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Mittl K, Hayashi F, Dandekar R, Schubert RD, Gerdts J, Oshiro L, Loudermilk R, Greenfield A, Augusto DG, Ramesh A, Tran E, Koshal K, Kizer K, Dreux J, Cagalingan A, Schustek F, Flood L, Moore T, Kirkemo LL, Cooper T, Harms M, Gomez R, Sibener L, Cree BAC, Hauser SL, Hollenbach JA, Gee M, Wilson MR, Zamvil SS, Sabatino JJ. Antigen-specificity of clonally-enriched CD8+ T cells in multiple sclerosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.07.611010. [PMID: 39282370 PMCID: PMC11398516 DOI: 10.1101/2024.09.07.611010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
CD8+ T cells are the dominant lymphocyte population in multiple sclerosis (MS) lesions where they are highly clonally expanded. The clonal identity, function, and antigen specificity of CD8+ T cells in MS are not well understood. Here we report a comprehensive single-cell RNA-seq and T cell receptor (TCR)-seq analysis of the cerebrospinal fluid (CSF) and blood from a cohort of treatment-naïve MS patients and control participants. A small subset of highly expanded and activated CSF-enriched CD8+ T cells were abundant in people with MS and displayed high cytotoxicity and tissue-homing transcriptional profiles. Using a combination of unbiased and targeted antigen discovery approaches, several MS-derived CD8+ T cell clonotypes recognizing Epstein-Barr virus (EBV) antigens and novel mimotopes were identified. These findings shed insight into the functions of CD8+ T cells in MS and may serve as potential disease biomarkers and therapeutic targets.
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Affiliation(s)
- Kristen Mittl
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Fumie Hayashi
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ravi Dandekar
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ryan D Schubert
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Josiah Gerdts
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Lindsay Oshiro
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Rita Loudermilk
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Ariele Greenfield
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Danillo G Augusto
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, NC, USA
| | - Akshaya Ramesh
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Edwina Tran
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Kaniskha Koshal
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | | | | | | | | | | | | | - Tiffany Cooper
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Meagan Harms
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Refujia Gomez
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | | | - Bruce A C Cree
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Stephen L Hauser
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Jill A Hollenbach
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
| | | | - Michael R Wilson
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Scott S Zamvil
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Joseph J Sabatino
- UCSF Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
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2
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Arneth B. Current Knowledge about CD3 +CD20 + T Cells in Patients with Multiple Sclerosis. Int J Mol Sci 2024; 25:8987. [PMID: 39201672 PMCID: PMC11354236 DOI: 10.3390/ijms25168987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 08/16/2024] [Accepted: 08/18/2024] [Indexed: 09/03/2024] Open
Abstract
Multiple sclerosis (MS) is a disease of the central nervous system (CNS) characterized by inflammation and autoimmune responses. This review explores the participation of T cells, particularly certain CD3+CD20+ T cells, in the clinical manifestations of MS and highlights their presence in diagnosed patients. These T cells show aberrant expression of CD20, normally considered a B-cell marker. In this review, relevant journal articles available in PubMed and CINAHL were identified by employing diverse search terms, such as MS, CD3+CD20+ T cells, the incidence and significance of CD3+CD20+ T cells in MS patients, and the impact of rituximab treatment. The search was limited to articles published in the ten-year period from 2014 to 2024. The results of this review suggest that most scholars agree on the presence of CD3+CD20+ T cells in cerebrospinal fluid. Emerging concepts relate to the fundamental role of CD20-expressing T cells in determining the target and efficacy of MS therapeutics and the presence of T cells in the cerebrospinal fluid of MS patients. The results clearly show that CD20+ T cells indicate disease chronicity and high disease activity.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Hospital of the Universities of Giessen and Marburg (UKGM), Justus Liebig University Giessen, Feulgenstr. 12, 35392 Giessen, Germany;
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Hospital of the Universities of Giessen and Marburg (UKGM), Philipps University Marburg, Baldinger Str., 35043 Marburg, Germany
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3
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Martins-Ferreira R, Calafell-Segura J, Chaves J, Ciudad L, Martins da Silva A, Pinho e Costa P, Leal B, Ballestar E. Purinergic exposure induces epigenomic and transcriptomic-mediated preconditioning resembling epilepsy-associated microglial states. iScience 2024; 27:110546. [PMID: 39184445 PMCID: PMC11342283 DOI: 10.1016/j.isci.2024.110546] [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: 07/10/2023] [Revised: 03/10/2024] [Accepted: 07/16/2024] [Indexed: 08/27/2024] Open
Abstract
Microglia play a crucial role in a range of neuropathologies through exacerbated activation. Microglial inflammatory responses can be influenced by prior exposures to noxious stimuli, like increased levels of extracellular adenosine and ATP. These are characteristic of brain insults like epileptic seizures and could potentially shape subsequent responses through epigenetic regulation. We investigated DNA methylation and expression changes in human microglia-like cells differentiated from monocytes following ATP-mediated preconditioning. We demonstrate that microglia-like cells display homeostatic microglial features, shown by surface markers, transcriptome, and DNA methylome. After exposure to ATP, TLR-mediated activation leads to an exacerbated pro-inflammatory response. These changes are accompanied by methylation and transcriptional reprogramming associated with enhanced immune-related functions. The reprogramming associated with ATP-mediated preconditioning leads to profiles found in microglial subsets linked to epilepsy. Purine-driven microglia immune preconditioning drives epigenetic and transcriptional changes that could contribute to altered functions of microglia during seizure development and progression.
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Affiliation(s)
- Ricardo Martins-Ferreira
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Josep Calafell-Segura
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - João Chaves
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Neurology Service, Centro Hospitalar Universitário de Santo António (CHUdSA), 4099-001 Porto, Portugal
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
| | - António Martins da Silva
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Neurophysiology Service, CHUdSA 4099-001 Porto, Portugal
| | - Paulo Pinho e Costa
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
- Department of Human Genetics, Instituto Nacional de Saúde Dr. Ricardo Jorge 4000-055 Porto, Portugal
| | - Bárbara Leal
- Immunogenetics Laboratory, Molecular Pathology and Immunology Department, Instituto de Ciências Biomédicas Abel Salazar – Universidade do Porto (ICBAS-UPorto), 4050-313 Porto, Portugal
- Autoimmunity and Neuroscience Group. Unit for Multidisciplinary Research in Biomedicine, ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
- ITR - Laboratory for Integrative and Translational Research in Population Health, Porto, Portugal
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai 200241, China
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Yazdani S, Lovik A, Seitz C, Ingre C, Fang F, Andersson J. T cell subset composition differs between blood and cerebrospinal fluid in amyotrophic lateral sclerosis. Clin Immunol 2024; 265:110270. [PMID: 38852806 DOI: 10.1016/j.clim.2024.110270] [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: 03/06/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/11/2024]
Abstract
Inflammation is a hallmark of amyotrophic lateral sclerosis (ALS) and is often assessed through biological samples. Due to the easier access, peripheral blood is more commonly phenotyped instead of cerebrospinal fluid (CSF) or affected tissues in ALS. Here, using flow cytometry, we compared the composition of T cell subsets in blood and CSF in ALS patients. We found consistent but weak correlations between blood and CSF for all T cell subsets examined. This finding implies that blood and CSF offer complementary information when characterizing T cell immunity in ALS and blood may not be used as a surrogate for CSF.
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Affiliation(s)
- Solmaz Yazdani
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Anikó Lovik
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Institute of Psychology, Leiden University, Leiden, the Netherlands
| | - Christina Seitz
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Ingre
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden; Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Fang Fang
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - John Andersson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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5
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Tuong ZK, van der Merwe R, Canete PF, Roco JA. Computational estimation of clonal diversity in autoimmunity. Immunol Cell Biol 2024. [PMID: 39010261 DOI: 10.1111/imcb.12801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024]
Abstract
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single-cell T-cell receptor and B-cell receptor sequencing. We also discuss two case studies where single-cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
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Affiliation(s)
- Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rohan van der Merwe
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Canete
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
- Clinical Hub for Interventional Research, College of Health & Medicine, The Australian National University, Canberra, ACT, Australia
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6
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Hanin A, Zhang L, Huttner AJ, Plu I, Mathon B, Bielle F, Navarro V, Hirsch LJ, Hafler DA. Single-Cell Transcriptomic Analyses of Brain Parenchyma in Patients With New-Onset Refractory Status Epilepticus (NORSE). NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200259. [PMID: 38810181 PMCID: PMC11139018 DOI: 10.1212/nxi.0000000000200259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/25/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND AND OBJECTIVES New-onset refractory status epilepticus (NORSE) occurs in previously healthy children or adults, often followed by refractory epilepsy and poor outcomes. The mechanisms that transform a normal brain into an epileptic one capable of seizing for prolonged periods despite treatment remain unclear. Nonetheless, several pieces of evidence suggest that immune dysregulation could contribute to hyperexcitability and modulate NORSE sequelae. METHODS We used single-nucleus RNA sequencing to delineate the composition and phenotypic states of the CNS of 4 patients with NORSE, to better understand the relationship between hyperexcitability and immune disturbances. We compared them with 4 patients with chronic temporal lobe epilepsy (TLE) and 2 controls with no known neurologic disorder. RESULTS Patients with NORSE and TLE exhibited a significantly higher proportion of excitatory neurons compared with controls, with no discernible difference in inhibitory GABAergic neurons. When examining the ratio between excitatory neurons and GABAergic neurons for each patient individually, we observed a higher ratio in patients with acute NORSE or TLE compared with controls. Furthermore, a negative correlation was found between the ratio of excitatory to GABAergic neurons and the proportion of GABAergic neurons. The ratio between excitatory neurons and GABAergic neurons correlated with the proportion of resident or infiltrating macrophages, suggesting the influence of microglial reactivity on neuronal excitability. Both patients with NORSE and TLE exhibited increased expression of genes associated with microglia activation, phagocytic activity, and NLRP3 inflammasome activation. However, patients with NORSE had decreased expression of genes related to the downregulation of the inflammatory response, potentially explaining the severity of their presentation. Microglial activation in patients with NORSE also correlated with astrocyte reactivity, possibly leading to higher degrees of demyelination. DISCUSSION Our study sheds light on the complex cellular dynamics in NORSE, revealing the potential roles of microglia, infiltrating macrophages, and astrocytes in hyperexcitability and demyelination, offering potential avenues for future research targeting the identified pathways.
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Affiliation(s)
- Aurélie Hanin
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Le Zhang
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Anita J Huttner
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Isabelle Plu
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Bertrand Mathon
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Franck Bielle
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Vincent Navarro
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Lawrence J Hirsch
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David A Hafler
- From the Departments of Neurology and Immunobiology (A.H., L.Z., D.A.H.); Comprehensive Epilepsy Center (A.H., L.J.H.), Department of Neurology, Yale University School of Medicine, New Haven, CT; Sorbonne Université (A.H., I.P., B.M., V.N.), Institut du Cerveau - Paris Brain Institute - ICM, Inserm, CNRS, APHP; AP-HP (A.H., V.N.), Epilepsy Unit and Clinical Neurophysiology Department, DMU Neurosciences, Hôpital de la Pitié-Salpêtrière, Paris, France; Department of Pathology (A.J.H.), Yale University School of Medicine, New Haven, CT; AP-HP (I.P., F.B.), Department of Neuropathology, DMU Neurosciences; AP-HP (B.M.), Department of Neurosurgery, Hôpital de la Pitié-Salpêtrière; and Center of Reference for Rare Epilepsies (V.N.), EpiCare, Hôpital de la Pitié-Salpêtrière, Paris, France
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7
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Lu IN, Cheung PFY, Heming M, Thomas C, Giglio G, Leo M, Erdemir M, Wirth T, König S, Dambietz CA, Schroeter CB, Nelke C, Siveke JT, Ruck T, Klotz L, Haider C, Höftberger R, Kleinschnitz C, Wiendl H, Hagenacker T, Meyer Zu Horste G. Cell-mediated cytotoxicity within CSF and brain parenchyma in spinal muscular atrophy unaltered by nusinersen treatment. Nat Commun 2024; 15:4120. [PMID: 38750052 PMCID: PMC11096380 DOI: 10.1038/s41467-024-48195-3] [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: 06/15/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
5q-associated spinal muscular atrophy (SMA) is a motoneuron disease caused by mutations in the survival motor neuron 1 (SMN1) gene. Adaptive immunity may contribute to SMA as described in other motoneuron diseases, yet mechanisms remain elusive. Nusinersen, an antisense treatment, enhances SMN2 expression, benefiting SMA patients. Here we have longitudinally investigated SMA and nusinersen effects on local immune responses in the cerebrospinal fluid (CSF) - a surrogate of central nervous system parenchyma. Single-cell transcriptomics (SMA: N = 9 versus Control: N = 9) reveal NK cell and CD8+ T cell expansions in untreated SMA CSF, exhibiting activation and degranulation markers. Spatial transcriptomics coupled with multiplex immunohistochemistry elucidate cytotoxicity near chromatolytic motoneurons (N = 4). Post-nusinersen treatment, CSF shows unaltered protein/transcriptional profiles. These findings underscore cytotoxicity's role in SMA pathogenesis and propose it as a therapeutic target. Our study illuminates cell-mediated cytotoxicity as shared features across motoneuron diseases, suggesting broader implications.
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Affiliation(s)
- I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Phyllis Fung-Yi Cheung
- Spatiotemporal Tumor Heterogeneity, German Cancer Consortium (DKTK), Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, DKTK, Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
| | - Michael Heming
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Giovanni Giglio
- Spatiotemporal Tumor Heterogeneity, German Cancer Consortium (DKTK), Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, DKTK, Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
| | - Markus Leo
- Department of Neurology and Center for Translational Neuro and Behavioral Science, University Hospital Essen, Essen, Germany
| | - Merve Erdemir
- Department of Neurology and Center for Translational Neuro and Behavioral Science, University Hospital Essen, Essen, Germany
| | - Timo Wirth
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Simone König
- Core Unit Proteomics, Interdisciplinary Center for Clinical Research, University of Münster, Münster, Germany
| | - Christine A Dambietz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Christina B Schroeter
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Nelke
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jens T Siveke
- Spatiotemporal Tumor Heterogeneity, German Cancer Consortium (DKTK), Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
- Bridge Institute of Experimental Tumor Therapy, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Division of Solid Tumor Translational Oncology, DKTK, Partner Site Essen, A Partnership Between German Cancer Research Center (DKFZ) and University Hospital Essen, Essen, Germany
| | - Tobias Ruck
- Department of Neurology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Carmen Haider
- Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Medical University of Vienna, Vienna, Austria
- Comprehensive Center for Clinical Neurosciences and Mental Health, Medical University of Vienna, Vienna, Austria
| | - Christoph Kleinschnitz
- Department of Neurology and Center for Translational Neuro and Behavioral Science, University Hospital Essen, Essen, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Tim Hagenacker
- Department of Neurology and Center for Translational Neuro and Behavioral Science, University Hospital Essen, Essen, Germany.
| | - Gerd Meyer Zu Horste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
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8
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Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet 2024; 56:838-845. [PMID: 38741015 DOI: 10.1038/s41588-024-01732-8] [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: 09/29/2021] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents determining whether the same allele is responsible, indicating a shared underlying mechanism. Here, using a collection of 129,058 cases and controls across 6 diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles twofold by combining cases and controls across diseases, allowing us to identify more expression quantitative trait loci driven by the shared alleles. The patterns indicate widespread sharing of pathogenic mechanisms but not a single global autoimmune mechanism. Our approach can be applied to any set of traits and is particularly valuable as sample collections become depleted.
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Affiliation(s)
- Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Division of Neurology at the Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Noah Connally
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - David van Heel
- Blizard Institute, Queen Mary University of London, London, UK
| | - Cisca Wijmenga
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leonid Padyukov
- Division of Rheumatology at the Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Robert R Graham
- Maze Therapeutics, South San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Vesalius Therapeutics, Cambridge, MA, USA.
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9
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Wang M, Yoon J, Reisert H, Das B, Orlinick B, Chiarella J, Halvas EK, Mellors J, Pang AP, Barakat LA, Fikrig M, Cyktor J, Kluger Y, Spudich S, Corley MJ, Farhadian SF. HIV-1-infected T cell clones are shared across cerebrospinal fluid and blood during ART. JCI Insight 2024; 9:e176208. [PMID: 38587074 PMCID: PMC11128194 DOI: 10.1172/jci.insight.176208] [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: 10/17/2023] [Accepted: 02/27/2024] [Indexed: 04/09/2024] Open
Abstract
The central nervous system HIV reservoir is incompletely understood and is a major barrier to HIV cure. We profiled people with HIV (PWH) and uninfected controls through single-cell transcriptomic and T cell receptor (TCR) sequencing to understand the dynamics of HIV persistence in the CNS. In PWH on ART, we found that most participants had single cells containing HIV-1 RNA, which was found predominantly in CD4 central memory T cells, in both cerebrospinal fluid (CSF) and blood. HIV-1 RNA-containing cells were found more frequently in CSF than blood, indicating a higher burden of reservoir cells in the CNS than blood for some PWH. Most CD4 T cell clones containing infected cells were compartment specific, while some (22%) - including rare clones with members of the clone containing detectable HIV RNA in both blood and CSF - were found in both CSF and blood. These results suggest that infected T cells trafficked between tissue compartments and that maintenance and expansion of infected T cell clones contributed to the CNS reservoir in PWH on ART.
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Affiliation(s)
- Meng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | | | | | | | | | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Elias K. Halvas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Mellors
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alina P.S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Joshua Cyktor
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Shelli F. Farhadian
- Section of Infectious Diseases, and
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
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10
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Tsagiopoulou M, Rashmi S, Aguilar-Fernandez S, Nieto J, Gut IG. Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions. Sci Data 2024; 11:316. [PMID: 38538617 PMCID: PMC10973478 DOI: 10.1038/s41597-024-03152-z] [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: 06/27/2023] [Accepted: 03/18/2024] [Indexed: 04/01/2024] Open
Abstract
Despite the wealth of publicly available single-cell datasets, our understanding of distinct resident immune cells and their unique features in diverse human organs remains limited. To address this, we compiled a meta-analysis dataset of 114,275 CD45+ immune cells sourced from 14 organs in healthy donors. While the transcriptome of immune cells remains relatively consistent across organs, our analysis has unveiled organ-specific gene expression differences (GTPX3 in kidney, DNTT and ACVR2B in thymus). These alterations are linked to different transcriptional factor activities and pathways including metabolism. TNF-α signaling through the NFkB pathway was found in several organs and immune compartments. The presence of distinct expression profiles for NFkB family genes and their target genes, including cytokines, underscores their pivotal role in cell positioning. Taken together, immune cells serve a dual role: safeguarding the organs and dynamically adjusting to the intricacies of the host organ environment, thereby actively contributing to its functionality and overall homeostasis.
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Affiliation(s)
| | - Sonal Rashmi
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | | | - Juan Nieto
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain
| | - Ivo G Gut
- Centro Nacional de Analisis Genomico (CNAG), Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
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11
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Ren H, Liu Q. Skull and vertebral bone marrow in central nervous system inflammation. FUNDAMENTAL RESEARCH 2024; 4:246-250. [PMID: 38933518 PMCID: PMC11197483 DOI: 10.1016/j.fmre.2023.01.012] [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: 11/04/2022] [Revised: 01/02/2023] [Accepted: 01/06/2023] [Indexed: 03/07/2023] Open
Abstract
Emerging evidence has highlighted the capacity of hematogenous cells in skull and vertebral bone marrow to enter the meningeal borders via ossified vascular channels and maintain immune homeostasis in the central nervous system (CNS). CNS-adjacent skull and vertebral bone marrow comprises hematopoietic niches that can sense CNS injury and supply specialized immune cells to fine-tune inflammatory responses. Here, we review recent advances in our understanding of skull and vertebral bone marrow-derived immune cells in homeostasis and inflammatory CNS diseases. Further, we discuss the implications for future development of therapies to mitigate CNS inflammation and its detrimental sequelae in neurological disorders.
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Affiliation(s)
- Honglei Ren
- Department of Neurology, Tianjin Neurological Institute, Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, International Joint Laboratory of Ocular Diseases, Ministry of Education, Haihe Laboratory of Cell Ecosystem, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Qiang Liu
- Department of Neurology, Tianjin Neurological Institute, Tianjin Institute of Immunology, State Key Laboratory of Experimental Hematology, International Joint Laboratory of Ocular Diseases, Ministry of Education, Haihe Laboratory of Cell Ecosystem, Tianjin Medical University General Hospital, Tianjin 300052, China
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12
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Ban M, Bredikhin D, Huang Y, Bonder MJ, Katarzyna K, Oliver AJ, Wilson NK, Coupland P, Hadfield J, Göttgens B, Madissoon E, Stegle O, Sawcer S. Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis. Brain 2024; 147:554-565. [PMID: 38038362 PMCID: PMC10834244 DOI: 10.1093/brain/awad404] [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: 08/04/2023] [Revised: 11/06/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Despite the overwhelming evidence that multiple sclerosis is an autoimmune disease, relatively little is known about the precise nature of the immune dysregulation underlying the development of the disease. Reasoning that the CSF from patients might be enriched for cells relevant in pathogenesis, we have completed a high-resolution single-cell analysis of 96 732 CSF cells collected from 33 patients with multiple sclerosis (n = 48 675) and 48 patients with other neurological diseases (n = 48 057). Completing comprehensive cell type annotation, we identified a rare population of CD8+ T cells, characterized by the upregulation of inhibitory receptors, increased in patients with multiple sclerosis. Applying a Multi-Omics Factor Analysis to these single-cell data further revealed that activity in pathways responsible for controlling inflammatory and type 1 interferon responses are altered in multiple sclerosis in both T cells and myeloid cells. We also undertook a systematic search for expression quantitative trait loci in the CSF cells. Of particular interest were two expression quantitative trait loci in CD8+ T cells that were fine mapped to multiple sclerosis susceptibility variants in the viral control genes ZC3HAV1 (rs10271373) and IFITM2 (rs1059091). Further analysis suggests that these associations likely reflect genetic effects on RNA splicing and cell-type specific gene expression respectively. Collectively, our study suggests that alterations in viral control mechanisms might be important in the development of multiple sclerosis.
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Affiliation(s)
- Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Danila Bredikhin
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yuanhua Huang
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kania Katarzyna
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul Coupland
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - James Hadfield
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Elo Madissoon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
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13
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Kousnetsov R, Bourque J, Surnov A, Fallahee I, Hawiger D. Single-cell sequencing analysis within biologically relevant dimensions. Cell Syst 2024; 15:83-103.e11. [PMID: 38198894 DOI: 10.1016/j.cels.2023.12.005] [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: 12/09/2022] [Revised: 05/23/2023] [Accepted: 12/14/2023] [Indexed: 01/12/2024]
Abstract
The currently predominant approach to transcriptomic and epigenomic single-cell analysis depends on a rigid perspective constrained by reduced dimensions and algorithmically derived and annotated clusters. Here, we developed Seqtometry (sequencing-to-measurement), a single-cell analytical strategy based on biologically relevant dimensions enabled by advanced scoring with multiple gene sets (signatures) for examination of gene expression and accessibility across various organ systems. By utilizing information only in the form of specific signatures, Seqtometry bypasses unsupervised clustering and individual annotations of clusters. Instead, Seqtometry combines qualitative and quantitative cell-type identification with specific characterization of diverse biological processes under experimental or disease conditions. Comprehensive analysis by Seqtometry of various immune cells as well as other cells from different organs and disease-induced states, including multiple myeloma and Alzheimer's disease, surpasses corresponding cluster-based analytical output. We propose Seqtometry as a single-cell sequencing analysis approach applicable for both basic and clinical research.
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Affiliation(s)
- Robert Kousnetsov
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Jessica Bourque
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Alexey Surnov
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Ian Fallahee
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA.
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14
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Gottlieb A, Pham HPT, Saltarrelli JG, Lindsey JW. Expanded T lymphocytes in the cerebrospinal fluid of multiple sclerosis patients are specific for Epstein-Barr-virus-infected B cells. Proc Natl Acad Sci U S A 2024; 121:e2315857121. [PMID: 38190525 PMCID: PMC10801919 DOI: 10.1073/pnas.2315857121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Epstein-Barr virus (EBV) infection has long been associated with multiple sclerosis (MS), but the role of EBV in the pathogenesis of MS is not clear. Our hypothesis is that a major fraction of the expanded clones of T lymphocytes in the cerebrospinal fluid (CSF) are specific for autologous EBV-infected B cells. We obtained blood and CSF samples from eight relapsing-remitting patients in the process of diagnosis. We stimulated cells from the blood with autologous EBV-infected lymphoblastoid cell lines (LCL), EBV, varicella zoster virus, influenza, and candida and sorted the responding cells with flow cytometry after 6 d. We sequenced the RNA for T cell receptors (TCR) from CSF, unselected blood cells, and the antigen-specific cells. We used the TCR Vβ CDR3 sequences from the antigen-specific cells to assign antigen specificity to the sequences from the CSF and blood. LCL-specific cells comprised 13.0 ± 4.3% (mean ± SD) of the total reads present in CSF and 13.3 ± 7.5% of the reads present in blood. The next most abundant antigen specificity was flu, which was 4.7 ± 1.7% of the reads in the CSF and 9.3 ± 6.6% in the blood. The prominence of LCL-specific reads was even more marked in the top 1% most abundant CSF clones with statistically significant 47% mean overlap with LCL. We conclude that LCL-specific sequences form a major portion of the TCR repertoire in both CSF and blood and that expanded clones specific for LCL are present in MS CSF. This has important implications for the pathogenesis of MS.
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Affiliation(s)
- Assaf Gottlieb
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX77030
| | - H. Phuong T. Pham
- Division of Multiple Sclerosis and Neuroimmunology, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX77030
| | - Jerome G. Saltarrelli
- Department of Surgery, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX77030
| | - J. William Lindsey
- Division of Multiple Sclerosis and Neuroimmunology, Department of Neurology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX77030
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15
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Kimura K, Nishigori R, Hamatani M, Sawamura M, Ashida S, Fujii C, Takata M, Lin Y, Sato W, Okamoto T, Kuzuya A, Takahashi R, Yamamura T, Kondo T. Resident Memory-like CD8 + T Cells Are Involved in Chronic Inflammatory and Neurodegenerative Diseases in the CNS. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200172. [PMID: 37949669 PMCID: PMC10691221 DOI: 10.1212/nxi.0000000000200172] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/29/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND AND OBJECTIVES Resident memory T (Trm) cells are a unique population that can survive and function in a compartmentalized tissue with inflammatory potential. We aim to investigate the alteration of Trm population in acute/chronic inflammatory and neurodegenerative diseases in the CNS. METHODS The frequencies of CD4+ and CD8+ T cells expressing both CD69 and CD103, the markers for Trm cells, were quantified in the peripheral blood and CSF (n = 80 and 44, respectively) in a cross-sectional manner. The transcriptional profile of Trm-like population in the CSF was further analyzed using a public single-cell dataset. RESULTS The frequency of CD69+CD103+CD8+ T cells was strikingly higher in the CSF than in the peripheral blood (among memory fraction, 13.5% vs 0.11%, difference (mean [SE]): 13.4% [2.9]). This CD69+CD103+CD8+ T-cell population was increased in the CSF from patients with chronic inflammatory diseases including multiple sclerosis and with neurodegenerative diseases such as Parkinson disease and Alzheimer disease compared with controls (11.5%, 13.0%, 8.1% vs 2.9%, respectively). By contrast, the frequency was not altered in acute inflammatory conditions in the CNS (4.0%). Single-cell RNAseq analysis confirmed Trm signature in CD69+CD103+CD8+ T cells in the CSF, supporting their Trm-like phenotype, which was not clear in controls. DISCUSSION Collectively, an increase in CD69+CD103+CD8+ Trm-like population in the CSF is related with both chronic neuroinflammatory and some neurodegenerative diseases in the CNS, suggesting a partially shared pathology in these diseases.
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Affiliation(s)
- Kimitoshi Kimura
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan.
| | - Ryusei Nishigori
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Mio Hamatani
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Masanori Sawamura
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Shinji Ashida
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Chihiro Fujii
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Masaki Takata
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Youwei Lin
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Wakiro Sato
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Tomoko Okamoto
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Akira Kuzuya
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Ryosuke Takahashi
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Takashi Yamamura
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
| | - Takayuki Kondo
- From the Department of Neurology (K.K., R.N., M.H., M.S., M.T., A.K., R.T.), Kyoto University Graduate School of Medicine; Department of Immunology (K.K., Y.L., W.S., T.O., T.Y.), National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira; Institute for the Advanced Study of Human Biology (M.H.), Kyoto University; Department of Neurology (S.A., C.F.), Graduate School of Medical Science, Kyoto Prefectural University of Medicine; and Department of Neurology (C.F., T.K.), Kansai Medical University Medical Center, Moriguchi, Japan
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16
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Zhu B, Wang Y, Ku LT, van Dijk D, Zhang L, Hafler DA, Zhao H. scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles. Genome Biol 2023; 24:292. [PMID: 38111007 PMCID: PMC10726524 DOI: 10.1186/s13059-023-03129-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) data for novel discoveries. We developed scNAT, a deep learning method that integrates paired scRNA-seq and scTCR-seq data to represent data in a unified latent space for downstream analysis. We demonstrate that scNAT is capable of removing batch effects, and identifying cell clusters and a T cell migration trajectory from blood to cerebrospinal fluid in multiple sclerosis.
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Affiliation(s)
- Biqing Zhu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Yuge Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - Li-Ting Ku
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - David van Dijk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Computer Science, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Le Zhang
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Hongyu Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA.
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA.
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17
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Kearns NA, Iatrou A, Flood DJ, De Tissera S, Mullaney ZM, Xu J, Gaiteri C, Bennett DA, Wang Y. Dissecting the human leptomeninges at single-cell resolution. Nat Commun 2023; 14:7036. [PMID: 37923721 PMCID: PMC10624900 DOI: 10.1038/s41467-023-42825-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023] Open
Abstract
Emerging evidence shows that the meninges conduct essential immune surveillance and immune defense at the brain border, and the dysfunction of meningeal immunity contributes to aging and neurodegeneration. However, no study exists on the molecular properties of cell types within human leptomeninges. Here, we provide single nuclei profiling of dissected postmortem leptomeninges from aged individuals. We detect diverse cell types, including unique meningeal endothelial, mural, and fibroblast subtypes. For immune cells, we show that most T cells express CD8 and bear characteristics of tissue-resident memory T cells. We also identify distinct subtypes of border-associated macrophages (BAMs) that display differential gene expressions from microglia and express risk genes for Alzheimer's Disease (AD), as nominated by genome-wide association studies (GWAS). We discover cell-type-specific differentially expressed genes in individuals with Alzheimer's dementia, particularly in fibroblasts and BAMs. Indeed, when cultured, leptomeningeal cells display the signature of ex vivo AD fibroblasts upon amyloid-β treatment. We further explore ligand-receptor interactions within the leptomeningeal niche and computationally infer intercellular communications in AD. Thus, our study establishes a molecular map of human leptomeningeal cell types, providing significant insight into the border immune and fibrotic responses in AD.
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Affiliation(s)
- Nicola A Kearns
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, 02478, USA
| | - Daniel J Flood
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Sashini De Tissera
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Zachary M Mullaney
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Jishu Xu
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Chris Gaiteri
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
- Department of Psychiatry, Upstate Medical University, Syracuse, NY, 13210, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA
| | - Yanling Wang
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, 60612, USA.
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, 60612, USA.
- Rush Graduate College, Rush University, Chicago IL, 60612, USA.
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18
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Touil H, Roostaei T, Calini D, Diaconu C, Epstein S, Raposo C, Onomichi K, Thakur KT, Craveiro L, Callegari I, Bryois J, Riley CS, Menon V, Derfuss T, De Jager PL, Malhotra D. A structured evaluation of cryopreservation in generating single-cell transcriptomes from cerebrospinal fluid. CELL REPORTS METHODS 2023; 3:100533. [PMID: 37533636 PMCID: PMC10391561 DOI: 10.1016/j.crmeth.2023.100533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/28/2023] [Accepted: 06/21/2023] [Indexed: 08/04/2023]
Abstract
Single-cell transcriptomics allows characterization of cerebrospinal fluid (CSF) cells at an unprecedented level. Here, we report a robust cryopreservation protocol adapted for the characterization of fragile CSF cells by single-cell RNA sequencing (RNA-seq) in moderate- to large-scale studies. Fresh CSF was collected from twenty-one participants at two independent sites. Each CSF sample was split into two fractions: one was processed fresh, while the second was cryopreserved for months and profiled after thawing. B and T cell receptor sequencing was also performed. Our comparison of fresh and cryopreserved data from the same individuals demonstrates highly efficient recovery of all known CSF cell types. We find no significant difference in cell type proportions and cellular transcriptomes between fresh and cryopreserved cells. Results were comparable at both sites and with different single-cell sequencing chemistries. Cryopreservation did not affect recovery of T and B cell clonotype diversity. Our CSF cell cryopreservation protocol provides an important alternative to fresh processing of fragile CSF cells.
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Affiliation(s)
- Hanane Touil
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tina Roostaei
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Daniela Calini
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claudiu Diaconu
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Samantha Epstein
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Catarina Raposo
- gRED OMNI-Biomarker Development, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, Basel, Switzerland
| | - Kaho Onomichi
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Kiran T. Thakur
- Program in Neuroinfectious Diseases, Division of Critical Care and Hospitalist Neurology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Licinio Craveiro
- Product Development Medical Affairs (PDMA) Neuroscience, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Ilaria Callegari
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Julien Bryois
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
| | - Claire S. Riley
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Vilas Menon
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tobias Derfuss
- University Hospital Basel, Department of Neurology and Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Philip L. De Jager
- Center for Translational & Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Columbia Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Dheeraj Malhotra
- Neuroscience and Rare Diseases (NRD), F. Hoffmann-La Roche, Ltd., Grenzacherstrasse, 4070 Basel, Switzerland
- MS Research Unit, Biogen, Cambridge, MA 02142, USA
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19
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Kastnes M, Aass KR, Bouma SA, Årseth C, Zahoor M, Yurchenko M, Standal T. The pro-tumorigenic cytokine IL-32 has a high turnover in multiple myeloma cells due to proteolysis regulated by oxygen-sensing cysteine dioxygenase and deubiquitinating enzymes. Front Oncol 2023; 13:1197542. [PMID: 37313466 PMCID: PMC10258340 DOI: 10.3389/fonc.2023.1197542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
IL-32 is a pro-inflammatory cytokine expressed by several types of cancer cells and immune cells. Currently, no treatment targeting IL-32 is available, and its intracellular and exosomal localization make IL-32 less accessible to drugs. We previously showed that hypoxia promotes IL-32 expression through HIF1α in multiple myeloma cells. Here, we demonstrate that high-speed translation and ubiquitin-dependent proteasomal degradation lead to a rapid IL-32 protein turnover. We find that IL-32 protein half-life is regulated by the oxygen-sensing cysteine-dioxygenase ADO and that deubiquitinases actively remove ubiquitin from IL-32 and promote protein stability. Deubiquitinase inhibitors promoted the degradation of IL-32 and may represent a strategy for reducing IL-32 levels in multiple myeloma. The fast turnover and enzymatic deubiquitination of IL-32 are conserved in primary human T cells; thus, deubiquitinase inhibitors may also affect T-cell responses in various diseases.
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Affiliation(s)
- Martin Kastnes
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kristin Roseth Aass
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Siri Anshushaug Bouma
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Charlotte Årseth
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Muhammad Zahoor
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Mariia Yurchenko
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Therese Standal
- Centre of Molecular Inflammation Research, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Hematology, St.Olavs University Hospital, Trondheim, Norway
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20
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Modvig S, Jeyakumar J, Marquart HV, Christensen C. Integrins and the Metastasis-like Dissemination of Acute Lymphoblastic Leukemia to the Central Nervous System. Cancers (Basel) 2023; 15:cancers15092504. [PMID: 37173970 PMCID: PMC10177281 DOI: 10.3390/cancers15092504] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) disseminates with high prevalence to the central nervous system (CNS) in a process resembling aspects of the CNS surveillance of normal immune cells as well as aspects of brain metastasis from solid cancers. Importantly, inside the CNS, the ALL blasts are typically confined within the cerebrospinal fluid (CSF)-filled cavities of the subarachnoid space, which they use as a sanctuary protected from both chemotherapy and immune cells. At present, high cumulative doses of intrathecal chemotherapy are administered to patients, but this is associated with neurotoxicity and CNS relapse still occurs. Thus, it is imperative to identify markers and novel therapy targets specific to CNS ALL. Integrins represent a family of adhesion molecules involved in cell-cell and cell-matrix interactions, implicated in the adhesion and migration of metastatic cancer cells, normal immune cells, and leukemic blasts. The ability of integrins to also facilitate cell-adhesion mediated drug resistance, combined with recent discoveries of integrin-dependent routes of leukemic cells into the CNS, have sparked a renewed interest in integrins as markers and therapeutic targets in CNS leukemia. Here, we review the roles of integrins in CNS surveillance by normal lymphocytes, dissemination to the CNS by ALL cells, and brain metastasis from solid cancers. Furthermore, we discuss whether ALL dissemination to the CNS abides by known hallmarks of metastasis, and the potential roles of integrins in this context.
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Affiliation(s)
- Signe Modvig
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jenani Jeyakumar
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
| | - Hanne Vibeke Marquart
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Claus Christensen
- Department of Clinical Immunology, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark
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21
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [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: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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22
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Wu GF. The cerebrospinal fluid immune cell landscape in animal models of multiple sclerosis. Front Mol Neurosci 2023; 16:1143498. [PMID: 37122618 PMCID: PMC10130411 DOI: 10.3389/fnmol.2023.1143498] [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: 01/13/2023] [Accepted: 02/15/2023] [Indexed: 05/02/2023] Open
Abstract
The fluid compartment surrounding the central nervous system (CNS) is a unique source of immune cells capable of reflecting the pathophysiology of neurologic diseases. While human clinical and experimental studies often employ cerebrospinal fluid (CSF) analysis, assessment of CSF in animal models of disease are wholly uncommon, particularly in examining the cellular component. Barriers to routine assessment of CSF in animal models of multiple sclerosis (MS) include limited sample volume, blood contamination, and lack of feasible longitudinal approaches. The few studies characterizing CSF immune cells in animal models of MS are largely outdated, but recent work employing transcriptomics have been used to explore new concepts in CNS inflammation and MS. Absence of extensive CSF data from rodent and other systems has curbed the overall impact of experimental models of MS. Future approaches, including examination of CSF myeloid subsets, single cell transcriptomics incorporating antigen receptor sequencing, and use of diverse animal models, may serve to overcome current limitations and provide critical insights into the pathogenesis of, and therapeutic developments for, MS.
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Affiliation(s)
- Gregory F. Wu
- Departments of Neurology and Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, United States
- Neurology Service, VA St. Louis Health Care System, St. Louis, MO, United States
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23
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Lv J, Zhu J, Wang P, Liu T, Yuan J, Yin H, Lan Y, Sun Q, Zhang Z, Ding G, Zhou C, Wang H, Wang Z, Wang Y. Artemisinin exerts a protective effect in the MPTP mouse model of Parkinson's disease by inhibiting microglial activation via the TLR4/Myd88/NF-KB pathway. CNS Neurosci Ther 2023; 29:1012-1023. [PMID: 36691817 PMCID: PMC10018080 DOI: 10.1111/cns.14063] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/23/2022] [Accepted: 12/02/2022] [Indexed: 01/25/2023] Open
Abstract
AIMS We performed cell and animal experiments to explore the therapeutic effect of artemisinin on Parkinson's disease (PD) and the TLR4/Myd88 signaling pathway. METHODS C57 mice were randomly divided into the blank, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced and artemisinin-treated groups. Clinical symptoms, the number of dopaminergic (DAergic) neurons in the substantia nigra, and microglial cell activation were compared among the three groups. Subsequently, BV-2 cell activation and TLR4/Myd88 pathway component expression were compared among the blank, MPP+ -treated, artemisinin-treated, and TLR4 activator-treated groups. RESULTS Behavioral symptoms were improved, the number of DAergic neurons in the substantia nigra of the midbrain was increased, and microglial cell activation was decreased in artemisinin-treated MPTP-induced PD model mice compared with control-treated MPTP-induced PD model mice (p < 0.05). The cell experiments revealed that artemisinin treatment reduced MPP+ -induced BV-2 cell activation and inhibited the TLR4/Myd88 signaling pathway. Moreover, the effect of artemisinin on the BV-2 cell model was inhibited by the TLR4 activator LPS (p < 0.05). CONCLUSION Artemisinin may reduce damage to DAergic neurons in a PD mouse model by decreasing microglial activation through the TLR4-mediated MyD88-dependent signaling pathway. However, this finding cannot explain the relationship between microglia and DAergic neurons.
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Affiliation(s)
- Jing Lv
- Department of Neurology, Graduate Training Base of Jinzhou Medical University, Affiliated Hospital of Hubei Medical College, Taihe Hospital, Shiyan, China.,Institute of Neuroscience, Hubei University of Medicine, Shiyan, China
| | - Jing Zhu
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China
| | - Peihan Wang
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Tongyu Liu
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Jiang Yuan
- Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Huan Yin
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, China
| | - Yiran Lan
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Qiang Sun
- Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Zhifeng Zhang
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China
| | - Guoda Ding
- Department of Neurology, Graduate Training Base of Jinzhou Medical University, Affiliated Hospital of Hubei Medical College, Taihe Hospital, Shiyan, China
| | - Chenxi Zhou
- Department of Neurology, Graduate Training Base of Jinzhou Medical University, Affiliated Hospital of Hubei Medical College, Taihe Hospital, Shiyan, China
| | - Huajie Wang
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Zihan Wang
- Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
| | - Yunfu Wang
- Department of Neurology, Graduate Training Base of Jinzhou Medical University, Affiliated Hospital of Hubei Medical College, Taihe Hospital, Shiyan, China.,Institute of Neuroscience, Hubei University of Medicine, Shiyan, China.,Department of Neurology, Taihe Hospital of Hubei University of Medicine, Shiyan, China
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24
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Serafini B, Rosicarelli B, Veroni C, Aloisi F. Tissue-resident memory T cells in the multiple sclerosis brain and their relationship to Epstein-Barr virus infected B cells. J Neuroimmunol 2023; 376:578036. [PMID: 36753806 DOI: 10.1016/j.jneuroim.2023.578036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Presence of EBV infected B cells and EBV-specific CD8 T cells in the multiple sclerosis (MS) brain suggests a role for virus-driven immunopathology in brain inflammation. Tissue-resident memory (Trm) T cells differentiating in MS lesions could provide local protection against EBV reactivation. Using immunohistochemical techniques to analyse canonical tissue residency markers in postmortem brains from control and MS cases, we report that CD103 and/or CD69 are mainly expressed in a subset of CD8+ T cells that intermingle with and contact EBV infected B cells in the infiltrated MS white matter and meninges, including B-cell follicles. Some Trm-like cells were found to express granzyme B and PD-1, mainly in white matter lesions. In the MS brain, Trm cells could fail to constrain EBV infection while contributing to sustain inflammation.
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Affiliation(s)
- Barbara Serafini
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Barbara Rosicarelli
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Caterina Veroni
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Francesca Aloisi
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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25
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Chow RD, Michaels T, Bellone S, Hartwich TM, Bonazzoli E, Iwasaki A, Song E, Santin AD. Distinct Mechanisms of Mismatch-Repair Deficiency Delineate Two Modes of Response to Anti-PD-1 Immunotherapy in Endometrial Carcinoma. Cancer Discov 2023; 13:312-331. [PMID: 36301137 PMCID: PMC9905265 DOI: 10.1158/2159-8290.cd-22-0686] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/29/2022] [Accepted: 10/19/2022] [Indexed: 02/07/2023]
Abstract
Mismatch repair-deficient (MMRd) cancers have varied responses to immune-checkpoint blockade (ICB). We conducted a phase II clinical trial of the PD-1 inhibitor pembrolizumab in 24 patients with MMRd endometrial cancer (NCT02899793). Patients with mutational MMRd tumors (6 patients) had higher response rates and longer survival than those with epigenetic MMRd tumors (18 patients). Mutation burden was higher in tumors with mutational MMRd compared with epigenetic MMRd; however, within each category of MMRd, mutation burden was not correlated with ICB response. Pretreatment JAK1 mutations were not associated with primary resistance to pembrolizumab. Longitudinal single-cell RNA-seq of circulating immune cells revealed contrasting modes of antitumor immunity for mutational versus epigenetic MMRd cancers. Whereas effector CD8+ T cells correlated with regression of mutational MMRd tumors, activated CD16+ NK cells were associated with ICB-responsive epigenetic MMRd tumors. These data highlight the interplay between tumor-intrinsic and tumor-extrinsic factors that influence ICB response. SIGNIFICANCE The molecular mechanism of MMRd is associated with response to anti-PD-1 immunotherapy in endometrial carcinoma. Tumors with epigenetic MMRd or mutational MMRd are correlated with NK cell or CD8+ T cell-driven immunity, respectively. Classifying tumors by the mechanism of MMRd may inform clinical decision-making regarding cancer immunotherapy. This article is highlighted in the In This Issue feature, p. 247.
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Affiliation(s)
- Ryan D. Chow
- Department of Genetics, Yale University, New Haven, Connecticut, USA
- System Biology Institute, Yale University, West Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Tai Michaels
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
| | - Stefania Bellone
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tobias M.P. Hartwich
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Elena Bonazzoli
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA
| | - Eric Song
- Department of Immunobiology, Yale University, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
| | - Alessandro D. Santin
- Smilow Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
- Corresponding authors: Correspondence to: Ryan D. Chow, Address: 850 West Campus Drive, ISTC 314, West Haven CT 06516, , Phone: 203-737-3825, Eric Song, Address: 300 Cedar Street, Suite S630, New Haven, CT 06519, , Phone: 203-785-2919, Alessandro D. Santin, Address: 333 Cedar Street, PO Box 208063, New Haven, CT 06511, , Phone: 203-737-2280
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26
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de Sèze J, Maillart E, Gueguen A, Laplaud DA, Michel L, Thouvenot E, Zephir H, Zimmer L, Biotti D, Liblau R. Anti-CD20 therapies in multiple sclerosis: From pathology to the clinic. Front Immunol 2023; 14:1004795. [PMID: 37033984 PMCID: PMC10076836 DOI: 10.3389/fimmu.2023.1004795] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/13/2023] [Indexed: 04/11/2023] Open
Abstract
The immune system plays a significant role in multiple sclerosis. While MS was historically thought to be T cell-mediated, multiple pieces of evidence now support the view that B cells are essential players in multiple sclerosis pathogenic processes. High-efficacy disease-modifying therapies that target the immune system have emerged over the past two decades. Anti-CD20 monoclonal antibodies selectively deplete CD20+ B and CD20+ T cells and efficiently suppress inflammatory disease activity. These monotherapies prevent relapses, reduce new or active magnetic resonance imaging brain lesions, and lessen disability progression in patients with relapsing multiple sclerosis. Rituximab, ocrelizumab, and ofatumumab are currently used in clinical practice, while phase III clinical trials for ublituximab have been recently completed. In this review, we compare the four anti-CD20 antibodies in terms of their mechanisms of action, routes of administration, immunological targets, and pharmacokinetic properties. A deeper understanding of the individual properties of these molecules in relation to their efficacy and safety profiles is critical for their use in clinical practice.
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Affiliation(s)
- Jérôme de Sèze
- Department of Neurology, Hôpital de Hautepierre, Clinical Investigation Center, Institut National de la Santé et de la Recherche Médicale (INSERM), Strasbourg, France
- Fédération de Médecine Translationelle, Institut National de la Santé et de la Recherche Médicale (INSERM), Strasbourg, France
- *Correspondence: Jérôme de Sèze,
| | - Elisabeth Maillart
- Department of Neurology, Pitié Salpêtrière Hospital, Paris, France
- Centre de Ressources et de Compétences Sclérose en Plaques, Paris, France
| | - Antoine Gueguen
- Department of Neurology, Rothschild Ophthalmologic Foundation, Paris, France
| | - David A. Laplaud
- Department of Neurology, Centre Hospitalier Universitaire (CHU) Nantes, Nantes Université, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre d’Investigation Clinique (CIC), Center for Research in Transplantation and Translational Immunology, UMR, UMR1064, Nantes, France
| | - Laure Michel
- Clinical Neuroscience Centre, CIC_P1414 Institut National de la Santé et de la Recherche Médicale (INSERM), Rennes University Hospital, Rennes University, Rennes, France
- Microenvironment, Cell Differentiation, Immunology and Cancer Unit, Institut National de la Santé et de la Recherche Médicale (INSERM), Rennes I University, French Blood Agency, Rennes, France
- Neurology Department, Rennes University Hospital, Rennes, France
| | - Eric Thouvenot
- Department of Neurology, Centre Hospitalier Universitaire (CHU) Nîmes, University of Montpellier, Nîmes, France
- Institut de Génomique Fonctionnelle, UMR, Institut National de la Santé et de la Recherche Médicale (INSERM), University of Montpellier, Montpellier, France
| | - Hélène Zephir
- University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM) U1172, Centre Hospitalier Universitaire (CHU), Lille, France
| | - Luc Zimmer
- Université Claude Bernard Lyon 1, Hospices Civils de Lyon, Institut National de la Santé et de la Recherche Médicale (INSERM), CNRS, Lyon Neuroscience Research Center, Lyon, France
| | - Damien Biotti
- Centre Ressources et Compétences Sclérose En Plaques (CRC-SEP) and Department of Neurology, Centre Hospitalier Universitaire (CHU) Toulouse Purpan – Hôpital Pierre-Paul Riquet, Toulouse, France
| | - Roland Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), UPS, Toulouse, France
- Department of Immunology, Toulouse University Hospital, Toulouse, France
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27
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Straeten F, Zhu J, Börsch AL, Zhang B, Li K, Lu IN, Gross C, Heming M, Li X, Rubin R, Ouyang Z, Wiendl H, Mingueneau M, Meyer zu Hörste G. Integrated single-cell transcriptomics of cerebrospinal fluid cells in treatment-naïve multiple sclerosis. J Neuroinflammation 2022; 19:306. [PMID: 36536441 PMCID: PMC9764586 DOI: 10.1186/s12974-022-02667-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic and often disabling autoimmune disease of the central nervous system (CNS). Cerebrospinal fluid (CSF) surrounds and protects the CNS. Analysis of CSF can aid the diagnosis of CNS diseases, help to identify the prognosis, and underlying mechanisms of diseases. Several recent studies have leveraged single-cell RNA-sequencing (scRNA-seq) to identify MS-associated changes in CSF cells that are considerably more altered than blood cells in MS. However, not all alterations were replicated across all studies. We therefore integrated multiple available scRNA-seq datasets of CSF cells from MS patients with early relapsing-remitting (RRMS) disease. We provide a searchable and interactive resource of this integrated analysis ( https://CSFinMS.bxgenomics.com ) facilitating diverse visualization and analysis methods without requiring computational skills. In the present joint analysis, we replicated the known expansion of B lineage and the recently described expansion of natural killer (NK) cells and some cytotoxic T cells and decrease of monocytes in the CSF in MS. The previous observation of the abundance of Th1-like Th17 effector memory cells in the CSF was not replicated. Expanded CSF B lineage cells resembled class-switched plasmablasts/-cells (e.g., SDC1/CD138, MZB1) as expected. Our integrative analysis thus validates increased cell type diversity and B cell maturation in the CSF in MS and improves accessibility of available data.
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Affiliation(s)
- Frederike Straeten
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Jing Zhu
- grid.417832.b0000 0004 0384 8146Department of Research, Biogen, Cambridge, MA USA
| | - Anna-Lena Börsch
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Baohong Zhang
- grid.417832.b0000 0004 0384 8146Department of Research, Biogen, Cambridge, MA USA
| | - Kejie Li
- grid.417832.b0000 0004 0384 8146Department of Research, Biogen, Cambridge, MA USA
| | - I-Na Lu
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Catharina Gross
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Michael Heming
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Xiaolin Li
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Rebekah Rubin
- grid.417832.b0000 0004 0384 8146Department of Research, Biogen, Cambridge, MA USA
| | | | - Heinz Wiendl
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
| | - Michael Mingueneau
- grid.417832.b0000 0004 0384 8146Department of Research, Biogen, Cambridge, MA USA
| | - Gerd Meyer zu Hörste
- grid.16149.3b0000 0004 0551 4246Department of Neurology with Institute of Translational Neurology, Medical Faculty, University Hospital Münster, Münster, Germany
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28
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Zeng L, Yang K, Zhang T, Zhu X, Hao W, Chen H, Ge J. Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review. J Autoimmun 2022; 133:102919. [PMID: 36242821 DOI: 10.1016/j.jaut.2022.102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/07/2022]
Abstract
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies or sensitized lymphocytes to its own tissues to cause an immune response. Immune disorders caused by autoimmunity can mediate autoimmune diseases. Autoimmune diseases have complicated pathogenesis due to the many types of cells involved, and the mechanism is still unclear. The emergence of single-cell research technology can solve the problem that ordinary transcriptome technology cannot be accurate to cell type. It provides unbiased results through independent analysis of cells in tissues and provides more mRNA information for identifying cell subpopulations, which provides a novel approach to study disruption of immune tolerance and disturbance of pro-inflammatory pathways on a cellular basis. It may fundamentally change the understanding of molecular pathways in the pathogenesis of autoimmune diseases and develop targeted drugs. Single-cell transcriptome sequencing (scRNA-seq) has been widely applied in autoimmune diseases, which provides a powerful tool for demonstrating the cellular heterogeneity of tissues involved in various immune inflammations, identifying pathogenic cell populations, and revealing the mechanism of disease occurrence and development. This review describes the principles of scRNA-seq, introduces common sequencing platforms and practical procedures, and focuses on the progress of scRNA-seq in 41 autoimmune diseases, which include 9 systemic autoimmune diseases and autoinflammatory diseases (rheumatoid arthritis, systemic lupus erythematosus, etc.) and 32 organ-specific autoimmune diseases (5 Skin diseases, 3 Nervous system diseases, 4 Eye diseases, 2 Respiratory system diseases, 2 Circulatory system diseases, 6 Liver, Gallbladder and Pancreas diseases, 2 Gastrointestinal system diseases, 3 Muscle, Bones and joint diseases, 3 Urinary system diseases, 2 Reproductive system diseases). This review also prospects the molecular mechanism targets of autoimmune diseases from the multi-molecular level and multi-dimensional analysis combined with single-cell multi-omics sequencing technology (such as scRNA-seq, Single cell ATAC-seq and single cell immune group library sequencing), which provides a reference for further exploring the pathogenesis and marker screening of autoimmune diseases and autoimmune inflammatory diseases in the future.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Tianqing Zhang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaofei Zhu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China; Hunan Academy of Chinese Medicine, Changsha, China.
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29
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Mix MR, Harty JT. Keeping T cell memories in mind. Trends Immunol 2022; 43:1018-1031. [PMID: 36369103 PMCID: PMC9691610 DOI: 10.1016/j.it.2022.10.001] [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: 09/01/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/09/2022]
Abstract
The mammalian central nervous system (CNS) contains a vibrant community of resident adaptive immune cells at homeostasis. Among these are memory CD8+ and CD4+ T cells, which reside in the CNS in the settings of health, aging, and neurological disease. These T cells commonly exhibit a tissue-resident memory (TRM) phenotype, suggesting that they are antigen-experienced and remain separate from the circulation. Despite these characterizations, T cell surveillance of the CNS has only recently been studied through the lens of TRM immunology. In this Review, we outline emerging concepts of CNS TRM generation, localization, maintenance, function, and specificity. In this way, we hope to highlight roles of CNS TRM in health and disease to inform future studies of adaptive neuroimmunity.
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Affiliation(s)
- Madison R Mix
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA
| | - John T Harty
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Medical Scientist Training Program, Carver College of Medicine, University of Iowa, Iowa City, IA, USA; Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, USA.
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30
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Ostkamp P, Deffner M, Schulte-Mecklenbeck A, Wünsch C, Lu IN, Wu GF, Goelz S, De Jager PL, Kuhlmann T, Gross CC, Klotz L, Meyer Zu Hörste G, Wiendl H, Schneider-Hohendorf T, Schwab N. A single-cell analysis framework allows for characterization of CSF leukocytes and their tissue of origin in multiple sclerosis. Sci Transl Med 2022; 14:eadc9778. [PMID: 36449599 DOI: 10.1126/scitranslmed.adc9778] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Peripheral central nervous system (CNS)-infiltrating lymphocytes are a hallmark of relapsing-remitting multiple sclerosis. Tissue-resident memory T cells (TRM) not only populate the healthy CNS parenchyma but also are suspected to contribute to multiple sclerosis pathology. Because cerebrospinal fluid (CSF), unlike CNS parenchyma, is accessible for diagnostics, we evaluated whether human CSF, apart from infiltrating cells, also contains TRM cells and CNS-resident myeloid cells draining from the parenchyma or border tissues. Using deep generative models, we integrated 41 CSF and 14 CNS parenchyma single-cell RNA sequencing (scRNAseq) samples from eight independent studies, encompassing 120,629 cells. By comparing CSF immune cells collected during multiple sclerosis relapse with cells collected during therapeutic very late antigen-4 blockade, we could identify immune subsets with tissue provenance across multiple lineages, including CNS border-associated macrophages, CD8 and CD4 TRM cells, and tissue-resident natural killer cells. All lymphocytic CNS-resident cells shared expression of CXCR6 but showed differential ITGAE expression (encoding CD103). A common signature defined CD4 and CD8 TRM cells by expression of ZFP36L2, DUSP1, and ID2. We further developed a user interface-driven application based on this analysis framework for atlas-level cell identity transfer onto new CSF scRNAseq data. Together, these results define CNS-resident immune cells involved in multiple sclerosis pathology that can be detected and monitored in CSF. Targeting these cell populations might be promising to modulate immunopathology in progressive multiple sclerosis and other neuroinflammatory diseases.
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Affiliation(s)
- Patrick Ostkamp
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Marie Deffner
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Andreas Schulte-Mecklenbeck
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Christian Wünsch
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - I-Na Lu
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Gregory F Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susan Goelz
- Oregon Health and Science University, Portland, OR 97239, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology and Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, Münster 48149, Germany
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Tilman Schneider-Hohendorf
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster 48149, Germany
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31
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Schneider-Hohendorf T, Gerdes LA, Pignolet B, Gittelman R, Ostkamp P, Rubelt F, Raposo C, Tackenberg B, Riepenhausen M, Janoschka C, Wünsch C, Bucciarelli F, Flierl-Hecht A, Beltrán E, Kümpfel T, Anslinger K, Gross CC, Chapman H, Kaplan I, Brassat D, Wekerle H, Kerschensteiner M, Klotz L, Lünemann JD, Hohlfeld R, Liblau R, Wiendl H, Schwab N. Broader Epstein-Barr virus-specific T cell receptor repertoire in patients with multiple sclerosis. J Exp Med 2022; 219:213431. [PMID: 36048016 PMCID: PMC9437111 DOI: 10.1084/jem.20220650] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/30/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) infection precedes multiple sclerosis (MS) pathology and cross-reactive antibodies might link EBV infection to CNS autoimmunity. As an altered anti-EBV T cell reaction was suggested in MS, we queried peripheral blood T cell receptor β chain (TCRβ) repertoires of 1,395 MS patients, 887 controls, and 35 monozygotic, MS-discordant twin pairs for multimer-confirmed, viral antigen-specific TCRβ sequences. We detected more MHC-I-restricted EBV-specific TCRβ sequences in MS patients. Differences in genetics or upbringing could be excluded by validation in monozygotic twin pairs discordant for MS. Anti-VLA-4 treatment amplified this observation, while interferon β- or anti-CD20 treatment did not modulate EBV-specific T cell occurrence. In healthy individuals, EBV-specific CD8+ T cells were of an effector-memory phenotype in peripheral blood and cerebrospinal fluid. In MS patients, cerebrospinal fluid also contained EBV-specific central-memory CD8+ T cells, suggesting recent priming. Therefore, MS is not only preceded by EBV infection, but also associated with broader EBV-specific TCR repertoires, consistent with an ongoing anti-EBV immune reaction in MS.
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Affiliation(s)
- Tilman Schneider-Hohendorf
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Lisa Ann Gerdes
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Béatrice Pignolet
- Toulouse Institute for infectious and inflammatory diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier, Toulouse, France
| | | | - Patrick Ostkamp
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | | | | | - Björn Tackenberg
- F. Hoffmann-La Roche Ltd, Basel, Switzerland.,Philipps-University, Department of Neurology, Marburg, Germany
| | - Marianne Riepenhausen
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Claudia Janoschka
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Christian Wünsch
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Florence Bucciarelli
- Toulouse Institute for infectious and inflammatory diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier, Toulouse, France
| | - Andrea Flierl-Hecht
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Katja Anslinger
- Institute of Legal Medicine, Ludwig-Maximilians Universität München, Munich, Germany
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | | | | | | | - Hartmut Wekerle
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Institute for Biological Intelligence, Martinsried, Germany
| | - Martin Kerschensteiner
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany.,Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Jan D Lünemann
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians Universität München, Munich, Germany.,Biomedical Center, Faculty of Medicine, Ludwig-Maximilians Universität München, Martinsried, Germany
| | - Roland Liblau
- Toulouse Institute for infectious and inflammatory diseases (Infinity), University of Toulouse, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, Université Paul Sabatier, Toulouse, France
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University of Münster, Münster, Germany
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Asashima H, Axisa PP, Pham THG, Longbrake EE, Ruff WE, Lele N, Cohen I, Raddassi K, Sumida TS, Hafler DA. Impaired TIGIT expression on B cells drives circulating follicular helper T cell expansion in multiple sclerosis. J Clin Invest 2022; 132:156254. [PMID: 36250467 PMCID: PMC9566906 DOI: 10.1172/jci156254] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
B cell depletion in patients with relapsing-remitting multiple sclerosis (RRMS) markedly prevents new MRI-detected lesions and disease activity, suggesting the hypothesis that altered B cell function leads to the activation of T cells driving disease pathogenesis. Here, we performed comprehensive analyses of CD40 ligand- (CD40L-) and IL-21-stimulated memory B cells from patients with MS and healthy age-matched controls, modeling the help of follicular helper T cells (Tfh cells), and found a differential gene expression signature in multiple B cell pathways. Most striking was the impaired TIGIT expression on MS-derived B cells mediated by dysregulation of the transcription factor TCF4. Activated circulating Tfh cells (cTfh cells) expressed CD155, the ligand of TIGIT, and TIGIT on B cells revealed their capacity to suppress the proliferation of IL-17-producing cTfh cells via the TIGIT/CD155 axis. Finally, CCR6+ cTfh cells were significantly increased in patients with MS, and their frequency was inversely correlated with that of TIGIT+ B cells. Together, these data suggest that the dysregulation of negative feedback loops between TIGIT+ memory B cells and cTfh cells in MS drives the activated immune system in this disease.
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Single-Cell Analysis to Better Understand the Mechanisms Involved in MS. Int J Mol Sci 2022; 23:ijms232012142. [PMID: 36292995 PMCID: PMC9602568 DOI: 10.3390/ijms232012142] [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: 09/09/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/17/2022] Open
Abstract
Multiple sclerosis is a chronic and inflammatory disease of the central nervous system. Although this disease is widely studied, many of the precise mechanisms involved are still not well known. Numerous studies currently focusing on multiple sclerosis highlight the involvement of many major immune cell subsets, such as CD4+ T cells, CD8+ T cells and more recently B cells. However, our vision of its pathology has remained too broad to allow the proper use of targeted therapeutics. This past decade, new technologies have emerged, enabling deeper research into the different cell subsets at the single-cell level both in the periphery and in the central nervous system. These technologies could allow us to identify new cell populations involved in the disease process and new therapeutic targets. In this review, we briefly introduce the major single-cell technologies currently used in studies before diving into the major findings from the multiple sclerosis research from the past 5 years. We focus on results that were obtained using single-cell technologies to study immune cells and cells from the central nervous system.
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Abstract
Inflammation is a biological process that dynamically alters the surrounding microenvironment, including participating immune cells. As a well-protected organ surrounded by specialized barriers and with immune privilege properties, the central nervous system (CNS) tightly regulates immune responses. Yet in neuroinflammatory conditions, pathogenic immunity can disrupt CNS structure and function. T cells in particular play a key role in promoting and restricting neuroinflammatory responses, while the inflamed CNS microenvironment can influence and reshape T cell function and identity. Still, the contraction of aberrant T cell responses within the CNS is not well understood. Using autoimmunity as a model, here we address the contribution of CD4 T helper (Th) cell subsets in promoting neuropathology and disease. To address the mechanisms antagonizing neuroinflammation, we focus on the control of the immune response by regulatory T cells (Tregs) and describe the counteracting processes that preserve their identity under inflammatory challenges. Finally, given the influence of the local microenvironment on immune regulation, we address how CNS-intrinsic signals reshape T cell function to mitigate abnormal immune T cell responses.
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Affiliation(s)
- Nail Benallegue
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Nantes Université, CHU Nantes, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France
| | - Hania Kebir
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Jorge I. Alvarez
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104
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35
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Dressman D, Buttrick T, Cimpean M, Bennett D, Menon V, Bradshaw EM, Vardarajan B, Elyaman W. Genotype-phenotype correlation of T-cell subtypes reveals senescent and cytotoxic genes in Alzheimer's disease. Hum Mol Genet 2022; 31:3355-3366. [PMID: 35640154 PMCID: PMC9523563 DOI: 10.1093/hmg/ddac126] [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: 11/18/2021] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/12/2022] Open
Abstract
Recent studies identifying expression quantitative trait loci (eQTLs) in immune cells have uncovered important links between disease risk alleles and gene expression trends in monocytes, T cells and other cell types. However, these studies are generally done with young, healthy subjects, limiting the utility of their findings for age-related conditions such as Alzheimer's disease (AD). We have performed RNA sequencing on four T-cell subsets in genome-wide genotyped and well-characterized AD subjects and age- and sex-matched controls from the Religious Orders Study/Memory and Aging Project. We correlated gene expression data with AD neuropathological traits and with single-nucleotide polymorphisms to detect eQTLs. We identified several significant genes involved in T-cell senescence and cytotoxicity, consistent with T-cell RNA sequencing studies in aged/AD cohorts. We identified unexpected eQTLs previously associated with neuropsychiatric disease traits. Finally, we discovered that pathways related to axon guidance and synaptic function were enriched among trans-eQTLs in coding regions of the genome. Our data strengthen the potential link between T-cell senescence and age-related neurodegenerative disease. In addition, our eQTL data suggest that T-cell phenotypes may influence neuropsychiatric disorders and can be influenced by genes involved in neurodevelopmental processes.
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Affiliation(s)
- Dallin Dressman
- Department of Pharmacology, Columbia University, New York, NY 10032, USA
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | | | | | - David Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL 60612, USA
| | - Vilas Menon
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Elizabeth M Bradshaw
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
| | - Wassim Elyaman
- Department of Neurology, Columbia University, New York, NY 10032, USA
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY 10032, USA
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36
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Xiao H, Xiao H, Zhang Y, Guo L, Dou Z, Liu L, Zhu L, Feng W, Liu B, Hu B, Chen T, Liu G, Wen T. High-throughput sequencing unravels the cell heterogeneity of cerebrospinal fluid in the bacterial meningitis of children. Front Immunol 2022; 13:872832. [PMID: 36119025 PMCID: PMC9478118 DOI: 10.3389/fimmu.2022.872832] [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: 02/10/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial meningitis (BM) is a common life-threatening infection in children that occurs in the central nervous system (CNS). The cytologic examination of cerebrospinal fluid (CSF) is a key parameter in the diagnosis of BM, but the heterogeneity of cells in the CSF has not been elucidated, which limits the current understanding of BM neuroinflammation. In this study, CSF samples were collected from a number of BM patients who were in different stages of disease progression. Single-cell RNA-sequencing (scRNA-seq), with additional bulk transcriptome sequencing, was conducted to decipher the characteristics of CSF cells in BM progression. A total of 18 immune cell clusters in CSF were identified, including two neutrophils, two monocytes, one macrophage, four myeloid dendritic cells, five T cells, one natural killer cell, one B cell, one plasmacytoid dendritic cell, and one plasma cell subtype. Their population profiles and dynamics in the initial onset, remission, and recovery stages during BM progression were also characterized, which showed decreased proportions of myeloid cells and increased proportions of lymphoid cells with disease progression. One novel neutrophil subtype, FFAR2+TNFAIP6+ neutrophils, and one novel monocyte subtype, THBS1+IL1B+ monocytes, were discovered, and their quantity changes positively correlated with the intensity of the inflammatory response in the CSF during BM. In addition, the CSF of BM patients with unsatisfactory therapeutic responses presented with different cell heterogeneity compared to the CSF of BM patients with satisfactory therapeutic responses, and their CSF featured altered intercellular communications and increased proportions of type II myeloid dendritic cells and plasmacytoid dendritic cells. Moreover, the bulk transcriptome profiles of autologous CSF cells and peripheral blood leukocytes of BM patients showed that the immune cells in these two physiological compartments exhibited distinct immune responses under different onset conditions. In particular, the CSF cells showed a high expression of macrophage characteristic genes and a low expression of platelet characteristic genes compared with peripheral blood leukocytes. Our study conducted an in-depth exploration of the characteristics of CSF cells in BM progression, which provided novel insights into immune cell engagement in acute CNS infection.
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Affiliation(s)
- Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haijuan Xiao
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lingyun Guo
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhenzhen Dou
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Linlin Liu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Liang Zhu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Wenya Feng
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Bing Liu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Bing Hu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Tianming Chen
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Gang Liu
- Department of Infectious Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Tingyi Wen, ; Gang Liu,
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Tingyi Wen, ; Gang Liu,
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37
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Hu D, Xia W, Weiner HL. CD8 + T cells in neurodegeneration: friend or foe? Mol Neurodegener 2022; 17:59. [PMID: 36056406 PMCID: PMC9437386 DOI: 10.1186/s13024-022-00563-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/17/2022] [Indexed: 12/31/2023] Open
Affiliation(s)
- Dan Hu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA. .,Geriatric Research Education and Clinical Center, Bedford VA Healthcare System, Bedford, MA, 01730, USA.
| | - Weiming Xia
- Geriatric Research Education and Clinical Center, Bedford VA Healthcare System, Bedford, MA, 01730, USA.,Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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38
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Nguyen M, Palm NW. Gut instincts in neuroimmunity from the eighteenth to twenty-first centuries. Semin Immunopathol 2022; 44:569-579. [PMID: 35786740 PMCID: PMC9519704 DOI: 10.1007/s00281-022-00948-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/29/2022] [Indexed: 02/08/2023]
Abstract
In the past two decades, work on the microbiota-gut-brain axis has led to a renewed appreciation for the interconnectedness between body systems in both clinical and scientific circles. In the USA alone, millions of adults are burdened with non-communicable chronic diseases whose putative etiologies were previously thought to be restricted to either the gut or brain, such as inflammatory bowel disease, irritable bowel syndrome, Parkinson's and Alzheimer's disease, and autism spectrum disorder. However, the recent explosion of research into the impacts of the gut microbiome on diverse aspects of human health has revealed the potentially critical importance of reciprocal interactions between the gut microbiota, the immune system, and the brain in diverse diseases and disorders. In this review, we revisit the history of gut-brain interactions in science and medicine, which dates back to at least the eighteenth century, and outline how concepts in this field have shifted and evolved across eras. Next, we highlight the modern resurgence of gut-brain axis research, focusing on neuro-immune-microbiota interactions and recent progress towards a mechanistic understanding of the diverse impacts of the microbiome on human health. Finally, we offer a forward-looking perspective on the future of microbiota-gut-brain research, which may eventually reveal new paths towards the treatment of diverse diseases influenced by the complex connections between the microbiota and the brain.
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Affiliation(s)
- Mytien Nguyen
- Department of Immunobiology, Yale University School of Medicine, 10 Amistad Street, New Haven, CT, 06520, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Noah W Palm
- Department of Immunobiology, Yale University School of Medicine, 10 Amistad Street, New Haven, CT, 06520, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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39
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Heming M, Börsch AL, Wiendl H, Meyer Zu Hörste G. High-dimensional investigation of the cerebrospinal fluid to explore and monitor CNS immune responses. Genome Med 2022; 14:94. [PMID: 35978442 PMCID: PMC9385102 DOI: 10.1186/s13073-022-01097-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/28/2022] [Indexed: 01/15/2023] Open
Abstract
The cerebrospinal fluid (CSF) features a unique immune cell composition and is in constant contact with the brain borders, thus permitting insights into the brain to diagnose and monitor diseases. Recently, the meninges, which are filled with CSF, were identified as a neuroimmunological interface, highlighting the potential of exploring central nervous system (CNS) immunity by studying CNS border compartments. Here, we summarize how single-cell transcriptomics of such border compartments advance our understanding of neurological diseases, the challenges that remain, and what opportunities novel multi-omic methods offer. Single-cell transcriptomics studies have detected cytotoxic CD4+ T cells and clonally expanded T and B cells in the CSF in the autoimmune disease multiple sclerosis; clonally expanded pathogenic CD8+ T cells were found in the CSF and in the brain adjacent to β-amyloid plaques of dementia patients; in patients with brain metastases, CD8+ T cell clonotypes were shared between the brain parenchyma and the CSF and persisted after therapy. We also outline how novel multi-omic approaches permit the simultaneous measurements of gene expression, chromatin accessibility, and protein in the same cells, which remain to be explored in the CSF. This calls for multicenter initiatives to create single-cell atlases, posing challenges in integrating patients and modalities across centers. While high-dimensional analyses of CSF cells are challenging, they hold potential for personalized medicine by better resolving heterogeneous diseases and stratifying patients.
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Affiliation(s)
- Michael Heming
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Anna-Lena Börsch
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany
| | - Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, Münster, Germany.
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40
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Merkler D, Vincenti I, Masson F, Liblau RS. Tissue-resident CD8 T cells in central nervous system inflammatory diseases: present at the crime scene and …guilty. Curr Opin Immunol 2022; 77:102211. [DOI: 10.1016/j.coi.2022.102211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 11/03/2022]
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41
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Su Y, Li Z, Rang X, Wang Y, Fu J. Integrated Analysis and Identification of CSF-Derived Risk miRNAs and Pivotal Genes in Multiple Sclerosis. J Mol Neurosci 2022; 72:1916-1928. [PMID: 35819635 DOI: 10.1007/s12031-022-02007-9] [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: 02/04/2022] [Accepted: 03/25/2022] [Indexed: 11/24/2022]
Abstract
Multiple sclerosis (MS) is a common chronic autoimmune disorder of the central nervous system that predominantly affects young adults. Mounting evidence indicates that deregulation of microRNAs (miRNAs) in cerebrospinal fluid (CSF) has been implicated in MS as a potential biomarker. However, comprehensive assessments of CSF miRNAs and their target genes are lacking. Here, aberrantly expressed CSF miRNAs of MS patients were obtained from numerous studies by manual search. With detailed information on these miRNAs, we utilized online databases to screen out immune-related target genes and further performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. To identify MS high-risk pathways and pivotal genes, pathway crosstalk and pathway-gene networks were constructed, followed by the establishment of a protein-protein interaction (PPI) network. The datasets collected from ArrayExpress were used to assess pivotal genes. Overall, 21 MS-related CSF miRNAs were included in this study. Subsequently, we identified 469 MS-related genes and 14 high-risk pathways. In the pathway-gene network, 27 critical MS-related genes participated in at least half of the high-risk pathways, and these genes were used to identify pivotal genes. Finally, miR-150, miR-328, and miR-34c-5p were determined to be risk miRNAs via the regulation of the pivotal risk genes MAPK1, AKT1, and VEGFA. Among them, VEGFA was validated to be significantly decreased in the CSF cells of MS patients by transcriptomic datasets. These findings may provide potential biomarkers or therapeutic targets and help elucidate the molecular mechanisms underlying the pathogenesis of MS.
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Affiliation(s)
- Yingchao Su
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Zhihui Li
- Department of Neurology, The Fourth Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin, China
| | - Xinming Rang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Yifei Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin, 150086, China
| | - Jin Fu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Heilongjiang Province, Harbin, 150086, China.
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42
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Farhadian SF, Lindenbaum O, Zhao J, Corley MJ, Im Y, Walsh H, Vecchio A, Garcia-Milian R, Chiarella J, Chintanaphol M, Calvi R, Wang G, Ndhlovu LC, Yoon J, Trotta D, Ma S, Kluger Y, Spudich S. HIV viral transcription and immune perturbations in the CNS of people with HIV despite ART. JCI Insight 2022; 7:e160267. [PMID: 35801589 PMCID: PMC9310520 DOI: 10.1172/jci.insight.160267] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 01/12/2023] Open
Abstract
People with HIV (PWH) on antiretroviral therapy (ART) experience elevated rates of neurological impairment, despite controlling for demographic factors and comorbidities, suggesting viral or neuroimmune etiologies for these deficits. Here, we apply multimodal and cross-compartmental single-cell analyses of paired cerebrospinal fluid (CSF) and peripheral blood in PWH and uninfected controls. We demonstrate that a subset of central memory CD4+ T cells in the CSF produced HIV-1 RNA, despite apparent systemic viral suppression, and that HIV-1-infected cells were more frequently found in the CSF than in the blood. Using cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq), we show that the cell surface marker CD204 is a reliable marker for rare microglia-like cells in the CSF, which have been implicated in HIV neuropathogenesis, but which we did not find to contain HIV transcripts. Through a feature selection method for supervised deep learning of single-cell transcriptomes, we find that abnormal CD8+ T cell activation, rather than CD4+ T cell abnormalities, predominated in the CSF of PWH compared with controls. Overall, these findings suggest ongoing CNS viral persistence and compartmentalized CNS neuroimmune effects of HIV infection during ART and demonstrate the power of single-cell studies of CSF to better understand the CNS reservoir during HIV infection.
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Affiliation(s)
- Shelli F. Farhadian
- Department of Medicine, Section of Infectious Diseases, and
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ofir Lindenbaum
- Program in Applied Mathematics, and
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Jun Zhao
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, and
- Feil Family Brain & Mind Institute, Weill Cornell Medicine, New York, New York, USA
| | - Yunju Im
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Hannah Walsh
- Department of Medicine, Section of Infectious Diseases, and
| | - Alyssa Vecchio
- University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, USA
| | - Rolando Garcia-Milian
- Bioinformatics Support Program, Cushing/Whitney Medical Library, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jennifer Chiarella
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Rachela Calvi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Guilin Wang
- Yale Center for Genome Analysis, Yale University, New Haven, Connecticut, USA
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, and
- Feil Family Brain & Mind Institute, Weill Cornell Medicine, New York, New York, USA
| | - Jennifer Yoon
- Department of Medicine, Section of Infectious Diseases, and
| | - Diane Trotta
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yuval Kluger
- Program in Applied Mathematics, and
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Serena Spudich
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
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43
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Proulx ST, Engelhardt B. Central nervous system zoning: How brain barriers establish subdivisions for CNS immune privilege and immune surveillance. J Intern Med 2022; 292:47-67. [PMID: 35184353 PMCID: PMC9314672 DOI: 10.1111/joim.13469] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The central nervous system (CNS) coordinates all our body functions. Neurons in the CNS parenchyma achieve this computational task by high speed communication via electrical and chemical signals and thus rely on a strictly regulated homeostatic environment, which does not tolerate uncontrolled entry of blood components including immune cells. The CNS thus has a unique relationship with the immune system known as CNS immune privilege. Previously ascribed to the presence of blood-brain barriers and the lack of lymphatic vessels in the CNS parenchyma prohibiting, respectively, efferent and afferent connections with the peripheral immune system, it is now appreciated that CNS immune surveillance is ensured by cellular and acellular brain barriers that limit immune cell and mediator accessibility to specific compartments at the borders of the CNS. CNS immune privilege is established by a brain barriers anatomy resembling the architecture of a medieval castle surrounded by two walls bordering a castle moat. Built for protection and defense this two-walled rampart at the outer perimeter of the CNS parenchyma allows for accommodation of different immune cell subsets and efficient monitoring of potential danger signals derived from inside or outside of the CNS parenchyma. It enables effective mounting of immune responses within the subarachnoid or perivascular spaces, while leaving the CNS parenchyma relatively undisturbed. In this study, we propose that CNS immune privilege rests on the proper function of the brain barriers, which allow for CNS immune surveillance but prohibit activation of immune responses from the CNS parenchyma unless it is directly injured.
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Affiliation(s)
- Steven T Proulx
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
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44
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Basic principles of neuroimmunology. Semin Immunopathol 2022; 44:685-695. [PMID: 35732977 DOI: 10.1007/s00281-022-00951-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 05/08/2022] [Indexed: 01/20/2023]
Abstract
The brain is an immune-privileged organ such that immune cell infiltration is highly regulated and better tolerating the introduction of antigen to reduce risk of harmful inflammation. Thus, the composition and the nature of the immune response is fundamentally different in the brain where avoiding immunopathology is prioritized compared to other peripheral organs. While the principle of immune privilege in the central nervous system (CNS) still holds true, the role of the immune system in the CNS has been revisited over the recent years. This redefining of immune privilege in the brain is a result of the recent re-discovery of the extensive CNS meningeal lymphatic system and the identification of resident T cells in the brain, meningeal layers, and its surrounding cerebrospinal fluid (CSF) in both humans and rodents. While neuro-immune interactions have been classically studied in the context of neuroinflammatory disease, recent works have also elucidated unconventional roles of immune-derived cytokines in neurological function, highlighting the many implications and potential of neuro-immune interactions. As a result, the study of neuro-immune interactions is becoming increasingly important in understanding both CNS homeostasis and disease. Here, we review the anatomically distinct immune compartments within the brain, the known mechanisms of leukocyte trafficking and infiltration into the CNS and unique transcriptional and functional characteristics of CNS-resident immune cells.
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Paley MA, Baker BJ, Dunham SR, Linskey N, Cantoni C, Lee K, Hassman LM, Laurent J, Roberson EDO, Clifford DB, Yokoyama WM. The CSF in neurosarcoidosis contains consistent clonal expansion of CD8 T cells, but not CD4 T cells. J Neuroimmunol 2022; 367:577860. [PMID: 35405431 PMCID: PMC9338453 DOI: 10.1016/j.jneuroim.2022.577860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Accepted: 03/29/2022] [Indexed: 01/02/2023]
Abstract
The tissue-specific drivers of neurosarcoidosis remain poorly defined. To identify cerebrospinal fluid (CSF) specific, antigen-driven T and B cell responses, we performed single-cell RNA sequencing of CSF and blood cells from neurosarcoid participants coupled to T and B cell receptor sequencing. In contrast to pulmonary sarcoidosis, which is driven by CD4 T cells, we found CD8 T cell clonal expansion enriched in the neurosarcoid CSF. These CSF-enriched CD8 T cells were composed of two subsets with differential expression of EBI2, CXCR3, and CXCR4. Lastly, our data suggest that IFNγ signaling may distinguish neurosarcoidosis from other neurological disorders.
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Affiliation(s)
- Michael A Paley
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States of America.
| | - Brandi J Baker
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - S Richard Dunham
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Nicole Linskey
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Claudia Cantoni
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Kenneth Lee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Lynn M Hassman
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Jennifer Laurent
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Elisha D O Roberson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States of America; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - David B Clifford
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, United States of America
| | - Wayne M Yokoyama
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States of America.
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Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones. Immunity 2022; 55:1013-1031.e7. [PMID: 35320704 PMCID: PMC9203927 DOI: 10.1016/j.immuni.2022.03.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/19/2022] [Accepted: 03/08/2022] [Indexed: 02/02/2023]
Abstract
Understanding the drivers and markers of clonally expanding HIV-1-infected CD4+ T cells is essential for HIV-1 eradication. We used single-cell ECCITE-seq, which captures surface protein expression, cellular transcriptome, HIV-1 RNA, and TCR sequences within the same single cell to track clonal expansion dynamics in longitudinally archived samples from six HIV-1-infected individuals (during viremia and after suppressive antiretroviral therapy) and two uninfected individuals, in unstimulated conditions and after CMV and HIV-1 antigen stimulation. Despite antiretroviral therapy, persistent antigen and TNF responses shaped T cell clonal expansion. HIV-1 resided in Th1-polarized, antigen-responding T cells expressing BCL2 and SERPINB9 that may resist cell death. HIV-1 RNA+ T cell clones were larger in clone size, established during viremia, persistent after viral suppression, and enriched in GZMB+ cytotoxic effector memory Th1 cells. Targeting HIV-1-infected cytotoxic CD4+ T cells and drivers of clonal expansion provides another direction for HIV-1 eradication.
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Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder which affects 6.1 million people worldwide. The neuropathological hallmarks include the loss of dopaminergic neurons in the substantia nigra, the presence of Lewy bodies and Lewy neurites caused by α-synuclein aggregation, and neuroinflammation in the brain. The prodromal phase happens years before the onset of PD during which time many patients show gastro-intestinal symptoms. These symptoms are in support of Braak’s theory and model where pathological α‐synuclein propagates from the gut to the brain. Importantly, immune responses play a determinant role in the pathogenesis of Parkinson’s disease. The innate immune responses triggered by microglia can cause neuronal death and disease progression. In addition, T cells infiltrate into the brains of PD patients and become involved in the adaptive immune responses. Interestingly, α‐synuclein is associated with both innate and adaptive immune responses by directly interacting with microglia and T cells. Here, we give a detailed review of the immunobiology of Parkinson’s disease, focusing on the role α-synuclein in the gut-brain axis hypothesis, the innate and adaptive immune responses involved in the disease, and current treatments.
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Single-cell multiomics in neuroinflammation. Curr Opin Immunol 2022; 76:102180. [DOI: 10.1016/j.coi.2022.102180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 03/21/2022] [Indexed: 11/17/2022]
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49
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Beliën J, Goris A, Matthys P. Natural Killer Cells in Multiple Sclerosis: Entering the Stage. Front Immunol 2022; 13:869447. [PMID: 35464427 PMCID: PMC9019710 DOI: 10.3389/fimmu.2022.869447] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/14/2022] [Indexed: 11/14/2022] Open
Abstract
Studies investigating the immunopathology of multiple sclerosis (MS) have largely focused on adaptive T and B lymphocytes. However, in recent years there has been an increased interest in the contribution of innate immune cells, amongst which the natural killer (NK) cells. Apart from their canonical role of controlling viral infections, cell stress and malignancies, NK cells are increasingly being recognized for their modulating effect on the adaptive immune system, both in health and autoimmune disease. From different lines of research there is now evidence that NK cells contribute to MS immunopathology. In this review, we provide an overview of studies that have investigated the role of NK cells in the pathogenesis of MS by use of the experimental autoimmune encephalomyelitis (EAE) animal model, MS genetics or through ex vivo and in vitro work into the immunology of MS patients. With the advent of modern hypothesis-free technologies such as single-cell transcriptomics, we are exposing an unexpected NK cell heterogeneity, increasingly blurring the boundaries between adaptive and innate immunity. We conclude that unravelling this heterogeneity, as well as the mechanistic link between innate and adaptive immune cell functions will lay the foundation for the use of NK cells as prognostic tools and therapeutic targets in MS and a myriad of other currently uncurable autoimmune disorders.
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Affiliation(s)
- Jarne Beliën
- Department of Neurosciences, Laboratory for Neuroimmunology, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - An Goris
- Department of Neurosciences, Laboratory for Neuroimmunology, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Patrick Matthys
- Department of Microbiology, Immunology and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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50
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Frieser D, Pignata A, Khajavi L, Shlesinger D, Gonzalez-Fierro C, Nguyen XH, Yermanos A, Merkler D, Höftberger R, Desestret V, Mair KM, Bauer J, Masson F, Liblau RS. Tissue-resident CD8 + T cells drive compartmentalized and chronic autoimmune damage against CNS neurons. Sci Transl Med 2022; 14:eabl6157. [PMID: 35417189 DOI: 10.1126/scitranslmed.abl6157] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mechanisms underlying the chronicity of autoimmune diseases of the central nervous system (CNS) are largely unknown. In particular, it is unclear whether tissue-resident memory T cells (TRM) contribute to lesion pathogenesis during chronic CNS autoimmunity. Here, we observed that a high frequency of brain-infiltrating CD8+ T cells exhibit a TRM-like phenotype in human autoimmune encephalitis. Using mouse models of neuronal autoimmunity and a combination of T single-cell transcriptomics, high-dimensional flow cytometry, and histopathology, we found that pathogenic CD8+ T cells behind the blood-brain barrier adopt a characteristic TRM differentiation program, and we revealed their phenotypic and functional heterogeneity. In the diseased CNS, autoreactive tissue-resident CD8+ T cells sustained focal neuroinflammation and progressive loss of neurons, independently of recirculating CD8+ T cells. Consistently, a large fraction of autoreactive tissue-resident CD8+ T cells exhibited proliferative potential as well as proinflammatory and cytotoxic properties. Persistence of tissue-resident CD8+ T cells in the CNS and their functional output, but not their initial differentiation, were crucially dependent on CD4+ T cells. Collectively, our results point to tissue-resident CD8+ T cells as essential drivers of chronic CNS autoimmunity and suggest that therapies targeting this compartmentalized autoreactive T cell subset might be effective for treating CNS autoimmune diseases.
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Affiliation(s)
- David Frieser
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | - Aurora Pignata
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | - Leila Khajavi
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | | | - Carmen Gonzalez-Fierro
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | - Xuan-Hung Nguyen
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | - Alexander Yermanos
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland.,Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.,Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland.,Division of Clinical Pathology, Geneva University Hospital, 1211 Geneva, Switzerland
| | - Romana Höftberger
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Virginie Desestret
- National Reference Center for Paraneoplastic Neurological Syndromes, MeLiS-UCBL-CNRS, INSERM, Hôpital Neurologique, Hospices Civils de Lyon, 69500 Lyon, France
| | - Katharina M Mair
- Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Jan Bauer
- Center for Brain Research, Medical University of Vienna, 1090 Vienna, Austria
| | - Frederick Masson
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France
| | - Roland S Liblau
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), University of Toulouse, CNRS, INSERM, UPS, 31024 Toulouse, France.,Department of Immunology, Toulouse University Hospital, 31300 Toulouse, France
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