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Johnson MB, Ogishi M, Domingo-Vila C, De Franco E, Wakeling MN, Imane Z, Resnick B, Williams E, Galão RP, Caswell R, Russ-Silsby J, Seeleuthner Y, Rinchai D, Fagniez I, Benson B, Dufort MJ, Speake C, Smithmyer ME, Hudson M, Dobbs R, Quandt Z, Hattersley AT, Zhang P, Boisson-Dupuis S, Anderson MS, Casanova JL, Tree TI, Oram RA. Human inherited PD-L1 deficiency is clinically and immunologically less severe than PD-1 deficiency. J Exp Med 2024; 221:e20231704. [PMID: 38634869 PMCID: PMC11032109 DOI: 10.1084/jem.20231704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/16/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
We previously reported two siblings with inherited PD-1 deficiency who died from autoimmune pneumonitis at 3 and 11 years of age after developing other autoimmune manifestations, including type 1 diabetes (T1D). We report here two siblings, aged 10 and 11 years, with neonatal-onset T1D (diagnosed at the ages of 1 day and 7 wk), who are homozygous for a splice-site variant of CD274 (encoding PD-L1). This variant results in the exclusive expression of an alternative, loss-of-function PD-L1 protein isoform in overexpression experiments and in the patients' primary leukocytes. Surprisingly, cytometric immunophenotyping and single-cell RNA sequencing analysis on blood leukocytes showed largely normal development and transcriptional profiles across lymphoid and myeloid subsets in the PD-L1-deficient siblings, contrasting with the extensive dysregulation of both lymphoid and myeloid leukocyte compartments in PD-1 deficiency. Our findings suggest that PD-1 and PD-L1 are essential for preventing early-onset T1D but that, unlike PD-1 deficiency, PD-L1 deficiency does not lead to fatal autoimmunity with extensive leukocytic dysregulation.
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Affiliation(s)
- Matthew B. Johnson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Clara Domingo-Vila
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Elisa De Franco
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Matthew N. Wakeling
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Zineb Imane
- Faculty of Medicine and Pharmacy, Mohammed 5 University of Rabat, Rabat, Morocco
| | - Brittany Resnick
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Evangelia Williams
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Rui Pedro Galão
- Department of Infectious Diseases, School of Immunobiology and Microbial Sciences, Kings College London, London, UK
| | - Richard Caswell
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - James Russ-Silsby
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Darawan Rinchai
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Iris Fagniez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Basilin Benson
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Matthew J. Dufort
- Center for Systems Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Cate Speake
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Megan E. Smithmyer
- Center for Interventional Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Michelle Hudson
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Rebecca Dobbs
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
- National Institute for Health and Care Research Exeter Clinical Research Facility, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Zoe Quandt
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Andrew T. Hattersley
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stephanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
| | - Mark S. Anderson
- Endocrine Division, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France
- Imagine Institute, Paris Cité University, Paris, France
- Department of Pediatrics, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, NY, USA
| | - Timothy I. Tree
- Department of Immunobiology, School of Immunology and Microbial Sciences, Kings College London, London, UK
| | - Richard A. Oram
- Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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2
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Waterman HR, Dufort MJ, Posso SE, Ni M, Li LZ, Zhu C, Raj P, Smith KD, Buckner JH, Hamerman JA. Lupus IgA1 autoantibodies synergize with IgG to enhance pDC responses to RNA-containing immune complexes. bioRxiv 2024:2023.09.07.556743. [PMID: 37745328 PMCID: PMC10515763 DOI: 10.1101/2023.09.07.556743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Autoantibodies to nuclear antigens are hallmarks of the autoimmune disease systemic lupus erythematosus (SLE) where they contribute to pathogenesis. However, there remains a gap in our knowledge regarding how different isotypes of autoantibodies contribute to disease, including the production of the critical type I interferon (IFN) cytokines by plasmacytoid dendritic cells (pDCs) in response to immune complexes (ICs). We focused on IgA, which is the second most prevalent isotype in serum, and along with IgG is deposited in glomeruli in lupus nephritis. Here, we show that individuals with SLE have IgA autoantibodies against most nuclear antigens, correlating with IgG against the same antigen. We investigated whether IgA autoantibodies against a major SLE autoantigen, Smith ribonucleoproteins (Sm/RNPs), play a role in IC activation of pDCs. We found that pDCs express the IgA-specific Fc receptor, FcαR, and there was a striking ability of IgA1 autoantibodies to synergize with IgG in RNA-containing ICs to generate robust pDC IFNα responses. pDC responses to these ICs required both FcαR and FcγRIIa, showing a potent synergy between these Fc receptors. Sm/RNP IC binding to and internalization by pDCs were greater when ICs contained both IgA1 and IgG. pDCs from individuals with SLE had higher binding of IgA1-containing ICs and higher expression of FcαR than pDCs from healthy control individuals. Whereas pDC FcαR expression correlated with blood ISG signature in SLE, TLR7 agonists, but not IFNα, upregulated pDC FcαR expression in vitro. Together, we show a new mechanism by which IgA1 autoantibodies contribute to SLE pathogenesis.
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Affiliation(s)
- Hayley R. Waterman
- Molecular and Cell Biology Program, University of Washington; Seattle, USA
- Center for Fundamental Immunology, Benaroya Research Institute; Seattle, USA
| | - Matthew J. Dufort
- Center for Systems Immunology, Benaroya Research Institute; Seattle, USA
| | - Sylvia E. Posso
- Center for Translational Immunology, Benaroya Research Institute
| | - Minjian Ni
- Center for Fundamental Immunology, Benaroya Research Institute; Seattle, USA
| | - Lucy Z. Li
- Molecular and Cell Biology Program, University of Washington; Seattle, USA
- Center for Fundamental Immunology, Benaroya Research Institute; Seattle, USA
| | - Chengsong Zhu
- Department of Immunology, Microarray and Immune Phenotyping Core Facility, University of Texas Southwestern Medical Center; Dallas, USA
| | - Prithvi Raj
- Department of Immunology, Microarray and Immune Phenotyping Core Facility, University of Texas Southwestern Medical Center; Dallas, USA
| | - Kelly D. Smith
- Department of Laboratory Medicine and Pathology, University of Washington; Seattle, USA
| | - Jane H. Buckner
- Center for Translational Immunology, Benaroya Research Institute
| | - Jessica A. Hamerman
- Molecular and Cell Biology Program, University of Washington; Seattle, USA
- Center for Fundamental Immunology, Benaroya Research Institute; Seattle, USA
- Department of Immunology, University of Washington; Seattle, USA
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3
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Doni Jayavelu N, Altman MC, Benson B, Dufort MJ, Vanderwall ER, Rich LM, White MP, Becker PM, Togias A, Jackson DJ, Debley JS. Type 2 inflammation reduces SARS-CoV-2 replication in the airway epithelium in allergic asthma through functional alteration of ciliated epithelial cells. J Allergy Clin Immunol 2023; 152:56-67. [PMID: 37001649 PMCID: PMC10052850 DOI: 10.1016/j.jaci.2023.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/05/2023] [Accepted: 03/23/2023] [Indexed: 03/31/2023]
Abstract
BACKGROUND Despite well-known susceptibilities to other respiratory viral infections, individuals with allergic asthma have shown reduced susceptibility to severe coronavirus disease 2019 (COVID-19). OBJECTIVE We sought to identify mechanisms whereby type 2 inflammation in the airway protects against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by using bronchial airway epithelial cells (AECs) from aeroallergen-sensitized children with asthma and healthy nonsensitized children. METHODS We measured SARS-CoV-2 replication and ACE2 protein and performed bulk and single-cell RNA sequencing of ex vivo infected AEC samples with SARS-CoV-2 infection and with or without IL-13 treatment. RESULTS We observed that viral replication was lower in AECs from children with allergic asthma than those from in healthy nonsensitized children and that IL-13 treatment reduced viral replication only in children with allergic asthma and not in healthy children. Lower viral transcript levels were associated with a downregulation of functional pathways of the ciliated epithelium related to differentiation as well as cilia and axoneme production and function, rather than lower ACE2 expression or increases in goblet cells or mucus secretion pathways. Moreover, single-cell RNA sequencing identified specific subsets of relatively undifferentiated ciliated epithelium (which are common in allergic asthma and highly responsive to IL-13) that directly accounted for impaired viral replication. CONCLUSION Our results identify a novel mechanism of innate protection against SARS-CoV-2 in allergic asthma that provides important molecular and clinical insights during the ongoing COVID-19 pandemic.
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Affiliation(s)
- Naresh Doni Jayavelu
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | - Matthew C Altman
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash; Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Wash.
| | - Basilin Benson
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Wash
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, Wash
| | - Elizabeth R Vanderwall
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Lucille M Rich
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Maria P White
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, Md
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, Md
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Jason S Debley
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash; Department of Pediatrics, Division of Pulmonary and Sleep Medicine, Seattle Children's Hospital, University of Washington, Seattle, Wash
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4
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Speake C, Habib T, Lambert K, Hundhausen C, Lord S, Dufort MJ, Skinner SO, Hu A, Kinsman M, Jones BE, Maerz MD, Tatum M, Hocking AM, Nepom GT, Greenbaum CJ, Buckner JH. IL-6-targeted therapies to block the cytokine or its receptor drive distinct alterations in T cell function. JCI Insight 2022; 7:159436. [PMID: 36282595 DOI: 10.1172/jci.insight.159436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 10/12/2022] [Indexed: 12/15/2022] Open
Abstract
Therapeutics that inhibit IL-6 at different points in its signaling pathway are in clinical use, yet whether the immunological effects of these interventions differ based on their molecular target is unknown. We performed short-term interventions in individuals with type 1 diabetes using anti-IL-6 (siltuximab) or anti-IL-6 receptor (IL-6R; tocilizumab) therapies and investigated the impact of this in vivo blockade on T cell fate and function. Immune outcomes were influenced by the target of the therapeutic intervention (IL-6 versus IL-6R) and by peak drug concentration. Tocilizumab reduced ICOS expression on T follicular helper cell populations and T cell receptor-driven (TCR-driven) STAT3 phosphorylation. Siltuximab reversed resistance to Treg-mediated suppression and increased TCR-driven phosphorylated STAT3 and production of IL-10, IL-21, and IL-27 by T effectors. Together, these findings indicate that the context of IL-6 blockade in vivo drives distinct T cell-intrinsic changes that may influence therapeutic outcomes.
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Affiliation(s)
| | | | | | | | | | | | | | - Alex Hu
- Center for Systems Immunology, and
| | | | | | | | | | | | - Gerald T Nepom
- Immune Tolerance Network, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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5
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Woodward Davis AS, Roozen HN, Dufort MJ, DeBerg HA, Delaney MA, Mair F, Erickson JR, Slichter CK, Berkson JD, Klock AM, Mack M, Lwo Y, Ko A, Brand RM, McGowan I, Linsley PS, Dixon DR, Prlic M. The human tissue-resident CCR5 + T cell compartment maintains protective and functional properties during inflammation. Sci Transl Med 2020; 11:11/521/eaaw8718. [PMID: 31801887 DOI: 10.1126/scitranslmed.aaw8718] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 07/19/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022]
Abstract
CCR5 is thought to play a central role in orchestrating migration of cells in response to inflammation. CCR5 antagonists can reduce inflammatory disease processes, which has led to an increased interest in using CCR5 antagonists in a wide range of inflammation-driven diseases. Paradoxically, these antagonists appear to function without negatively affecting host immunity at barrier sites. We reasoned that the resolution to this paradox may lie in the CCR5+ T cell populations that permanently reside in tissues. We used a single-cell analysis approach to examine the human CCR5+ T cell compartment in the blood, healthy, and inflamed mucosal tissues to resolve these seemingly contradictory observations. We found that 65% of the CD4 tissue-resident memory T (TRM) cell compartment expressed CCR5. These CCR5+ TRM cells were enriched in and near the epithelial layer and not only limited to TH1-type cells but also contained a large TH17-producing and a stable regulatory T cell population. The CCR5+ TRM compartment was stably maintained even in inflamed tissues including the preservation of TH17 and regulatory T cell populations. Further, using tissues from the CHARM-03 clinical trial, we found that CCR5+ TRM are preserved in human mucosal tissue during treatment with the CCR5 antagonist Maraviroc. Our data suggest that the human CCR5+ TRM compartment is functionally and spatially equipped to maintain barrier immunity even in the absence of CCR5-mediated, de novo T cell recruitment from the periphery.
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Affiliation(s)
- Amanda S Woodward Davis
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Hayley N Roozen
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Hannah A DeBerg
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Martha A Delaney
- Department of Comparative Medicine, University of Washington, Seattle, WA 98195, USA
| | - Florian Mair
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Jami R Erickson
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Chloe K Slichter
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA.,Department of Global Health, University of Washington, Seattle, WA 98195, USA
| | - Julia D Berkson
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA
| | - Alexis M Klock
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthias Mack
- Department of Internal Medicine-Nephrology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Yu Lwo
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Alexander Ko
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Rhonda M Brand
- Department of Internal Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.,Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Ian McGowan
- University of Miami Miller School of Medicine, Miami, FL 33136, USA.,Orion Biotechnology, Ottawa, ON, K1S 1N4, Canada
| | - Peter S Linsley
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Douglas R Dixon
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Martin Prlic
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA. .,Department of Global Health, University of Washington, Seattle, WA 98195, USA.,Department of Immunology, University of Washington, Seattle, WA 98109, USA
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6
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Rodrigues KB, Dufort MJ, Llibre A, Speake C, Rahman MJ, Bondet V, Quiel J, Linsley PS, Greenbaum CJ, Duffy D, Tarbell KV. Innate immune stimulation of whole blood reveals IFN-1 hyper-responsiveness in type 1 diabetes. Diabetologia 2020; 63:1576-1587. [PMID: 32500289 PMCID: PMC10091865 DOI: 10.1007/s00125-020-05179-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/17/2020] [Indexed: 01/05/2023]
Abstract
AIMS/HYPOTHESIS Self-antigen-specific T cell responses drive type 1 diabetes pathogenesis, but alterations in innate immune responses are also critical and not as well understood. Innate immunity in human type 1 diabetes has primarily been assessed via gene-expression analysis of unstimulated peripheral blood mononuclear cells, without the immune activation that could amplify disease-associated signals. Increased responsiveness in each of the two main innate immune pathways, driven by either type 1 IFN (IFN-1) or IL-1, have been detected in type 1 diabetes, but the dominant innate pathway is still unclear. This study aimed to determine the key innate pathway in type 1 diabetes and assess the whole blood immune stimulation assay as a tool to investigate this. METHODS The TruCulture whole blood ex vivo stimulation assay, paired with gene expression and cytokine measurements, was used to characterise changes in the stimulated innate immune response in type 1 diabetes. We applied specific cytokine-induced signatures to our data, pre-defined from the same assays measured in a separate cohort of healthy individuals. In addition, NOD mice were stimulated with CpG and monocyte gene expression was measured. RESULTS Monocytes from NOD mice showed lower baseline vs diabetes-resistant B6.g7 mice, but higher induced IFN-1-associated gene expression. In human participants, ex vivo whole blood stimulation revealed higher induced IFN-1 responses in type 1 diabetes, as compared with healthy control participants. In contrast, neither the IL-1-induced gene signature nor response to the adaptive immune stimulant Staphylococcal enterotoxin B were significantly altered in type 1 diabetes samples vs healthy control participants. Targeted gene-expression analysis showed that this enhanced IFN response was specific to IFN-1, as IFN-γ-driven responses were not significantly different. CONCLUSIONS/INTERPRETATION Our study identifies increased responsiveness to IFN-1 as a feature of both the NOD mouse model of autoimmune diabetes and human established type 1 diabetes. A stimulated IFN-1 gene signature may be a potential biomarker for type 1 diabetes and used to evaluate the effects of therapies targeting this pathway. DATA AVAILABILITY Mouse gene expression data are found in the gene expression omnibus (GEO) repository, accession GSE146452 ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146452 ). Nanostring count data from the human experiments were deposited in the GEO repository, accession GSE146338 ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146338 ). Data files and R code for all analyses are available at https://github.com/rodriguesk/T1D_truculture_diabetologia . Graphical abstract.
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Affiliation(s)
- Kameron B Rodrigues
- Immune Tolerance Section, Diabetes Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
- Pathology Department, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Alba Llibre
- Immunobiology of Dendritic Cells/Inserm U1223, Département d'Immunologie, Institut Pasteur, 25 rue de Dr. Roux, 75724, Paris, France
| | - Cate Speake
- Diabetes Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - M Jubayer Rahman
- Immune Tolerance Section, Diabetes Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Vincent Bondet
- Immunobiology of Dendritic Cells/Inserm U1223, Département d'Immunologie, Institut Pasteur, 25 rue de Dr. Roux, 75724, Paris, France
| | - Juan Quiel
- Immune Tolerance Section, Diabetes Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Peter S Linsley
- Systems Immunology Division, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Carla J Greenbaum
- Diabetes Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Darragh Duffy
- Immunobiology of Dendritic Cells/Inserm U1223, Département d'Immunologie, Institut Pasteur, 25 rue de Dr. Roux, 75724, Paris, France.
| | - Kristin V Tarbell
- Immune Tolerance Section, Diabetes Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
- Amgen Discovery Research, 1120 Veterans Blvd, South San Francisco, CA, 94080, USA.
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7
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Wiedeman AE, Muir VS, Rosasco MG, DeBerg HA, Presnell S, Haas B, Dufort MJ, Speake C, Greenbaum CJ, Serti E, Nepom GT, Blahnik G, Kus AM, James EA, Linsley PS, Long SA. Autoreactive CD8+ T cell exhaustion distinguishes subjects with slow type 1 diabetes progression. J Clin Invest 2020; 130:480-490. [PMID: 31815738 PMCID: PMC6934185 DOI: 10.1172/jci126595] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 10/08/2019] [Indexed: 12/22/2022] Open
Abstract
Although most patients with type 1 diabetes (T1D) retain some functional insulin-producing islet β cells at the time of diagnosis, the rate of further β cell loss varies across individuals. It is not clear what drives this differential progression rate. CD8+ T cells have been implicated in the autoimmune destruction of β cells. Here, we addressed whether the phenotype and function of autoreactive CD8+ T cells influence disease progression. We identified islet-specific CD8+ T cells using high-content, single-cell mass cytometry in combination with peptide-loaded MHC tetramer staining. We applied a new analytical method, DISCOV-R, to characterize these rare subsets. Autoreactive T cells were phenotypically heterogeneous, and their phenotype differed by rate of disease progression. Activated islet-specific CD8+ memory T cells were prevalent in subjects with T1D who experienced rapid loss of C-peptide; in contrast, slow disease progression was associated with an exhaustion-like profile, with expression of multiple inhibitory receptors, limited cytokine production, and reduced proliferative capacity. This relationship between properties of autoreactive CD8+ T cells and the rate of T1D disease progression after onset make these phenotypes attractive putative biomarkers of disease trajectory and treatment response and reveal potential targets for therapeutic intervention.
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Affiliation(s)
| | | | | | | | | | | | | | - Cate Speake
- Diabetes Program, Benaroya Research Institute (BRI) at Virginia Mason, Seattle, Washington, USA
| | - Carla J. Greenbaum
- Diabetes Program, Benaroya Research Institute (BRI) at Virginia Mason, Seattle, Washington, USA
| | | | - Gerald T. Nepom
- Translational Research Program
- Immune Tolerance Network (ITN), Bethesda, Maryland, USA
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8
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Speake C, Skinner SO, Berel D, Whalen E, Dufort MJ, Young WC, Odegard JM, Pesenacker AM, Gorus FK, James EA, Levings MK, Linsley PS, Akirav EM, Pugliese A, Hessner MJ, Nepom GT, Gottardo R, Long SA. A composite immune signature parallels disease progression across T1D subjects. JCI Insight 2019; 4:126917. [PMID: 31671072 PMCID: PMC6962023 DOI: 10.1172/jci.insight.126917] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 10/29/2019] [Indexed: 02/06/2023] Open
Abstract
At diagnosis, most people with type 1 diabetes (T1D) produce measurable levels of endogenous insulin, but the rate at which insulin secretion declines is heterogeneous. To explain this heterogeneity, we sought to identify a composite signature predictive of insulin secretion, using a collaborative assay evaluation and analysis pipeline that incorporated multiple cellular and serum measures reflecting β cell health and immune system activity. The ability to predict decline in insulin secretion would be useful for patient stratification for clinical trial enrollment or therapeutic selection. Analytes from 12 qualified assays were measured in shared samples from subjects newly diagnosed with T1D. We developed a computational tool (DIFAcTO, Data Integration Flexible to Account for different Types of data and Outcomes) to identify a composite panel associated with decline in insulin secretion over 2 years following diagnosis. DIFAcTO uses multiple filtering steps to reduce data dimensionality, incorporates error estimation techniques including cross-validation and sensitivity analysis, and is flexible to assay type, clinical outcome, and disease setting. Using this novel analytical tool, we identified a panel of immune markers that, in combination, are highly associated with loss of insulin secretion. The methods used here represent a potentially novel process for identifying combined immune signatures that predict outcomes relevant for complex and heterogeneous diseases like T1D.
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Affiliation(s)
- Cate Speake
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Samuel O. Skinner
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Dror Berel
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Elizabeth Whalen
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Matthew J. Dufort
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - William Chad Young
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jared M. Odegard
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Anne M. Pesenacker
- University of British Columbia BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Frans K. Gorus
- Diabetes Research Center, Medical School and University Hospital (UZ Brussel), Brussels Free University Vrije Universiteit Brussel, Brussels, Belgium
| | - Eddie A. James
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Megan K. Levings
- University of British Columbia BC Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Peter S. Linsley
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Eitan M. Akirav
- Research Institute, Islet Biology, New York University Winthrop Hospital, Mineola, New York, USA
- Stony Brook University School of Medicine, Stony Brook, New York, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Department of Medicine, Division of Diabetes Endocrinology and Metabolism, Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | | | - Gerald T. Nepom
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
- Immune Tolerance Network, Bethesda, Maryland, USA
| | - Raphael Gottardo
- Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - S. Alice Long
- Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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Herold KC, Bundy BN, Long SA, Bluestone JA, DiMeglio LA, Dufort MJ, Gitelman SE, Gottlieb PA, Krischer JP, Linsley PS, Marks JB, Moore W, Moran A, Rodriguez H, Russell WE, Schatz D, Skyler JS, Tsalikian E, Wherrett DK, Ziegler AG, Greenbaum CJ. An Anti-CD3 Antibody, Teplizumab, in Relatives at Risk for Type 1 Diabetes. N Engl J Med 2019; 381:603-613. [PMID: 31180194 PMCID: PMC6776880 DOI: 10.1056/nejmoa1902226] [Citation(s) in RCA: 508] [Impact Index Per Article: 101.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Type 1 diabetes is a chronic autoimmune disease that leads to destruction of insulin-producing beta cells and dependence on exogenous insulin for survival. Some interventions have delayed the loss of insulin production in patients with type 1 diabetes, but interventions that might affect clinical progression before diagnosis are needed. METHODS We conducted a phase 2, randomized, placebo-controlled, double-blind trial of teplizumab (an Fc receptor-nonbinding anti-CD3 monoclonal antibody) involving relatives of patients with type 1 diabetes who did not have diabetes but were at high risk for development of clinical disease. Patients were randomly assigned to a single 14-day course of teplizumab or placebo, and follow-up for progression to clinical type 1 diabetes was performed with the use of oral glucose-tolerance tests at 6-month intervals. RESULTS A total of 76 participants (55 [72%] of whom were ≤18 years of age) underwent randomization - 44 to the teplizumab group and 32 to the placebo group. The median time to the diagnosis of type 1 diabetes was 48.4 months in the teplizumab group and 24.4 months in the placebo group; the disease was diagnosed in 19 (43%) of the participants who received teplizumab and in 23 (72%) of those who received placebo. The hazard ratio for the diagnosis of type 1 diabetes (teplizumab vs. placebo) was 0.41 (95% confidence interval, 0.22 to 0.78; P = 0.006 by adjusted Cox proportional-hazards model). The annualized rates of diagnosis of diabetes were 14.9% per year in the teplizumab group and 35.9% per year in the placebo group. There were expected adverse events of rash and transient lymphopenia. KLRG1+TIGIT+CD8+ T cells were more common in the teplizumab group than in the placebo group. Among the participants who were HLA-DR3-negative, HLA-DR4-positive, or anti-zinc transporter 8 antibody-negative, fewer participants in the teplizumab group than in the placebo group had diabetes diagnosed. CONCLUSIONS Teplizumab delayed progression to clinical type 1 diabetes in high-risk participants. (Funded by the National Institutes of Health and others; ClinicalTrials.gov number, NCT01030861.).
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Affiliation(s)
- Kevan C Herold
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Brian N Bundy
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - S Alice Long
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Jeffrey A Bluestone
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Linda A DiMeglio
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Matthew J Dufort
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Stephen E Gitelman
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Peter A Gottlieb
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Jeffrey P Krischer
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Peter S Linsley
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Jennifer B Marks
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Wayne Moore
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Antoinette Moran
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Henry Rodriguez
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - William E Russell
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Desmond Schatz
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Jay S Skyler
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Eva Tsalikian
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Diane K Wherrett
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Anette-Gabriele Ziegler
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
| | - Carla J Greenbaum
- From the Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT (K.C.H.); the Departments of Epidemiology and Pediatrics, University of South Florida, Tampa (B.N.B., J.P.K., H.R.), the Department of Medicine, University of Miami, Miami (J.B.M., J.S.S.), and the Department of Pediatrics, University of Florida, Gainesville (D.S.) - all in Florida; Benaroya Research Institute, Seattle (S.A.L., M.J.D., P.S.L., C.J.G.); the Diabetes Center, University of California at San Francisco, San Francisco (J.A.B., S.E.G.); the Department of Pediatrics, Indiana University, Indianapolis (L.A.D.); the Barbara Davis Diabetes Center, University of Colorado, Anschultz (P.A.G.); Children's Mercy Hospital, Kansas City, MO (W.M.); the Department of Pediatrics, University of Minnesota, Minneapolis (A.M.); the Department of Pediatrics and Cell and Developmental Biology, Vanderbilt University, Nashville (W.E.R.); the Department of Pediatrics, University of Iowa, Iowa City (E.T.); the Hospital for Sick Children, University of Toronto, Toronto (D.K.W.); and Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany (A.-G.Z.)
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Linsley PS, Greenbaum CJ, Rosasco M, Presnell S, Herold KC, Dufort MJ. Elevated T cell levels in peripheral blood predict poor clinical response following rituximab treatment in new-onset type 1 diabetes. Genes Immun 2019; 20:293-307. [PMID: 29925930 PMCID: PMC6477779 DOI: 10.1038/s41435-018-0032-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/05/2018] [Accepted: 04/09/2018] [Indexed: 12/11/2022]
Abstract
Biologic treatment of type 1 diabetes (T1D) with agents including anti-CD3 (otelixizumab and teplizumab), anti-CD20 (rituximab), LFA3Ig (alafacept), and CTLA4Ig (abatacept) results in transient stabilization of insulin C-peptide, a surrogate for endogenous insulin secretion. With the goal of inducing more robust immune tolerance, we used systems biology approaches to elucidate mechanisms associated with C-peptide stabilization in clinical trial blood samples from new-onset T1D subjects treated with the B cell-depleting drug, rituximab. RNA sequencing (RNA-seq) analysis of whole-blood samples from this trial revealed a transient increase in heterogeneous T cell populations, which were associated with decreased pharmacodynamic activity of rituximab, increased proliferative responses to islet antigens, and more rapid C-peptide loss. Our findings illustrate complexity in hematopoietic remodeling that accompanies B cell depletion by rituximab, which impacts and predicts therapeutic efficacy in T1D. Our data also suggest that a combination of rituximab with therapy targeting CD4 + T cells may be beneficial for T1D subjects.
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Affiliation(s)
- Peter S Linsley
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA.
| | - Carla J Greenbaum
- Diabetes Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Mario Rosasco
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Scott Presnell
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
| | - Kevan C Herold
- Departments of Immunobiology and Internal Medicine, Yale University, New Haven, CT, 06520, USA
| | - Matthew J Dufort
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA, USA
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11
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Linsley PS, Greenbaum CJ, Speake C, Long SA, Dufort MJ. B lymphocyte alterations accompany abatacept resistance in new-onset type 1 diabetes. JCI Insight 2019; 4:126136. [PMID: 30830871 DOI: 10.1172/jci.insight.126136] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 01/17/2019] [Indexed: 02/06/2023] Open
Abstract
Costimulatory interactions control T cell activation at sites of activated antigen-presenting cells, including B cells. Blockade of the CD28/CD80/CD86 costimulatory axis with CTLA4Ig (abatacept) is widely used to treat certain autoimmune diseases. While transiently effective in subjects with new-onset type 1 diabetes (T1D), abatacept did not induce long-lasting immune tolerance. To elucidate mechanisms limiting immune tolerance in T1D, we performed unbiased analysis of whole blood transcriptomes and targeted measurements of cell subset levels in subjects from a clinical trial of abatacept in new-onset T1D. We showed that individual subjects displayed age-related immune phenotypes ("immunotypes") at baseline, characterized by elevated levels of B cells or neutrophils, that accompanied rapid or slow progression, respectively, in both abatacept- and placebo-treated groups. A more pronounced immunotype was exhibited by a subset of subjects showing poor response (resistance) to abatacept. This resistance immunotype was characterized by a transient increase in activated B cells (one of the cell types that binds abatacept), reprogrammed costimulatory ligand gene expression, and reduced inhibition of anti-insulin antibodies. Our findings identify immunotypes in T1D subjects that are linked to the rate of disease progression, both in placebo- and abatacept-treated subjects. Furthermore, our results suggest therapeutic approaches to restore immune tolerance in T1D.
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Affiliation(s)
| | | | | | - S Alice Long
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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12
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Dufort MJ, Greenbaum CJ, Speake C, Linsley PS. Cell type-specific immune phenotypes predict loss of insulin secretion in new-onset type 1 diabetes. JCI Insight 2019; 4:125556. [PMID: 30830868 DOI: 10.1172/jci.insight.125556] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 01/17/2019] [Indexed: 12/12/2022] Open
Abstract
The rate of decline in insulin secretion after diagnosis with type 1 diabetes (T1D) varies substantially among individuals and with age at diagnosis, but the mechanism(s) behind this heterogeneity are not well understood. We investigated the loss of pancreatic β cell function in new-onset T1D subjects using unbiased whole blood RNA-seq and verified key findings by targeted cell count measurements. We found that patients who lost insulin secretion more rapidly had immune phenotypes ("immunotypes") characterized by higher levels of B cells and lower levels of neutrophils, especially neutrophils expressing primary granule genes. The B cell and neutrophil immunotypes showed strong age dependence, with B cell levels in particular predicting rate of progression in young subjects only. This age relationship suggested that therapy targeting B cells in T1D would be most effective in young subjects with high pretreatment B cell levels, a prediction which was supported by data from a clinical trial of rituximab in new-onset subjects. These findings demonstrate a link between age-related immunotypes and disease outcome in new-onset T1D. Furthermore, our data suggest that greater success could be achieved by targeted use of immunomodulatory therapy in specific T1D populations defined by age and immune characteristics.
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Affiliation(s)
| | - Carla J Greenbaum
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Cate Speake
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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13
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Vecchio F, Lo Buono N, Stabilini A, Nigi L, Dufort MJ, Geyer S, Rancoita PM, Cugnata F, Mandelli A, Valle A, Leete P, Mancarella F, Linsley PS, Krogvold L, Herold KC, Elding Larsson H, Richardson SJ, Morgan NG, Dahl-Jørgensen K, Sebastiani G, Dotta F, Bosi E, Battaglia M. Abnormal neutrophil signature in the blood and pancreas of presymptomatic and symptomatic type 1 diabetes. JCI Insight 2018; 3:122146. [PMID: 30232284 DOI: 10.1172/jci.insight.122146] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 08/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Neutrophils and their inflammatory mediators are key pathogenic components in multiple autoimmune diseases, while their role in human type 1 diabetes (T1D), a disease that progresses sequentially through identifiable stages prior to the clinical onset, is not well understood. We previously reported that the number of circulating neutrophils is reduced in patients with T1D and in presymptomatic at-risk subjects. The aim of the present work was to identify possible changes in circulating and pancreas-residing neutrophils throughout the disease course to better elucidate neutrophil involvement in human T1D. METHODS Data collected from 389 subjects at risk of developing T1D, and enrolled in 4 distinct studies performed by TrialNet, were analyzed with comprehensive statistical approaches to determine whether the number of circulating neutrophils correlates with pancreas function. To obtain a broad analysis of pancreas-infiltrating neutrophils throughout all disease stages, pancreas sections collected worldwide from 4 different cohorts (i.e., nPOD, DiViD, Siena, and Exeter) were analyzed by immunohistochemistry and immunofluorescence. Finally, circulating neutrophils were purified from unrelated nondiabetic subjects and donors at various T1D stages and their transcriptomic signature was determined by RNA sequencing. RESULTS Here, we show that the decline in β cell function is greatest in individuals with the lowest peripheral neutrophil numbers. Neutrophils infiltrate the pancreas prior to the onset of symptoms and they continue to do so as the disease progresses. Of interest, a fraction of these pancreas-infiltrating neutrophils also extrudes neutrophil extracellular traps (NETs), suggesting a tissue-specific pathogenic role. Whole-transcriptome analysis of purified blood neutrophils revealed a unique molecular signature that is distinguished by an overabundance of IFN-associated genes; despite being healthy, said signature is already present in T1D-autoantibody-negative at-risk subjects. CONCLUSIONS These results reveal an unexpected abnormality in neutrophil disposition both in the circulation and in the pancreas of presymptomatic and symptomatic T1D subjects, implying that targeting neutrophils might represent a previously unrecognized therapeutic modality. FUNDING Juvenile Diabetes Research Foundation (JDRF), NIH, Diabetes UK.
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Affiliation(s)
- Federica Vecchio
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Lo Buono
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Angela Stabilini
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Nigi
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Matthew J Dufort
- Systems Immunology Division, Benaroya Research Institute, Seattle, Washington, USA
| | - Susan Geyer
- University of South Florida, TNCC, Tampa, Florida, USA
| | - Paola Maria Rancoita
- Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy
| | - Federica Cugnata
- Centre of Statistics for Biomedical Sciences (CUSSB), Vita-Salute San Raffaele University, Milan, Italy
| | - Alessandra Mandelli
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Valle
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Pia Leete
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Francesca Mancarella
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Peter S Linsley
- Systems Immunology Division, Benaroya Research Institute, Seattle, Washington, USA
| | - Lars Krogvold
- Pediatric Department, Oslo University Hospital HF, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kevan C Herold
- Departments of Immunobiology and Internal Medicine, Yale University, New Haven, Connecticut, USA
| | - Helena Elding Larsson
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital SUS, Malmo, Sweden
| | - Sarah J Richardson
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Noel G Morgan
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building Barrack Road, Exeter, Devon, United Kingdom
| | - Knut Dahl-Jørgensen
- Pediatric Department, Oslo University Hospital HF, Oslo, Norway; Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Guido Sebastiani
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Francesco Dotta
- Diabetes Unit, Department of Medicine, Surgery and Neuroscience, University of Siena, and Fondazione Umberto Di Mario ONLUS c/o Toscana Life Science, Siena, Italy
| | - Emanuele Bosi
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy, and the Department of Internal Medicine, IRCCS San Raffaele Hospital, Milan, Italy.,TrialNet Clinical Center, IRCCS San Raffaele Hospital, Milan, Italy
| | | | | | - Manuela Battaglia
- Diabetes Research Institute, IRCCS San Raffaele Scientific Institute, Milan, Italy.,TrialNet Clinical Center, IRCCS San Raffaele Hospital, Milan, Italy
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Cerosaletti K, Barahmand-Pour-Whitman F, Yang J, DeBerg HA, Dufort MJ, Murray SA, Israelsson E, Speake C, Gersuk VH, Eddy JA, Reijonen H, Greenbaum CJ, Kwok WW, Wambre E, Prlic M, Gottardo R, Nepom GT, Linsley PS. Single-Cell RNA Sequencing Reveals Expanded Clones of Islet Antigen-Reactive CD4 + T Cells in Peripheral Blood of Subjects with Type 1 Diabetes. J Immunol 2017; 199:323-335. [PMID: 28566371 DOI: 10.4049/jimmunol.1700172] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022]
Abstract
The significance of islet Ag-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects is unclear, partly because similar cells are also found in healthy control (HC) subjects. We hypothesized that key disease-associated cells would show evidence of prior Ag exposure, inferred from expanded TCR clonotypes, and essential phenotypic properties in their transcriptomes. To test this, we developed single-cell RNA sequencing procedures for identifying TCR clonotypes and transcript phenotypes in individual T cells. We applied these procedures to analysis of islet Ag-reactive CD4+ memory T cells from the blood of T1D and HC individuals after activation with pooled immunodominant islet peptides. We found extensive TCR clonotype sharing in Ag-activated cells, especially from individual T1D subjects, consistent with in vivo T cell expansion during disease progression. The expanded clonotype from one T1D subject was detected at repeat visits spanning >15 mo, demonstrating clonotype stability. Notably, we found no clonotype sharing between subjects, indicating a predominance of "private" TCR specificities. Expanded clones from two T1D subjects recognized distinct IGRP peptides, implicating this molecule as a trigger for CD4+ T cell expansion. Although overall transcript profiles of cells from HC and T1D subjects were similar, profiles from the most expanded clones were distinctive. Our findings demonstrate that islet Ag-reactive CD4+ memory T cells with unique Ag specificities and phenotypes are expanded during disease progression and can be detected by single-cell analysis of peripheral blood.
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Affiliation(s)
- Karen Cerosaletti
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101;
| | | | - Junbao Yang
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Hannah A DeBerg
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Matthew J Dufort
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Sara A Murray
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Elisabeth Israelsson
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Cate Speake
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Vivian H Gersuk
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - James A Eddy
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Helena Reijonen
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Carla J Greenbaum
- Diabetes Clinical Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - William W Kwok
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Erik Wambre
- Translational Research Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101
| | - Martin Prlic
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109; and
| | | | - Peter S Linsley
- Systems Immunology Program, Benaroya Research Institute at Virginia Mason, Seattle, WA 98101;
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Dufort MJ, Hanniffy S, Álvarez RC, Gorvel VA, Altman MC, Khaenam P, Solera J, Gersuk VH, Bosilkovski M, Moriyón I, Linsley PS, Gorvel JP. Gene expression profiles predict treatment outcomes in Brucellosis. The Journal of Immunology 2016. [DOI: 10.4049/jimmunol.196.supp.66.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Brucellosis is a zoonotic disease caused by Brucella bacteria, acquired by humans through contact with or consumption of products from infected animals. Treatment outcomes vary widely; some patients recover, others relapse, and others develop chronic symptoms despite therapy. We employed expression profiling using RNA sequencing (RNAseq) to better understand variation in outcomes and investigate disease mechanisms. We performed RNAseq analysis of whole blood samples from 125 Brucellosis patients and 51 healthy controls from Macedonia. Patients were subdivided based on disease history into primary, secondary, and chronic infection. Secondary and chronic cases did not show differences in gene expression from healthy controls or from each other. Primary cases displayed numerous transcriptional changes relative to healthy controls. Up-regulated genes were enriched for response to interferon-gamma, cytolysis, T cell proliferation, and cell cycle; down-regulated genes, for B cell proliferation. Primary cases were further subdivided based on outcome into those who resolved with treatment and those who developed disease relapse during treatment. In comparison to healthy controls, relapse cases showed larger magnitude differences in expression at diagnosis than resolution cases; this suggests that relapse could potentially be predicted based on transcription levels at time of diagnosis. Differences in gene expression observed at diagnosis were no longer present 6–9 months after diagnosis. Our results indicate opportunities to prognostically identify patients that may require more intensive treatment and monitoring, and to better understand the symptomology of and immune response to Brucella infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Mile Bosilkovski
- 5Univ. Clin. for Infectious Diseases and Febrile Conditions, Skopje, Rep. of Macedonia
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Dufort MJ. An augmented supermatrix phylogeny of the avian family Picidae reveals uncertainty deep in the family tree. Mol Phylogenet Evol 2016; 94:313-26. [DOI: 10.1016/j.ympev.2015.08.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 08/22/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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Dufort MJ, Keith Barker F. Range dynamics, rather than convergent selection, explain the mosaic distribution of red-winged blackbird phenotypes. Ecol Evol 2013; 3:4910-24. [PMID: 24455125 PMCID: PMC3892357 DOI: 10.1002/ece3.859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 09/26/2013] [Accepted: 09/30/2013] [Indexed: 11/24/2022] Open
Abstract
Geographic distributions of genetic and phenotypic characters can illuminate historical evolutionary processes. In particular, mosaic distributions of phenotypically similar populations can arise from parallel evolution or from irregular patterns of dispersal and colonization by divergent forms. Two phenotypically divergent forms of the red-winged blackbird (Agelaius phoeniceus) show a mosaic phenotypic distribution, with a "bicolored" form occurring disjunctly in California and Mexico. We analyzed the relationships among these bicolored populations and neighboring typical populations, using ∼600 bp of mitochondrial DNA sequence data and 10 nuclear short tandem repeat loci. We find that bicolored populations, although separated by ∼3000 km, are genetically more similar to one other than they are to typical populations separated by ∼400 km. We also find evidence of ongoing gene flow among populations, including some evidence of asymmetric gene flow. We conclude that the current distribution of bicolored forms represents incomplete speciation, where recent asymmetric hybridization with typical A. phoeniceus is dividing the range of a formerly widespread bicolored form. This hypothesis predicts that bicolored forms may suffer extinction by hybridization. Future work will use fine-scaled geographical sampling and nuclear sequence data to test for hybrid origins of currently typical populations and to more precisely quantify the directionality of gene flow.
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Affiliation(s)
- Matthew J Dufort
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
| | - F Keith Barker
- Department of Ecology, Evolution and Behavior, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108 ; Bell Museum of Natural History, University of Minnesota 100 Ecology Building, 1987 Upper Buford Circle, Saint Paul, Minnesota, 55108
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Barker FK, Bell JJ, Bogdanowicz SM, Bonatto SL, Cezilly F, Collins SM, Dubreuil C, Dufort MJ, Eraud C, Fuseya R, Heap EA, Jacobsen N, Madders M, McEwing R, Michel AP, Mougeot F, Ogden RS, Orantes LC, Othman AS, Parent E, Pulido-Santacruz P, Rioux-Paré R, Roberts MF, Rosazlina R, Sakamoto T, De-León PS, Sévigny JM, St-Onge P, Terraube J, Tingay RE, Tremblay R, Watanabe S, Wattier RA. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 June 2011-31 July 2011. Mol Ecol Resour 2011; 11:1124-6. [PMID: 21951598 DOI: 10.1111/j.1755-0998.2011.03068.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This article documents the addition of 112 microsatellite marker loci and 24 pairs of single nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Agelaius phoeniceus, Austrolittorina cincta, Circus cyaneus, Circus macrourus, Circus pygargus, Cryptocoryne × purpurea Ridl. nothovar. purpurea, Mya arenaria, Patagioenas squamosa, Prochilodus mariae, Scylla serrata and Scytalopus speluncae. These loci were cross-tested on the following species: Cryptocoryne × purpurea nothovar. purpurea, Cryptocoryne affinis, Cryptocoryne ciliata, Cryptocoryne cordata var. cordata, Cryptocoryne elliptica, Cryptocoryne griffithii, Cryptocoryne minima, Cryptocoryne nurii and Cryptocoryne schulzei. This article also documents the addition of 24 sequencing primer pairs and 24 allele-specific primers or probes for Aphis glycines.
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Affiliation(s)
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- Department of Ecology, Evolution, and Behavior, University of Minnesota, 100 Ecology Building, 1987 Upper Buford Circle, St. Paul, MN 55108, USA
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