1
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Kohlgruber AC, Dezfulian MH, Sie BM, Wang CI, Kula T, Laserson U, Larman HB, Elledge SJ. High-throughput discovery of MHC class I- and II-restricted T cell epitopes using synthetic cellular circuits. Nat Biotechnol 2024:10.1038/s41587-024-02248-6. [PMID: 38956325 DOI: 10.1038/s41587-024-02248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 04/16/2024] [Indexed: 07/04/2024]
Abstract
Antigen discovery technologies have largely focused on major histocompatibility complex (MHC) class I-restricted human T cell receptors (TCRs), leaving methods for MHC class II-restricted and mouse TCR reactivities relatively undeveloped. Here we present TCR mapping of antigenic peptides (TCR-MAP), an antigen discovery method that uses a synthetic TCR-stimulated circuit in immortalized T cells to activate sortase-mediated tagging of engineered antigen-presenting cells (APCs) expressing processed peptides on MHCs. Live, tagged APCs can be directly purified for deconvolution by sequencing, enabling TCRs with unknown specificity to be queried against barcoded peptide libraries in a pooled screening context. TCR-MAP accurately captures self-reactivities or viral reactivities with high throughput and sensitivity for both MHC class I-restricted and class II-restricted TCRs. We elucidate problematic cross-reactivities of clinical TCRs targeting the cancer/testis melanoma-associated antigen A3 and discover targets of myocarditis-inciting autoreactive T cells in mice. TCR-MAP has the potential to accelerate T cell antigen discovery efforts in the context of cancer, infectious disease and autoimmunity.
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Affiliation(s)
- Ayano C Kohlgruber
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Brandon M Sie
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Charlotte I Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Tomasz Kula
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Genetics, Harvard University Medical School, Boston, MA, USA
- Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Stephen J Elledge
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Genetics, Harvard University Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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2
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Linsley PS, Nakayama M, Balmas E, Chen J, Barahmand-Pour-Whitman F, Bansal S, Bottorff T, Serti E, Speake C, Pugliese A, Cerosaletti K. Germline-like TCR-α chains shared between autoreactive T cells in blood and pancreas. Nat Commun 2024; 15:4971. [PMID: 38871688 PMCID: PMC11176301 DOI: 10.1038/s41467-024-48833-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024] Open
Abstract
Human type 1 diabetes (T1D) is caused by autoimmune attack on the insulin-producing pancreatic beta cells by islet antigen-reactive T cells. How human islet antigen-reactive (IAR) CD4+ memory T cells from peripheral blood affect T1D progression in the pancreas is poorly understood. Here, we aim to determine if IAR T cells in blood could be detected in pancreas. We identify paired αβ (TRA/TRB) T cell receptors (TCRs) in IAR T cells from the blood of healthy, at-risk, new-onset, and established T1D donors, and measured sequence overlap with TCRs in pancreata from healthy, at risk and T1D organ donors. We report extensive TRA junction sharing between IAR T cells and pancreas-infiltrating T cells (PIT), with perfect-match or single-mismatch TRA junction amino acid sequences comprising ~29% total unique IAR TRA junctions (942/3,264). PIT-matched TRA junctions were largely public and enriched for TRAV41 usage, showing significant nucleotide sequence convergence, increased use of germline-encoded versus non-templated residues in epitope engagement, and a potential for cross-reactivity. Our findings thus link T cells with distinctive germline-like TRA chains in the peripheral blood with T cells in the pancreas.
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Affiliation(s)
- Peter S Linsley
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Elisa Balmas
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Janice Chen
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | | | - Shubham Bansal
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Ty Bottorff
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | | | - Cate Speake
- Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Alberto Pugliese
- Department of Diabetes Immunology & The Wanek Family Project for Type 1 Diabetes, Arthur Riggs Diabetes & Metabolism Research Institute, City of Hope, Duarte, CA, USA
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3
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Karnaukhov VK, Le Gac AL, Bilonda Mutala L, Darbois A, Perrin L, Legoux F, Walczak AM, Mora T, Lantz O. Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proc Natl Acad Sci U S A 2024; 121:e2311348121. [PMID: 38530897 PMCID: PMC10998581 DOI: 10.1073/pnas.2311348121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/09/2024] [Indexed: 03/28/2024] Open
Abstract
How T-cell receptor (TCR) characteristics determine subset commitment during T-cell development is still unclear. Here, we addressed this question for innate-like T cells, mucosal-associated invariant T (MAIT) cells, and invariant natural killer T (iNKT) cells. MAIT and iNKT cells have similar developmental paths, leading in mice to two effector subsets, cytotoxic (MAIT1/iNKT1) and IL17-secreting (MAIT17/iNKT17). For iNKT1 vs iNKT17 fate choice, an instructive role for TCR affinity was proposed but recent data argue against this model. Herein, we examined TCR role in MAIT and iNKT subset commitment through scRNAseq and TCR repertoire analysis. In our dataset of thymic MAIT cells, we found pairs of T-cell clones with identical amino acid TCR sequences originating from distinct precursors, one of which committed to MAIT1 and the other to MAIT17 fates. Quantitative in silico simulations indicated that the number of such cases is best explained by lineage choice being independent of TCR characteristics. Comparison of TCR features of MAIT1 and MAIT17 clonotypes demonstrated that the subsets cannot be distinguished based on TCR sequence. To pinpoint the developmental stage associated with MAIT sublineage choice, we demonstrated that proliferation takes place both before and after MAIT fate commitment. Altogether, we propose a model of MAIT cell development in which noncommitted, intermediate-stage MAIT cells undergo a first round of proliferation, followed by TCR characteristics-independent commitment to MAIT1 or MAIT17 lineage, followed by an additional round of proliferation. Reanalyzing a published iNKT TCR dataset, we showed that this model is also relevant for iNKT cell development.
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Affiliation(s)
- Vadim K. Karnaukhov
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Anne-Laure Le Gac
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Linda Bilonda Mutala
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Aurélie Darbois
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Laetitia Perrin
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Francois Legoux
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- INSERM Equipe de Recherche Labellisée 1305, CNRSUMR6290, Université de Rennes, Institut de Génétique & Développement de Rennes35000, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Olivier Lantz
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- Laboratoire d’Immunologie Clinique, Département de médecine diagnostique et théranostique, Institut Curie, Paris75005, France
- Centre d’Investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris75005, France
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4
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De Boer RJ, Kesmir C, Perelson AS, Borghans JAM. Is the exquisite specificity of lymphocytes generated by thymic selection or due to evolution? Front Immunol 2024; 15:1266349. [PMID: 38605941 PMCID: PMC11008227 DOI: 10.3389/fimmu.2024.1266349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024] Open
Abstract
We have previously argued that the antigen receptors of T and B lymphocytes evolved to be sufficiently specific to avoid massive deletion of clonotypes by negative selection. Their optimal 'specificity' level, i.e., probability of binding any particular epitope, was shown to be inversely related to the number of self-antigens that the cells have to be tolerant to. Experiments have demonstrated that T lymphocytes also become more specific during negative selection in the thymus, because cells expressing the most crossreactive receptors have the highest likelihood of binding a self-antigen, and hence to be tolerized (i.e., deleted, anergized, or diverted into a regulatory T cell phenotype). Thus, there are two -not mutually exclusive- explanations for the exquisite specificity of T cells, one involving evolution and the other thymic selection. To better understand the impact of both, we extend a previously developed mathematical model by allowing for T cells with very different binding probabilities in the pre-selection repertoire. We confirm that negative selection tends to tolerize the most crossreactive clonotypes. As a result, the average level of specificity in the functional post-selection repertoire depends on the number of self-antigens, even if there is no evolutionary optimization of binding probabilities. However, the evolutionary optimal range of binding probabilities in the pre-selection repertoire also depends on the number of self-antigens. Species with more self antigens need more specific pre-selection repertoires to avoid excessive loss of T cells during thymic selection, and hence mount protective immune responses. We conclude that both evolution and negative selection are responsible for the high level of specificity of lymphocytes.
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Affiliation(s)
- Rob J. De Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Can Kesmir
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Alan S. Perelson
- Department of Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - José A. M. Borghans
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
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5
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Yin R, Melton S, Huseby ES, Kardar M, Chakraborty AK. How persistent infection overcomes peripheral tolerance mechanisms to cause T cell-mediated autoimmune disease. Proc Natl Acad Sci U S A 2024; 121:e2318599121. [PMID: 38446856 PMCID: PMC10945823 DOI: 10.1073/pnas.2318599121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024] Open
Abstract
T cells help orchestrate immune responses to pathogens, and their aberrant regulation can trigger autoimmunity. Recent studies highlight that a threshold number of T cells (a quorum) must be activated in a tissue to mount a functional immune response. These collective effects allow the T cell repertoire to respond to pathogens while suppressing autoimmunity due to circulating autoreactive T cells. Our computational studies show that increasing numbers of pathogenic peptides targeted by T cells during persistent or severe viral infections increase the probability of activating T cells that are weakly reactive to self-antigens (molecular mimicry). These T cells are easily re-activated by the self-antigens and contribute to exceeding the quorum threshold required to mount autoimmune responses. Rare peptides that activate many T cells are sampled more readily during severe/persistent infections than in acute infections, which amplifies these effects. Experiments in mice to test predictions from these mechanistic insights are suggested.
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Affiliation(s)
- Rose Yin
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Samuel Melton
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Eric S. Huseby
- Basic Pathology, Department of Pathology, University of Massachusetts Medical School, Worcester, MA01655
| | - Mehran Kardar
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
| | - Arup K. Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA02139
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA02139
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA02139
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6
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Borna S, Meffre E, Bacchetta R. FOXP3 deficiency, from the mechanisms of the disease to curative strategies. Immunol Rev 2024; 322:244-258. [PMID: 37994657 DOI: 10.1111/imr.13289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
FOXP3 gene is a key transcription factor driving immune tolerance and its deficiency causes immune dysregulation, polyendocrinopathy, enteropathy X-linked syndrome (IPEX), a prototypic primary immune regulatory disorder (PIRD) with defective regulatory T (Treg) cells. Although life-threatening, the increased awareness and early diagnosis have contributed to improved control of the disease. IPEX currently comprises a broad spectrum of clinical autoimmune manifestations from severe early onset organ involvement to moderate, recurrent manifestations. This review focuses on the mechanistic advancements that, since the IPEX discovery in early 2000, have informed the role of the human FOXP3+ Treg cells in controlling peripheral tolerance and shaping the overall immune landscape of IPEX patients and carrier mothers, contributing to defining new treatments.
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Affiliation(s)
- Simon Borna
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Eric Meffre
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, USA
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, California, USA
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7
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Aba Ü, Maslak İC, İpşir C, Pehlivan D, Warnock NI, Tumes DJ, Cildir G, Erman B. A Novel Homozygous Germline Mutation in Transferrin Receptor 1 (TfR1) Leads to Combined Immunodeficiency and Provides New Insights into Iron-Immunity Axis. J Clin Immunol 2024; 44:55. [PMID: 38270687 PMCID: PMC10811203 DOI: 10.1007/s10875-024-01658-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
A homozygous missense mutation in the transferrin receptor 1 (TfR1), also known as CD71, leads to a rare inborn error of immunity (IEI) characterized by the impaired lymphocyte activation and proliferation due to defective iron uptake of cells. However, only one causative mutation (c.58T > C, p.Y20H) in the TFRC gene coding for TfR1 has been reported so far. We herein identified a new disease-causing homozygous germline mutation in the TFRC gene (c.64C > T, p.R22W) (referred to as TfR1R22W from now on) in a Turkish patient with combined immunodeficiency (CID). TfR1R22W results in impaired TfR1 internalization similar to previously defined TfR1Y20H mutation. We found that TfR1R22W is associated with severely restricted B and T lymphocyte clonal diversity and impaired T cell activation and cytokine production as well as defective mitochondrial oxidative phosphorylation in helper T cells. In addition, circulating NK, Treg, and MAIT cell populations were significantly decreased in the patient. Using whole transcriptome analysis, we found dysregulated immune homeostasis and novel biological processes associated with TfR1R22W. We also identified a considerable expansion of circulating low-density neutrophils (LDNs) in patient's PBMCs. Overall, TfR1R22W mutation expands the current understanding of the IEI associated with TfR1 dysfunction and provides new insights underlying impaired immune function, lymphocyte diversity, and granulocyte homeostasis.
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Affiliation(s)
- Ümran Aba
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Türkiye
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Türkiye
| | - İbrahim Cemal Maslak
- Division of Pediatric Allergy and Immunology, Süleyman Demirel University, Isparta, Türkiye
| | - Canberk İpşir
- Department of Pediatric Immunology, Institute of Child Health, Hacettepe University, Ankara, Türkiye
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Türkiye
| | - Damla Pehlivan
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Türkiye
| | - Nicholas I Warnock
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, 5000, Australia
| | - Damon J Tumes
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, 5000, Australia
| | - Gökhan Cildir
- Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, SA, 5000, Australia.
- UniSA Bradley Building, North Terrace, Adelaide, SA, 5000, Australia.
| | - Baran Erman
- Can Sucak Research Laboratory for Translational Immunology, Hacettepe University, Ankara, Türkiye.
- Institute of Child Health, Hacettepe University, Ankara, Türkiye.
- Beytepe Campus of Hacettepe University, HUNITEK Building, Floor 1, 06800, Ankara, Türkiye.
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8
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Li R, Wang J, Li X, Liang Y, Jiang Y, Zhang Y, Xu P, Deng L, Wang Z, Sun T, Wu J, Xie H, Wang Y. T-cell receptor sequencing reveals hepatocellular carcinoma immune characteristics according to Barcelona Clinic liver cancer stages within liver tissue and peripheral blood. Cancer Sci 2024; 115:94-108. [PMID: 37962061 PMCID: PMC10823291 DOI: 10.1111/cas.16013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Analysis of T-cell receptor (TCR) repertoires in different stages of hepatocellular carcinoma (HCC) might help to elucidate its pathogenesis and progression. This study aimed to investigate TCR profiles in liver biopsies and peripheral blood mononuclear cells (PBMCs) in different Barcelona Clinic liver cancer (BCLC) stages of HCC. Ten patients in early stage (BCLC_A), 10 patients in middle stage (BCLC_B), and 10 patients in late stage (BCLC_C) cancer were prospectively enrolled. The liver tumor tissues, adjacent tissues, and PBMCs of each patient were collected and examined by TCR β sequencing. Based on the ImMunoGeneTics (IMGT) database, we aligned the V, D, J, and C gene segments and identified the frequency of CDR3 sequences and amino acids sequence. Diversity of TCR in PBMCs was higher than in both tumor tissues and adjacent tissues, regardless of BCLC stage and postoperative recurrence. TCR clonality was increased in T cells from peripheral blood in advanced HCC, compared with the early and middle stages. No statistical differences were observed between different BCLC stages, either in tumors or adjacent tissues. TCR clonality revealed no significant difference between recurrent tumor and non-recurrent tumor, therefore PBMCs was better to be representative of TCR characteristics in different stages of HCC compared to tumor tissues. Clonal expansion of T cells was associated with low risk of recurrence in HCC patients.
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Affiliation(s)
- Rui Li
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Junxiao Wang
- Interventional Radiology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
- Aerospace Medical Center, Aerospace Center HospitalPeking University Aerospace Clinical CollegeBeijingChina
| | - Xiubin Li
- Department of Urology, The Third Medical CenterChinese PLA General HospitalBeijingChina
| | - Yining Liang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Yiyun Jiang
- Department of Pathology and Hepatology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
| | - Yuwei Zhang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Pengfei Xu
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
| | - Ling Deng
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
| | - Zhe Wang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
| | - Tao Sun
- Hangzhou ImmuQuad BiotechnologiesHangzhouChina
- Institute of Wenzhou, Zhejiang UniversityWenzhouChina
| | - Jian Wu
- Department of Laboratory MedicineThe Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical UniversitySuzhouChina
| | - Hui Xie
- Interventional Radiology, The Fifth Medical CenterChinese PLA General HospitalBeijingChina
| | - Yijin Wang
- School of MedicineSouthern University of Science and TechnologyShenzhenChina
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9
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Borna Š, Lee E, Nideffer J, Ramachandran A, Wang B, Baker J, Mavers M, Lakshmanan U, Narula M, Garrett AKH, Schulze J, Olek S, Marois L, Gernez Y, Bhatia M, Chong HJ, Walter J, Kitcharoensakkul M, Lang A, Cooper MA, Bertaina A, Roncarolo MG, Meffre E, Bacchetta R. Identification of unstable regulatory and autoreactive effector T cells that are expanded in patients with FOXP3 mutations. Sci Transl Med 2023; 15:eadg6822. [PMID: 38117899 PMCID: PMC11070150 DOI: 10.1126/scitranslmed.adg6822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 11/17/2023] [Indexed: 12/22/2023]
Abstract
Studies of the monogenic autoimmune disease immunodysregulation polyendocrinopathy enteropathy X-linked syndrome (IPEX) have elucidated the essential function of the transcription factor FOXP3 and thymic-derived regulatory T cells (Tregs) in controlling peripheral tolerance. However, the presence and the source of autoreactive T cells in IPEX remain undetermined. Here, we investigated how FOXP3 deficiency affects the T cell receptor (TCR) repertoire and Treg stability in vivo and compared T cell abnormalities in patients with IPEX with those in patients with autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy syndrome (APECED). To study Tregs independently of their phenotype and to analyze T cell autoreactivity, we combined Treg-specific demethylation region analyses, single-cell multiomic profiling, and bulk TCR sequencing. We found that patients with IPEX, unlike patients with APECED, have expanded autoreactive T cells originating from both autoreactive effector T cells (Teffs) and Tregs. In addition, a fraction of the expanded Tregs from patients with IPEX lost their phenotypic and functional markers, including CD25 and FOXP3. Functional experiments with CRISPR-Cas9-mediated FOXP3 knockout Tregs and Tregs from patients with IPEX indicated that the patients' Tregs gain a TH2-skewed Teff-like function, which is consistent with immune dysregulation observed in these patients. Analyses of FOXP3 mutation-carrier mothers and a patient with IPEX after hematopoietic stem cell transplantation indicated that Tregs expressing nonmutated FOXP3 prevent the accumulation of autoreactive Teffs and unstable Tregs. These findings could be directly used for diagnostic and prognostic purposes and for monitoring the effects of immunomodulatory treatments.
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Affiliation(s)
- Šimon Borna
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Esmond Lee
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jason Nideffer
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Akshaya Ramachandran
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bing Wang
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeanette Baker
- Department of Medicine, Division of Blood and Marrow Transplantation, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melissa Mavers
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Uma Lakshmanan
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mansi Narula
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Amy Kang-hee Garrett
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Sven Olek
- Ivana Turbachova Laboratory for Epigenetics, Precision for Medicine GmbH, Berlin, 12489, Germany
| | - Louis Marois
- Department of Medicine, Immunology and Allergy Service, CHU de Québec – Laval University, Quebec, G1V 4G2, Canada
| | - Yael Gernez
- Department of Pediatrics, Division of Allergy, Rheumatology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Monica Bhatia
- Columbia University Irving Medical Center, NY, NY 10032, USA
| | - Hey Jin Chong
- Division of Allergy and Immunology, University of Pittsburgh Medical Center Children’s Hospital of Pittsburgh, Pittsburgh, 15224, Pa, USA
| | - Jolan Walter
- Division of Allergy and Immunology, Department of Pediatrics, Johns Hopkins All Children’s Hospital, University of South Florida, St. Petersburg, 33701, FL, USA
| | - Maleewan Kitcharoensakkul
- Divisions of Rheumatology/Immunology, and Allergy and Pulmonary Medicine, Department of Pediatrics, Washington University in St. Louis, St. Louis, Missouri, 63110, USA
| | - Abigail Lang
- Department of Pediatrics, Division of Allergy and Immunology, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Megan A. Cooper
- Department of pediatrics, division of Rheumatology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, 63110, USA
| | - Alice Bertaina
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Eric Meffre
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, 269 Campus Drive West, Stanford, CA 94305, USA
| | - Rosa Bacchetta
- Department of Pediatrics, Division of Hematology, Oncology, Stem Cell Transplantation and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Center for Definitive and Curative Medicine (CDCM), Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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Textor J, Buytenhuijs F, Rogers D, Gauthier ÈM, Sultan S, Wortel IMN, Kalies K, Fähnrich A, Pagel R, Melichar HJ, Westermann J, Mandl JN. Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity. Cell Syst 2023; 14:1059-1073.e5. [PMID: 38061355 DOI: 10.1016/j.cels.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The T cell receptor (TCR) determines specificity and affinity for both foreign and self-peptides presented by the major histocompatibility complex (MHC). Although the strength of TCR interactions with self-pMHC impacts T cell function, it has been challenging to identify TCR sequence features that predict T cell fate. To discern patterns distinguishing TCRs from naive CD4+ T cells with low versus high self-reactivity, we used data from 42 mice to train a machine learning (ML) algorithm that identifies population-level differences between TCRβ sequence sets. This approach revealed that weakly self-reactive T cell populations were enriched for longer CDR3β regions and acidic amino acids. We tested our ML predictions of self-reactivity using retrogenic mice with fixed TCRβ sequences. Extrapolating our analyses to independent datasets, we predicted high self-reactivity for regulatory T cells and slightly reduced self-reactivity for T cells responding to chronic infections. Our analyses suggest a potential trade-off between TCR repertoire diversity and self-reactivity. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Johannes Textor
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands.
| | - Franka Buytenhuijs
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Ève Mallet Gauthier
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Shabaz Sultan
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Inge M N Wortel
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Kathrin Kalies
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Anke Fähnrich
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - René Pagel
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Medicine, Université de Montréal, Montréal, QC H1T 2M4, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | | | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada.
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11
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Mitchell AM, Baschal EE, McDaniel KA, Fleury T, Choi H, Pyle L, Yu L, Rewers MJ, Nakayama M, Michels AW. Tracking DNA-based antigen-specific T cell receptors during progression to type 1 diabetes. SCIENCE ADVANCES 2023; 9:eadj6975. [PMID: 38064552 PMCID: PMC10708189 DOI: 10.1126/sciadv.adj6975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/09/2023] [Indexed: 12/18/2023]
Abstract
T cells targeting self-proteins are important mediators in autoimmune diseases. T cells express unique cell-surface receptors (TCRs) that recognize peptides presented by major histocompatibility molecules. TCRs have been identified from blood and pancreatic islets of individuals with type 1 diabetes (T1D). Here, we tracked ~1700 known antigen-specific TCR sequences, islet antigen or viral reactive, in bulk TCRβ sequencing from longitudinal blood DNA samples in at-risk cases who progressed to T1D, age/sex/human leukocyte antigen-matched controls, and a new-onset T1D cohort. Shared and frequent antigen-specific TCRβ sequences were identified in all three cohorts, and viral sequences were present across all ages. Islet sequences had different patterns of accumulation based upon antigen specificity in the at-risk cases. Furthermore, 73 islet-antigen TCRβ sequences were present in higher frequencies and numbers in T1D samples relative to controls. The total number of these disease-associated TCRβ sequences inversely correlated with age at clinical diagnosis, indicating the potential to use disease-relevant TCR sequences as biomarkers in autoimmune disorders.
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Affiliation(s)
- Angela M. Mitchell
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Erin E. Baschal
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kristen A. McDaniel
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Theodore Fleury
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Hyelin Choi
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Laura Pyle
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Biostatistics and Informatics, University of Colorado School of Public Health, Aurora, CO, USA
| | - Liping Yu
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Marian J. Rewers
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Aaron W. Michels
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA
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12
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Pang Z, Lu MM, Zhang Y, Gao Y, Bai JJ, Gu JY, Xie L, Wu WZ. Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges. Biomark Res 2023; 11:104. [PMID: 38037114 PMCID: PMC10690996 DOI: 10.1186/s40364-023-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising approach for cancer therapy with an expectation of no significant side effects. In the human body, mature T cells are armed with an incredible diversity of T cell receptors (TCRs) that theoretically react to the variety of random mutations generated by tumor cells. The outcomes, however, of current clinical trials using TCR-T cell therapies are not very successful especially involving solid tumors. The therapy still faces numerous challenges in the efficient screening of tumor-specific antigens and their cognate TCRs. In this review, we first introduce TCR structure-based antigen recognition and signaling, then describe recent advances in neoantigens and their specific TCR screening technologies, and finally summarize ongoing clinical trials of TCR-T therapies against neoantigens. More importantly, we also present the current challenges of TCR-T cell-based immunotherapies, e.g., the safety of viral vectors, the mismatch of T cell receptor, the impediment of suppressive tumor microenvironment. Finally, we highlight new insights and directions for personalized TCR-T therapy.
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Affiliation(s)
- Zhi Pang
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Man-Man Lu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yu Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan Gao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jin-Jin Bai
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Ying Gu
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Wei-Zhong Wu
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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13
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Ishikawa T, Horie K, Takakura Y, Ohki H, Maruyama Y, Hayama M, Miyauchi M, Miyao T, Hagiwara N, Kobayashi TJ, Akiyama N, Akiyama T. T-cell receptor repertoire analysis of CD4-positive T cells from blood and an affected organ in an autoimmune mouse model. Genes Cells 2023; 28:929-941. [PMID: 37909727 DOI: 10.1111/gtc.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/15/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
Abstract
One hallmark of some autoimmune diseases is the variability of symptoms among individuals. Organs affected by the disease differ between patients, posing a challenge in diagnosing the affected organs. Although numerous studies have investigated the correlation between T cell antigen receptor (TCR) repertoires and the development of infectious and immune diseases, the correlation between TCR repertoires and variations in disease symptoms among individuals remains unclear. This study aimed to investigate the correlation of TCRα and β repertoires in blood T cells with the extent of autoimmune signs that varies among individuals. We sequenced TCRα and β of CD4+ CD44high CD62Llow T cells in the blood and stomachs of mice deficient in autoimmune regulator (Aire) (AIRE KO), a mouse model of human autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. Data analysis revealed that the degree of similarity in TCR sequences between the blood and stomach varied among individual AIRE KO mice and reflected the extent of T cell infiltration in the stomach. We identified a set of TCR sequences whose frequencies in blood might correlate with extent of the stomach manifestations. Our results propose a potential of using TCR repertoires not only for diagnosing disease development but also for diagnosing affected organs in autoimmune diseases.
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Affiliation(s)
- Tatsuya Ishikawa
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Kenta Horie
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuki Takakura
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Houko Ohki
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yuya Maruyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Mio Hayama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Maki Miyauchi
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Takahisa Miyao
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Naho Hagiwara
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Nobuko Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Taishin Akiyama
- Laboratory of Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
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14
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Linsley P, Nakayama M, Balmas E, Chen J, Pour F, Bansal S, Serti E, Speake C, Pugliese A, Cerosaletti K. Self-reactive germline-like TCR alpha chains shared between blood and pancreas. RESEARCH SQUARE 2023:rs.3.rs-3446917. [PMID: 37886513 PMCID: PMC10602137 DOI: 10.21203/rs.3.rs-3446917/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Human islet antigen reactive CD4 + memory T cells (IAR T cells) from peripheral blood have been studied extensively for their role in the pathogenesis of autoimmune type 1 diabetes (T1D). However, IAR T cells are rare, and it remains poorly understood how they affect T1D progression in the pancreas. Using single cell RNA-sequencing coupled with a multiplexed activation induced marker (AIM) enrichment assay, we identified paired TCR alpha/beta (TRA/TRB) T cell receptors (TCRs) in IAR T cells from the blood of healthy, at-risk, new onset, and established T1D donors. Using TCR sequences as barcodes, we measured infiltration of IAR T cells from blood into pancreas of organ donors with and without T1D. We detected extensive TCR sharing between IAR T cells from peripheral blood and pancreatic infiltrating T cells (PIT), with perfectly matched or single mismatched TRA junctions and J gene regions, comprising ~ 34% of unique IAR TCRs. PIT-matching IAR T cells had public TRA chains that showed increased use of germline-encoded residues in epitope engagement and a propensity for cross-reactivity. The link with T cells in the pancreas implicates autoreactive IAR T cells with shared TRA junctions and increased levels in blood with the prediabetic and new onset phases of T1D progression.
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15
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Lagattuta KA, Nathan A, Rumker L, Birnbaum ME, Raychaudhuri S. The T cell receptor sequence influences the likelihood of T cell memory formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.20.549939. [PMID: 37502994 PMCID: PMC10370203 DOI: 10.1101/2023.07.20.549939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
T cell differentiation depends on activation through the T cell receptor (TCR), whose amino acid sequence varies cell to cell. Particular TCR amino acid sequences nearly guarantee Mucosal-Associated Invariant T (MAIT) and Natural Killer T (NKT) cell fates. To comprehensively define how TCR amino acids affects all T cell fates, we analyze the paired αβTCR sequence and transcriptome of 819,772 single cells. We find that hydrophobic CDR3 residues promote regulatory T cell transcriptional states in both the CD8 and CD4 lineages. Most strikingly, we find a set of TCR sequence features, concentrated in CDR2α, that promotes positive selection in the thymus as well as transition from naïve to memory in the periphery. Even among T cells that recognize the same antigen, these TCR sequence features help to explain which T cells form immunological memory, which is essential for effective pathogen response.
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Affiliation(s)
- Kaitlyn A. Lagattuta
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Laurie Rumker
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael E. Birnbaum
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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16
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Mora T, Walczak AM. Towards a quantitative theory of tolerance. Trends Immunol 2023; 44:512-518. [PMID: 37263823 DOI: 10.1016/j.it.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023]
Abstract
A cornerstone of the classical view of tolerance is the elimination of self-reactive T cells via negative selection in the thymus. However, high-throughput T cell receptor (TCR) sequencing data have so far failed to detect substantial signatures of negative selection in the observed repertoires. In addition, quantitative estimates as well as recent experiments suggest that the elimination of self-reactive T cells is at best incomplete. We discuss several recent theoretical ideas that might explain tolerance while being consistent with these observations, including collective decision-making through quorum sensing, and sensitivity to change through dynamic tuning and adaptation. We propose that a unified quantitative theory of tolerance should combine these elements to help to explain the plasticity of the immune system and its robustness to autoimmunity.
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Affiliation(s)
- Thierry Mora
- Laboratoire de Physique de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Université Paris Sciences et Lettres (PSL University), Sorbonne Université, and Université Paris-Cité, 75005 Paris, France.
| | - Aleksandra M Walczak
- Laboratoire de Physique de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique (CNRS), Université Paris Sciences et Lettres (PSL University), Sorbonne Université, and Université Paris-Cité, 75005 Paris, France.
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17
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Pille M, Avila J, Sanchez GS, Goetgeluk G, De Munter S, Jansen H, Billiet L, Weening K, Xue H, Bonte S, Ingels J, De Cock L, Pascal E, Deseins L, Kerre T, Taghon T, Leclercq G, Vermijlen D, Davis B, Vandekerckhove B. The Wiskott-Aldrich syndrome protein is required for positive selection during T-cell lineage differentiation. Front Immunol 2023; 14:1188099. [PMID: 37350958 PMCID: PMC10282776 DOI: 10.3389/fimmu.2023.1188099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/15/2023] [Indexed: 06/24/2023] Open
Abstract
The Wiskott-Aldrich syndrome (WAS) is an X-linked primary immune deficiency caused by a mutation in the WAS gene. This leads to altered or absent WAS protein (WASp) expression and function resulting in thrombocytopenia, eczema, recurrent infections, and autoimmunity. In T cells, WASp is required for immune synapse formation. Patients with WAS show reduced numbers of peripheral blood T lymphocytes and an altered T-cell receptor repertoire. In vitro, their peripheral T cells show decreased proliferation and cytokine production upon aCD3/aCD28 stimulation. It is unclear whether these T-cell defects are acquired during peripheral activation or are, in part, generated during thymic development. Here, we assessed the role of WASp during T-cell differentiation using artificial thymic organoid cultures and in the thymus of humanized mice. Although CRISPR/Cas9 WAS knockout hematopoietic stem and progenitor cells (HSPCs) rearranged the T-cell receptor and differentiated to T-cell receptor (TCR)+ CD4+ CD8+ double-positive (DP) cells similar to wild-type HSPCs, a partial defect in the generation of CD8 single-positive (SP) cells was observed, suggesting that WASp is involved in their positive selection. TCR repertoire analysis of the DP and CD8+ SP population, however, showed a polyclonal repertoire with no bias toward autoreactivity. To our knowledge, this is the first study of the role of WASp in human T-cell differentiation and on TCR repertoire generation.
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Affiliation(s)
- Melissa Pille
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - John Avila
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Glenn Goetgeluk
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Stijn De Munter
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Hanne Jansen
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Lore Billiet
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Karin Weening
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Haipeng Xue
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Sarah Bonte
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Joline Ingels
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Laurenz De Cock
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Pascal
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lucas Deseins
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Tessa Kerre
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Tom Taghon
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB Center for Research in Immunology (U-CRI), Université Libre de Bruxelles (ULB), Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Brian Davis
- Brown Foundation Institute of Molecular Medicine, Mc Govern Medical School, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Bart Vandekerckhove
- Laboratory of Experimental Immunology, Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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18
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Billiet L, De Cock L, Sanchez Sanchez G, Mayer RL, Goetgeluk G, De Munter S, Pille M, Ingels J, Jansen H, Weening K, Pascal E, Raes K, Bonte S, Kerre T, Vandamme N, Seurinck R, Roels J, Lavaert M, Van Nieuwerburgh F, Leclercq G, Taghon T, Impens F, Menten B, Vermijlen D, Vandekerckhove B. Single-cell profiling identifies a novel human polyclonal unconventional T cell lineage. J Exp Med 2023; 220:e20220942. [PMID: 36939517 PMCID: PMC10037106 DOI: 10.1084/jem.20220942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 12/22/2022] [Accepted: 02/27/2023] [Indexed: 03/21/2023] Open
Abstract
In the human thymus, a CD10+ PD-1+ TCRαβ+ differentiation pathway diverges from the conventional single positive T cell lineages at the early double-positive stage. Here, we identify the progeny of this unconventional lineage in antigen-inexperienced blood. These unconventional T cells (UTCs) in thymus and blood share a transcriptomic profile, characterized by hallmark transcription factors (i.e., ZNF683 and IKZF2), and a polyclonal TCR repertoire with autoreactive features, exhibiting a bias toward early TCRα chain rearrangements. Single-cell RNA sequencing confirms a common developmental trajectory between the thymic and blood UTCs and clearly delineates this unconventional lineage in blood. Besides MME+ recent thymic emigrants, effector-like clusters are identified in this heterogeneous lineage. Expression of Helios and KIR and a decreased CD8β expression are characteristics of this lineage. This UTC lineage could be identified in adult blood and intestinal tissues. In summary, our data provide a comprehensive characterization of the polyclonal unconventional lineage in antigen-inexperienced blood and identify the adult progeny.
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Affiliation(s)
- Lore Billiet
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Laurenz De Cock
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Guillem Sanchez Sanchez
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles, Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles, Brussels, Belgium
- Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Rupert L. Mayer
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Stijn De Munter
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Melissa Pille
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Joline Ingels
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Hanne Jansen
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Karin Weening
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Eva Pascal
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Killian Raes
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Sarah Bonte
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Tessa Kerre
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Niels Vandamme
- VIB Single Cell Core, VIB, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Jana Roels
- VIB Single Cell Core, VIB, Ghent, Belgium
- Data Mining and Modeling for Biomedicine, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Marieke Lavaert
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Cancer Research Institute Ghent, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Björn Menten
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - David Vermijlen
- Department of Pharmacotherapy and Pharmaceutics, Université Libre de Bruxelles, Brussels, Belgium
- Institute for Medical Immunology, Université Libre de Bruxelles, Brussels, Belgium
- Université Libre de Bruxelles Center for Research in Immunology, Université Libre de Bruxelles, Brussels, Belgium
- WELBIO Department, WEL Research Institute, Wavre, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
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19
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Kalinina A, Persiyantseva N, Britanova O, Lupyr K, Shagina I, Khromykh L, Kazansky D. Unique features of the TCR repertoire of reactivated memory T cells in the experimental mouse tumor model. Comput Struct Biotechnol J 2023; 21:3196-3209. [PMID: 37333858 PMCID: PMC10275742 DOI: 10.1016/j.csbj.2023.05.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023] Open
Abstract
T cell engineering with T cell receptors (TCR) specific to tumor antigens has become a breakthrough towards personalized cancer adoptive cell immunotherapy. However, the search for therapeutic TCRs is often challenging, and effective strategies are strongly required for the identification and enrichment of tumor-specific T cells that express TCRs with superior functional characteristics. Using an experimental mouse tumor model, we studied sequential changes in TCR repertoire features of T cells involved in the primary and secondary immune responses to allogeneic tumor antigens. In-depth bioinformatics analysis of TCR repertoires showed differences in reactivated memory T cells compared to primarily activated effectors. After cognate antigen re-encounter, memory cells were enriched with clonotypes that express α-chain TCR with high potential cross-reactivity and enhanced strength of interaction with both MHC and docked peptides. Our findings suggest that functionally true memory T cells could be a better source of therapeutic TCRs for adoptive cell therapy. No marked changes were observed in the physicochemical characteristics of TCRβ in reactivated memory clonotypes, indicative of the dominant role of TCRα in the secondary allogeneic immune response. The results of this study could further contribute to the development of TCR-modified T cell products based on the phenomenon of TCR chain centricity.
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Affiliation(s)
- Anastasiia Kalinina
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Nadezda Persiyantseva
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Olga Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russian Federation
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1, 17997 Moscow, Russian Federation
| | - Ksenia Lupyr
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoi boulevard 30c1, 121205 Moscow, Russian Federation
- Institute of Translational Medicine, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1,build. 1, 17997 Moscow, Russian Federation
| | - Irina Shagina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya st. 16/10, 117997 Moscow, Russian Federation
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova st.1, 17997 Moscow, Russian Federation
| | - Ludmila Khromykh
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
| | - Dmitry Kazansky
- N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Kashirskoe sh. 24, 115478 Moscow, Russian Federation
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20
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Friman V, Quinti I, Davydov AN, Shugay M, Farroni C, Engström E, Pour Akaber S, Barresi S, Mohamed A, Pulvirenti F, Milito C, Granata G, Giorda E, Ahlström S, Karlsson J, Marasco E, Marcellini V, Bocci C, Cascioli S, Scarsella M, Phad G, Tilevik A, Tartaglia M, Bemark M, Chudakov DM, Carsetti R, Grimsholm O. Defective peripheral B cell selection in common variable immune deficiency patients with autoimmune manifestations. Cell Rep 2023; 42:112446. [PMID: 37119135 DOI: 10.1016/j.celrep.2023.112446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/15/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Common variable immune deficiency (CVID) is a heterogeneous disorder characterized by recurrent infections, low levels of serum immunoglobulins, and impaired vaccine responses. Autoimmune manifestations are common, but B cell central and peripheral selection mechanisms in CVID are incompletely understood. Here, we find that receptor editing, a measure of central tolerance, is increased in transitional B cells from CVID patients and that these cells have a higher immunoglobulin κ:λ ratio in CVID patients with autoimmune manifestations than in those with infection only. Contrariwise, the selection pressure in the germinal center on CD27bright memory B cells is decreased in CVID patients with autoimmune manifestations. Finally, functionally, T cell-dependent activation showed that naive B cells in CVID patients are badly equipped for activation and induction of mismatch repair genes. We conclude that central tolerance is functional whereas peripheral selection is defective in CVID patients with autoimmune manifestations, which could underpin the development of autoimmunity.
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Affiliation(s)
- Vanda Friman
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Isabella Quinti
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Mikhail Shugay
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Chiara Farroni
- Translational Research Unit, National Institute for Infectious Diseases Lazzaro Spallanzani (IRCCS), Rome, Italy; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Erik Engström
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Shirin Pour Akaber
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Ahmed Mohamed
- Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Faculty of Health Sciences, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Federica Pulvirenti
- Centre for Primary Immune Deficiency, AUO Policlinico Umberto I, Rome, Italy
| | - Cinzia Milito
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Guido Granata
- Clinical and Research Department for Infectious Diseases, National Institute for Infectious Diseases L. Spallanzani (IRCCS), 00149 Rome, Italy
| | - Ezio Giorda
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Sara Ahlström
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Karlsson
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Emiliano Marasco
- Division of Rheumatology, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | | | - Chiara Bocci
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Simona Cascioli
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Marco Scarsella
- Research Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ganesh Phad
- Institute for Research in Biomedicine (IRB), Università della Svizzera Italiana (USI), Bellinzona, Switzerland
| | | | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy
| | - Mats Bemark
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Immunology and Transfusion Medicine, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Dmitriy M Chudakov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Central European Institute of Technology, Brno, Czech Republic
| | - Rita Carsetti
- B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy; Unit of Diagnostic Immunology, Department of Laboratories, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ola Grimsholm
- Institute of Pathophysiology and Allergy Research, Centre for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Vienna, Austria; Department of Rheumatology and Inflammation Research, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; B Cell Pathophysiology Unit, Immunology Research Area, Ospedale Pediatrico Bambino Gesù IRCCS, Rome, Italy.
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21
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Stadinski BD, Cleveland SB, Brehm MA, Greiner DL, Huseby PG, Huseby ES. I-A g7 β56/57 polymorphisms regulate non-cognate negative selection to CD4 + T cell orchestrators of type 1 diabetes. Nat Immunol 2023; 24:652-663. [PMID: 36807641 PMCID: PMC10623581 DOI: 10.1038/s41590-023-01441-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 01/20/2023] [Indexed: 02/22/2023]
Abstract
Genetic susceptibility to type 1 diabetes is associated with homozygous expression of major histocompatibility complex class II alleles that carry specific beta chain polymorphisms. Why heterozygous expression of these major histocompatibility complex class II alleles does not confer a similar predisposition is unresolved. Using a nonobese diabetic mouse model, here we show that heterozygous expression of the type 1 diabetes-protective allele I-Ag7 β56P/57D induces negative selection to the I-Ag7-restricted T cell repertoire, including beta-islet-specific CD4+ T cells. Surprisingly, negative selection occurs despite I-Ag7 β56P/57D having a reduced ability to present beta-islet antigens to CD4+ T cells. Peripheral manifestations of non-cognate negative selection include a near complete loss of beta-islet-specific CXCR6+ CD4+ T cells, an inability to cross-prime islet-specific glucose-6-phosphatase catalytic subunit-related protein and insulin-specific CD8+ T cells and disease arrest at the insulitis stage. These data reveal that negative selection on non-cognate self-antigens in the thymus can promote T cell tolerance and protection from autoimmunity.
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Affiliation(s)
- Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sarah B Cleveland
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Michael A Brehm
- Department of Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Dale L Greiner
- Department of Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, MA, USA
| | - Priya G Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA.
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22
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MHC-II heterozygosity limits type 1 diabetes susceptibility through negative selection. Nat Immunol 2023; 24:573-574. [PMID: 36829075 DOI: 10.1038/s41590-023-01446-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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23
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Camaglia F, Ryvkin A, Greenstein E, Reich-Zeliger S, Chain B, Mora T, Walczak AM, Friedman N. Quantifying changes in the T cell receptor repertoire during thymic development. eLife 2023; 12:81622. [PMID: 36661220 PMCID: PMC9934861 DOI: 10.7554/elife.81622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
One of the feats of adaptive immunity is its ability to recognize foreign pathogens while sparing the self. During maturation in the thymus, T cells are selected through the binding properties of their antigen-specific T-cell receptor (TCR), through the elimination of both weakly (positive selection) and strongly (negative selection) self-reactive receptors. However, the impact of thymic selection on the TCR repertoire is poorly understood. Here, we use transgenic Nur77-mice expressing a T-cell activation reporter to study the repertoires of thymic T cells at various stages of their development, including cells that do not pass selection. We combine high-throughput repertoire sequencing with statistical inference techniques to characterize the selection of the TCR in these distinct subsets. We find small but significant differences in the TCR repertoire parameters between the maturation stages, which recapitulate known differentiation pathways leading to the CD4+ and CD8+ subtypes. These differences can be simulated by simple models of selection acting linearly on the sequence features. We find no evidence of specific sequences or sequence motifs or features that are suppressed by negative selection. These results favour a collective or statistical model for T-cell self non-self discrimination, where negative selection biases the repertoire away from self recognition, rather than ensuring lack of self-reactivity at the single-cell level.
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Affiliation(s)
- Francesco Camaglia
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de ParisParisFrance
| | - Arie Ryvkin
- Department of Immunology, Weizmann Institute of ScienceRehovotIsrael
| | - Erez Greenstein
- Department of Immunology, Weizmann Institute of ScienceRehovotIsrael
| | | | - Benny Chain
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Thierry Mora
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de ParisParisFrance
| | - Aleksandra M Walczak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de ParisParisFrance
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of ScienceRehovotIsrael
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24
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Raveney BJE, El‐Darawish Y, Sato W, Arinuma Y, Yamaoka K, Hori S, Yamamura T, Oki S. Neuropilin-1 (NRP1) expression distinguishes self-reactive helper T cells in systemic autoimmune disease. EMBO Mol Med 2022; 14:e15864. [PMID: 36069030 PMCID: PMC9549730 DOI: 10.15252/emmm.202215864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 02/05/2023] Open
Abstract
Pathogenic T helper cells (Th cells) that respond to self-antigen cannot be easily distinguished from beneficial Th cells. These cells can generate systemic autoimmune disease in response to widely expressed self-antigens. In this study, we have identified neuropilin-1 (NRP1) as a cell surface marker of self-reactive Th cells. NRP1+ Th cells, absent in non-regulatory T cell subsets in normal mice, appeared in models of systemic autoimmune disease and strongly correlated with disease symptoms. NRP1+ Th cells were greatly reduced in Nr4a2 cKO mice, which have reduced self-reactive responses but showed normal responses against exogenous antigens. Transfer of NRP1+ Th cells was sufficient to initiate or accelerate systemic autoimmune disease, and targeting NRP1-expressing Th cells therapeutically ameliorated SLE-like autoimmune symptoms in BXSB-Yaa mice. Peripheral NRP1+ Th cells were significantly increased in human SLE patients. Our data suggest that self-reactive Th cells can be phenotypically distinguished within the Th cell pool. These findings offer a novel approach to identify self-reactive Th cells and target them to treat systemic autoimmune disease.
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Affiliation(s)
- Ben JE Raveney
- Department of ImmunologyNational Institute of NeuroscienceTokyoJapan
| | - Yosif El‐Darawish
- Department of ImmunologyNational Institute of NeuroscienceTokyoJapan
| | - Wakiro Sato
- Department of ImmunologyNational Institute of NeuroscienceTokyoJapan
| | - Yoshiyuki Arinuma
- Department of Rheumatology and Infectious DiseasesKitasato University School of MedicineSagamiharaJapan
| | - Kunihiro Yamaoka
- Department of Rheumatology and Infectious DiseasesKitasato University School of MedicineSagamiharaJapan
| | - Shohei Hori
- Laboratory for Immunology and MicrobiologyGraduate School of Pharmaceutical Sciences, The University of TokyoTokyoJapan
| | - Takashi Yamamura
- Department of ImmunologyNational Institute of NeuroscienceTokyoJapan
| | - Shinji Oki
- Department of ImmunologyNational Institute of NeuroscienceTokyoJapan
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25
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Mulinacci G, Palermo A, Gerussi A, Asselta R, Gershwin ME, Invernizzi P. New insights on the role of human leukocyte antigen complex in primary biliary cholangitis. Front Immunol 2022; 13:975115. [PMID: 36119102 PMCID: PMC9471323 DOI: 10.3389/fimmu.2022.975115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/11/2022] [Indexed: 01/04/2023] Open
Abstract
Primary Biliary Cholangitis (PBC) is a rare autoimmune cholangiopathy. Genetic studies have shown that the strongest statistical association with PBC has been mapped in the human leukocyte antigen (HLA) locus, a highly polymorphic area that mostly contribute to the genetic variance of the disease. Furthermore, PBC presents high variability throughout different population groups, which may explain the different geoepidemiology of the disease. A major role in defining HLA genetic contribution has been given by genome-wide association studies (GWAS) studies; more recently, new technologies have been developed to allow a deeper understanding. The study of the altered peptides transcribed by genetic alterations also allowed the development of novel therapeutic strategies in the context of immunotolerance. This review summarizes what is known about the immunogenetics of PBC with a focus on the HLA locus, the different distribution of HLA alleles worldwide, and how HLA modifications are associated with the pathogenesis of PBC. Novel therapeutic strategies are also outlined.
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Affiliation(s)
- Giacomo Mulinacci
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Andrea Palermo
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Merrill Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
- *Correspondence: Pietro Invernizzi,
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26
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Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus. Nat Commun 2022; 13:4951. [PMID: 35999236 PMCID: PMC9399087 DOI: 10.1038/s41467-022-32692-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy. Differentiation and activation of T cells are normally modulated by non-covalent interactions between T cell receptor (TCR) and antigenic peptides. Here the authors use step-wise mutations, biochemical characterization and structural insights to describe the contributions of natural covalent bonds between TCR and antigenic peptides during these processes.
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27
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Hou X, Hong X, Ou M, Meng S, Wang T, Liao S, He J, Yu H, Liu L, Yin L, Liu D, Tang D, Dai Y. Analysis of Gene Expression and TCR/B Cell Receptor Profiling of Immune Cells in Primary Sjögren's Syndrome by Single-Cell Sequencing. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:238-249. [PMID: 35705251 DOI: 10.4049/jimmunol.2100803] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/18/2022] [Indexed: 01/07/2023]
Abstract
Primary Sjögren's syndrome (pSS) is a chronic autoimmune disease that is estimated to affect 35 million people worldwide and is characterized by lymphocytic infiltration, elevated circulating autoantibodies, and proinflammatory cytokines. The key immune cell subset changes and the TCR/BCR repertoire alterations in pSS patients remain unclear. In this study, we sought to comprehensively characterize the transcriptional changes in PBMCs of pSS patients by single-cell RNA sequencing and single-cell V(D)J sequencing. Naive CD8+ T cells and mucosal-associated invariant T cells were markedly decreased but regulatory T cells were increased in pSS patients. There were a large number of differentially expressed genes shared by multiple subpopulations of T cells and B cells. Abnormal signaling pathways, including Ag processing and presentation, the BCR signaling pathway, the TCR signaling pathway, and Epstein-Barr virus infection, were highly enriched in pSS patients. Moreover, there were obvious differences in the CD30, FLT3, IFN-II, IL-1, IL-2, IL-6, IL-10, RESISTIN, TGF-β, TNF, and VEGF signaling networks between pSS patients and healthy controls. Single-cell TCR and BCR repertoire analysis showed that there was a lower diversity of T cells in pSS patients than in healthy controls; however, there was no significant difference in the degree of clonal expansion, CDR3 length distribution, or degree of sequence sharing. Notably, our results further emphasize the functional importance of αβ pairing in determining Ag specificity. In conclusion, our analysis provides a comprehensive single-cell map of gene expression and TCR/BCR profiles in pSS patients for a better understanding of the pathogenesis, diagnosis, and treatment of pSS.
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Affiliation(s)
- Xianliang Hou
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - Xiaoping Hong
- Department of Rheumatology and Immunology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Minglin Ou
- Central Laboratory, Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, The Second Affiliated Hospital of Guilin Medical University, Guilin, China; and
| | - Shuhui Meng
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Tingting Wang
- Department of Rheumatology and Immunology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Shengyou Liao
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Jingquan He
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Haiyan Yu
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Lixiong Liu
- Department of Rheumatology and Immunology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Rheumatology and Immunology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China;
| | - Donge Tang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China;
| | - Yong Dai
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China;
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28
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Katayama Y, Yokota R, Akiyama T, Kobayashi TJ. Machine Learning Approaches to TCR Repertoire Analysis. Front Immunol 2022; 13:858057. [PMID: 35911778 PMCID: PMC9334875 DOI: 10.3389/fimmu.2022.858057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sparked by the development of genome sequencing technology, the quantity and quality of data handled in immunological research have been changing dramatically. Various data and database platforms are now driving the rapid progress of machine learning for immunological data analysis. Of various topics in immunology, T cell receptor repertoire analysis is one of the most important targets of machine learning for assessing the state and abnormalities of immune systems. In this paper, we review recent repertoire analysis methods based on machine learning and deep learning and discuss their prospects.
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Affiliation(s)
- Yotaro Katayama
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yotaro Katayama,
| | - Ryo Yokota
- National Research Institute of Police Science, Kashiwa, Chiba, Japan
| | - Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tetsuya J. Kobayashi
- Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
- Institute of Industrial Science, The University of Tokyo, Tokyo, Japan
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29
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Huseby ES, Teixeiro E. The perception and response of T cells to a changing environment are based on the law of initial value. Sci Signal 2022; 15:eabj9842. [PMID: 35639856 PMCID: PMC9290192 DOI: 10.1126/scisignal.abj9842] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
αβ T cells are critical components of the adaptive immune system and are capable of inducing sterilizing immunity after pathogen infection and eliminating transformed tumor cells. The development and function of T cells are controlled through the T cell antigen receptor, which recognizes peptides displayed on major histocompatibility complex (MHC) molecules. Here, we review how T cells generate the ability to recognize self-peptide-bound MHC molecules and use signals derived from these interactions to instruct cellular development, activation thresholds, and functional specialization in the steady state and during immune responses. We argue that the basic tenants of T cell development and function follow Weber-Fetcher's law of just noticeable differences and Wilder's law of initial value. Together, these laws argue that the ability of a system to respond and the quality of that response are scalable to the basal state of that system. Manifestation of these laws in T cells generates clone-specific activation thresholds that are based on perceivable differences between homeostasis and pathogen encounter (self versus nonself discrimination), as well as poised states for subsequent differentiation into specific effector cell lineages.
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Affiliation(s)
- Eric S. Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
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30
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Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
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Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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31
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Ishigaki K, Lagattuta KA, Luo Y, James EA, Buckner JH, Raychaudhuri S. HLA autoimmune risk alleles restrict the hypervariable region of T cell receptors. Nat Genet 2022; 54:393-402. [PMID: 35332318 PMCID: PMC9010379 DOI: 10.1038/s41588-022-01032-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 02/04/2022] [Indexed: 12/16/2022]
Abstract
Polymorphisms in the human leukocyte antigen (HLA) genes strongly influence autoimmune disease risk. HLA risk alleles may influence thymic selection to increase the frequency of T cell receptors (TCRs) reactive to autoantigens (central hypothesis). However, research in human autoimmunity has provided little evidence supporting the central hypothesis. Here we investigated the influence of HLA alleles on TCR composition at the highly diverse complementarity determining region 3 (CDR3), which confers antigen recognition. We observed unexpectedly strong HLA-CDR3 associations. The strongest association was found at HLA-DRB1 amino acid position 13, the position that mediates genetic risk for multiple autoimmune diseases. We identified multiple CDR3 amino acid features enriched by HLA risk alleles. Moreover, the CDR3 features promoted by the HLA risk alleles are more enriched in candidate pathogenic TCRs than control TCRs (for example, citrullinated epitope-specific TCRs in patients with rheumatoid arthritis). Together, these results provide genetic evidence supporting the central hypothesis.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eddie A James
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Jane H Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. .,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK.
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32
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Pauken KE, Lagattuta KA, Lu BY, Lucca LE, Daud AI, Hafler DA, Kluger HM, Raychaudhuri S, Sharpe AH. TCR-sequencing in cancer and autoimmunity: barcodes and beyond. Trends Immunol 2022; 43:180-194. [PMID: 35090787 PMCID: PMC8882139 DOI: 10.1016/j.it.2022.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/21/2023]
Abstract
The T cell receptor (TCR) endows T cells with antigen specificity and is central to nearly all aspects of T cell function. Each naïve T cell has a unique TCR sequence that is stably maintained during cell division. In this way, the TCR serves as a molecular barcode that tracks processes such as migration, differentiation, and proliferation of T cells. Recent technological advances have enabled sequencing of the TCR from single cells alongside deep molecular phenotypes on an unprecedented scale. In this review, we discuss strengths and limitations of TCR sequences as molecular barcodes and their application to study immune responses following Programmed Death-1 (PD-1) blockade in cancer. Additionally, we consider applications of TCR data beyond use as a barcode.
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Affiliation(s)
- Kristen E Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benjamin Y Lu
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Liliana E Lucca
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Adil I Daud
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David A Hafler
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Harriet M Kluger
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PL, UK
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA; Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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33
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Lagattuta KA, Kang JB, Nathan A, Pauken KE, Jonsson AH, Rao DA, Sharpe AH, Ishigaki K, Raychaudhuri S. Repertoire analyses reveal T cell antigen receptor sequence features that influence T cell fate. Nat Immunol 2022; 23:446-457. [PMID: 35177831 PMCID: PMC8904286 DOI: 10.1038/s41590-022-01129-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 01/05/2022] [Indexed: 01/02/2023]
Abstract
T cells acquire a regulatory phenotype when their T cell receptors (TCRs) experience an intermediate-to-high affinity interaction with a self-peptide presented via the major histocompatibility complex (MHC). Using TCRβ sequences from flow-sorted human cells, we identified TCR features that promote regulatory T cell (Treg) fate. From these results, we developed a scoring system to quantify TCR-intrinsic regulatory potential (TiRP). When applied to the tumor microenvironment, TiRP scoring helped to explain why only some T cell clones maintained the Tconv phenotype through expansion. To elucidate drivers of these predictive TCR features, we then examined the two elements of the Treg TCR ligand separately: the self-peptide, and the human MHC II molecule. These analyses revealed that hydrophobicity in the third complementarity determining region (CDR3β) of the TCR promotes reactivity to self-peptides, while TCR variable gene (TRBV gene) usage shapes the TCR’s general propensity for human MHC II-restricted activation.
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Affiliation(s)
- Kaitlyn A Lagattuta
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kristen E Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arlene H Sharpe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA. .,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA. .,Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.
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34
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Shao MM, Yi FS, Huang ZY, Peng P, Wu FY, Shi HZ, Zhai K. T Cell Receptor Repertoire Analysis Reveals Signatures of T Cell Responses to Human Mycobacterium tuberculosis. Front Microbiol 2022; 13:829694. [PMID: 35197957 PMCID: PMC8859175 DOI: 10.3389/fmicb.2022.829694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/03/2022] [Indexed: 11/17/2022] Open
Abstract
Characterization of T cell receptor (TCR) repertoires is essential for understanding the mechanisms of Mycobacterium tuberculosis (Mtb) infection involving T cell adaptive immunity. The characteristics of TCR sequences and distinctive signatures of T cell subsets in tuberculous patients are still unclear. By combining single-cell TCR sequencing (sc-TCR seq) with single-cell RNA sequencing (sc-RNA seq) and flow cytometry to characterize T cells in tuberculous pleural effusions (TPEs), we identified 41,718 CD3+ T cells in TPEs and paired blood samples, including 30,515 CD4+ T cells and 11,203 CD8+ T cells. Compared with controls, no differences in length and profile of length distribution were observed in complementarity determining region 3 (CDR3) in both CD4+ and CD8+ T cells in TPE. Altered hydrophobicity was demonstrated in CDR3 in CD8+ T cells and a significant imbalance in the TCR usage pattern of T cells with preferential expression of TRBV4-1 in TPE. A significant increase in clonality was observed in TCR repertoires in CD4+ T cells, but not in CD8+ T cells, although both enriched CD4+ and CD8+ T cells showed TH1 and cytotoxic signatures. Furthermore, we identified a new subset of polyfunctional CD4+ T cells with CD1-restricted, TH1, and cytotoxic characteristics, and this subset might provide protective immunity against Mtb.
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Affiliation(s)
- Ming-Ming Shao
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Feng-Shuang Yi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhong-Yin Huang
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Peng Peng
- Department of Respiratory and Critical Care Medicine, Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, Wuhan, China
| | - Feng-Yao Wu
- Department of Tuberculosis, Nanning Fourth People’s Hospital, Nanning, China
| | - Huan-Zhong Shi
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Kan Zhai
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- *Correspondence: Kan Zhai,
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35
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Li W, Jia Y, Wang Y, Zhao Q, Yang L, Zeng T, Niu L, Dai R, Li Y, Zhao X, Wu J. WASp Deficiency Selectively Affects the TCR Diversity of Different Memory T Cell Subsets in WAS Chimeric Mice. Front Immunol 2022; 12:794795. [PMID: 35116029 PMCID: PMC8803657 DOI: 10.3389/fimmu.2021.794795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Background The T cell receptor (TCR) diversity is essential for effective T cell immunity. Previous studies showed that TCR diversity in Wiskott–Aldrich Syndrome (WAS) patients was severely impaired, especially in the memory T cell populations. Whether this defect was caused by intrinsic WASp deficiency or extrinsic reasons is still unclear. Methods We sorted different T cell subsets from the bone marrow chimeric mice model using both magnetic beads and flow cytometry. TCR repertoires of memory T cells, especially CD4+ effector memory T (TEM) cells and CD8+ central memory T (TCM) cells, were analyzed using the UMI quantitative high-throughput sequencing (HTS). Results An average of 5.51 million sequencing reads of 32 samples was obtained from the Illumina sequencing platform. Bioinformatic analyses showed that compared with wild type (WT), WAS knock out (KO)-CD4+ TEM cells exhibited increased Simpson index and decreased D50 index (P <0.05); The rank abundance curve of KO-CD4+ TEM cells was shorter and steeper than that of WT, and the angle of qD and q in KO-CD4+ TEM cells was lower than that of WT, while these indexes showed few changes between WT and KO chimeric mice in the CD8+TCM population. Therefore, it indicated that the restriction on the TCRVβ repertoires is majorly in KO-CD4+ TEM cells but not KO- CD8+ TCM cells. Principal Component Analysis (PCA), a comprehensive parameter for TCRVβ diversity, successfully segregated CD4+ TEM cells from WT and KO, but failed in CD8+ TCM cells. Among the total sequences of TRB, the usage of TRBV12.2, TRBV30, TRBV31, TRBV4, TRBD1, TRBD2, TRBJ1.1, and TRBJ1.4 showed a significant difference between WT-CD4+ TEM cells and KO-CD4+ TEM cells (P <0.05), while in CD8+ TCM cells, only the usage of TRBV12.2 and TRBV20 showed a substantial difference between WT and KO (P <0.05). No significant differences in the hydrophobicity and sequence length of TCRVβ were found between the WT and KO groups. Conclusion WASp deficiency selectively affected the TCR diversity of different memory T cell subsets, and it had more impact on the TCRVβ diversity of CD4+ TEM cells than CD8+ TCM cells. Moreover, the limitation of TCRVβ diversity of CD4+ TEM cells and CD8+ TCM cells in WAS was not severe but intrinsic.
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Affiliation(s)
- Wenyan Li
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yanjun Jia
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yanping Wang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Qin Zhao
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Yang
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Ting Zeng
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Linlin Niu
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Rongxin Dai
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Yanan Li
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaodong Zhao
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Junfeng Wu, ; Xiaodong Zhao,
| | - Junfeng Wu
- National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Child Infection and Immunity, Chongqing Key Laboratory of Pediatrics, Children’s Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology and Immunology, Children’s Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Junfeng Wu, ; Xiaodong Zhao,
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36
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Integrating T cell receptor sequences and transcriptional profiles by clonotype neighbor graph analysis (CoNGA). Nat Biotechnol 2022; 40:54-63. [PMID: 34426704 PMCID: PMC8832949 DOI: 10.1038/s41587-021-00989-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
Links between T cell clonotypes, as defined by T cell receptor (TCR) sequences, and phenotype, as reflected in gene expression (GEX) profiles, surface protein expression and peptide:major histocompatibility complex binding, can reveal functional relationships beyond the features shared by clonally related cells. Here we present clonotype neighbor graph analysis (CoNGA), a graph theoretic approach that identifies correlations between GEX profile and TCR sequence through statistical analysis of GEX and TCR similarity graphs. Using CoNGA, we uncovered associations between TCR sequence and GEX profiles that include a previously undescribed 'natural lymphocyte' population of human circulating CD8+ T cells and a set of TCR sequence determinants of differentiation in thymocytes. These examples show that CoNGA might help elucidate complex relationships between TCR sequence and T cell phenotype in large, heterogeneous, single-cell datasets.
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37
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B Cells in Primary Membranous Nephropathy: Escape from Immune Tolerance and Implications for Patient Management. Int J Mol Sci 2021; 22:ijms222413560. [PMID: 34948358 PMCID: PMC8708506 DOI: 10.3390/ijms222413560] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Membranous nephropathy (MN) is an important cause of nephrotic syndrome and chronic kidney disease (CKD) in adults. The pathogenic significance of B cells in MN is increasingly recognized, especially following the discovery of various autoantibodies that target specific podocytic antigens and the promising treatment responses seen with B cell depleting therapies. The presence of autoreactive B cells and autoantibodies that bind to antigens on podocyte surfaces are characteristic features of MN, and are the result of breaches in central and peripheral tolerance of B lymphocytes. These perturbations in B cell tolerance include altered B lymphocyte subsets, dysregulation of genes that govern immunoglobulin production, aberrant somatic hypermutation and co-stimulatory signalling, abnormal expression of B cell-related cytokines, and increased B cell infiltrates and organized tertiary lymphoid structures within the kidneys. An understanding of the role of B cell tolerance and homeostasis may have important implications for patient management in MN, as conventional immunosuppressive treatments and novel B cell-targeted therapies show distinct effects on proliferation, differentiation and reconstitution in different B cell subsets. Circulating B lymphocytes and related cytokines may serve as potential biomarkers for treatment selection, monitoring of therapeutic response and prediction of disease relapse. These recent advances in the understanding of B cell tolerance in MN have provided greater insight into its immunopathogenesis and potential novel strategies for disease monitoring and treatment.
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38
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Fang M, Su Z, Abolhassani H, Zhang W, Jiang C, Cheng B, Luo L, Wu J, Wang S, Lin L, Wang X, Wang L, Aghamohammadi A, Li T, Zhang X, Hammarström L, Liu X. T Cell Repertoire Abnormality in Immunodeficiency Patients with DNA Repair and Methylation Defects. J Clin Immunol 2021; 42:375-393. [PMID: 34825286 PMCID: PMC8821531 DOI: 10.1007/s10875-021-01178-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/25/2022]
Abstract
Both DNA damage response and methylation play a crucial role in antigen receptor recombination by creating a diverse repertoire in developing lymphocytes, but how their defects relate to T cell repertoire and phenotypic heterogeneity of immunodeficiency remains obscure. We studied the TCR repertoire in patients with the mutation in different genes (ATM, DNMT3B, ZBTB24, RAG1, DCLRE1C, and JAK3) and uncovered distinct characteristics of repertoire diversity. We propose that early aberrancies in thymus T cell development predispose to the heterogeneous phenotypes of the immunodeficiency spectrum. Shorter CDR3 lengths in ATM-deficient patients, resulting from a decreased number of nucleotide insertions during VDJ recombination in the pre-selected TCR repertoire, as well as the increment of CDR3 tyrosine residues, lead to the enrichment of pathology-associated TCRs, which may contribute to the phenotypes of ATM deficiency. Furthermore, patients with DNMT3B and ZBTB24 mutations who exhibit discrepant phenotypes present longer CDR3 lengths and reduced number of known pathology-associated TCRs.
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Affiliation(s)
- Mingyan Fang
- BGI-Shenzhen, Shenzhen, 518083, China.,Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - Zheng Su
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, The University of New South Wales, Sydney, NSW, Australia
| | - Hassan Abolhassani
- Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden.,Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | | | | | - Lihua Luo
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | | | - Liya Lin
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xie Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Asghar Aghamohammadi
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Tao Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Lennart Hammarström
- BGI-Shenzhen, Shenzhen, 518083, China. .,Division of Clinical Immunology at the Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden. .,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, 518083, China. .,Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
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39
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Fu J, Khosravi-Maharlooei M, Sykes M. High Throughput Human T Cell Receptor Sequencing: A New Window Into Repertoire Establishment and Alloreactivity. Front Immunol 2021; 12:777756. [PMID: 34804070 PMCID: PMC8604183 DOI: 10.3389/fimmu.2021.777756] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high throughput sequencing (HTS) of T cell receptors (TCRs) and in transcriptomic analysis, particularly at the single cell level, have opened the door to a new level of understanding of human immunology and immune-related diseases. In this article, we discuss the use of HTS of TCRs to discern the factors controlling human T cell repertoire development and how this approach can be used in combination with human immune system (HIS) mouse models to understand human repertoire selection in an unprecedented manner. An exceptionally high proportion of human T cells has alloreactive potential, which can best be understood as a consequence of the processes governing thymic selection. High throughput TCR sequencing has allowed assessment of the development, magnitude and nature of the human alloresponse at a new level and has provided a tool for tracking the fate of pre-transplant-defined donor- and host-reactive TCRs following transplantation. New insights into human allograft rejection and tolerance obtained with this method in combination with single cell transcriptional analyses are reviewed here.
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Affiliation(s)
- Jianing Fu
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Mohsen Khosravi-Maharlooei
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University, New York, NY, United States
- Department of Surgery, Columbia University, New York, NY, United States
- Department of Microbiology & Immunology, Columbia University, New York, NY, United States
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40
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Delmonte OM, Bergerson JRE, Kawai T, Kuehn HS, McDermott DH, Cortese I, Zimmermann MT, Dobbs AK, Bosticardo M, Fink D, Majumdar S, Palterer B, Pala F, Dsouza NR, Pouzolles M, Taylor N, Calvo KR, Daley SR, Velez D, Agharahimi A, Myint-Hpu K, Dropulic LK, Lyons JJ, Holland SM, Freeman AF, Ghosh R, Similuk MB, Niemela JE, Stoddard J, Kuhns DB, Urrutia R, Rosenzweig SD, Walkiewicz MA, Murphy PM, Notarangelo LD. SASH3 variants cause a novel form of X-linked combined immunodeficiency with immune dysregulation. Blood 2021; 138:1019-1033. [PMID: 33876203 PMCID: PMC8462359 DOI: 10.1182/blood.2020008629] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sterile alpha motif (SAM) and Src homology-3 (SH3) domain-containing 3 (SASH3), also called SH3-containing lymphocyte protein (SLY1), is a putative adaptor protein that is postulated to play an important role in the organization of signaling complexes and propagation of signal transduction cascades in lymphocytes. The SASH3 gene is located on the X-chromosome. Here, we identified 3 novel SASH3 deleterious variants in 4 unrelated male patients with a history of combined immunodeficiency and immune dysregulation that manifested as recurrent sinopulmonary, cutaneous, and mucosal infections and refractory autoimmune cytopenias. Patients exhibited CD4+ T-cell lymphopenia, decreased T-cell proliferation, cell cycle progression, and increased T-cell apoptosis in response to mitogens. In vitro T-cell differentiation of CD34+ cells and molecular signatures of rearrangements at the T-cell receptor α (TRA) locus were indicative of impaired thymocyte survival. These patients also manifested neutropenia and B-cell and natural killer (NK)-cell lymphopenia. Lentivirus-mediated transfer of the SASH3 complementary DNA-corrected protein expression, in vitro proliferation, and signaling in SASH3-deficient Jurkat and patient-derived T cells. These findings define a new type of X-linked combined immunodeficiency in humans that recapitulates many of the abnormalities reported in mice with Sly1-/- and Sly1Δ/Δ mutations, highlighting an important role of SASH3 in human lymphocyte function and survival.
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MESH Headings
- Animals
- B-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/immunology
- Child, Preschool
- Chromosomes, Human, X/genetics
- Chromosomes, Human, X/immunology
- Genetic Loci
- Humans
- Jurkat Cells
- Killer Cells, Natural/immunology
- Lymphopenia/genetics
- Lymphopenia/immunology
- Male
- Mice
- Mice, Knockout
- Mutation
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- X-Linked Combined Immunodeficiency Diseases/genetics
- X-Linked Combined Immunodeficiency Diseases/immunology
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Affiliation(s)
- Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jenna R E Bergerson
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Tomoki Kawai
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hye Sun Kuehn
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Irene Cortese
- Neuroimmunology Clinic, Division of Neuroimmunology and Neurovirology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD
| | - Michael T Zimmermann
- Division of Research, Genomics Sciences & Precision Medicine Center, Milwaukee, WI
- Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI
| | - A Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Danielle Fink
- Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Shamik Majumdar
- Molecular Signaling Section, Laboratory of Molecular Immunology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Boaz Palterer
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Nikita R Dsouza
- Division of Research, Genomics Sciences & Precision Medicine Center, Milwaukee, WI
| | - Marie Pouzolles
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Naomi Taylor
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
- Institut de Genetique Moleculaire de Montpellier, Centre National de la Recherche Scientifique Unité Mixte de Recherche (UMR) 5535, Universite de Montpellier, Montpellier, France
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Stephen R Daley
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Daniel Velez
- Molecular Signaling Section, Laboratory of Molecular Immunology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Anahita Agharahimi
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Katherine Myint-Hpu
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Jonathan J Lyons
- Division of Intramural Research, Laboratory of Allergic Diseases, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD and
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Alexandra F Freeman
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Rajarshi Ghosh
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Morgan B Similuk
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Julie E Niemela
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Jennifer Stoddard
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Douglas B Kuhns
- Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Raul Urrutia
- Division of Research, Genomics Sciences & Precision Medicine Center, Milwaukee, WI
- Department of Surgery, Medical College of Wisconsin, Milwaukee, WI
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Magdalena A Walkiewicz
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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41
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Bainter W, Lougaris V, Wallace JG, Badran Y, Hoyos-Bachiloglu R, Peters Z, Wilkie H, Das M, Janssen E, Beano A, Farhat KB, Kam C, Bercich L, Incardona P, Villanacci V, Bondioni MP, Meini A, Baronio M, Abarzua P, Parolini S, Tabellini G, Maio S, Schmidt B, Goldsmith JD, Murphy G, Hollander G, Plebani A, Chou J, Geha RS. Combined immunodeficiency with autoimmunity caused by a homozygous missense mutation in inhibitor of nuclear factor 𝛋B kinase alpha (IKKα). Sci Immunol 2021; 6:eabf6723. [PMID: 34533979 DOI: 10.1126/sciimmunol.abf6723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Wayne Bainter
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vassilios Lougaris
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Jacqueline G Wallace
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yousef Badran
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Zachary Peters
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hazel Wilkie
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mrinmoy Das
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Erin Janssen
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Abdallah Beano
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Khaoula Ben Farhat
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christy Kam
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luisa Bercich
- Department of Pathology, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Paolo Incardona
- Department of Pathology, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Vincenzo Villanacci
- Department of Pathology, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Maria Pia Bondioni
- Department of Pediatric Radiology, University of Brescia, ASST Spedali Civili of Brescia, Brescia, Italy
| | - Antonella Meini
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Manuela Baronio
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Phammela Abarzua
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Silvia Parolini
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Giovanna Tabellini
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Stefano Maio
- Department of Paediatrics, the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Birgitta Schmidt
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey D Goldsmith
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - George Murphy
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Georg Hollander
- Department of Paediatrics, the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Paediatric Immunology, Department of Biomedicine, University of Basel, University Children's Hospital Basel, Basel, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Alessandro Plebani
- Pediatrics Clinic, Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia, ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Janet Chou
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Raif S Geha
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
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42
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Wirasinha RC, Davies AR, Srivastava M, Sheridan JM, Sng XYX, Delmonte OM, Dobbs K, Loh KL, Miosge LA, Lee CE, Chand R, Chan A, Yap JY, Keller MD, Chen K, Rossjohn J, La Gruta NL, Vinuesa CG, Reid HH, Lionakis MS, Notarangelo LD, Gray DHD, Goodnow CC, Cook MC, Daley SR. Nfkb2 variants reveal a p100-degradation threshold that defines autoimmune susceptibility. J Exp Med 2021; 218:211502. [PMID: 33107914 PMCID: PMC7595743 DOI: 10.1084/jem.20200476] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/16/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022] Open
Abstract
NF-κB2/p100 (p100) is an inhibitor of κB (IκB) protein that is partially degraded to produce the NF-κB2/p52 (p52) transcription factor. Heterozygous NFKB2 mutations cause a human syndrome of immunodeficiency and autoimmunity, but whether autoimmunity arises from insufficiency of p52 or IκB function of mutated p100 is unclear. Here, we studied mice bearing mutations in the p100 degron, a domain that harbors most of the clinically recognized mutations and is required for signal-dependent p100 degradation. Distinct mutations caused graded increases in p100-degradation resistance. Severe p100-degradation resistance, due to inheritance of one highly degradation-resistant allele or two subclinical alleles, caused thymic medullary hypoplasia and autoimmune disease, whereas the absence of p100 and p52 did not. We inferred a similar mechanism occurs in humans, as the T cell receptor repertoires of affected humans and mice contained a hydrophobic signature of increased self-reactivity. Autoimmunity in autosomal dominant NFKB2 syndrome arises largely from defects in nonhematopoietic cells caused by the IκB function of degradation-resistant p100.
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Affiliation(s)
- Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Ainsley R Davies
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Translational Research Unit, Department of Immunology, The Canberra Hospital, Canberra, Australia.,Centre for Personalised Immunology (NHMRC Centre of Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Monika Srivastava
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Julie M Sheridan
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Xavier Y X Sng
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Ottavia M Delmonte
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Kerry Dobbs
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Khai L Loh
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Lisa A Miosge
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Cindy Eunhee Lee
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Translational Research Unit, Department of Immunology, The Canberra Hospital, Canberra, Australia
| | - Rochna Chand
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Translational Research Unit, Department of Immunology, The Canberra Hospital, Canberra, Australia
| | - Anna Chan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Jin Yan Yap
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Michael D Keller
- Division of Allergy and Immunology, Children's National Medical Center, Washington, DC
| | - Karin Chen
- Department of Pediatrics, University of Utah, Salt Lake City, UT.,Department of Pediatrics, Seattle Children's Hospital, University of Washington School of Medicine, Seattle, WA
| | - Jamie Rossjohn
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Nicole L La Gruta
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Centre for Personalised Immunology (NHMRC Centre of Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Hugh H Reid
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Daniel H D Gray
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Christopher C Goodnow
- Garvan Institute of Medical Research & Cellular Genomics Futures Institute, University of New South Wales, Sydney, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Translational Research Unit, Department of Immunology, The Canberra Hospital, Canberra, Australia.,Centre for Personalised Immunology (NHMRC Centre of Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
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43
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Shelyakin PV, Lupyr KR, Egorov ES, Kofiadi IA, Staroverov DB, Kasatskaya SA, Kriukova VV, Shagina IA, Merzlyak EM, Nakonechnaya TO, Latysheva EA, Manto IA, Khaitov MR, Lukyanov SA, Chudakov DM, Britanova OV. Naïve Regulatory T Cell Subset Is Altered in X-Linked Agammaglobulinemia. Front Immunol 2021; 12:697307. [PMID: 34489944 PMCID: PMC8417104 DOI: 10.3389/fimmu.2021.697307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/29/2021] [Indexed: 11/14/2022] Open
Abstract
The interplay between T- and B-cell compartments during naïve, effector and memory T cell maturation is critical for a balanced immune response. Primary B-cell immunodeficiency arising from X-linked agammaglobulinemia (XLA) offers a model to explore B cell impact on T cell subsets, starting from the thymic selection. Here we investigated characteristics of naïve and effector T cell subsets in XLA patients, revealing prominent alterations in the corresponding T-cell receptor (TCR) repertoires. We observed immunosenescence in terms of decreased diversity of naïve CD4+ and CD8+ TCR repertoires in XLA donors. The most substantial alterations were found within naïve CD4+ subsets, and we have investigated these in greater detail. In particular, increased clonality and convergence, along with shorter CDR3 regions, suggested narrower focused antigen-specific maturation of thymus-derived naïve Treg (CD4+CD45RA+CD27+CD25+) in the absence of B cells - normally presenting diverse self and commensal antigens. The naïve Treg proportion among naïve CD4 T cells was decreased in XLA patients, supporting the concept of impaired thymic naïve Treg selection. Furthermore, the naïve Treg subset showed prominent differences at the transcriptome level, including increased expression of genes specific for antigen-presenting and myeloid cells. Altogether, our findings suggest active B cell involvement in CD4 T cell subsets maturation, including B cell-dependent expansion of the naïve Treg TCR repertoire that enables better control of self-reactive T cells.
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Affiliation(s)
- Pavel V Shelyakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ksenia R Lupyr
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgeny S Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Ilya A Kofiadi
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Dmitriy B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Sofya A Kasatskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Valeriia V Kriukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Irina A Shagina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ekaterina M Merzlyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Tatiana O Nakonechnaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Irina A Manto
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Musa R Khaitov
- FSBI "NRC Institute of Immunology" FMBA of Russia, Moscow, Russia
| | - Sergey A Lukyanov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitriy M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.,Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Olga V Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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44
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Binz C, Bubke A, Sandrock I, Prinz I. αβ T cells replacing dermal and epidermal γδ T cells in Tcrd -/- mice express an MHC-independent TCR repertoire. Eur J Immunol 2021; 51:2618-2632. [PMID: 34398456 DOI: 10.1002/eji.202149243] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 06/23/2021] [Accepted: 08/12/2021] [Indexed: 12/15/2022]
Abstract
The epidermis of mouse skin is usually populated by dendritic epidermal T cells (γδDETC) expressing an invariant Vγ5Vδ1+ TCR. In Tcrd-/- mice, skin-resident γδDETC are replaced by αβDETC carrying polyclonal αβ TCRs. Although they exhibit a dendritic morphology, αβDETC were reported to be less functional than genuine γδDETC, likely because their TCR is unable to interact with the original TCR ligands of γδDETC. However, the TCR repertoire of those replacement DETC in Tcrd-/- mice might provide clues for understanding the development and selection of canonical γδDETC. Here, we compare the phenotype and TCR repertoires of wild-type and Tcrd-/- mouse skin T cells. Our data reveal that αβDETC are CD4/CD8 double negative and express an MHC-independent TCR repertoire. Furthermore, we identify a second MHC-independent population of CD103hi CD4/ CD8 double-negative αβ T cells in the dermis of Tcrd-/- mice.
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Affiliation(s)
- Christoph Binz
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Anja Bubke
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Inga Sandrock
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Immo Prinz
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,Institute of Systems Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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45
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Barthlott T, Handel AE, Teh HY, Wirasinha RC, Hafen K, Žuklys S, Roch B, Orkin SH, de Villartay JP, Daley SR, Holländer GA. Indispensable epigenetic control of thymic epithelial cell development and function by polycomb repressive complex 2. Nat Commun 2021; 12:3933. [PMID: 34168132 PMCID: PMC8225857 DOI: 10.1038/s41467-021-24158-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Thymic T cell development and T cell receptor repertoire selection are dependent on essential molecular cues provided by thymic epithelial cells (TEC). TEC development and function are regulated by their epigenetic landscape, in which the repressive H3K27me3 epigenetic marks are catalyzed by polycomb repressive complex 2 (PRC2). Here we show that a TEC-targeted deficiency of PRC2 function results in a hypoplastic thymus with reduced ability to express antigens and select a normal repertoire of T cells. The absence of PRC2 activity reveals a transcriptomically distinct medullary TEC lineage that incompletely off-sets the shortage of canonically-derived medullary TEC whereas cortical TEC numbers remain unchanged. This alternative TEC development is associated with the generation of reduced TCR diversity. Hence, normal PRC2 activity and placement of H3K27me3 marks are required for TEC lineage differentiation and function and, in their absence, the thymus is unable to compensate for the loss of a normal TEC scaffold.
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Affiliation(s)
- Thomas Barthlott
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Adam E Handel
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Hong Ying Teh
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
| | - Katrin Hafen
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Saulius Žuklys
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland
| | - Benoit Roch
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stuart H Orkin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Jean-Pierre de Villartay
- Genome Dynamics in the Immune System Laboratory, INSERM UMR 1163, Université de Paris, Imagine Institute, Paris, France
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
- School of Health and Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Georg A Holländer
- Department of Biomedicine and University Children's Hospital of Basel, University of Basel, Basel, Switzerland.
- Department of Paediatrics and the Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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46
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Structures suggest an approach for converting weak self-peptide tumor antigens into superagonists for CD8 T cells in cancer. Proc Natl Acad Sci U S A 2021; 118:2100588118. [PMID: 34074778 PMCID: PMC8201969 DOI: 10.1073/pnas.2100588118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Tumor vaccines using modified self-antigens that structurally enhance T cell receptor–peptide–major histocompatibility complex interactions greatly improve a T cell protective response against the tumor’s unmodified self-antigen. X-ray crystal structures of these interactions explain how the native and modified peptides can interact with the same T cell receptor, but with different affinities and abilities to drive T cell proliferation and differentiation. Tumors frequently express unmutated self-tumor–associated antigens (self-TAAs). However, trial results using self-TAAs as vaccine targets against cancer are mixed, often attributed to deletion of T cells with high-affinity receptors (TCRs) for self-TAAs during T cell development. Mutating these weak self-TAAs to produce higher affinity, effective vaccines is challenging, since the mutations may not benefit all members of the broad self-TAA–specific T cell repertoire. We previously identified a common weak murine self-TAA that we converted to a highly effective antitumor vaccine by a single amino acid substitution. In this case the modified and natural self-TAAs still raised very similar sets of CD8 T cells. Our structural studies herein show that the modification of the self-TAA resulted in a subtle change in the major histocompatibility complex I–TAA structure. This amino acid substitution allowed a dramatic conformational change in the peptide during subsequent TCR engagement, creating a large increase in TCR affinity and accounting for the efficacy of the modified self-TAA as a vaccine. These results show that carefully selected, well-characterized modifications to a poorly immunogenic self-TAA can rescue the immune response of the large repertoire of weakly responding natural self-TAA–specific CD8 T cells, driving them to proliferate and differentiate into functional effectors. Subsequently, the unmodified self-TAA on the tumor cells, while unable to drive this response, is nevertheless a sufficient target for the CD8 cytotoxic effectors. Our results suggest a pathway for more efficiently identifying variants of common self-TAAs, which could be useful in vaccine development, complementing other current nonantigen-specific immunotherapies.
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47
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Fulford TS, Grumont R, Wirasinha RC, Ellis D, Barugahare A, Turner SJ, Naeem H, Powell D, Lyons PA, Smith KGC, Scheer S, Zaph C, Klein U, Daley SR, Gerondakis S. c-Rel employs multiple mechanisms to promote the thymic development and peripheral function of regulatory T cells in mice. Eur J Immunol 2021; 51:2006-2026. [PMID: 33960413 DOI: 10.1002/eji.202048900] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 03/12/2021] [Accepted: 05/05/2021] [Indexed: 01/03/2023]
Abstract
The NF-κB transcription factor c-Rel is a critical regulator of Treg ontogeny, controlling multiple points of the stepwise developmental pathway. Here, we found that the thymic Treg defect in c-Rel-deficient (cRel-/- ) mice is quantitative, not qualitative, based on analyses of TCR repertoire and TCR signaling strength. However, these parameters are altered in the thymic Treg-precursor population, which is also markedly diminished in cRel-/- mice. Moreover, c-Rel governs the transcriptional programme of both thymic and peripheral Tregs, controlling a core of genes involved with immune signaling, and separately in the periphery, cell cycle progression. Last, the immune suppressive function of peripheral cRel-/- tTregs is diminished in a lymphopenic model of T cell proliferation and is associated with decreased stability of Foxp3 expression. Collectively, we show that c-Rel is a transcriptional regulator that controls multiple aspects of Treg development, differentiation, and function via distinct mechanisms.
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Affiliation(s)
- Thomas S Fulford
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Raelene Grumont
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Darcy Ellis
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Adele Barugahare
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Monash Bioinformatics Platform, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - Stephen J Turner
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia.,Department of Microbiology, Monash University, Melbourne, Australia
| | - Haroon Naeem
- Monash Bioinformatics Platform, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - David Powell
- Monash Bioinformatics Platform, School of Biomedical Sciences, Monash University, Melbourne, Australia
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, England, UK.,Department of Medicine, University of Cambridge, University of Cambridge School of Clinical Medicine, Cambridge, England, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, England, UK.,Department of Medicine, University of Cambridge, University of Cambridge School of Clinical Medicine, Cambridge, England, UK
| | - Sebastian Scheer
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Colby Zaph
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Ulf Klein
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James's, University of Leeds, Leeds, LS2 7TF
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Steve Gerondakis
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
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48
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Bosticardo M, Pala F, Notarangelo LD. RAG deficiencies: Recent advances in disease pathogenesis and novel therapeutic approaches. Eur J Immunol 2021; 51:1028-1038. [PMID: 33682138 PMCID: PMC8325549 DOI: 10.1002/eji.202048880] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/13/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022]
Abstract
The RAG1 and RAG2 proteins initiate the process of V(D)J recombination and therefore play an essential role in adaptive immunity. While null mutations in the RAG genes cause severe combined immune deficiency with lack of T and B cells (T- B- SCID) and susceptibility to life-threatening, early-onset infections, studies in humans and mice have demonstrated that hypomorphic RAG mutations are associated with defects of central and peripheral tolerance resulting in immune dysregulation. In this review, we provide an overview of the extended spectrum of RAG deficiencies and their associated clinical and immunological phenotypes in humans. We discuss recent advances in the mechanisms that control RAG expression and function, the effects of perturbed RAG activity on lymphoid development and immune homeostasis, and propose novel approaches to correct this group of disorders.
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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49
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Gao A, Chen Z, Amitai A, Doelger J, Mallajosyula V, Sundquist E, Pereyra Segal F, Carrington M, Davis MM, Streeck H, Chakraborty AK, Julg B. Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2. iScience 2021; 24:102311. [PMID: 33748696 PMCID: PMC7956900 DOI: 10.1016/j.isci.2021.102311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/22/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
We describe a physics-based learning model for predicting the immunogenicity of cytotoxic T lymphocyte (CTL) epitopes derived from diverse pathogens including SARS-CoV-2. The model was trained and optimized on the relative immunodominance of CTL epitopes in human immunodeficiency virus infection. Its accuracy was tested against experimental data from patients with COVID-19. Our model predicts that only some SARS-CoV-2 epitopes predicted to bind to HLA molecules are immunogenic. The immunogenic CTL epitopes across all SARS-CoV-2 proteins are predicted to provide broad population coverage, but those from the SARS-CoV-2 spike protein alone are unlikely to do so. Our model also predicts that several immunogenic SARS-CoV-2 CTL epitopes are identical to seasonal coronaviruses circulating in the population and such cross-reactive CD8+ T cells can indeed be detected in prepandemic blood donors, suggesting that some level of CTL immunity against COVID-19 may be present in some individuals before SARS-CoV-2 infection.
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Affiliation(s)
- Ang Gao
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zhilin Chen
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | - Assaf Amitai
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Julia Doelger
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Emily Sundquist
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
| | | | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Mark M. Davis
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Hendrik Streeck
- Institut für Virologie, Universitätsklinikum Bonn, 53127 Bonn, Germany
| | - Arup K. Chakraborty
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Boris Julg
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, 400 Technology Sq., Cambridge, MA 02139, USA
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50
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Lo WL, Weiss A. Adapting T Cell Receptor Ligand Discrimination Capability via LAT. Front Immunol 2021; 12:673196. [PMID: 33936119 PMCID: PMC8085316 DOI: 10.3389/fimmu.2021.673196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Self- and non-self ligand discrimination is a core principle underlying T cell-mediated immunity. Mature αβ T cells can respond to a foreign peptide ligand presented by major histocompatibility complex molecules (pMHCs) on antigen presenting cells, on a background of continuously sensed self-pMHCs. How αβ T cells can properly balance high sensitivity and high specificity to foreign pMHCs, while surrounded by a sea of self-peptide ligands is not well understood. Such discrimination cannot be explained solely by the affinity parameters of T cell antigen receptor (TCR) and pMHC interaction. In this review, we will discuss how T cell ligand discrimination may be molecularly defined by events downstream of the TCR-pMHC interaction. We will discuss new evidence in support of the kinetic proofreading model of TCR ligand discrimination, and in particular how the kinetics of specific phosphorylation sites within the adaptor protein linker for activation of T cells (LAT) determine the outcome of TCR signaling. In addition, we will discuss emerging data regarding how some kinases, including ZAP-70 and LCK, may possess scaffolding functions to more efficiently direct their kinase activities.
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Affiliation(s)
- Wan-Lin Lo
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Arthur Weiss
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Arthritis Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, United States
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