressed immunoregulatory checkpoints PD-L1, TIM-3, and the tryptophan-catabolizing protein IDO, at the same level as macrophages. Expression of these molecules increased with age. We also found that classical monocytes are important signaling hubs, potentially controlling the retention of cDC2 and ThExh via CCR1-, CCR4-, CCR5-, and CXCR3-dependent signaling. Enrichment of the cDC2-monocyte-macrophage network in diagnostic biopsies is associated with early treatment failure. These results reveal unanticipated complexity and spatial polarization within the MNP compartment, further demonstrating their potential roles in immune evasion by cHL.
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Affiliation(s)
- Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Martin Fergie
- Division of Informatics, Imaging and Data Sciences, University of Manchester, Manchester, United Kingdom
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Claire Jones
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Ashwin Sachdeva
- Genito-urinary Cancer Research Group, Division of Cancer Sciences, Oglesby Cancer Research Building, University of Manchester, Manchester, United Kingdom
- Department of Surgery, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Alex Blain
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - Chris M Bacon
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Vikki Rand
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
- National Horizons Centre, Teesside University, Darlington, United Kingdom
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Kylie R James
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge Biorepository for Translational Medicine, Cambridge, United Kingdom
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Nicolaas Jonas
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge Biorepository for Translational Medicine, Cambridge, United Kingdom
| | - Matthew Collin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Christopher D Carey
- Newcastle upon Tyne NHS Hospitals Foundation Trust, Newcastle upon Tyne, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
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17
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Inaba A, Tuong ZK, Zhao TX, Stewart AP, Mathews R, Truman L, Sriranjan R, Kennet J, Saeb-Parsy K, Wicker L, Waldron-Lynch F, Cheriyan J, Todd JA, Mallat Z, Clatworthy MR. Low-dose IL-2 enhances the generation of IL-10-producing immunoregulatory B cells. Nat Commun 2023; 14:2071. [PMID: 37045832 PMCID: PMC10097719 DOI: 10.1038/s41467-023-37424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/16/2023] [Indexed: 04/14/2023] Open
Abstract
Dysfunction of interleukin-10 producing regulatory B cells has been associated with the pathogenesis of autoimmune diseases, but whether regulatory B cells can be therapeutically induced in humans is currently unknown. Here we demonstrate that a subset of activated B cells expresses CD25, and the addition of low-dose recombinant IL-2 to in vitro stimulated peripheral blood and splenic human B cells augments IL-10 secretion. Administration of low dose IL-2, aldesleukin, to patients increases IL-10-producing B cells. Single-cell RNA sequencing of circulating immune cells isolated from low dose IL2-treated patients reveals an increase in plasmablast and plasma cell populations that are enriched for a regulatory B cell gene signature. The transcriptional repressor BACH2 is significantly down-regulated in plasma cells from IL-2-treated patients, BACH2 binds to the IL-10 gene promoter, and Bach2 depletion or genetic deficiency increases B cell IL-10, implicating BACH2 suppression as an important mechanism by which IL-2 may promote an immunoregulatory phenotype in B cells.
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Affiliation(s)
- Akimichi Inaba
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Tian X Zhao
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
| | - Andrew P Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rebeccah Mathews
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Lucy Truman
- Ear, Nose Throat Department, West Suffolk Hospital, Bury St Edmunds, UK
| | - Rouchelle Sriranjan
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jane Kennet
- Wellcome-MRC Institute of Metabolic Science-Metabolic Research Laboratories and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
| | - Linda Wicker
- Medical Sciences Division, University of Oxford, Oxford, UK
| | - Frank Waldron-Lynch
- Novartis Institutes for BioMedical Research, Autoimmunity Transplantation Inflammation, Basel, Switzerland
| | - Joseph Cheriyan
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, UK
| | - John A Todd
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Ziad Mallat
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge, UK
- Universite de Paris and INSERM, Paris, France
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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18
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Scott KM, Chong YT, Park S, Wijeyekoon RS, Hayat S, Mathews RJ, Fitzpatrick Z, Tyers P, Wright G, Whitby J, Barker RA, Hu MT, Williams-Gray CH, Clatworthy MR. B lymphocyte responses in Parkinson's disease and their possible significance in disease progression. Brain Commun 2023; 5:fcad060. [PMID: 36993946 PMCID: PMC10042276 DOI: 10.1093/braincomms/fcad060] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 09/27/2022] [Accepted: 03/08/2023] [Indexed: 03/11/2023] Open
Abstract
Inflammation contributes to Parkinson's disease pathogenesis. We hypothesized that B lymphocytes are involved in Parkinson's disease progression. We measured antibodies to alpha-synuclein and tau in serum from patients with rapid eye movement sleep behaviour disorder (n = 79), early Parkinson's disease (n = 50) and matched controls (n = 50). Rapid eye movement sleep behaviour disorder cases were stratified by risk of progression to Parkinson's disease (low risk = 30, high risk = 49). We also measured B-cell activating factor of the tumour necrosis factor receptor family, C-reactive protein and total immunoglobulin G. We found elevated levels of antibodies to alpha-synuclein fibrils in rapid eye movement sleep behaviour disorder patients at high risk of Parkinson's disease conversion (ANOVA, P < 0.001) and lower S129D peptide-specific antibodies in those at low risk (ANOVA, P < 0.001). An early humoral response to alpha-synuclein is therefore detectable prior to the development of Parkinson's disease. Peripheral B lymphocyte phenotyping using flow cytometry in early Parkinson's disease patients and matched controls (n = 41 per group) revealed reduced B cells in Parkinson's disease, particularly in those at higher risk of developing an early dementia [t(3) = 2.87, P = 0.01]. Patients with a greater proportion of regulatory B cells had better motor scores [F(4,24) = 3.612, P = 0.019], suggesting they have a protective role in Parkinson's disease. In contrast, B cells isolated from Parkinson's disease patients at higher risk of dementia had greater cytokine (interleukin 6 and interleukin 10) responses following in vitro stimulation. We assessed peripheral blood lymphocytes in alpha-synuclein transgenic mouse models of Parkinson's disease: they also had reduced B cells, suggesting this is related to alpha-synuclein pathology. In a toxin-based mouse model of Parkinson's disease, B-cell deficiency or depletion resulted in worse pathological and behavioural outcomes, supporting the conclusion that B cells play an early protective role in dopaminergic cell loss. In conclusion, we found changes in the B-cell compartment associated with risk of disease progression in rapid eye movement sleep behaviour disorder (higher alpha-synuclein antibodies) and early Parkinson's disease (lower levels of B lymphocytes that were more reactive to stimulation). Regulatory B cells play a protective role in a mouse model, potentially by attenuating inflammation and dopaminergic cell loss. B cells are therefore likely to be involved in the pathogenesis of Parkinson's disease, albeit in a complex way, and thus warrant consideration as a therapeutic target.
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Affiliation(s)
- Kirsten M Scott
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, UK
| | - Yen Ting Chong
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Seoyoung Park
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Ruwani S Wijeyekoon
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Shaista Hayat
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Rebeccah J Mathews
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, UK
| | - Zachary Fitzpatrick
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, UK
| | - Pam Tyers
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Georgia Wright
- University of Cambridge Clinical School of Medicine, Cambridge CB2 OQQ, UK
| | - Jennifer Whitby
- University of Cambridge Clinical School of Medicine, Cambridge CB2 OQQ, UK
| | - Roger A Barker
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Michele T Hu
- Division of Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Caroline H Williams-Gray
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, UK
- Cellular Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
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19
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Dutcher EG, Lopez-Cruz L, Pama EAC, Lynall ME, Bevers ICR, Jones JA, Khan S, Sawiak SJ, Milton AL, Clatworthy MR, Robbins TW, Bullmore ET, Dalley JW. Early-life stress biases responding to negative feedback and increases amygdala volume and vulnerability to later-life stress. Transl Psychiatry 2023; 13:81. [PMID: 36882404 PMCID: PMC9992709 DOI: 10.1038/s41398-023-02385-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Early-life stress (ELS) or adversity, particularly in the form of childhood neglect and abuse, is associated with poor mental and physical health outcomes in adulthood. However, whether these relationships are mediated by the consequences of ELS itself or by other exposures that frequently co-occur with ELS is unclear. To address this question, we carried out a longitudinal study in rats to isolate the effects of ELS on regional brain volumes and behavioral phenotypes relevant to anxiety and depression. We used the repeated maternal separation (RMS) model of chronic ELS, and conducted behavioral measurements throughout adulthood, including of probabilistic reversal learning (PRL), responding on a progressive ratio task, sucrose preference, novelty preference, novelty reactivity, and putative anxiety-like behavior on the elevated plus maze. Our behavioral assessment was combined with magnetic resonance imaging (MRI) for quantitation of regional brain volumes at three time points: immediately following RMS, young adulthood without further stress, and late adulthood with further stress. We found that RMS caused long-lasting, sexually dimorphic biased responding to negative feedback on the PRL task. RMS also slowed response time on the PRL task, but without this directly impacting task performance. RMS animals were also uniquely sensitive to a second stressor, which disproportionately impaired their performance and slowed their responding on the PRL task. MRI at the time of the adult stress revealed a larger amygdala volume in RMS animals compared with controls. These behavioral and neurobiological effects persisted well into adulthood despite a lack of effects on conventional tests of 'depression-like' and 'anxiety-like' behavior, and a lack of any evidence of anhedonia. Our findings indicate that ELS has long-lasting cognitive and neurobehavioral effects that interact with stress in adulthood and may have relevance for understanding the etiology of anxiety and depression in humans.
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Affiliation(s)
- Ethan G Dutcher
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - Laura Lopez-Cruz
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - E A Claudia Pama
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - Mary-Ellen Lynall
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 0SZ, UK
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, CB2 OQH, UK
| | - Iris C R Bevers
- Faculty of Medical Sciences, Radboud University, Nijmegen, 6525 XZ, The Netherlands
| | - Jolyon A Jones
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - Shahid Khan
- GlaxoSmithKline Research & Development, Stevenage, SG1 2NY, UK
| | - Stephen J Sawiak
- Department of Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, CB2 3EL, UK
- Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, Cambridge, CB2 0QQ, UK
| | - Amy L Milton
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge, CB2 OQH, UK
| | - Trevor W Robbins
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK
| | - Edward T Bullmore
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 0SZ, UK
| | - Jeffrey W Dalley
- Department of Psychology, University of Cambridge, Cambridge, CB2 3EB, UK.
- Department of Psychiatry, University of Cambridge, Cambridge, CB2 0SZ, UK.
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20
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Guo SA, Bowyer GS, Ferdinand JR, Maes M, Tuong ZK, Gillman E, Liao M, Lindeboom RGH, Yoshida M, Worlock K, Gopee H, Stephenson E, Gao CA, Lyons PA, Smith KGC, Haniffa M, Meyer KB, Nikolić MZ, Zhang Z, Wunderink RG, Misharin AV, Dougan G, Navapurkar V, Teichmann SA, Conway Morris A, Clatworthy MR. Obesity Is Associated with Attenuated Tissue Immunity in COVID-19. Am J Respir Crit Care Med 2023; 207:566-576. [PMID: 36095143 PMCID: PMC10870921 DOI: 10.1164/rccm.202204-0751oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 09/12/2022] [Indexed: 02/03/2023] Open
Abstract
Rationale: Obesity affects 40% of U.S. adults, is associated with a proinflammatory state, and presents a significant risk factor for the development of severe coronavirus disease (COVID-19). To date, there is limited information on how obesity might affect immune cell responses in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Objectives: To determine the impact of obesity on respiratory tract immunity in COVID-19 across the human lifespan. Methods: We analyzed single-cell transcriptomes from BAL in three ventilated adult cohorts with (n = 24) or without (n = 9) COVID-19 from nasal immune cells in children with (n = 14) or without (n = 19) COVID-19, and from peripheral blood mononuclear cells in an independent adult COVID-19 cohort (n = 42), comparing obese and nonobese subjects. Measurements and Main Results: Surprisingly, we found that obese adult subjects had attenuated lung immune or inflammatory responses in SARS-CoV-2 infection, with decreased expression of IFN-α, IFN-γ, and TNF-α (tumor necrosis factor α) response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Peripheral blood immune cells in an independent adult cohort showed a similar but less marked reduction in type-I IFN and IFNγ response genes, as well as decreased serum IFNα, in obese patients with SARS-CoV-2. Nasal immune cells from obese children with COVID-19 also showed reduced enrichment of IFN-α and IFN-γ response genes. Conclusions: These findings show blunted tissue immune responses in obese patients with COVID-19, with implications for treatment stratification, supporting the specific application of inhaled recombinant type-I IFNs in this vulnerable subset.
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Affiliation(s)
- Shuang A. Guo
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Georgina S. Bowyer
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
| | - John R. Ferdinand
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
| | - Mailis Maes
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
| | - Zewen K. Tuong
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Eleanor Gillman
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
| | - Mingfeng Liao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, China
| | | | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Kaylee Worlock
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Hudaa Gopee
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Catherine A. Gao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Paul A. Lyons
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; and
| | - Kenneth G. C. Smith
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; and
| | - Muzlifah Haniffa
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kerstin B. Meyer
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Marko Z. Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, China
| | - Richard G. Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alexander V. Misharin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Gordon Dougan
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; and
| | - Vilas Navapurkar
- John V. Farman Intensive Care Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Andrew Conway Morris
- Division of Anaesthesia, Department of Medicine
- Division of Immunology, Department of Pathology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, United Kingdom
- John V. Farman Intensive Care Unit, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Menna R. Clatworthy
- Molecular Immunity Unit
- Cambridge Institute for Therapeutic Immunology and Infectious Disease
- Department of Medicine, Cambridge Biomedical Campus
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; and
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21
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Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R, Pett JP, Huang N, Xu C, He P, Dabrowska M, Pritchard S, Tuck L, Prigmore E, Perera S, Knights A, Oszlanczi A, Hunter A, Vieira SF, Patel M, Lindeboom RGH, Campos LS, Matsuo K, Nakayama T, Yoshida M, Worlock KB, Nikolić MZ, Georgakopoulos N, Mahbubani KT, Saeb-Parsy K, Bayraktar OA, Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet 2023; 55:66-77. [PMID: 36543915 PMCID: PMC9839452 DOI: 10.1038/s41588-022-01243-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
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Affiliation(s)
- Elo Madissoon
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Ana Ribeiro Orsi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Andrew Knights
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | | | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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22
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Li R, Ferdinand JR, Loudon KW, Bowyer GS, Laidlaw S, Muyas F, Mamanova L, Neves JB, Bolt L, Fasouli ES, Lawson ARJ, Young MD, Hooks Y, Oliver TRW, Butler TM, Armitage JN, Aho T, Riddick ACP, Gnanapragasam V, Welsh SJ, Meyer KB, Warren AY, Tran MGB, Stewart GD, Cortés-Ciriano I, Behjati S, Clatworthy MR, Campbell PJ, Teichmann SA, Mitchell TJ. Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell 2022; 40:1583-1599.e10. [PMID: 36423636 PMCID: PMC9767677 DOI: 10.1016/j.ccell.2022.11.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/12/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
Tumor behavior is intricately dependent on the oncogenic properties of cancer cells and their multi-cellular interactions. To understand these dependencies within the wider microenvironment, we studied over 270,000 single-cell transcriptomes and 100 microdissected whole exomes from 12 patients with kidney tumors, prior to validation using spatial transcriptomics. Tissues were sampled from multiple regions of the tumor core, the tumor-normal interface, normal surrounding tissues, and peripheral blood. We find that the tissue-type location of CD8+ T cell clonotypes largely defines their exhaustion state with intra-tumoral spatial heterogeneity that is not well explained by somatic heterogeneity. De novo mutation calling from single-cell RNA-sequencing data allows us to broadly infer the clonality of stromal cells and lineage-trace myeloid cell development. We report six conserved meta-programs that distinguish tumor cell function, and find an epithelial-mesenchymal transition meta-program highly enriched at the tumor-normal interface that co-localizes with IL1B-expressing macrophages, offering a potential therapeutic target.
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Affiliation(s)
- Ruoyan Li
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Georgina S Bowyer
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sean Laidlaw
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Francesc Muyas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Joana B Neves
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK; Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Liam Bolt
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Eirini S Fasouli
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Andrew R J Lawson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Matthew D Young
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvette Hooks
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Thomas R W Oliver
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Timothy M Butler
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - James N Armitage
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Tev Aho
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Antony C P Riddick
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Vincent Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Sarah J Welsh
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Kerstin B Meyer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK; Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Isidro Cortés-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Menna R Clatworthy
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Department of Physics, Cavendish Laboratory, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Thomas J Mitchell
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge University Hospitals NHS Foundation Trust and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK.
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23
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Richoz N, Tuong ZK, Loudon KW, Patiño-Martínez E, Ferdinand JR, Portet A, Bashant KR, Thevenon E, Rucci F, Hoyler T, Junt T, Kaplan MJ, Siegel RM, Clatworthy MR. Distinct pathogenic roles for resident and monocyte-derived macrophages in lupus nephritis. JCI Insight 2022; 7:159751. [PMID: 36345939 PMCID: PMC9675473 DOI: 10.1172/jci.insight.159751] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/06/2022] [Indexed: 11/09/2022] Open
Abstract
Lupus nephritis is a serious complication of systemic lupus erythematosus, mediated by IgG immune complex (IC) deposition in kidneys, with limited treatment options. Kidney macrophages are critical tissue sentinels that express IgG-binding Fcγ receptors (FcγRs), with previous studies identifying prenatally seeded resident macrophages as major IC responders. Using single-cell transcriptomic and spatial analyses in murine and human lupus nephritis, we sought to understand macrophage heterogeneity and subset-specific contributions in disease. In lupus nephritis, the cell fate trajectories of tissue-resident (TrMac) and monocyte-derived (MoMac) kidney macrophages were perturbed, with disease-associated transcriptional states indicating distinct pathogenic roles for TrMac and MoMac subsets. Lupus nephritis-associated MoMac subsets showed marked induction of FcγR response genes, avidly internalized circulating ICs, and presented IC-opsonized antigen. In contrast, lupus nephritis-associated TrMac subsets demonstrated limited IC uptake, but expressed monocyte chemoattractants, and their depletion attenuated monocyte recruitment to the kidney. TrMacs also produced B cell tissue niche factors, suggesting a role in supporting autoantibody-producing lymphoid aggregates. Extensive similarities were observed with human kidney macrophages, revealing cross-species transcriptional disruption in lupus nephritis. Overall, our study suggests a division of labor in the kidney macrophage response in lupus nephritis, with treatment implications - TrMacs orchestrate leukocyte recruitment while MoMacs take up and present IC antigen.
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Affiliation(s)
- Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom.,National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Zewen K. Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom.,Cellular Genetics programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Kevin W. Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom
| | - Eduardo Patiño-Martínez
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John R. Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom
| | - Anaïs Portet
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom
| | - Kathleen R. Bashant
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Francesca Rucci
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Thomas Hoyler
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Tobias Junt
- Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Mariana J. Kaplan
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Richard M. Siegel
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA.,Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Menna R. Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, Department of Medicine, University of Cambridge School of Clinical Medicine, United Kingdom.,Cellular Genetics programme, Wellcome Sanger Institute, Hinxton, United Kingdom
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24
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Lynall ME, Soskic B, Hayhurst J, Schwartzentruber J, Levey DF, Pathak GA, Polimanti R, Gelernter J, Stein MB, Trynka G, Clatworthy MR, Bullmore E. Genetic variants associated with psychiatric disorders are enriched at epigenetically active sites in lymphoid cells. Nat Commun 2022; 13:6102. [PMID: 36243721 PMCID: PMC9569335 DOI: 10.1038/s41467-022-33885-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 10/06/2022] [Indexed: 02/06/2023] Open
Abstract
Multiple psychiatric disorders have been associated with abnormalities in both the innate and adaptive immune systems. The role of these abnormalities in pathogenesis, and whether they are driven by psychiatric risk variants, remains unclear. We test for enrichment of GWAS variants associated with multiple psychiatric disorders (cross-disorder or trans-diagnostic risk), or 5 specific disorders (cis-diagnostic risk), in regulatory elements in immune cells. We use three independent epigenetic datasets representing multiple organ systems and immune cell subsets. Trans-diagnostic and cis-diagnostic risk variants (for schizophrenia and depression) are enriched at epigenetically active sites in brain tissues and in lymphoid cells, especially stimulated CD4+ T cells. There is no evidence for enrichment of either trans-risk or cis-risk variants for schizophrenia or depression in myeloid cells. This suggests a possible model where environmental stimuli activate T cells to unmask the effects of psychiatric risk variants, contributing to the pathogenesis of mental health disorders.
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Affiliation(s)
- Mary-Ellen Lynall
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK.
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK.
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK.
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK.
| | - Blagoje Soskic
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
- Human Technopole, Milan, Italy
| | | | | | - Daniel F Levey
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Gita A Pathak
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Renato Polimanti
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Joel Gelernter
- VA Connecticut Healthcare System, West Haven, CT, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- Departments of Genetics and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Murray B Stein
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Ed Bullmore
- Department of Psychiatry, Herchel Smith Building of Brain & Mind Sciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0SZ, UK
- Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
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25
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Riding AM, Loudon KW, Guo A, Ferdinand JR, Lok LS, Richoz N, Stewart A, Castro-Dopico T, Tuong ZK, Fiancette R, Bowyer GS, Fleming A, Gillman ES, Suchanek O, Mahbubani KT, Saeb-Parsy K, Withers D, Dougan G, Clare S, Clatworthy MR. Group 3 innate lymphocytes make a distinct contribution to type 17 immunity in bladder defence. iScience 2022; 25:104660. [PMID: 35845169 PMCID: PMC9283510 DOI: 10.1016/j.isci.2022.104660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 03/08/2022] [Accepted: 06/16/2022] [Indexed: 02/02/2023] Open
Abstract
Bladder infection affects a hundred million people annually, but our understanding of bladder immunity is incomplete. We found type 17 immune response genes among the most up-regulated networks in mouse bladder following uropathogenic Escherichia coli (UPEC) challenge. Intravital imaging revealed submucosal Rorc+ cells responsive to UPEC challenge, and we found increased Il17 and IL22 transcripts in wild-type and Rag2 -/- mice, implicating group 3 innate lymphoid cells (ILC3s) as a source of these cytokines. NCR-positive and negative ILC3 subsets were identified in murine and human bladders, with local proliferation increasing IL17-producing ILC3s post infection. ILC3s made a more limited contribution to bladder IL22, with prominent early induction of IL22 evident in Th17 cells. Single-cell RNA sequencing revealed bladder NCR-negative ILC3s as the source of IL17 and identified putative ILC3-myeloid cell interactions, including via lymphotoxin-β-LTBR. Altogether, our data provide important insights into the orchestration and execution of type 17 immunity in bladder defense.
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Affiliation(s)
- Alexandra M. Riding
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Kevin W. Loudon
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Andrew Guo
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Laurence S.C. Lok
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Andrew Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Tomas Castro-Dopico
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
| | - Remi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Georgina S. Bowyer
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Aaron Fleming
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Eleanor S. Gillman
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | | | - Kourosh Saeb-Parsy
- University of Cambridge Department of Surgery, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
| | - David Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Gordan Dougan
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Simon Clare
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Menna R. Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
- Cambridge Institute for Therapeutic Immunology and Infectious Diseases (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Puddicombe Way, Cambridge CB2 0AW, UK
- Cellular Generics, Wellcome Sanger Institute, Hinxton, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Parasites and Microbes, Wellcome Sanger Institute, Hinxton, UK
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26
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Yao Y, Du Jiang P, Chao BN, Cagdas D, Kubo S, Balasubramaniyam A, Zhang Y, Shadur B, NaserEddin A, Folio LR, Schwarz B, Bohrnsen E, Zheng L, Lynberg M, Gottlieb S, Leney-Greene MA, Park AY, Tezcan I, Akdogan A, Gocmen R, Onder S, Rosenberg A, Soilleux EJ, Johnson E, Jackson PK, Demeter J, Chauvin SD, Paul F, Selbach M, Bulut H, Clatworthy MR, Tuong ZK, Zhang H, Stewart BJ, Bosio CM, Stepensky P, Clare S, Ganesan S, Pascall JC, Daumke O, Butcher GW, McMichael AJ, Simon AK, Lenardo MJ. GIMAP6 regulates autophagy, immune competence, and inflammation in mice and humans. J Exp Med 2022; 219:213217. [PMID: 35551368 PMCID: PMC9111091 DOI: 10.1084/jem.20201405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 11/26/2022] Open
Abstract
Inborn errors of immunity (IEIs) unveil regulatory pathways of human immunity. We describe a new IEI caused by mutations in the GTPase of the immune-associated protein 6 (GIMAP6) gene in patients with infections, lymphoproliferation, autoimmunity, and multiorgan vasculitis. Patients and Gimap6−/− mice show defects in autophagy, redox regulation, and polyunsaturated fatty acid (PUFA)–containing lipids. We find that GIMAP6 complexes with GABARAPL2 and GIMAP7 to regulate GTPase activity. Also, GIMAP6 is induced by IFN-γ and plays a critical role in antibacterial immunity. Finally, we observed that Gimap6−/− mice died prematurely from microangiopathic glomerulosclerosis most likely due to GIMAP6 deficiency in kidney endothelial cells.
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Affiliation(s)
- Yikun Yao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ping Du Jiang
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Brittany N Chao
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Deniz Cagdas
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Satoshi Kubo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Arasu Balasubramaniyam
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Bella Shadur
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel.,The Garvan Institute of Medical Research, Immunology Division, Darlinghurst, Sydney, Australia.,St Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, Australia
| | - Adeeb NaserEddin
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Les R Folio
- Clinical Center, National Institutes of Health, Bethesda, MD
| | - Benjamin Schwarz
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Eric Bohrnsen
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Lixin Zheng
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Matthew Lynberg
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Simone Gottlieb
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Michael A Leney-Greene
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Ann Y Park
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Ilhan Tezcan
- Division of Immunology, Department of Pediatrics, Hacettepe University Faculty of Medicine, Ankara, Turkey.,Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Turkey.,Ihsan Dogramaci Childrens Hospital, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ali Akdogan
- Division of Rheumatology, Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Rahsan Gocmen
- Department of Radiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Sevgen Onder
- Department of Pathology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Avi Rosenberg
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD.,Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | | | - Errin Johnson
- The Dunn School of Pathology, South Parks Road, Oxford, UK
| | - Peter K Jackson
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Janos Demeter
- Baxter Laboratory, Departments of Microbiology & Immunology and Pathology Stanford University School of Medicine, Stanford, CA
| | - Samuel D Chauvin
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
| | - Florian Paul
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Matthias Selbach
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Haydar Bulut
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Zewen K Tuong
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Hanlin Zhang
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Catharine M Bosio
- Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - Polina Stepensky
- Hadassah University Medical Center, Department of Bone Marrow Transplantation and Cancer Immunotherapy, Jerusalem, Israel
| | - Simon Clare
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Sundar Ganesan
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, Rockville, MD
| | - John C Pascall
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Oliver Daumke
- Crystallography, Max-Delbrück-Centrum for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Institute for Chemistry and Biochemistry, Freie Universität Berlin, Takustrasse 6, Berlin, Germany
| | - Geoffrey W Butcher
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Andrew J McMichael
- Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Anna Katharina Simon
- Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Michael J Lenardo
- Molecular Development of the Immune System Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,National Institute of Allergy and Infectious Diseases Clinical Genomics Program, Rockville, MD
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27
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Li Z, Tuong ZK, Dean I, Willis C, Gaspal F, Fiancette R, Idris S, Kennedy B, Ferdinand JR, Peñalver A, Cabantous M, Murtuza Baker S, Fry JW, Carlesso G, Hammond SA, Dovedi SJ, Hepworth MR, Clatworthy MR, Withers DR. In vivo labeling reveals continuous trafficking of TCF-1+ T cells between tumor and lymphoid tissue. J Exp Med 2022; 219:e20210749. [PMID: 35472220 PMCID: PMC9048291 DOI: 10.1084/jem.20210749] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 01/14/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
Improving the efficacy of immune checkpoint therapies will require a better understanding of how immune cells are recruited and sustained in tumors. Here, we used the photoconversion of the tumor immune cell compartment to identify newly entering lymphocytes, determine how they change over time, and investigate their egress from the tumor. Combining single-cell transcriptomics and flow cytometry, we found that while a diverse mix of CD8 T cell subsets enter the tumor, all CD8 T cells retained within this environment for more than 72 h developed an exhausted phenotype, revealing the rapid establishment of this program. Rather than forming tumor-resident populations, non-effector subsets, which express TCF-1 and include memory and stem-like cells, were continuously recruited into the tumor, but this recruitment was balanced by concurrent egress to the tumor-draining lymph node. Thus, the TCF-1+ CD8 T cell niche in tumors is highly dynamic, with the circulation of cells between the tumor and peripheral lymphoid tissue to bridge systemic and intratumoral responses.
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Affiliation(s)
- Zhi Li
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Zewen K. Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Isaac Dean
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Claire Willis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabrina Gaspal
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Rémi Fiancette
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Suaad Idris
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Bethany Kennedy
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ana Peñalver
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Mia Cabantous
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Syed Murtuza Baker
- Division of Informatics, Imaging & Data Science, Faculty of Biology, Medicine and Health, the University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jeremy W. Fry
- ProImmune Ltd., The Magdalen Centre, Oxford Science Park, Oxford, UK
| | | | | | | | - Matthew R. Hepworth
- Lydia Becker Institute of Immunology and Inflammation, Division of Infection, Immunity and Respiratory Medicine, Faculty of Biology, Medicine and Health, the University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - David R. Withers
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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28
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Beaman GM, Woolf AS, Lopes FM, Guo SA, Harkness JR, Cervellione RM, Keene D, Mushtaq I, Clatworthy MR, Newman WG. Narrowing the chromosome 22q11.2 locus duplicated in bladder exstrophy-epispadias complex. J Pediatr Urol 2022; 18:362.e1-362.e8. [PMID: 35491304 DOI: 10.1016/j.jpurol.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/15/2022] [Accepted: 04/03/2022] [Indexed: 10/18/2022]
Abstract
INTRODUCTION Bladder exstrophy-epispadias complex (BEEC) comprises a spectrum of anterior midline congenital malformations, involving the lower urinary tract. BEEC is usually sporadic, but families with more than one affected member have been reported, and a twin concordance study supported a genetic contribution to pathogenesis. Moreover, diverse chromosomal aberrations have been reported in a small subset of individuals with BEEC. The commonest are 22q11.2 microduplications, identified in approximately 3% of BEEC index cases. OBJECTIVES We aimed to refine the chromosome 22q11.2 locus, and to determine whether the encompassed genes are expressed in normal developing and mature human urinary bladders. RESULTS Using DNA from an individual with CBE, the 22q11.2 duplicated locus was refined by identification of a maternally inherited 314 kb duplication (chr22:21,147,293-21,461,017), as depicted in this image. Moreover, the eight protein coding genes within the locus were found to be expressed during normal developing and mature bladders. To determine whether duplications in any of these individual genes were associated with CBE, we undertook copy number analyses in 115 individuals with CBE without duplications of the whole locus. No duplications of individual genes were found. DISCUSSION The current study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes are expressed in human bladders both during antenatal development and postnatally. Nevertheless, the precise biological explanation as to why duplication of the phenocritical region of 22q11 confers increased susceptibility to BEEC remains to be determined. The fact that individuals with CBE without duplications of the whole locus also lacked duplication of any of the individual genes suggests that in individuals with BEEC and duplication of the 22q11.2 locus altered dosage of more than one gene may be important in BEEC etiology. CONCLUSIONS The study has refined the 22q11.2 locus associated with BEEC and has shown that the eight protein coding genes within this locus are expressed in human bladders.
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Affiliation(s)
- Glenda M Beaman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Filipa M Lopes
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QH, United Kingdom; Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom
| | - J Robert Harkness
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Raimondo M Cervellione
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - David Keene
- Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Imran Mushtaq
- Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton CB10 1RQ, United Kingdom; Department of Paediatric Urology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - William G Newman
- Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.
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29
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Domínguez Conde C, Xu C, Jarvis LB, Rainbow DB, Wells SB, Gomes T, Howlett SK, Suchanek O, Polanski K, King HW, Mamanova L, Huang N, Szabo PA, Richardson L, Bolt L, Fasouli ES, Mahbubani KT, Prete M, Tuck L, Richoz N, Tuong ZK, Campos L, Mousa HS, Needham EJ, Pritchard S, Li T, Elmentaite R, Park J, Rahmani E, Chen D, Menon DK, Bayraktar OA, James LK, Meyer KB, Yosef N, Clatworthy MR, Sims PA, Farber DL, Saeb-Parsy K, Jones JL, Teichmann SA. Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science 2022; 376:eabl5197. [PMID: 35549406 PMCID: PMC7612735 DOI: 10.1126/science.abl5197] [Citation(s) in RCA: 191] [Impact Index Per Article: 95.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite their crucial role in health and disease, our knowledge of immune cells within human tissues remains limited. We surveyed the immune compartment of 16 tissues from 12 adult donors by single-cell RNA sequencing and VDJ sequencing generating a dataset of ~360,000 cells. To systematically resolve immune cell heterogeneity across tissues, we developed CellTypist, a machine learning tool for rapid and precise cell type annotation. Using this approach, combined with detailed curation, we determined the tissue distribution of finely phenotyped immune cell types, revealing hitherto unappreciated tissue-specific features and clonal architecture of T and B cells. Our multitissue approach lays the foundation for identifying highly resolved immune cell types by leveraging a common reference dataset, tissue-integrated expression analysis, and antigen receptor sequencing.
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Affiliation(s)
- C Domínguez Conde
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - C Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LB Jarvis
- Department of Clinical Neurosciences, University of Cambridge
| | - DB Rainbow
- Department of Clinical Neurosciences, University of Cambridge
| | - SB Wells
- Department of Systems Biology, Columbia University Irving Medical Center
| | - T Gomes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - SK Howlett
- Department of Clinical Neurosciences, University of Cambridge
| | - O Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - K Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - HW King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - L Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - PA Szabo
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - L Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - ES Fasouli
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - KT Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - M Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - L Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - ZK Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - L Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- West Suffolk Hospital NHS Trust, Bury Saint Edmunds, UK
| | - HS Mousa
- Department of Clinical Neurosciences, University of Cambridge
| | - EJ Needham
- Department of Clinical Neurosciences, University of Cambridge
| | - S Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - T Li
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - R Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - J Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - E Rahmani
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - D Chen
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DK Menon
- Department of Anaesthesia, University of Cambridge, Cambridge, UK
| | - OA Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - LK James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - KB Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - N Yosef
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - MR Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - PA Sims
- Department of Systems Biology, Columbia University Irving Medical Center
| | - DL Farber
- Department of Microbiology and Immunology, Columbia University Irving Medical Center
| | - K Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - JL Jones
- Department of Clinical Neurosciences, University of Cambridge
| | - SA Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, JJ Thomson Ave, Cambridge CB3 0HE, UK
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30
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Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. Mapping the developing human immune system across organs. Science 2022; 376:eabo0510. [PMID: 35549310 PMCID: PMC7612819 DOI: 10.1126/science.abo0510] [Citation(s) in RCA: 87] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell genomics studies have decoded the immune-cell composition of several human prenatal organs but were limited in understanding the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells prior to peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Paediatrics, Cambridge University Hospitals, Hills Road, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Haematology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadav Yayon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mohi Miah
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK.,Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
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31
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Banham GD, Lee CYC, Ferdinand JR, Matthews RJ, Jing C, Smithers N, Prinjha RK, Clatworthy MR. Bromodomain Inhibitors Modulate FcγR-Mediated Mononuclear Phagocyte Activation and Chemotaxis. Front Immunol 2022; 13:885101. [PMID: 35619690 PMCID: PMC9127238 DOI: 10.3389/fimmu.2022.885101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
IgG antibodies form immune complexes (IC) that propagate inflammation and tissue damage in autoimmune diseases such as systemic lupus erythematosus. IgG IC engage Fcγ receptors (FcγR) on mononuclear phagocytes (MNP), leading to widespread changes in gene expression that mediate antibody effector function. Bromodomain and extra-terminal domain (BET) proteins are involved in governing gene transcription. We investigated the capacity of BET protein inhibitors (iBET) to alter IgG FcγR-mediated MNP activation. We found that iBET dampened IgG IC-induced pro-inflammatory gene expression and decreased activating FcγR expression on MNPs, reducing their ability to respond to IgG IC. Despite FcγR downregulation, iBET-treated macrophages demonstrated increased phagocytosis of protein antigen, IgG IC, and apoptotic cells. iBET also altered cell morphology, generating more amoeboid MNPs with reduced adhesion. iBET treatment impaired chemotaxis towards a CCL19 gradient in IC-stimulated dendritic cells (DC) in vitro, and inhibited IC-induced DC migration to draining lymph nodes in vivo, in a DC-intrinsic manner. Altogether, our data show that iBET modulates FcγR-mediated MNP activation and migration, revealing the therapeutic potential of BET protein inhibition in antibody-mediated diseases.
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Affiliation(s)
- Gemma D. Banham
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Colin Y. C. Lee
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Rebeccah J. Matthews
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Chenzhi Jing
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Smithers
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Rab K. Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, United Kingdom
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, United Kingdom
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32
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Zhang Y, Garcia-Ibanez L, Ulbricht C, Lok LSC, Pike JA, Mueller-Winkler J, Dennison TW, Ferdinand JR, Burnett CJM, Yam-Puc JC, Zhang L, Alfaro RM, Takahama Y, Ohigashi I, Brown G, Kurosaki T, Tybulewicz VLJ, Rot A, Hauser AE, Clatworthy MR, Toellner KM. Recycling of memory B cells between germinal center and lymph node subcapsular sinus supports affinity maturation to antigenic drift. Nat Commun 2022; 13:2460. [PMID: 35513371 PMCID: PMC9072412 DOI: 10.1038/s41467-022-29978-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
Infection or vaccination leads to the development of germinal centers (GC) where B cells evolve high affinity antigen receptors, eventually producing antibody-forming plasma cells or memory B cells. Here we follow the migratory pathways of B cells emerging from germinal centers (BEM) and find that many BEM cells migrate into the lymph node subcapsular sinus (SCS) guided by sphingosine-1-phosphate (S1P). From the SCS, BEM cells may exit the lymph node to enter distant tissues, while some BEM cells interact with and take up antigen from SCS macrophages, followed by CCL21-guided return towards the GC. Disruption of local CCL21 gradients inhibits the recycling of BEM cells and results in less efficient adaption to antigenic variation. Our findings thus suggest that the recycling of antigen variant-specific BEM cells and transport of antigen back to GC may support affinity maturation to antigenic drift.
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Affiliation(s)
- Yang Zhang
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Laura Garcia-Ibanez
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Carolin Ulbricht
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Charitéplatz 1, 10117, Berlin, Germany
| | - Laurence S C Lok
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Jeremy A Pike
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Birmingham, UK
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Thomas W Dennison
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - John R Ferdinand
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Cameron J M Burnett
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Juan C Yam-Puc
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Lingling Zhang
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- The Francis Crick Institute, London, UK
| | - Raul Maqueda Alfaro
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Department of Cell Biology, Center for Research and Advanced Studies, The National Polytechnic Institute, Cinvestav-IPN, Av. IPN 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima, 770-8503, Japan
| | - Geoffrey Brown
- Department of Cell Biology, Center for Research and Advanced Studies, The National Polytechnic Institute, Cinvestav-IPN, Av. IPN 2508, San Pedro Zacatenco, Gustavo A. Madero, 07360, Mexico City, Mexico
| | - Tomohiro Kurosaki
- Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, Osaka University, Osaka, 565-0871, Japan
- Laboratory of Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, Kanagawa, 230-0045, Japan
| | | | - Antal Rot
- Centre for Microvascular Research, The William Harvey Research Institute, Queen Mary University London, EC1M 6BQ, London, UK
- Centre for Inflammation and Therapeutic Innovation, Queen Mary University London, EC1M 6BQ, London, UK
- Institute for Cardiovascular Prevention, Ludwig-Maximilians University, 80336, Munich, Germany
| | - Anja E Hauser
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
- Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Charitéplatz 1, 10117, Berlin, Germany
| | - Menna R Clatworthy
- University of Cambridge Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Kai-Michael Toellner
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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Abstract
The bladder is a major component of the urinary tract, an organ system that expels metabolic waste and excess water, which necessitates proximity to the external environment and its pathogens. It also houses a commensal microbiome. Therefore, its tissue immunity must resist pathogen invasion while maintaining tolerance to commensals. Bacterial infection of the bladder is common, with half of women globally experiencing one or more episodes of cystitis in their lifetime. Despite this, our knowledge of bladder immunity, particularly in humans, is incomplete. Here we consider the current view of tissue immunity in the bladder, with a focus on defense against infection. The urothelium has robust immune functionality, and its defensive capabilities are supported by resident immune cells, including macrophages, dendritic cells, natural killer cells, and γδ T cells. We discuss each in turn and consider why adaptive immune responses are often ineffective in preventing recurrent infection, as well as areas of priority for future research.
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Affiliation(s)
- Georgina S Bowyer
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom;
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
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34
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Thompson ER, Sewpaul A, Figuereido R, Bates L, Tingle SJ, Ferdinand JR, Situmorang GR, Ladak SS, Connelly CM, Hosgood SA, Nicholson ML, Clatworthy MR, Ali S, Wilson CH, Sheerin NS. MicroRNA antagonist therapy during normothermic machine perfusion of donor kidneys. Am J Transplant 2022; 22:1088-1100. [PMID: 34932895 DOI: 10.1111/ajt.16929] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 12/12/2021] [Accepted: 12/14/2021] [Indexed: 01/25/2023]
Abstract
Normothermic machine perfusion (NMP) is a novel clinical approach to overcome the limitations of traditional hypothermic organ preservation. NMP can be used to assess and recondition organs prior to transplant and is the subject of clinical trials in solid organ transplantation. In addition, NMP provides an opportunity to deliver therapeutic agents directly to the organ, thus avoiding many limitations associated with systemic treatment of the recipient. We report the delivery of oligonucleotide-based therapy to human kidneys during NMP, in this case to target microRNA function (antagomir). An antagomir targeting mir-24-3p localized to the endothelium and proximal tubular epithelium. Endosomal uptake during NMP conditions facilitated antagomir co-localization with proteins involved in the RNA-induced silencing complex (RISC) and demonstrated engagement of the miRNA target. This pattern of uptake was not seen during cold perfusion. Targeting mir-24-3p action increased expression of genes controlled by this microRNA, including heme oxygenase-1 and sphingosine-1-phosphate receptor 1. The expression of genes not under the control of mir-24-3p was unchanged, indicating specificity of the antagomir effect. In summary, this is the first report of ex vivo gymnotic delivery of oligonucleotide to the human kidney and demonstrates that NMP provides the platform to bind and block detrimental microRNAs in donor kidneys prior to transplantation.
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Affiliation(s)
- Emily R Thompson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Avinash Sewpaul
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Rodrigo Figuereido
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Lucy Bates
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Samuel J Tingle
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - John R Ferdinand
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Gerhard R Situmorang
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Shameem S Ladak
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Chloe M Connelly
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah A Hosgood
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK.,Department of Surgery, University of Cambridge, Cambridge, UK
| | - Michael L Nicholson
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK.,Department of Surgery, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Simi Ali
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Colin H Wilson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
| | - Neil S Sheerin
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne, UK.,NIHR Blood and Transplant Research Unit in Organ Donation and Transplantation, Newcastle upon Tyne, UK
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35
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Di Marco Barros R, Fitzpatrick Z, Clatworthy MR. The gut-meningeal immune axis: Priming brain defense against the most likely invaders. J Exp Med 2022; 219:213031. [PMID: 35195681 PMCID: PMC8932540 DOI: 10.1084/jem.20211520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/02/2023] Open
Abstract
The gastrointestinal tract contains trillions of microorganisms that exist symbiotically with the host due to a tolerant, regulatory cell–rich intestinal immune system. However, this intimate relationship with the microbiome inevitably comes with risks, with intestinal organisms being the most common cause of bacteremia. The vasculature of the brain-lining meninges contains fenestrated endothelium, conferring vulnerability to invasion by circulating microbes. We propose that this has evolutionarily led to close links between gut and meningeal immunity, to prime the central nervous system defense against the most likely invaders. This paradigm is exemplified by the dural venous sinus IgA defense system, where the antibody repertoire mirrors that of the gut.
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Affiliation(s)
| | | | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
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36
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Kotagiri P, Mescia F, Hanson AL, Turner L, Bergamaschi L, Peñalver A, Richoz N, Moore SD, Ortmann BM, Dunmore BJ, Morgan MD, Tuong ZK, Göttgens B, Toshner M, Hess C, Maxwell PH, Clatworthy MR, Nathan JA, Bradley JR, Lyons PA, Burrows N, Smith KGC. The impact of hypoxia on B cells in COVID-19. EBioMedicine 2022; 77:103878. [PMID: 35189575 PMCID: PMC8856886 DOI: 10.1016/j.ebiom.2022.103878] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Prominent early features of COVID-19 include severe, often clinically silent, hypoxia and a pronounced reduction in B cells, the latter important in defence against SARS-CoV-2. This presentation resembles the phenotype of mice with VHL-deficient B cells, in which Hypoxia-Inducible Factors are constitutively active, suggesting hypoxia might drive B cell abnormalities in COVID-19. METHODS Detailed B cell phenotyping was undertaken by flow-cytometry on longitudinal samples from patients with COVID-19 across a range of severities (NIHR Cambridge BioResource). The impact of hypoxia on the transcriptome was assessed by single-cell and whole blood RNA sequencing analysis. The direct effect of hypoxia on B cells was determined through immunisation studies in genetically modified and hypoxia-exposed mice. FINDINGS We demonstrate the breadth of early and persistent defects in B cell subsets in moderate/severe COVID-19, including reduced marginal zone-like, memory and transitional B cells, changes also observed in B cell VHL-deficient mice. These findings were associated with hypoxia-related transcriptional changes in COVID-19 patient B cells, and similar B cell abnormalities were seen in mice kept in hypoxic conditions. INTERPRETATION Hypoxia may contribute to the pronounced and persistent B cell pathology observed in acute COVID-19 pneumonia. Assessment of the impact of early oxygen therapy on these immune defects should be considered, as their correction could contribute to improved outcomes. FUNDING Evelyn Trust, Addenbrooke's Charitable Trust, UKRI/NIHR, Wellcome Trust.
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Affiliation(s)
- Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Aimee L Hanson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Ana Peñalver
- Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge
| | - Nathan Richoz
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - Stephen D Moore
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Brian M Ortmann
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Benjamin J Dunmore
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Michael D Morgan
- Cancer Research UK - Cambridge Institute, Robinson Way, Cambridge CB2 0RE, United Kingdom; EMBL-EBI, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Zewen Kelvin Tuong
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, United Kingdom
| | - Mark Toshner
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Heart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Patrick H Maxwell
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cellular Genetics, Wellcome Sanger Institute, Hinxton. United Kingdom
| | - James A Nathan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - John R Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, United Kingdom
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom
| | - Natalie Burrows
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom; Cambridge Institute for Medical Research, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Cambridge.
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, United Kingdom; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, United Kingdom.
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37
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Kotagiri P, Mescia F, Rae WM, Bergamaschi L, Tuong ZK, Turner L, Hunter K, Gerber PP, Hosmillo M, Hess C, Clatworthy MR, Goodfellow IG, Matheson NJ, McKinney EF, Wills MR, Gupta RK, Bradley JR, Bashford-Rogers RJM, Lyons PA, Smith KGC. B cell receptor repertoire kinetics after SARS-CoV-2 infection and vaccination. Cell Rep 2022; 38:110393. [PMID: 35143756 PMCID: PMC8801326 DOI: 10.1016/j.celrep.2022.110393] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/28/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
B cells are important in immunity to both severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, but B cell receptor (BCR) repertoire development in these contexts has not been compared. We analyze serial samples from 171 SARS-CoV-2-infected individuals and 63 vaccine recipients and find the global BCR repertoire differs between them. Following infection, immunoglobulin (Ig)G1/3 and IgA1 BCRs increase, somatic hypermutation (SHM) decreases, and, in severe disease, IgM and IgA clones are expanded. In contrast, after vaccination, the proportion of IgD/M BCRs increase, SHM is unchanged, and expansion of IgG clones is prominent. VH1-24, which targets the N-terminal domain (NTD) and contributes to neutralization, is expanded post infection except in the most severe disease. Infection generates a broad distribution of SARS-CoV-2-specific clones predicted to target the spike protein, while a more focused response after vaccination mainly targets the spike's receptor-binding domain. Thus, the nature of SARS-CoV-2 exposure differentially affects BCR repertoire development, potentially informing vaccine strategies.
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Affiliation(s)
- Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - William M Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Zewen K Tuong
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Lorinda Turner
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Kelvin Hunter
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Pehuén P Gerber
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Myra Hosmillo
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Christoph Hess
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Department of Biomedicine, University and University Hospital Basel, Basel 4031, Switzerland; Botnar Research Centre for Child Health (BRCCH) University Basel and ETH Zurich, Basel 4059, Switzerland
| | - Menna R Clatworthy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, Cambridge CB10 1RQ, UK
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Nicholas J Matheson
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NHS Blood and Transplant, Cambridge CB2 1PT, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Mark R Wills
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | | | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK.
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Yoshida M, Worlock KB, Huang N, Lindeboom RGH, Butler CR, Kumasaka N, Dominguez Conde C, Mamanova L, Bolt L, Richardson L, Polanski K, Madissoon E, Barnes JL, Allen-Hyttinen J, Kilich E, Jones BC, de Wilton A, Wilbrey-Clark A, Sungnak W, Pett JP, Weller J, Prigmore E, Yung H, Mehta P, Saleh A, Saigal A, Chu V, Cohen JM, Cane C, Iordanidou A, Shibuya S, Reuschl AK, Herczeg IT, Argento AC, Wunderink RG, Smith SB, Poor TA, Gao CA, Dematte JE, Reynolds G, Haniffa M, Bowyer GS, Coates M, Clatworthy MR, Calero-Nieto FJ, Göttgens B, O'Callaghan C, Sebire NJ, Jolly C, De Coppi P, Smith CM, Misharin AV, Janes SM, Teichmann SA, Nikolić MZ, Meyer KB. Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature 2022; 602:321-327. [PMID: 34937051 PMCID: PMC8828466 DOI: 10.1038/s41586-021-04345-x] [Citation(s) in RCA: 147] [Impact Index Per Article: 73.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 12/14/2021] [Indexed: 02/03/2023]
Abstract
It is not fully understood why COVID-19 is typically milder in children1-3. Here, to examine the differences between children and adults in their response to SARS-CoV-2 infection, we analysed paediatric and adult patients with COVID-19 as well as healthy control individuals (total n = 93) using single-cell multi-omic profiling of matched nasal, tracheal, bronchial and blood samples. In the airways of healthy paediatric individuals, we observed cells that were already in an interferon-activated state, which after SARS-CoV-2 infection was further induced especially in airway immune cells. We postulate that higher paediatric innate interferon responses restrict viral replication and disease progression. The systemic response in children was characterized by increases in naive lymphocytes and a depletion of natural killer cells, whereas, in adults, cytotoxic T cells and interferon-stimulated subpopulations were significantly increased. We provide evidence that dendritic cells initiate interferon signalling in early infection, and identify epithelial cell states associated with COVID-19 and age. Our matching nasal and blood data show a strong interferon response in the airways with the induction of systemic interferon-stimulated populations, which were substantially reduced in paediatric patients. Together, we provide several mechanisms that explain the milder clinical syndrome observed in children.
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Affiliation(s)
- Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
- Division of Respiratory Diseases, Department of Internal Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Ni Huang
- Wellcome Sanger Institute, Cambridge, UK
| | | | - Colin R Butler
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | | | | | | | - Liam Bolt
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Elo Madissoon
- Wellcome Sanger Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Eliz Kilich
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Brendan C Jones
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Angus de Wilton
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | | | | | | | | | - Henry Yung
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Puja Mehta
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Anita Saigal
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Vivian Chu
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Jonathan M Cohen
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Clare Cane
- Royal Free Hospital NHS Foundation Trust, London, UK
| | | | - Soichi Shibuya
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
| | - Ann-Kathrin Reuschl
- UCL Division of Infection and Immunity, University College London, London, UK
| | - Iván T Herczeg
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - A Christine Argento
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sean B Smith
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Taylor A Poor
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Catherine A Gao
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jane E Dematte
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Matthew Coates
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Berthold Göttgens
- Wellcome, MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Christopher O'Callaghan
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil J Sebire
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Clare Jolly
- UCL Division of Infection and Immunity, University College London, London, UK
| | - Paolo De Coppi
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Claire M Smith
- NIHR Great Ormond Street BRC and UCL Institute of Child Health, London, UK
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK.
- University College London Hospitals NHS Foundation Trust, London, UK.
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Fleming A, Castro‐Dopico T, Clatworthy MR. B cell class switching in intestinal immunity in health and disease. Scand J Immunol 2022; 95:e13139. [PMID: 34978077 PMCID: PMC9285483 DOI: 10.1111/sji.13139] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/31/2021] [Accepted: 12/31/2021] [Indexed: 12/12/2022]
Abstract
The gastrointestinal tract is colonized by trillions of commensal microorganisms that collectively form the microbiome and make essential contributions to organism homeostasis. The intestinal immune system must tolerate these beneficial commensals, whilst preventing pathogenic organisms from systemic spread. Humoral immunity plays a key role in this process, with large quantities of immunoglobulin (Ig)A secreted into the lumen on a daily basis, regulating the microbiome and preventing bacteria from encroaching on the epithelium. However, there is an increasing appreciation of the role of IgG antibodies in intestinal immunity, including beneficial effects in neonatal immune development, pathogen and tumour resistance, but also of pathological effects in driving chronic inflammation in inflammatory bowel disease (IBD). These antibody isotypes differ in effector function, with IgG exhibiting more proinflammatory capabilities compared with IgA. Therefore, the process that leads to the generation of different antibody isotypes, class-switch recombination (CSR), requires careful regulation and is orchestrated by the immunological cues generated by the prevalent local challenge. In general, an initiating signal such as CD40 ligation on B cells leads to the induction of activation-induced cytidine deaminase (AID), but a second cytokine-mediated signal determines which Ig heavy chain is expressed. Whilst the cytokines driving intestinal IgA responses are well-studied, there is less clarity on how IgG responses are generated in the intestine, and how these cues might become dysfunctional in IBD. Here, we review the key mechanisms regulating class switching to IgA vs IgG in the intestine, processes that could be therapeutically manipulated in infection and IBD.
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Affiliation(s)
- Aaron Fleming
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
| | - Tomas Castro‐Dopico
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
- The Francis Crick InstituteLondonUK
| | - Menna R. Clatworthy
- Molecular Immunity UnitDepartment of MedicineCambridge Institute of Therapeutic Immunology and Infectious DiseasesUniversity of CambridgeCambridgeUK
- Cellular GeneticsWellcome Trust Sanger InstituteHinxtonUK
- NIHR Cambridge Biomedical Research CentreCambridgeUK
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40
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Moro F, Pischiutta F, Portet A, Needham EJ, Norton EJ, Ferdinand JR, Vegliante G, Sammali E, Pascente R, Caruso E, Micotti E, Tolomeo D, di Marco Barros R, Fraunberger E, Wang KKW, Esser MJ, Menon DK, Clatworthy MR, Zanier ER. Ageing is associated with maladaptive immune response and worse outcome after traumatic brain injury. Brain Commun 2022; 4:fcac036. [PMID: 35350551 PMCID: PMC8947244 DOI: 10.1093/braincomms/fcac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/23/2021] [Accepted: 02/14/2022] [Indexed: 11/15/2022] Open
Abstract
Traumatic brain injury is increasingly common in older individuals. Older age is one of the strongest predictors for poor prognosis after brain trauma, a phenomenon driven by the presence of extra-cranial comorbidities as well as pre-existent pathologies associated with cognitive impairment and brain volume loss (such as cerebrovascular disease or age-related neurodegeneration). Furthermore, ageing is associated with a dysregulated immune response, which includes attenuated responses to infection and vaccination, and a failure to resolve inflammation leading to chronic inflammatory states. In traumatic brain injury, where the immune response is imperative for the clearance of cellular debris and survey of the injured milieu, an appropriate self-limiting response is vital to promote recovery. Currently, our understanding of age-related factors that contribute to the outcome is limited; but a more complete understanding is essential for the development of tailored therapeutic strategies to mitigate the consequences of traumatic brain injury. Here we show greater functional deficits, white matter abnormalities and worse long-term outcomes in aged compared with young C57BL/6J mice after either moderate or severe traumatic brain injury. These effects are associated with altered systemic, meningeal and brain tissue immune response. Importantly, the impaired acute systemic immune response in the mice was similar to the findings observed in our clinical cohort. Traumatic brain-injured patient cohort over 70 years of age showed lower monocyte and lymphocyte counts compared with those under 45 years. In mice, traumatic brain injury was associated with alterations in peripheral immune subsets, which differed in aged compared with adult mice. There was a significant increase in transcription of immune and inflammatory genes in the meninges post-traumatic brain injury, including monocyte/leucocyte-recruiting chemokines. Immune cells were recruited to the region of the dural injury, with a significantly higher number of CD11b+ myeloid cells in aged compared with the adult mice. In brain tissue, when compared with the young adult mice, we observed a more pronounced and widespread reactive astrogliosis 1 month after trauma in aged mice, sustained by an early and persistent induction of proinflammatory astrocytic state. These findings provide important insights regarding age-related exacerbation of neurological damage after brain trauma.
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Affiliation(s)
- Federico Moro
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Francesca Pischiutta
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Anaïs Portet
- Molecular Immunity Unit, Department of Medicine, Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, UK
| | - Edward J. Needham
- Division of Anaesthesia, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QH, UK
| | - Emma J. Norton
- Division of Anaesthesia, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QH, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, UK
| | - Gloria Vegliante
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Eliana Sammali
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Rosaria Pascente
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Enrico Caruso
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Neuroscience Intensive Care Unit, Department of Anesthesia and Critical Care, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Edoardo Micotti
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Daniele Tolomeo
- Laboratory of Biology of Neurodegenerative Disorders, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Rafael di Marco Barros
- Molecular Immunity Unit, Department of Medicine, Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, UK
| | - Erik Fraunberger
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Cumming School of Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Kevin K. W. Wang
- Program for Neurotrauma, Neuroproteomics and Biomarker Research, Departments of Emergency Medicine, Psychiatry and Neuroscience, University of Florida, Gainesville, FL, USA
| | - Michael J. Esser
- Cumming School of Medicine, Alberta Children’s Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - David K. Menon
- Division of Anaesthesia, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QH, UK
| | - Menna R. Clatworthy
- Molecular Immunity Unit, Department of Medicine, Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, UK
| | - Elisa R. Zanier
- Laboratory of Acute Brain Injury and Therapeutic Strategies, Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Correspondence to: Elisa R. Zanier Laboratory of Acute Brain Injury and Therapeutic Strategies Department of Neuroscience Istituto di Ricerche Farmacologiche Mario Negri IRCCS 20156 Milan, Italy E-mail:
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41
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Zhao TX, Sriranjan RS, Tuong ZK, Lu Y, Sage AP, Nus M, Hubsch A, Kaloyirou F, Vamvaka E, Helmy J, Kostapanos M, Jalaludeen N, Klatzmann D, Tedgui A, Rudd JHF, Horton SJ, Huntly BJP, Hoole SP, Bond SP, Clatworthy MR, Cheriyan J, Mallat Z. Regulatory T-Cell Response to Low-Dose Interleukin-2 in Ischemic Heart Disease. NEJM Evid 2022; 1:EVIDoa2100009. [PMID: 38319239 DOI: 10.1056/evidoa2100009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Regulatory T-Cell Response to Low-Dose Interleukin-2 in Ischemic Heart Disease This phase 1b/2a, randomized, double-blind, placebo-controlled, dose-escalation trial tested low-dose subcutaneous aldesleukin (recombinant IL-2) in patients with ischemic heart disease. Low-dose IL-2 expanded Tregs, without adverse events of major concern. Single-cell RNA-sequencing of circulating immune cells was used to provide mechanistic assessment of the treatment's effects.
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Affiliation(s)
- Tian X Zhao
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Rouchelle S Sriranjan
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Yuning Lu
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Andrew P Sage
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Meritxell Nus
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Annette Hubsch
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Fotini Kaloyirou
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Evangelia Vamvaka
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Joanna Helmy
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michalis Kostapanos
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Navazh Jalaludeen
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - David Klatzmann
- Department of Inflammation, Immunopathology, and Biotherapy, Pitié-Salpêtrière Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Alain Tedgui
- Paris Cardiovascular Research Center, Université de Paris, Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - James H F Rudd
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Horton
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Brian J P Huntly
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Stephen P Hoole
- Department of Cardiology, Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Simon P Bond
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Joseph Cheriyan
- Division of Experimental Medicine and Immunotherapeutics, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Cambridge Clinical Trials Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ziad Mallat
- Division of Cardiovascular Medicine, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Paris Cardiovascular Research Center, Université de Paris, Institut National de la Santé et de la Recherche Médicale, Paris, France
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42
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Tuong ZK, Loudon KW, Berry B, Richoz N, Jones J, Tan X, Nguyen Q, George A, Hori S, Field S, Lynch AG, Kania K, Coupland P, Babbage A, Grenfell R, Barrett T, Warren AY, Gnanapragasam V, Massie C, Clatworthy MR. Resolving the immune landscape of human prostate at a single-cell level in health and cancer. Cell Rep 2021; 37:110132. [PMID: 34936871 PMCID: PMC8721283 DOI: 10.1016/j.celrep.2021.110132] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 09/01/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022] Open
Abstract
The prostate gland produces prostatic fluid, high in zinc and citrate and essential for the maintenance of spermatozoa. Prostate cancer is a common condition with limited treatment efficacy in castration-resistant metastatic disease, including with immune checkpoint inhibitors. Using single-cell RNA-sequencing to perform an unbiased assessment of the cellular landscape of human prostate, we identify a subset of tumor-enriched androgen receptor-negative luminal epithelial cells with increased expression of cancer-associated genes. We also find a variety of innate and adaptive immune cells in normal prostate that were transcriptionally perturbed in prostate cancer. An exception is a prostate-specific, zinc transporter-expressing macrophage population (MAC-MT) that contributes to tissue zinc accumulation in homeostasis but shows enhanced inflammatory gene expression in tumors, including T cell-recruiting chemokines. Remarkably, enrichment of the MAC-MT signature in cancer biopsies is associated with improved disease-free survival, suggesting beneficial antitumor functions.
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Affiliation(s)
- Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Brendan Berry
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | | | - Xiao Tan
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Quan Nguyen
- Division of Genetics and Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Anne George
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Early Detection Programme, CRUK Cambridge Centre, Cambridge, UK
| | - Satoshi Hori
- Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK
| | | | - Andy G Lynch
- CRUK Cambridge Institute, Cambridge, UK; School of Mathematics and Statistics/School of Medicine, University of St Andrews, St Andrews, UK
| | | | | | - Anne Babbage
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Tristan Barrett
- Department of Radiology, University of Cambridge, Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Vincent Gnanapragasam
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge Biomedical Campus, Cambridge, UK
| | - Charlie Massie
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; CRUK Cambridge Institute, Cambridge, UK; Early Detection Programme, CRUK Cambridge Centre, Cambridge, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK; NIHR Cambridge Biomedical Research Centre, Cambridge, UK; Cambridge Institute of Therapeutic Immunology & Infectious Diseases, Cambridge, UK.
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43
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Clatworthy MR. The meninges-a cradle and school for nurturing and educating developing B cells. Immunity 2021; 54:2688-2690. [PMID: 34910935 DOI: 10.1016/j.immuni.2021.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
B cell development is thought to be limited to the bone marrow. In this issue of Immunity, Wang et al. find that the meninges, the membranes that surround the brain and spinal cord, contain developing B cells, and they provide evidence that the B cells are there to be tolerized to central nervous system antigens.
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Affiliation(s)
- Menna R Clatworthy
- Molecular Immunity Unit, Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge Department of Medicine, Cambridge, UK; Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.
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44
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Mulderrig L, Garaycoechea JI, Tuong ZK, Millington CL, Dingler FA, Ferdinand JR, Gaul L, Tadross JA, Arends MJ, O'Rahilly S, Crossan GP, Clatworthy MR, Patel KJ. Aldehyde-driven transcriptional stress triggers an anorexic DNA damage response. Nature 2021; 600:158-163. [PMID: 34819667 DOI: 10.1038/s41586-021-04133-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 10/13/2021] [Indexed: 01/14/2023]
Abstract
Endogenous DNA damage can perturb transcription, triggering a multifaceted cellular response that repairs the damage, degrades RNA polymerase II and shuts down global transcription1-4. This response is absent in the human disease Cockayne syndrome, which is caused by loss of the Cockayne syndrome A (CSA) or CSB proteins5-7. However, the source of endogenous DNA damage and how this leads to the prominent degenerative features of this disease remain unknown. Here we find that endogenous formaldehyde impedes transcription, with marked physiological consequences. Mice deficient in formaldehyde clearance (Adh5-/-) and CSB (Csbm/m; Csb is also known as Ercc6) develop cachexia and neurodegeneration, and succumb to kidney failure, features that resemble human Cockayne syndrome. Using single-cell RNA sequencing, we find that formaldehyde-driven transcriptional stress stimulates the expression of the anorexiogenic peptide GDF15 by a subset of kidney proximal tubule cells. Blocking this response with an anti-GDF15 antibody alleviates cachexia in Adh5-/-Csbm/m mice. Therefore, CSB provides protection to the kidney and brain against DNA damage caused by endogenous formaldehyde, while also suppressing an anorexic endocrine signal. The activation of this signal might contribute to the cachexia observed in Cockayne syndrome as well as chemotherapy-induced anorectic weight loss. A plausible evolutionary purpose for such a response is to ensure aversion to genotoxins in food.
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Affiliation(s)
- Lee Mulderrig
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Zewen K Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Christopher L Millington
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Felix A Dingler
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Liam Gaul
- The Francis Crick Institute, London, UK
| | - John A Tadross
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Mark J Arends
- Division of Pathology, University of Edinburgh, Cancer Research UK Edinburgh Centre, IGMM, Edinburgh, UK
| | - Stephen O'Rahilly
- MRC Metabolic Diseases Unit, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | | | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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45
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Tuong ZK, Stewart BJ, Guo SA, Clatworthy MR. Epigenetics and tissue immunity-Translating environmental cues into functional adaptations. Immunol Rev 2021; 305:111-136. [PMID: 34821397 DOI: 10.1111/imr.13036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
There is an increasing appreciation that many innate and adaptive immune cell subsets permanently reside within non-lymphoid organs, playing a critical role in tissue homeostasis and defense. The best characterized are macrophages and tissue-resident T lymphocytes that work in concert with organ structural cells to generate appropriate immune responses and are functionally shaped by organ-specific environmental cues. The interaction of tissue epithelial, endothelial and stromal cells is also required to attract, differentiate, polarize and maintain organ immune cells in their tissue niche. All of these processes require dynamic regulation of cellular transcriptional programmes, with epigenetic mechanisms playing a critical role, including DNA methylation and post-translational histone modifications. A failure to appropriately regulate immune cell transcription inevitably results in inadequate or inappropriate immune responses and organ pathology. Here, with a focus on the mammalian kidney, an organ which generates differing regional environmental cues (including hypersalinity and hypoxia) due to its physiological functions, we will review the basic concepts of tissue immunity, discuss the technologies available to profile epigenetic modifications in tissue immune cells, including those that enable single-cell profiling, and consider how these mechanisms influence the development, phenotype, activation and function of different tissue immune cell subsets, as well as the immunological function of structural cells.
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Affiliation(s)
- Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Shuang Andrew Guo
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC-Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK
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46
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Tuong ZK, Lukowski SW, Nguyen QH, Chandra J, Zhou C, Gillinder K, Bashaw AA, Ferdinand JR, Stewart BJ, Teoh SM, Hanson SJ, Devitt K, Clatworthy MR, Powell JE, Frazer IH. A model of impaired Langerhans cell maturation associated with HPV induced epithelial hyperplasia. iScience 2021; 24:103326. [PMID: 34805788 PMCID: PMC8586807 DOI: 10.1016/j.isci.2021.103326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/29/2021] [Accepted: 10/19/2021] [Indexed: 12/24/2022] Open
Abstract
Langerhans cells (LC) are skin-resident antigen-presenting cells that regulate immune responses to epithelial microorganisms. Human papillomavirus (HPV) infection can promote malignant epithelial transformation. As LCs are considered important for controlling HPV infection, we compared the transcriptome of murine LCs from skin transformed by K14E7 oncoprotein and from healthy skin. We identified transcriptome heterogeneity at the single cell level amongst LCs in normal skin, associated with ontogeny, cell cycle, and maturation. We identified a balanced co-existence of immune-stimulatory and immune-inhibitory LC cell states in normal skin that was significantly disturbed in HPV16 E7-transformed skin. Hyperplastic skin was depleted of immune-stimulatory LCs and enriched for LCs with an immune-inhibitory gene signature, and LC-keratinocyte crosstalk was dysregulated. We identified reduced expression of interleukin (IL)-34, a critical molecule for LC homeostasis. Enrichment of an immune-inhibitory LC gene signature and reduced levels of epithelial IL-34 were also found in human HPV-associated cervical epithelial cancers. Single cell atlas of Langerhans cells in cutaneous skin Stimulatory and inhibitory Langerhans cell states are in balance Inhibitory Langerhans cell states dominate HPV-transformed hyperplastic skin Langerhans cell imbalance is associated with disrupted IL-34 signaling
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Affiliation(s)
- Zewen K Tuong
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia.,Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Samuel W Lukowski
- Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Quan H Nguyen
- Australia Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Janin Chandra
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Chenhao Zhou
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Kevin Gillinder
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Abate A Bashaw
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - John R Ferdinand
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK
| | - Siok Min Teoh
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sarah J Hanson
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Katharina Devitt
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Menna R Clatworthy
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC-Laboratory of Molecular Biology, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ian H Frazer
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia
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47
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Burrows N, Bashford-Rogers RJM, Bhute VJ, Peñalver A, Ferdinand JR, Stewart BJ, Smith JEG, Deobagkar-Lele M, Giudice G, Connor TM, Inaba A, Bergamaschi L, Smith S, Tran MGB, Petsalaki E, Lyons PA, Espeli M, Huntly BJP, Smith KGC, Cornall RJ, Clatworthy MR, Maxwell PH. Author Correction: Dynamic regulation of hypoxia-inducible factor-1α activity is essential for normal B cell development. Nat Immunol 2021; 22:1465. [PMID: 34522040 DOI: 10.1038/s41590-021-01036-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Natalie Burrows
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK. .,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
| | - Rachael J M Bashford-Rogers
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford, UK
| | - Vijesh J Bhute
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Ana Peñalver
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Benjamin J Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Joscelin E G Smith
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mukta Deobagkar-Lele
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Girolamo Giudice
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Thomas M Connor
- Oxford Kidney Unit, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Akimichi Inaba
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Laura Bergamaschi
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sam Smith
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London, UK.,Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
| | - Evangelia Petsalaki
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Paul A Lyons
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Marion Espeli
- Université de Paris, Institut de Recherche Saint Louis, EMiLy, Inserm U1160, Paris, France
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Department of Haematology, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Richard J Cornall
- Nuffield Department of Medicine, Wellcome Centre for Human Genetics, Oxford, UK.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Patrick H Maxwell
- Cambridge Institute for Medical Research, The Keith Peters Building, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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48
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Lok LSC, Walker JA, Jolin HE, Scanlon ST, Ishii M, Fallon PG, McKenzie ANJ, Clatworthy MR. Group 2 Innate Lymphoid Cells Exhibit Tissue-Specific Dynamic Behaviour During Type 2 Immune Responses. Front Immunol 2021; 12:711907. [PMID: 34484215 PMCID: PMC8415880 DOI: 10.3389/fimmu.2021.711907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/29/2021] [Indexed: 12/25/2022] Open
Abstract
Group 2 innate lymphoid cells (ILC2s) are early effectors of mucosal type 2 immunity, producing cytokines such as interleukin (IL)-13 to mediate responses to helminth infection and allergen-induced inflammation. ILC2s are also present in lymph nodes (LNs) and can express molecules required for antigen presentation, but to date there are limited data on their dynamic behaviour. We used a CD2/IL-13 dual fluorescent reporter mouse for in vivo imaging of ILC2s and Th2 T cells in real time following a type 2 priming helminth infection or egg injection. After helminth challenge, we found that ILC2s were the main source of IL-13 in lymphoid organs (Peyer’s patches and peripheral LNs), and were located in T cell areas. Intravital imaging demonstrated an increase in IL-13+ ILC2 size and movement following helminth infection, but reduced duration of interactions with T cells compared with those in homeostasis. In contrast, in the intestinal mucosa, we observed an increase in ILC2-T cell interactions post-infection, including some of prolonged duration, as well as increased IL-13+ ILC2 movement. These data suggest that ILC2 activation enhances cell motility, with the potential to increase the area of distribution of cytokines to optimise the early generation of type 2 responses. The prolonged ILC2 interactions with T cells within the intestinal mucosa are consistent with the conclusion that contact-based T cell activation may occur within inflamed tissues rather than lymphoid organs. Our findings have important implications for our understanding of the in vivo biology of ILC2s and the way in which these cells facilitate adaptive immune responses.
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Affiliation(s)
- Laurence S C Lok
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom.,Department of Immunology and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Jennifer A Walker
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Helen E Jolin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Seth T Scanlon
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Masaru Ishii
- Department of Immunology and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | | | - Andrew N J McKenzie
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge, United Kingdom.,Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, United Kingdom.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
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49
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Elmentaite R, Kumasaka N, Roberts K, Fleming A, Dann E, King HW, Kleshchevnikov V, Dabrowska M, Pritchard S, Bolt L, Vieira SF, Mamanova L, Huang N, Perrone F, Goh Kai'En I, Lisgo SN, Katan M, Leonard S, Oliver TRW, Hook CE, Nayak K, Campos LS, Domínguez Conde C, Stephenson E, Engelbert J, Botting RA, Polanski K, van Dongen S, Patel M, Morgan MD, Marioni JC, Bayraktar OA, Meyer KB, He X, Barker RA, Uhlig HH, Mahbubani KT, Saeb-Parsy K, Zilbauer M, Clatworthy MR, Haniffa M, James KR, Teichmann SA. Cells of the human intestinal tract mapped across space and time. Nature 2021; 597:250-255. [PMID: 34497389 PMCID: PMC8426186 DOI: 10.1038/s41586-021-03852-1] [Citation(s) in RCA: 213] [Impact Index Per Article: 71.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.
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Affiliation(s)
- Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Aaron Fleming
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Hamish W King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | | | | | | | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Issac Goh Kai'En
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matilda Katan
- Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Steven Leonard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - C Elizabeth Hook
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Komal Nayak
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Michael D Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, Department of Clinical Neurosciences and Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Holm H Uhlig
- Translational Gastroenterology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals Trust, Cambridge, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kylie R James
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Garvan Institute of Medical Research, The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
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50
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Abstract
Neutrophils are traditionally considered short‐lived, circulating innate immune cells that are rapidly recruited to sites of inflammation in response to infectious and inflammatory stimuli. Neutrophils efficiently internalize, kill or entrap pathogens, but their effector molecules may cause collateral tissue damage. More recently, it has been appreciated that neutrophils can also influence adaptive immunity. Lymph nodes (LNs) are immune cell‐rich secondary lymphoid organs that provide an ideal platform for cellular interaction and the integration of immunological information collected from local tissues. A variety of peripheral stimuli promote neutrophil migration to draining LNs via blood or lymphatics, utilizing differing molecular cues depending on the site of entry. Within LNs, neutrophils interact with other innate and adaptive cells. Crosstalk with subcapsular sinus macrophages contributes to the control of pathogen spread beyond the LN. Neutrophils can influence antigen presentation indirectly by interacting with DCs or directly by expressing major histocompatibility complex (MHC) and costimulatory molecules for antigen presentation. Interactions between neutrophils and adaptive lymphocytes can alter B‐cell antibody responses. Studies have shown conflicting results on whether neutrophils exert stimulatory or inhibitory effects on other LN immune cells, with stimulus‐specific and temporal differences in the outcome of these interactions. Furthermore, neutrophils have also been shown to traffick to LNs in homeostasis, with a potential role in immune surveillance, antigen capture and in shaping early adaptive responses in LNs. Understanding the mechanisms underpinning the effects of neutrophils on LN immune cells and adaptive immunity could facilitate the development of neutrophil‐targeted therapies in inflammatory diseases.
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Affiliation(s)
- Laurence S C Lok
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, University of Cambridge Department of Medicine, Cambridge, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Department of Immunology and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Osaka, Japan
| | - Menna R Clatworthy
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, University of Cambridge Department of Medicine, Cambridge, UK.,Cambridge Institute for Therapeutic Immunology and Infectious Diseases, University of Cambridge, Cambridge, UK.,Cellular Genetics, Wellcome Sanger Institute, Hinxton, UK
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