1
|
Pogorelyy MV, Kirk AM, Adhikari S, Minervina AA, Sundararaman B, Vegesana K, Brice DC, Scott ZB, Thomas PG. TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613345. [PMID: 39345544 PMCID: PMC11430070 DOI: 10.1101/2024.09.16.613345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
α/β T cells are key players in adaptive immunity. The specificity of T cells is determined by the sequences of the hypervariable T cell receptor (TCR) α and β chains. Although bulk TCR sequencing offers a cost-effective approach for in-depth TCR repertoire profiling, it does not provide chain pairings, which are essential for determining T cell specificity. In contrast, single-cell TCR sequencing technologies produce paired chain data, but are limited in throughput to thousands of cells and are cost-prohibitive for cohort-scale studies. Here, we present TIRTL-seq (Throughput-Intensive Rapid TCR Library sequencing), a novel approach that generates ready-to-sequence TCR libraries from live cells in less than 7 hours. The protocol is optimized for use with non-contact liquid handlers in an automation-friendly 384-well plate format. Reaction volume miniaturization reduces library preparation costs to <$0.50 per well. The core principle of TIRTL-seq is the parallel generation of hundreds of libraries providing multiple biological replicates from a single sample that allows precise inference of both frequencies of individual clones and TCR chain pairings from well-occurrence patterns. We demonstrate scalability of our approach up to 1 million unique paired αβTCR clonotypes corresponding to over 30 million T cells per sample at a cost of less than $2000. For a sample of 10 million cells the cost is ~$200. We benchmarked TIRTL-seq against state-of-the-art 5'RACE bulk TCR-seq and 10x Genomics Chromium technologies on longitudinal samples. We show that TIRTL-seq is able to quantitatively identify expanding and contracting clonotypes between timepoints while providing accurate TCR chain pairings, including distinct temporal dynamics of SARS-CoV-2-specific and EBV-specific CD8+ T cell responses after infection. While clonal expansion was followed by sharp contraction for SARS-CoV-2 specific TCRs, EBV-specific TCRs remained stable once established. The sequences of both α and β TCR chains are essential for determining T cell specificity. As the field moves towards greater applications in diagnostics and immunotherapy that rely on TCR specificity, we anticipate that our scalable paired TCR sequencing methodology will be instrumental for collecting large paired-chain datasets and ultimately extracting therapeutically relevant information from the TCR repertoire.
Collapse
Affiliation(s)
| | | | | | | | | | - Kasi Vegesana
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David C Brice
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Paul G Thomas
- St. Jude Children's Research Hospital, Memphis, TN, USA
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Abbadessa G, Lepore MT, Bruzzaniti S, Piemonte E, Miele G, Signoriello E, Perna F, De Falco C, Lus G, Matarese G, Bonavita S, Galgani M. Ocrelizumab Alters Cytotoxic Lymphocyte Function While Reducing EBV-Specific CD8 + T-Cell Proliferation in Patients With Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200250. [PMID: 38662990 PMCID: PMC11087045 DOI: 10.1212/nxi.0000000000200250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 03/08/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND AND OBJECTIVES The role of B cells in the pathogenic events leading to relapsing multiple sclerosis (R-MS) has only been recently elucidated. A pivotal step in defining this role has been provided by therapeutic efficacy of anti-CD20 monoclonal antibodies. Indeed, treatment with anti-CD20 can also alter number and function of other immune cells not directly expressing CD20 on their cell surface, whose activities can contribute to unknown aspects influencing therapeutic efficacy. We examined the phenotype and function of cytotoxic lymphocytes and Epstein-Barr virus (EBV)-specific immune responses in people with R-MS before and after ocrelizumab treatment. METHODS In this prospective study, we collected blood samples from people with R-MS (n = 41) before and 6 and 12 months after initiating ocrelizumab to assess the immune phenotype and the indirect impact on cytotoxic functions of CD8+ T and NK cells. In addition, we evaluated the specific anti-EBV proliferative responses of both CD8+ T and NK lymphocytes as surrogate markers of anti-EBV activity. RESULTS We observed that while ocrelizumab depleted circulating B cells, it also reduced the expression of activation and migratory markers on both CD8+ T and NK cells as well as their in vitro cytotoxic activity. A comparable pattern in the modulation of immune molecules by ocrelizumab was observed in cytotoxic cells even when patients with R-MS were divided into groups based on their prior disease-modifying treatment. These effects were accompanied by a significant and selective reduction of CD8+ T-cell proliferation in response to EBV antigenic peptides. DISCUSSION Taken together, our findings suggest that ocrelizumab-while depleting B cells-affects the cytotoxic function of CD8+ and NK cells, whose reduced cross-activity against myelin antigens might also contribute to its therapeutic efficacy during MS.
Collapse
MESH Headings
- Humans
- Antibodies, Monoclonal, Humanized/pharmacology
- Female
- Adult
- Male
- Herpesvirus 4, Human/immunology
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- Middle Aged
- Immunologic Factors/pharmacology
- Multiple Sclerosis, Relapsing-Remitting/drug therapy
- Multiple Sclerosis, Relapsing-Remitting/immunology
- Multiple Sclerosis, Relapsing-Remitting/blood
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- Prospective Studies
- Cell Proliferation/drug effects
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Lymphocyte Activation/drug effects
Collapse
Affiliation(s)
- Gianmarco Abbadessa
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Maria Teresa Lepore
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Sara Bruzzaniti
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Erica Piemonte
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Giuseppina Miele
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Elisabetta Signoriello
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Francesco Perna
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Chiara De Falco
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - G Lus
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Giuseppe Matarese
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Simona Bonavita
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| | - Mario Galgani
- From the Department of Advanced Medical and Surgical Sciences (G.A., G. Miele, E.S., G.L., S. Bonavita), University of Campania Luigi Vanvitelli; Istituto per l'Endocrinologia e l'Oncologia Sperimentale "G.Salvatore" - Consiglio Nazionale delle Ricerche (M.T.L., S. Bruzzaniti, G. Matarese, M.G.); Department of Molecular Medicine and Medical Biotechnologies (E.P., G. Matarese, M.G.); Department of Clinical Medicine and Surgery (F.P.), University of Naples "Federico II"; and UOC Biochimica Clinica - Ospedali dei Colli (C.D.F.), Naples, Italy
| |
Collapse
|
4
|
Hu Y, Huang J, Wang S, Sun X, Wang X, Yu H. Deciphering Autoimmune Diseases: Unveiling the Diagnostic, Therapeutic, and Prognostic Potential of Immune Repertoire Sequencing. Inflammation 2024:10.1007/s10753-024-02079-2. [PMID: 38914737 DOI: 10.1007/s10753-024-02079-2] [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: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/08/2024] [Indexed: 06/26/2024]
Abstract
Autoimmune diseases (AIDs) are immune system disorders where the body exhibits an immune response to its own antigens, causing damage to its own tissues and organs. The pathogenesis of AIDs is incompletely understood. However, recent advances in immune repertoire sequencing (IR-seq) technology have opened-up a new avenue to study the IR. These studies have revealed the prevalence in IR alterations, potentially inducing AIDs by disrupting immune tolerance and thereby contributing to our comprehension of AIDs. IR-seq harbors significant potential for the clinical diagnosis, personalized treatment, and prognosis of AIDs. This article reviews the application and progress of IR-seq in diseases, such as multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and type 1 diabetes, to enhance our understanding of the pathogenesis of AIDs and offer valuable references for the diagnosis and treatment of AIDs.
Collapse
Affiliation(s)
- Yuelin Hu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Jialing Huang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Shuqing Wang
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Sun
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Xin Wang
- School of Basic Medical Sciences, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou, P.R. China.
| |
Collapse
|
5
|
Münz C. Altered EBV specific immune control in multiple sclerosis. J Neuroimmunol 2024; 390:578343. [PMID: 38615370 DOI: 10.1016/j.jneuroim.2024.578343] [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: 02/03/2024] [Revised: 03/23/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Since the 1980s it is known that immune responses to the Epstein-Barr virus (EBV) are elevated in multiple sclerosis (MS) patients. Recent seroepidemiologial data have shown that this alteration after primary EBV infection identifies individuals with a more than 30-fold increased risk to develop MS. The mechanisms by which EBV infection might erode tolerance for the central nervous system (CNS) in these individuals, years prior to clinical MS onset, remain unclear. In this review I will discuss altered frequencies of EBV life cycle stages and their tissue distribution, EBV with CNS autoantigen cross-reactive immune responses and loss of immune control for autoreactive B and T cells as possible mechanisms. This discussion is intended to stimulate future studies into these mechanisms with the aim to identify candidates for interventions that might correct EBV specific immune control and/or resulting cross-reactivities with CNS autoantigens in MS patients and thereby ameliorate disease activity.
Collapse
Affiliation(s)
- Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Switzerland.
| |
Collapse
|
6
|
Dungan L, Dunne J, Savio M, Kalaszi M, McElheron M, Lynagh Y, O'Driscoll K, Roche C, Qureshi A, Crowley B, Conlon N, Kearney H. Disease-Modifying Treatments for Multiple Sclerosis Affect Measures of Cellular Immune Responses to EBNA-1 Peptides. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200217. [PMID: 38547427 DOI: 10.1212/nxi.0000000000200217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/19/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND AND OBJECTIVES Epstein-Barr virus (EBV) has been strongly implicated in the pathogenesis of multiple sclerosis (MS). Despite this, there are no routinely used tests to measure cellular response to EBV. In this study, we analyzed the cellular response to EBV nuclear antigen-1 (EBNA-1) in people with MS (pwMS) using a whole blood assay. METHODS This cross-sectional study took place in a dedicated MS clinic in a university hospital. We recruited healthy controls, people with epilepsy (PWE), and pwMS taking a range of disease-modifying treatments (DMTs) including natalizumab, anti-CD20 monoclonal antibodies (mAbs), dimethyl fumarate (DMF), and also treatment naïve. Whole blood samples were stimulated with commercially available PepTivator EBNA1 peptides and a control virus-cytomegalovirus (CMV) peptide. We recorded the cellular response to stimulation with both interferon gamma (IFN-γ) and interleukin-2 (IL-2). We also compared the cellular responses to EBNA1 with IgG responses to EBNA1, viral capsid antigen (VCA), and EBV viral load. RESULTS We recruited 86 pwMS, with relapsing remitting MS, in this group, and we observed a higher level of cellular response recorded with IFN-γ (0.79 IU/mL ± 1.36) vs healthy controls (0.29 IU/mL ± 0.90, p = 0.0048) and PWE (0.17 IU/mL ± 0.33, p = 0.0088). Treatment with either anti-CD20 mAbs (0.28 IU/mL ± 0.57) or DMF (0.07 IU/mL ± 0.15) resulted in a cellular response equivalent to control levels or in PWE (p = 0.26). The results of recording IL-2 response were concordant with IFN-γ: with suppression also seen with anti-CD20 mAbs and DMF. By contrast, we did not record any differential effect of DMTs on the levels of IgG to either EBNA-1 or VCA. Nor did we observe differences in cellular response to cytomegalovirus between groups. DISCUSSION This study demonstrates how testing and recording the cellular response to EBNA-1 in pwMS may be beneficial. EBNA-1 stimulation of whole blood samples produced higher levels of IFN-γ and IL-2 in pwMS compared with controls and PWE. In addition, we show a differential effect of currently available DMTs on this response. The functional assay deployed uses whole blood samples with minimal preprocessing suggesting that employment as a treatment response measure in clinical trials targeting EBV may be possible.
Collapse
Affiliation(s)
- Lara Dungan
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Jean Dunne
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Michael Savio
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Marianna Kalaszi
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Matt McElheron
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Yvonne Lynagh
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Kate O'Driscoll
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Carmel Roche
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Ammara Qureshi
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Brendan Crowley
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Niall Conlon
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| | - Hugh Kearney
- From the Department of Immunology (L.D., J.D., N.C.), St James's Hospital; School of Medicine (M.S., N.C.), Trinity College Dublin; MS Unit (M.K., H.K.), Department of Neurology, St James's Hospital; Department of Medical Gerontology (M.M.), School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin; Virology Laboratory (Y.L., K.O.D., C.R., A.Q., B.C.), St James's Hospital; and FutureNeuro SFI Research Centre (H.K.), Academic Unit of Neurology, School of Medicine, Trinity College Dublin, Ireland
| |
Collapse
|
7
|
Serafini B, Benincasa L, Rosicarelli B, Aloisi F. EBV infected cells in the multiple sclerosis brain express PD-L1: How the virus and its niche may escape immune surveillance. J Neuroimmunol 2024; 389:578314. [PMID: 38422689 DOI: 10.1016/j.jneuroim.2024.578314] [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: 11/30/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024]
Abstract
The presence of EBV infected B cells in postmortem multiple sclerosis (MS) brain tissue suggests immune evasion strategies. Using immunohistochemical techniques we analysed the expression of the immune checkpoint molecule PD-L1 and its receptor PD-1 in MS brains containing B cell-enriched perivascular infiltrates and meningeal follicles, a major EBV reservoir. PD-1 and PD-L1 immunoreactivities were restricted to CNS-infiltrating immune cells. PD-L1 was expressed on B cells, including EBV infected B cells, while PD-1 was expressed on many CD8+ T cells, including EBV-specific CD8+ T-cells, and fewer CD4+ T cells. PD-L1+ cells and EBV infected cells were in close contact with PD-1+ T cells. PD-L1 expressed by EBV infected B cells could favour local immune evasion leading to EBV persistence and immunopathology in the MS brain.
Collapse
Affiliation(s)
- Barbara Serafini
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Lucia Benincasa
- 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.
| | - Francesca Aloisi
- Department of Neuroscience, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| |
Collapse
|
8
|
Fang J, Lei J, He B, Wu Y, Chen P, Sun Z, Wu N, Huang Y, Wei P, Yin L, Chen Y. Decoding the transcriptional heterogeneity, differentiation lineage, clinical significance in tissue-resident memory CD8 T cell of the small intestine by single-cell analysis. J Transl Med 2024; 22:203. [PMID: 38403590 PMCID: PMC10895748 DOI: 10.1186/s12967-024-04978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/11/2024] [Indexed: 02/27/2024] Open
Abstract
Resident memory T (Trm) cells which are specifically located in non-lymphoid tissues showed distinct phenotypes and functions compared to circulating memory T cells and were vital for the initiation of robust immune response within tissues. However, the heterogeneity in the transcriptional features, development pathways, and cancer response of Trm cells in the small intestine was not demonstrated. Here, we integrated scRNA-seq and scTCR-seq data pan-tissue T cells to explore the heterogeneity of Trm cells and their development pathways. Trm were enriched in tissue-specific immune response and those in the DUO specially interacted with B cells via TNF and MHC-I signatures. T cell lineage analyses demonstrated that Trm might be derived from the T_CD4/CD8 subset within the same organ or migrated from spleen and mesenteric lymph nodes. We compared the immune repertoire of Trm among organs and implied that clonotypes in both DUO and ILE were less expanded and hydrophilic TRB CDR3s were enriched in the DUO. We further demonstrated that Trm in the intestine infiltrated the colorectal cancer and several effector molecules were highly expressed. Finally, the TCGA dataset of colorectal cancer implied that the infiltration of Trm from the DUO and the ILE was beneficial for overall survival and the response to immune checkpoint blockade.
Collapse
Affiliation(s)
- Jialing Fang
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jun Lei
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
- Department of Laboratory Medicine, Xixi Hospital of Hangzhou, Hangzhou, China
| | - Boxiao He
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Yankang Wu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Peng Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Zaiqiao Sun
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Ning Wu
- Department of Immunology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yafei Huang
- Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pengcheng Wei
- School of Medicine, Guangxi University, Nanning, 530004, China
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO, 80206, USA
| | - Lei Yin
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.
| | - Yongshun Chen
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Lehikoinen J, Valori M, Jääskeläinen AJ, Laakso SM, Arstila TP, Tienari PJ. High Epstein-Barr virus capsid antigen IgG level associates with the carriership of CD8+ T cell somatic mutations in the STAT3 SH2 domain. Clin Immunol 2023; 255:109733. [PMID: 37572949 DOI: 10.1016/j.clim.2023.109733] [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: 07/05/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
High carrier prevalence of STAT3 SH2 domain somatic mutations was recently discovered in CD8+ T cells. We found these low-allele-fraction clones in 26% of donors, without difference between multiple sclerosis (MS) patients and controls. Here we tested whether anti-viral antibodies associate with the carriership of these mutant clones. We compared antibody responses against common viruses in mutation carriers vs. non-carriers. Plasma samples of 152 donors (92 MS patients, 60 controls) were analyzed for antibodies against cytomegalovirus (CMV), Epstein-Barr virus (EBV), human herpesvirus-6A and parvovirus B19. The mutation carrier status associated with EBV VCA IgG level (p = 0.005) and remained significant after logistic regression (p = 0.036). This association was contributed similarly by MS patients and controls. These results suggest that EBV contributes to the generation or growth of these clones. The pathogenic role of the STAT3 mutant clones in MS is presently unclear, but their detailed characterization warrants further study.
Collapse
Affiliation(s)
- Joonas Lehikoinen
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland.
| | - Miko Valori
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Anne J Jääskeläinen
- HUS Diagnostic Center, Clinical Microbiology, University of Helsinki and Helsinki University Hospital
| | - Sini M Laakso
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland
| | - T Petteri Arstila
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Bacteriology and Immunology, Medicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pentti J Tienari
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland; Department of Neurology, Brain Center, Helsinki University Hospital, Helsinki, Finland
| |
Collapse
|
11
|
Massey J, Artuz C, Dyer Z, Jackson K, Khoo M, Visweswaran M, Withers B, Moore J, Ma D, Sutton I. Diversification and expansion of the EBV-reactive cytotoxic T lymphocyte repertoire following autologous haematopoietic stem cell transplant for multiple sclerosis. Clin Immunol 2023; 254:109709. [PMID: 37495004 DOI: 10.1016/j.clim.2023.109709] [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: 06/05/2023] [Revised: 07/07/2023] [Accepted: 07/23/2023] [Indexed: 07/28/2023]
Abstract
Both genetic susceptibility and environmental exposures are thought to be involved in multiple sclerosis (MS) pathogenesis. Of all viruses potentially relevant to MS aetiology, Epstein-Barr virus (EBV) is the best-studied. EBV is a B cell lymphotropic virus which is able to evade the immune system by establishing latent infection in memory B cells, and EBV reactivation is restricted by CD8 cytotoxic T cell (CTL) responses in immune competent individuals. Autologous haematopoietic stem cell transplantation (AHSCT) is considered to be the most effective therapy in the treatment of relapsing MS even though chemotherapy-induced lymphopenia can associate with the re-emergence of latent viruses. Despite the increasing interest in EBV and MS pathogenesis the relationship between AHSCT, EBV and viral immunity in people with MS has not been investigated to date. This study analysed immune responses to EBV in a well characterised cohort of 13 individuals with MS by utilising pre-AHSCT, and 6-, 12- and 24-month post AHSCT bio-banked peripheral blood mononuclear cells and plasma samples. It is demonstrated that the infused stem cell product contains latently EBV-infected memory B cells, and that EBV viremia occurs in the immune-compromised recipient post-transplant. High throughput TCR analysis detected expansion and diversification of the CD8 CTL responses reactive with EBV lytic and latent antigens from 6 to 24 months following AHSCT. Increased levels of latent EBV infection found within the B cell pool following treatment, as measured by EBV genomic detection, did not associate with disease relapse. This is the first study of EBV immunity following application of AHSCT in the treatment of MS and not only raises important questions about the role of EBV infection in MS pathogenesis, but is of clinical importance given the expanding clinical trials of adoptive EBV-specific CTLs in MS.
Collapse
Affiliation(s)
- Jennifer Massey
- Department of Neurology, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia.
| | - Crisbel Artuz
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia
| | - Zoe Dyer
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia
| | - Katherine Jackson
- Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Melissa Khoo
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia
| | - Malini Visweswaran
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia
| | - Barbara Withers
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia; Department of Haematology, St Vincent's Hospital; Darlinghurst, NSW 2010, Australia
| | - John Moore
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia; Department of Haematology, St Vincent's Hospital; Darlinghurst, NSW 2010, Australia
| | - David Ma
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical Research, Darlinghurst, NSW 2010, Australia; School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia; Department of Haematology, St Vincent's Hospital; Darlinghurst, NSW 2010, Australia
| | - Ian Sutton
- School of Clinical Medicine, St Vincent's Healthcare Clinical Campus, Faculty of Medicine and Health, UNSW, Sydney, Australia; Department of Neurology, St Vincent's Clinic; Darlinghurst, NSW 2010, Australia
| |
Collapse
|
12
|
Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
Collapse
Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
| |
Collapse
|
13
|
Nozuma S, Matsuura E, Tanaka M, Kodama D, Matsuzaki T, Yoshimura A, Sakiyama Y, Nakahata S, Morishita K, Enose-Akahata Y, Jacoboson S, Kubota R, Takashima H. Identification and tracking of HTLV-1-infected T cell clones in virus-associated neurologic disease. JCI Insight 2023; 8:167422. [PMID: 37036006 PMCID: PMC10132145 DOI: 10.1172/jci.insight.167422] [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: 11/22/2022] [Accepted: 02/21/2023] [Indexed: 04/11/2023] Open
Abstract
Human T lymphotropic virus type 1-assoicated (HTLV-1-associated) myelopathy/tropical spastic paraparesis (HAM/TSP) is a neuroinflammatory disease caused by the persistent proliferation of HTLV-1-infected T cells. Here, we performed a T cell receptor (TCR) repertoire analysis focused on HTLV-1-infected cells to identify and track the infected T cell clones that are preserved in patients with HAM/TSP and migrate to the CNS. TCRβ repertoire analysis revealed higher clonal expansion in HTLV-1-infected cells compared with noninfected cells from patients with HAM/TSP and asymptomatic carriers (ACs). TCR clonality in HTLV-1-infected cells was similar in patients with HAM/TSP and ACs. Longitudinal analysis showed that the TCR repertoire signature in HTLV-1-infected cells remained stable, and highly expanded infected clones were preserved within each patient with HAM/TSP over years. Expanded HTLV-1-infected clones revealed different distributions between cerebrospinal fluid (CSF) and peripheral blood and were enriched in the CSF of patients with HAM/TSP. Cluster analysis showed similarity in TCRβ sequences in HTLV-1-infected cells, suggesting that they proliferate after common antigen stimulation. Our results indicate that exploring TCR repertoires of HTLV-1-infected cells can elucidate individual clonal dynamics and identify potential pathogenic clones expanded in the CNS.
Collapse
Affiliation(s)
- Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Masakazu Tanaka
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Daisuke Kodama
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Toshio Matsuzaki
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yusuke Sakiyama
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Shingo Nakahata
- Division of HTLV-1/ATL Carcinogenesis and Therapeutics, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
| | - Kazuhiro Morishita
- Project for Advanced Medical Research and Development, Project Research Division, Frontier Science Research Center, University of Miyazaki, Miyazaki, Japan
| | - Yoshimi Enose-Akahata
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Steven Jacoboson
- Viral Immunology Section, Neuroimmunology Branch, National Institute of Neurological Disorder and Stroke, NIH, Bethesda, Maryland, USA
| | - Ryuji Kubota
- Division of Neuroimmunology, Joint Research Center for Human Retrovirus Infection, and
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| |
Collapse
|
14
|
Aloisi F, Giovannoni G, Salvetti M. Epstein-Barr virus as a cause of multiple sclerosis: opportunities for prevention and therapy. Lancet Neurol 2023; 22:338-349. [PMID: 36764322 DOI: 10.1016/s1474-4422(22)00471-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 02/10/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the CNS that results from the interplay between heritable and environmental factors. Mounting evidence from different fields of research supports the pivotal role of the Epstein-Barr virus (EBV) in the development of multiple sclerosis. However, translating this knowledge into clinically actionable information requires a better understanding of the mechanisms linking EBV to pathophysiology. Ongoing research is trying to clarify whether EBV causes neuroinflammation via autoimmunity or antiviral immunity, and if the interaction of EBV with genetic susceptibility to multiple sclerosis can explain why a ubiquitous virus promotes immune dysfunction in susceptible individuals. If EBV also has a role in driving disease activity, the characterisation of this role will help diagnosis, prognosis, and treatment in people with multiple sclerosis. Ongoing clinical trials targeting EBV and new anti-EBV vaccines provide hope for future treatments and preventive interventions.
Collapse
Affiliation(s)
- Francesca Aloisi
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy.
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Preventive Medicine and Blizard Institute, Queen Mary University, London, UK
| | - Marco Salvetti
- Department of Neurosciences, Mental Health and Sensory Organs, Sapienza University of Rome, Rome, Italy; IRCCS Neuromed, Pozzilli, Italy
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Bjornevik K, Münz C, Cohen JI, Ascherio A. Epstein-Barr virus as a leading cause of multiple sclerosis: mechanisms and implications. Nat Rev Neurol 2023; 19:160-171. [PMID: 36759741 DOI: 10.1038/s41582-023-00775-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2023] [Indexed: 02/11/2023]
Abstract
Epidemiological studies have provided compelling evidence that multiple sclerosis (MS) is a rare complication of infection with the Epstein-Barr virus (EBV), a herpesvirus that infects more than 90% of the global population. This link was long suspected because the risk of MS increases markedly after infectious mononucleosis (symptomatic primary EBV infection) and with high titres of antibodies to specific EBV antigens. However, it was not until 2022 that a longitudinal study demonstrated that MS risk is minimal in individuals who are not infected with EBV and that it increases over 30-fold following EBV infection. Over the past few years, a number of studies have provided clues on the underlying mechanisms, which might help us to develop more targeted treatments for MS. In this Review, we discuss the evidence linking EBV to the development of MS and the mechanisms by which the virus is thought to cause the disease. Furthermore, we discuss implications for the treatment and prevention of MS, including the use of antivirals and vaccines.
Collapse
Affiliation(s)
- Kjetil Bjornevik
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | - Alberto Ascherio
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
17
|
Dyer Z, Tscharke D, Sutton I, Massey J. From bedside to bench: how existing therapies inform the relationship between Epstein-Barr virus and multiple sclerosis. Clin Transl Immunology 2023; 12:e1437. [PMID: 36844913 PMCID: PMC9947628 DOI: 10.1002/cti2.1437] [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: 12/15/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 02/25/2023] Open
Abstract
Therapy for relapsing-remitting multiple sclerosis (MS) has advanced dramatically despite incomplete understanding of the cause of the condition. Current treatment involves inducing broad effects on immune cell populations with consequent off-target side effects, and no treatment can completely prevent disability progression. Further therapeutic advancement will require a better understanding of the pathobiology of MS. Interest in the role of Epstein-Barr virus (EBV) in multiple sclerosis has intensified based on strong epidemiological evidence of an association between EBV seroprevalence and MS. Hypotheses proposed to explain the biological relationship between EBV and MS include molecular mimicry, EBV immortalised autoreactive B cells and infection of glial cells by EBV. Examining the interaction between EBV and immunotherapies that have demonstrated efficacy in MS offers clues to the validity of these hypotheses. The efficacy of B cell depleting therapies could be consistent with a hypothesis that EBV-infected B cells drive MS; however, loss of T cell control of B cells does not exacerbate MS. A number of MS therapies invoke change in EBV-specific T cell populations, but pathogenic EBV-specific T cells with cross-reactivity to CNS antigen have not been identified. Immune reconstitution therapies induce EBV viraemia and expansion of EBV-specific T cell clones, but this does not correlate with relapse. Much remains unknown regarding the role of EBV in MS pathogenesis. We discuss future translational research that could fill important knowledge gaps.
Collapse
Affiliation(s)
- Zoe Dyer
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical ResearchDarlinghurstNSWAustralia,St. Vincent's Clinical School, Faculty of MedicineUniversity of New South Wales (UNSW)DarlinghurstNSWAustralia
| | - David Tscharke
- John Curtin School of Medical ResearchAustralian National UniversityCanberraACTAustralia
| | - Ian Sutton
- St. Vincent's Clinical School, Faculty of MedicineUniversity of New South Wales (UNSW)DarlinghurstNSWAustralia,Department of NeurologySt Vincent's ClinicDarlinghurstNSWAustralia
| | - Jennifer Massey
- Blood Stem Cell and Cancer Research Group, St Vincent's Centre for Applied Medical ResearchDarlinghurstNSWAustralia,St. Vincent's Clinical School, Faculty of MedicineUniversity of New South Wales (UNSW)DarlinghurstNSWAustralia,Department of NeurologySt Vincent's ClinicDarlinghurstNSWAustralia,Department of NeurologySt Vincent's HospitalDarlinghurstNSWAustralia
| |
Collapse
|
18
|
Sorosina M, Santoro S, Ferrè L, Mascia E, Clarelli F, Giordano A, Cannizzaro M, Lucia M, Martinelli V, Filippi M, Esposito F. Risk HLA Variants Affect the T-Cell Repertoire in Multiple Sclerosis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2023; 10:10/3/e200093. [PMID: 36792371 PMCID: PMC9931183 DOI: 10.1212/nxi.0000000000200093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 12/14/2022] [Indexed: 02/17/2023]
Abstract
BACKGROUND AND OBJECTIVES The major histocompatibility complex (MHC) locus has a predominant role in the genetic predisposition to multiple sclerosis (MS), with 32 associations found to be involved. We aimed to investigate the impact of MHC MS-risk alleles on T-cell repertoire in patients with MS. METHODS We studied 161 untreated patients with relapsing-remitting MS for whom Class I and II human leukocyte antigen (HLA) alleles were inferred from whole-genome genotyping data, and T-cell receptor (TCR) CDR3 sequences were obtained through next-generation sequencing. T-cell repertoire features including diversity, public clones, and architecture were evaluated. RESULTS We identified 5 MS-risk loci associated with TCR diversity: HLA-DRB1*15:01 (7.65 × 10-3), rs9271366 (1.96 × 10-3), rs766848979 A (1.89 × 10-2), rs9277626 (2.95 × 10-2), and rs11751659 (1.92 × 10-2), with evidence of expanded clonotypes in carriers of risk alleles. Moreover, HLA-DRB1*15:01 (4.99 × 10-3), rs9271366 (6.54 × 10-3), rs1049079 C (4.37 × 10-2), AA DQΒ1 position -5 L (1.05 × 10-3), and AA DQΒ1 position 221 Q (9.39 × 10-4) showed an association with the CDR3 aminoacidic sequence architecture, suggesting an impact on the antigen recognition breadth as well. Evaluating the sharing of clones across MS-risk allele carrier individuals revealed the presence of highly shared clonotypes predicted to target viral antigens, including Epstein-Barr virus. DISCUSSION Our study supports the association between MHC-risk alleles and macrofeatures of the T-cell repertoire in the context of MS. Further studies are needed to understand the underlying molecular mechanisms.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Federica Esposito
- From the Laboratory of Neurological Complex Disorders (M.S., S.S., L.F., E.M., F.C., A.G., M.C., F.E.), Division of Neuroscience, Institute of Experimental Neurology (INSPE), IRCCS San Raffaele Scientific Institute; Neurology and Neurorehabilitation Unit (L.F., A.G., M.C., M.L., V.M., M.F., F.E.), IRCCS San Raffaele Scientific Institute, Milan, Italy; Vita-Salute San Raffaele University (M.F.); Neurophysiology Unit (M.F.), IRCCS San Raffaele Scientific Institute; and Neuroimaging Research Unit, Division of Neuroscience, Institute of Experimental Neurology (INSPE) (P.F.), IRCCS San Raffaele Scientific Institute, Milan, Italy.
| |
Collapse
|
19
|
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:e20220650. [PMID: 36048016 PMCID: PMC9437111 DOI: 10.1084/jem.20220650] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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.
Collapse
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
| |
Collapse
|
20
|
MINI-review of Epstein-Barr virus involvement in multiple sclerosis etiology and pathogenesis. J Neuroimmunol 2022; 371:577935. [DOI: 10.1016/j.jneuroim.2022.577935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/11/2022] [Accepted: 07/24/2022] [Indexed: 11/18/2022]
|
21
|
Boziki M, Bakirtzis C, Sintila SA, Kesidou E, Gounari E, Ioakimidou A, Tsavdaridou V, Skoura L, Fylaktou A, Nikolaidou V, Stangou M, Nikolaidis I, Giantzi V, Karafoulidou E, Theotokis P, Grigoriadis N. Ocrelizumab in Patients with Active Primary Progressive Multiple Sclerosis: Clinical Outcomes and Immune Markers of Treatment Response. Cells 2022; 11:cells11121959. [PMID: 35741088 PMCID: PMC9222195 DOI: 10.3390/cells11121959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/04/2023] Open
Abstract
Ocrelizumab is a B-cell-depleting monoclonal antibody approved for the treatment of relapsing-remitting multiple sclerosis (RRMS) and active primary progressive MS (aPPMS). This prospective, uncontrolled, open-label, observational study aimed to assess the efficacy of ocrelizumab in patients with aPPMS and to dissect the clinical, radiological and laboratory attributes of treatment response. In total, 22 patients with aPPMS followed for 24 months were included. The primary efficacy outcome was the proportion of patients with optimal response at 24 months, defined as patients free of relapses, free of confirmed disability accumulation (CDA) and free of T1 Gd-enhancing lesions and new/enlarging T2 lesions on the brain and cervical MRI. In total, 14 (63.6%) patients and 13 patients (59.1%) were classified as responders at 12 and 24 months, respectively. Time exhibited a significant effect on mean absolute and normalized gray matter cerebellar volume (F = 4.342, p = 0.23 and F = 4.279, p = 0.024, respectively). Responders at 24 months exhibited reduced peripheral blood ((%) of CD19+ cells) plasmablasts compared to non-responders at the 6-month point estimate (7.69 ± 4.4 vs. 22.66 ± 7.19, respectively, p = 0.043). Response to ocrelizumab was linked to lower total and gray matter cerebellar volume loss over time. Reduced plasmablast depletion was linked for the first time to sub-optimal response to ocrelizumab in aPPMS.
Collapse
Affiliation(s)
- Marina Boziki
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Christos Bakirtzis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Styliani-Aggeliki Sintila
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Evangelia Kesidou
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Evdoxia Gounari
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Aliki Ioakimidou
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Vasiliki Tsavdaridou
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Lemonia Skoura
- Microbiology Laboratory, Department of Immunology, AHEPA University Hospital, 54636 Thessaloniki, Greece; (E.G.); (A.I.); (V.T.); (L.S.)
| | - Asimina Fylaktou
- National Peripheral Histocompatibility Center, Immunology Department, Hippokration General Hospital, 54642 Thessaloniki, Greece; (A.F.); (V.N.)
| | - Vasiliki Nikolaidou
- National Peripheral Histocompatibility Center, Immunology Department, Hippokration General Hospital, 54642 Thessaloniki, Greece; (A.F.); (V.N.)
| | - Maria Stangou
- Department of Nephrology, Medical School, Aristotle University of Thessaloniki, Hippokration Hospital, 54642 Thessaloniki, Greece;
| | - Ioannis Nikolaidis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Virginia Giantzi
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Eleni Karafoulidou
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Paschalis Theotokis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
| | - Nikolaos Grigoriadis
- Multiple Sclerosis Center of the 2nd Neurological University Department, School of Medicine, Aristotle University of Thessaloniki, AHEPA General University Hospital, 54636 Thessaloniki, Greece; (M.B.); (C.B.); (S.-A.S.); (E.K.); (I.N.); (V.G.); (E.K.); (P.T.)
- Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
- Correspondence:
| |
Collapse
|
22
|
Bedri SK, Evertsson B, Khademi M, Al Nimer F, Olsson T, Hillert J, Glaser A. Copy number variations across the blood-brain barrier in multiple sclerosis. Ann Clin Transl Neurol 2022; 9:962-976. [PMID: 35560551 PMCID: PMC9268884 DOI: 10.1002/acn3.51573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/30/2022] [Accepted: 04/12/2022] [Indexed: 12/29/2022] Open
Abstract
Objective Multiple sclerosis (MS) is a neuroinflammatory disease where immune cells cross the blood–brain barrier (BBB) into the central nervous system (CNS). What predisposes these immune cells to cross the BBB is still unknown. Here, we examine the possibility that genomic rearrangements could predisposespecific immune cells in the peripheral blood to cross the BBB and form sub‐populations of cells involved in the inflammatory process in the CNS. Methods We compared copy number variations in paired peripheral blood mononuclear cells (PBMCs) and cerebrospinal fluid (CSF) cells from MS patients. Thereafter, using next generation sequencing, we studied the T‐cell receptor beta (TRB) locus rearrangements and profiled the αβ T cell repertoire in peripheral CD4+ and CD8+ T cells and in the CSF. Results We identified deletions in the T‐cell receptor alpha/delta (TRA/D), gamma (TRG), and TRB loci in CSF cells compared to PBMCs. Further characterization revealed diversity of the TRB locus which was used to describe the character and clonal expansion of T cells in the CNS. T‐cell repertoire profiling from either side of the BBB concluded that the most frequent clones in the CSF samples are unique to an individual. Furthermore, we observed a difference in the proportion of expanded T‐cell clones when comparing samples from MS patients in relapse and remission with opposite trends in CSF and peripheral blood. Interpretation This study provides a characterization of the T cells in the CSF and might indicate a role of expanded clones in MS pathogenicity.
Collapse
Affiliation(s)
- Sahl Khalid Bedri
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Evertsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Mohsen Khademi
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Faiez Al Nimer
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Karolinska University Hospital, Tema Neuro, Stockholm, Sweden
| | - Anna Glaser
- Department of Clinical Neuroscience and Centrum for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
23
|
Lima M, Aloizou AM, Siokas V, Bakirtzis C, Liampas I, Tsouris Z, Bogdanos DP, Baloyannis SJ, Dardiotis E. Coronaviruses and their relationship with multiple sclerosis: is the prevalence of multiple sclerosis going to increase after the Covid-19 pandemia? Rev Neurosci 2022; 33:703-720. [PMID: 35258237 DOI: 10.1515/revneuro-2021-0148] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
The purpose of this review is to examine whether there is a possible (etiological/triggering) relationship between infection with various Coronaviruses, including Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2), the virus responsible for the Coronavirus disease-19 (Covid-19) pandemia, and Multiple Sclerosis (MS), and whether an increase of the prevalence of MS after the current Covid-19 pandemia should be expected, examining new and preexisting data. Although the exact pathogenesis of MS remains unknown, environmental agents seem to greatly influence the onset of the disease, with viruses being the most popular candidate. Existing data support this possible etiological relationship between viruses and MS, and experimental studies show that Coronaviruses can actually induce an MS-like demyelinating disease in animal models. Findings in MS patients could also be compatible with this coronaviral MS hypothesis. More importantly, current data from the Covid-19 pandemia show that SARS-CoV-2 can trigger autoimmunity and possibly induce autoimmune diseases, in the Central Nervous System as well, strengthening the viral hypothesis of MS. If we accept that Coronaviruses can induce MS, it is reasonable to expect an increase in the prevalence of MS after the Covid-19 pandemia. This knowledge is of great importance in order to protect the aging groups that are more vulnerable against autoimmune diseases and MS specifically, and to establish proper vaccination and health policies.
Collapse
Affiliation(s)
- Maria Lima
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| | - Athina-Maria Aloizou
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| | - Christos Bakirtzis
- B' Department of Neurology, Multiple Sclerosis Center, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636, Thessaloniki, Greece
| | - Ioannis Liampas
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| | - Zisis Tsouris
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| | - Dimitrios P Bogdanos
- Department of Rheumatology and clinical Immunology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 40500 Viopolis, Larissa, Greece
| | - Stavros J Baloyannis
- Research Institute for Alzheimer's disease, Aristotle University of Thessaloniki, 57200 Iraklio Lagkada, Thessaloniki, Greece.,1st Department of Neurology, AHEPA University Hospital, Aristotle University of Thessaloniki, 54636, Thessaloniki, Greece
| | - Efthimios Dardiotis
- Department of Neurology, University General Hospital of Larissa, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41100, Larissa, Greece
| |
Collapse
|
24
|
Massey J, Jackson K, Singh M, Hughes B, Withers B, Ford C, Khoo M, Hendrawan K, Zaunders J, Charmeteau-De Muylder B, Cheynier R, Luciani F, Ma D, Moore J, Sutton I. Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis. Front Immunol 2022; 13:798300. [PMID: 35197974 PMCID: PMC8859174 DOI: 10.3389/fimmu.2022.798300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/13/2022] [Indexed: 12/29/2022] Open
Abstract
Autologous haematopoietic stem cell transplantation (AHSCT) is a vital therapeutic option for patients with highly active multiple sclerosis (MS). Rates of remission suggest AHSCT is the most effective form of immunotherapy in controlling the disease. Despite an evolving understanding of the biology of immune reconstitution following AHSCT, the mechanism by which AHSCT enables sustained disease remission beyond the period of lymphopenia remains to be elucidated. Auto-reactive T cells are considered central to MS pathogenesis. Here, we analyse T cell reconstitution for 36 months following AHSCT in a cohort of highly active MS patients. Through longitudinal analysis of sorted naïve and memory T cell clones, we establish that AHSCT induces profound changes in the dominant T cell landscape of both CD4+ and CD8+ memory T cell clones. Lymphopenia induced homeostatic proliferation is followed by clonal attrition; with only 19% of dominant CD4 (p <0.025) and 13% of dominant CD8 (p <0.005) clones from the pre-transplant repertoire detected at 36 months. Recovery of a thymically-derived CD4 naïve T cell repertoire occurs at 12 months and is ongoing at 36 months, however diversity of the naïve populations is not increased from baseline suggesting the principal mechanism of durable remission from MS after AHSCT relates to depletion of putative auto-reactive clones. In a cohort of MS patients expressing the MS risk allele HLA DRB1*15:01, public clones are probed as potential biomarkers of disease. AHSCT appears to induce sustained periods of disease remission with dynamic changes in the clonal T cell repertoire out to 36 months post-transplant.
Collapse
Affiliation(s)
- Jennifer Massey
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- *Correspondence: Jennifer Massey,
| | - Katherine Jackson
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mandeep Singh
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Brendan Hughes
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - Barbara Withers
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Carole Ford
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Melissa Khoo
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - Kevin Hendrawan
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | - John Zaunders
- Immunology Laboratory, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
| | | | - Rémi Cheynier
- Université de Paris, INSERM, CNRS, Institut Cochin, Paris, France
| | - Fabio Luciani
- School of Medical Sciences and Kirby Institute for Infection and Immunity, University of New South Wales (UNSW), Kensington, NSW, Australia
| | - David Ma
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - John Moore
- Department of Haematology, St Vincent’s Hospital, Darlinghurst, NSW, Australia
- Blood Stem Cell and Cancer Research Group, St Vincent’s Centre for Applied Medical Research, Darlinghurst, NSW, Australia
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
| | - Ian Sutton
- St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales (UNSW), Darlinghurst, NSW, Australia
- Department of Neurology, St Vincent’s Clinic, Darlinghurst, NSW, Australia
| |
Collapse
|
25
|
Jivanjee T, Ibrahim S, Nyquist SK, Gatter GJ, Bromley JD, Jaiswal S, Berger B, Behar SM, Love JC, Shalek AK. Enriching and Characterizing T Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products. Methods Mol Biol 2022; 2574:159-182. [PMID: 36087201 DOI: 10.1007/978-1-0716-2712-9_7] [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] [Indexed: 05/09/2023]
Abstract
Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full-length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process; however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods.Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer result in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq WTA libraries.
Collapse
Affiliation(s)
- Tasneem Jivanjee
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samira Ibrahim
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sarah K Nyquist
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - G James Gatter
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joshua D Bromley
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Swati Jaiswal
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bonnie Berger
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samuel M Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Alex K Shalek
- Institute for Medical Engineering & Science and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
26
|
Amoriello R, Mariottini A, Ballerini C. Immunosenescence and Autoimmunity: Exploiting the T-Cell Receptor Repertoire to Investigate the Impact of Aging on Multiple Sclerosis. Front Immunol 2021; 12:799380. [PMID: 34925384 PMCID: PMC8673061 DOI: 10.3389/fimmu.2021.799380] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023] Open
Abstract
T-cell receptor (TCR) repertoire diversity is a determining factor for the immune system capability in fighting infections and preventing autoimmunity. During life, the TCR repertoire diversity progressively declines as a physiological aging progress. The investigation of TCR repertoire dynamics over life represents a powerful tool unraveling the impact of immunosenescence in health and disease. Multiple Sclerosis (MS) is a demyelinating, inflammatory, T-cell mediated autoimmune disease of the Central Nervous System in which age is crucial: it is the most widespread neurological disease among young adults and, furthermore, patients age may impact on MS progression and treatments outcome. Crossing knowledge on the TCR repertoire dynamics over MS patients' life is fundamental to investigate disease mechanisms, and the advent of high- throughput sequencing (HTS) has significantly increased our knowledge on the topic. Here we report an overview of current literature about the impact of immunosenescence and age-related TCR dynamics variation in autoimmunity, including MS.
Collapse
Affiliation(s)
- Roberta Amoriello
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Florence, Italy
| |
Collapse
|
27
|
Meier UC, Cipian RC, Karimi A, Ramasamy R, Middeldorp JM. Cumulative Roles for Epstein-Barr Virus, Human Endogenous Retroviruses, and Human Herpes Virus-6 in Driving an Inflammatory Cascade Underlying MS Pathogenesis. Front Immunol 2021; 12:757302. [PMID: 34790199 PMCID: PMC8592026 DOI: 10.3389/fimmu.2021.757302] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
Roles for viral infections and aberrant immune responses in driving localized neuroinflammation and neurodegeneration in multiple sclerosis (MS) are the focus of intense research. Epstein-Barr virus (EBV), as a persistent and frequently reactivating virus with major immunogenic influences and a near 100% epidemiological association with MS, is considered to play a leading role in MS pathogenesis, triggering localized inflammation near or within the central nervous system (CNS). This triggering may occur directly via viral products (RNA and protein) and/or indirectly via antigenic mimicry involving B-cells, T-cells and cytokine-activated astrocytes and microglia cells damaging the myelin sheath of neurons. The genetic MS-risk factor HLA-DR2b (DRB1*1501β, DRA1*0101α) may contribute to aberrant EBV antigen-presentation and anti-EBV reactivity but also to mimicry-induced autoimmune responses characteristic of MS. A central role is proposed for inflammatory EBER1, EBV-miRNA and LMP1 containing exosomes secreted by viable reactivating EBV+ B-cells and repetitive release of EBNA1-DNA complexes from apoptotic EBV+ B-cells, forming reactive immune complexes with EBNA1-IgG and complement. This may be accompanied by cytokine- or EBV-induced expression of human endogenous retrovirus-W/-K (HERV-W/-K) elements and possibly by activation of human herpesvirus-6A (HHV-6A) in early-stage CNS lesions, each contributing to an inflammatory cascade causing the relapsing-remitting neuro-inflammatory and/or progressive features characteristic of MS. Elimination of EBV-carrying B-cells by antibody- and EBV-specific T-cell therapy may hold the promise of reducing EBV activity in the CNS, thereby limiting CNS inflammation, MS symptoms and possibly reversing disease. Other approaches targeting HHV-6 and HERV-W and limiting inflammatory kinase-signaling to treat MS are also being tested with promising results. This article presents an overview of the evidence that EBV, HHV-6, and HERV-W may have a pathogenic role in initiating and promoting MS and possible approaches to mitigate development of the disease.
Collapse
Affiliation(s)
- Ute-Christiane Meier
- Institut für Laboratoriumsmedizin, Klinikum der Universität München, München, Germany.,Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | | | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | |
Collapse
|
28
|
Zhang J, Wang Y, Yu H, Chen G, Wang L, Liu F, Yuan J, Ni Q, Xia X, Wan Y. Mapping the spatial distribution of T cells in repertoire dimension. Mol Immunol 2021; 138:161-171. [PMID: 34428621 DOI: 10.1016/j.molimm.2021.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 08/15/2021] [Indexed: 01/13/2023]
Abstract
T cells mediate adaptive immunity in diverse anatomic compartments through recognition of specific antigens via unique T cell receptor (TCR) structures. However, little is known about the spatial distribution of an organism's TCR repertoire. Here, using high-throughput TCR sequencing (TCRseq), we investigated the TCR repertoires of sixteen tissues in healthy C57B/L6 mice. We found that TCR repertoires generally classified into three categories (lymph nodes, non-lymph node tissues and small intestine) based on sequence similarity. Clonal distribution and diversity analyses showed that small intestine compartment had a more skewed repertoire as compared to lymph nodes and non-lymph node tissues. However, analysis of TRBV and TRBJ gene usage across tissue compartments, as well as comparison of CDR3 length distributions, showed no significant tissue-dependent differences. Interestingly, analysis of clonotype sharing between mice showed that although non-redundant public clonotypes were found more easily in lymph nodes, small intestinal CD4 + T cells harbored more abundant public clonotypes. These findings under healthy physiological conditions offer an important reference dataset, which may contribute to our ability to better manipulate T cell responses against infection and vaccination.
Collapse
Affiliation(s)
- Junying Zhang
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, 401331, China
| | - Yu Wang
- Zunyi Medical University, Zunyi, 563003, China
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Liting Wang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Fang Liu
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China
| | - Jiangbei Yuan
- Hepato-Pancreato-Biliary Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Guangdong Province, 518036, China
| | - Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China.
| | - Xuefeng Xia
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing, 401331, China.
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China; Chongqing Key Laboratory of Cytomics, Chongqing, 400038, China; School of Big Data & Software Engineering, Chongqing University, Chongqing, 401331, China.
| |
Collapse
|
29
|
Song R, Jia X, Zhao J, Du P, Zhang JA. T cell receptor revision and immune repertoire changes in autoimmune diseases. Int Rev Immunol 2021; 41:517-533. [PMID: 34243694 DOI: 10.1080/08830185.2021.1929954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Autoimmune disease (AID) is a condition in which the immune system breaks down and starts to attack the body. Some common AIDs include systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes mellitus and so forth. The changes in T-cell receptor (TCR) repertoire have been found in several autoimmune diseases, and may be responsible for the breakdown of peripheral immune tolerance. In this review, we discussed the processes of TCR revision in peripheral immune environment, the changes in TCR repertoire that occurred in various AIDs, and the specifically expanded T cell clones. We hope our discussion can provide insights for the future studies, helping with the discovery of disease biomarkers and expanding the strategies of immune-targeted therapy. HighlightsRestricted TCR repertoire and biased TCR-usage are found in a variety of AIDs.TCR repertoire shows tissue specificity in a variety of AID diseases.The relationship between TCR repertoire diversity and disease activity is still controversial in AIDs.Dominant TCR clonotypes may help to discover new disease biomarkers and expand the strategies of immune-targeted therapy.
Collapse
Affiliation(s)
- Ronghua Song
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Xi Jia
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jing Zhao
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Peng Du
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| | - Jin-An Zhang
- Department of Endocrinology, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai, China
| |
Collapse
|
30
|
Veroni C, Aloisi F. The CD8 T Cell-Epstein-Barr Virus-B Cell Trialogue: A Central Issue in Multiple Sclerosis Pathogenesis. Front Immunol 2021; 12:665718. [PMID: 34305896 PMCID: PMC8292956 DOI: 10.3389/fimmu.2021.665718] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
The cause and the pathogenic mechanisms leading to multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system (CNS), are still under scrutiny. During the last decade, awareness has increased that multiple genetic and environmental factors act in concert to modulate MS risk. Likewise, the landscape of cells of the adaptive immune system that are believed to play a role in MS immunopathogenesis has expanded by including not only CD4 T helper cells but also cytotoxic CD8 T cells and B cells. Once the key cellular players are identified, the main challenge is to define precisely how they act and interact to induce neuroinflammation and the neurodegenerative cascade in MS. CD8 T cells have been implicated in MS pathogenesis since the 80's when it was shown that CD8 T cells predominate in MS brain lesions. Interest in the role of CD8 T cells in MS was revived in 2000 and the years thereafter by studies showing that CNS-recruited CD8 T cells are clonally expanded and have a memory effector phenotype indicating in situ antigen-driven reactivation. The association of certain MHC class I alleles with MS genetic risk implicates CD8 T cells in disease pathogenesis. Moreover, experimental studies have highlighted the detrimental effects of CD8 T cell activation on neural cells. While the antigens responsible for T cell recruitment and activation in the CNS remain elusive, the high efficacy of B-cell depleting drugs in MS and a growing number of studies implicate B cells and Epstein-Barr virus (EBV), a B-lymphotropic herpesvirus that is strongly associated with MS, in the activation of pathogenic T cells. This article reviews the results of human studies that have contributed to elucidate the role of CD8 T cells in MS immunopathogenesis, and discusses them in light of current understanding of autoreactivity, B-cell and EBV involvement in MS, and mechanism of action of different MS treatments. Based on the available evidences, an immunopathological model of MS is proposed that entails a persistent EBV infection of CNS-infiltrating B cells as the target of a dysregulated cytotoxic CD8 T cell response causing CNS tissue damage.
Collapse
Affiliation(s)
| | - Francesca Aloisi
- Department of Neuroscience, Istituto Superiore di Sanità, Rome, Italy
| |
Collapse
|
31
|
Amoriello R, Chernigovskaya M, Greiff V, Carnasciali A, Massacesi L, Barilaro A, Repice AM, Biagioli T, Aldinucci A, Muraro PA, Laplaud DA, Lossius A, Ballerini C. TCR repertoire diversity in Multiple Sclerosis: High-dimensional bioinformatics analysis of sequences from brain, cerebrospinal fluid and peripheral blood. EBioMedicine 2021; 68:103429. [PMID: 34127432 PMCID: PMC8245901 DOI: 10.1016/j.ebiom.2021.103429] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND T cells play a key role in the pathogenesis of multiple sclerosis (MS), a chronic, inflammatory, demyelinating disease of the central nervous system (CNS). Although several studies recently investigated the T-cell receptor (TCR) repertoire in cerebrospinal fluid (CSF) of MS patients by high-throughput sequencing (HTS), a deep analysis on repertoire similarities and differences among compartments is still missing. METHODS We performed comprehensive bioinformatics on high-dimensional TCR Vβ sequencing data from published and unpublished MS and healthy donors (HD) studies. We evaluated repertoire polarization, clone distribution, shared CDR3 amino acid sequences (CDR3s-a.a.) across repertoires, clone overlap with public databases, and TCR similarity architecture. FINDINGS CSF repertoires showed a significantly higher public clones percentage and sequence similarity compared to peripheral blood (PB). On the other hand, we failed to reject the null hypothesis that the repertoire polarization is the same between CSF and PB. One Primary-Progressive MS (PPMS) CSF repertoire differed from the others in terms of TCR similarity architecture. Cluster analysis splits MS from HD. INTERPRETATION In MS patients, the presence of a physiological barrier, the blood-brain barrier, does not impact clone prevalence and distribution, but impacts public clones, indicating CSF as a more private site. We reported a high Vβ sequence similarity in the CSF-TCR architecture in one PPMS. If confirmed it may be an interesting insight into MS progressive inflammatory mechanisms. The clustering of MS repertoires from HD suggests that disease shapes the TCR Vβ clonal profile. FUNDING This study was partly financially supported by the Italian Multiple Sclerosis Foundation (FISM), that contributed to Ballerini-DB data collection (grant #2015 R02).
Collapse
Affiliation(s)
- Roberta Amoriello
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | | | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Alberto Carnasciali
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy
| | - Luca Massacesi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Italy
| | - Alessandro Barilaro
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Italy
| | - Anna M Repice
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Italy
| | - Tiziana Biagioli
- Laboratorio Generale, Careggi University Hospital, Florence, Italy
| | | | - Paolo A Muraro
- Wolfson Neuroscience Laboratory, Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - David A Laplaud
- CRTI-Inserm U1064, CIC0004 and Service de Neurologie, CHU de Nantes, Hôpital Nord Laënnec, Nantes, France
| | - Andreas Lossius
- Institute of Clinical Medicine, University of Oslo, Postboks 1105, Blindern 0317 Oslo, Norway.
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), Laboratory of Neuroimmunology, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy.
| |
Collapse
|
32
|
Wu M, Zhao M, Wu H, Lu Q. Immune repertoire: Revealing the "real-time" adaptive immune response in autoimmune diseases. Autoimmunity 2021; 54:61-75. [PMID: 33650440 DOI: 10.1080/08916934.2021.1887149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The diversity of the immune repertoire (IR) enables the human immune system to distinguish multifarious antigens (Ags) that humans may encounter throughout life. At the same time, bias or abnormalities in the IR also pay a contribution to the pathogenesis of autoimmune diseases. Rapid advancements in high-throughput sequencing (HTS) technology have ushered in a new era of immune studies, revealing novel molecules and pathways that might result in autoimmunity. In the field of IR, HTS can monitor the immune response status and identify disease-specific immune repertoires. In this review, we summarize updated progress on the mechanisms of the IR and current related studies on four autoimmune diseases, particularly focusing on systemic lupus erythematosus (SLE). These autoimmune diseases can exhibit slightly or significantly skewed IRs and provide novel insights that inform our comprehending of disease pathogenesis and provide potential targets for diagnosis and treatment.
Collapse
Affiliation(s)
- Meiyu Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
| |
Collapse
|
33
|
Tsamis KI, Sakkas H, Giannakis A, Ryu HS, Gartzonika C, Nikas IP. Evaluating Infectious, Neoplastic, Immunological, and Degenerative Diseases of the Central Nervous System with Cerebrospinal Fluid-Based Next-Generation Sequencing. Mol Diagn Ther 2021; 25:207-229. [PMID: 33646562 PMCID: PMC7917176 DOI: 10.1007/s40291-021-00513-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2021] [Indexed: 12/24/2022]
Abstract
Cerebrospinal fluid (CSF) is a clear and paucicellular fluid that circulates within the ventricular system and the subarachnoid space of the central nervous system (CNS), and diverse CNS disorders can impact its composition, volume, and flow. As conventional CSF testing suffers from suboptimal sensitivity, this review aimed to evaluate the role of next-generation sequencing (NGS) in the work-up of infectious, neoplastic, neuroimmunological, and neurodegenerative CNS diseases. Metagenomic NGS showed improved sensitivity—compared to traditional methods—to detect bacterial, viral, parasitic, and fungal infections, while the overall performance was maximized in some studies when all diagnostic modalities were used. In patients with primary CNS cancer, NGS findings in the CSF were largely concordant with the molecular signatures derived from tissue-based molecular analysis; of interest, additional mutations were identified in the CSF in some glioma studies, reflecting intratumoral heterogeneity. In patients with metastasis to the CNS, NGS facilitated diagnosis, prognosis, therapeutic management, and monitoring, exhibiting higher sensitivity than neuroimaging, cytology, and plasma-based molecular analysis. Although evidence is still rudimentary, NGS could enhance the diagnosis and pathogenetic understanding of multiple sclerosis in addition to Alzheimer and Parkinson disease. To conclude, NGS has shown potential to aid the research, facilitate the diagnostic approach, and improve the management outcomes of all the aforementioned CNS diseases. However, to establish its role in clinical practice, the clinical validity and utility of each NGS protocol should be determined. Lastly, as most evidence has been derived from small and retrospective studies, results from randomized control trials could be of significant value.
Collapse
Affiliation(s)
- Konstantinos I Tsamis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece. .,School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus.
| | - Hercules Sakkas
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Alexandros Giannakis
- Department of Neurology, University Hospital of Ioannina, 45500, Ioannina, Greece
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, 03080, Korea
| | - Constantina Gartzonika
- Microbiology Department, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
| | - Ilias P Nikas
- School of Medicine, European University Cyprus, 2404, Nicosia, Cyprus
| |
Collapse
|
34
|
Nozuma S, Enose-Akahata Y, Johnson KR, Monaco MC, Ngouth N, Elkahloun A, Ohayon J, Zhu J, Jacobson S. Immunopathogenic CSF TCR repertoire signatures in virus-associated neurologic disease. JCI Insight 2021; 6:144869. [PMID: 33616082 PMCID: PMC7934934 DOI: 10.1172/jci.insight.144869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 01/13/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we examined and characterized disease-specific TCR signatures in cerebrospinal fluid (CSF) of patients with HTLV-1–associated myelopathy/tropical spastic paraparesis (HAM/TSP). TCR β libraries using unique molecular identifier–based methodologies were sequenced in paired peripheral blood mononuclear cells (PBMCs) and CSF cells from HAM/TSP patients and normal healthy donors (NDs). The sequence analysis demonstrated that TCR β repertoires in CSF of HAM/TSP patients were highly expanded and contained both TCR clonotypes shared with PBMCs and uniquely enriched within the CSF. In addition, we analyzed TCR β repertoires of highly expanded and potentially immunopathologic HTLV-1 Tax11-19–specific CD8+ T cells from PBMCs of HLA-A*0201+ HAM/TSP and identified a conserved motif (PGLAG) in the CDR3 region. Importantly, TCR β clonotypes of expanded clones in HTLV-1 Tax11-19–specific CD8+ T cells were also expanded and enriched in the CSF of the same patient. These results suggest that exploring TCR repertoires of CSF and antigen-specific T cells may provide a TCR repertoire signature in virus-associated neurologic disorders.
Collapse
Affiliation(s)
| | | | - Kory R Johnson
- Bioinformatics Section, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | | | - Nyater Ngouth
- Viral Immunology Section, Neuroimmunology Branch and
| | - Abdel Elkahloun
- Comparative Genomics and Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Joan Ohayon
- Neuroimmunology Clinic, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, Maryland, USA
| | - Jun Zhu
- Mokobio Biotechnology R&D Center, Rockville, Maryland, USA
| | | |
Collapse
|
35
|
Oh H, Leventhal O, Channappa D, Henderson VW, Wyss-Coray T, Lehallier B, Gate D. Methods to investigate intrathecal adaptive immunity in neurodegeneration. Mol Neurodegener 2021; 16:3. [PMID: 33482851 PMCID: PMC7824942 DOI: 10.1186/s13024-021-00423-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Cerebrospinal fluid (CSF) provides basic mechanical and immunological protection to the brain. Historically, analysis of CSF has focused on protein changes, yet recent studies have shed light on cellular alterations. Evidence now exists for involvement of intrathecal T cells in the pathobiology of neurodegenerative diseases. However, a standardized method for long-term preservation of CSF immune cells is lacking. Further, the functional role of CSF T cells and their cognate antigens in neurodegenerative diseases are largely unknown. Results We present a method for long-term cryopreservation of CSF immune cells for downstream single cell RNA and T cell receptor sequencing (scRNA-TCRseq) analysis. We observe preservation of CSF immune cells, consisting primarily of memory CD4+ and CD8+ T cells. We then utilize unbiased bioinformatics approaches to quantify and visualize TCR sequence similarity within and between disease groups. By this method, we identify clusters of disease-associated, antigen-specific TCRs from clonally expanded CSF T cells of patients with neurodegenerative diseases. Conclusions Here, we provide a standardized approach for long-term storage of CSF immune cells. Additionally, we present unbiased bioinformatic approaches that will facilitate the discovery of target antigens of clonally expanded T cells in neurodegenerative diseases. These novel methods will help improve our understanding of adaptive immunity in the central nervous system. Supplementary Information The online version contains supplementary material available at 10.1186/s13024-021-00423-w.
Collapse
Affiliation(s)
- Hamilton Oh
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Olivia Leventhal
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Victor W Henderson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.,Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA
| | - David Gate
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, California, USA.
| |
Collapse
|
36
|
Diagnostic differentiation of Zika and dengue virus exposure by analyzing T cell receptor sequences from peripheral blood of infected HLA-A2 transgenic mice. PLoS Negl Trop Dis 2020; 14:e0008896. [PMID: 33270635 PMCID: PMC7738164 DOI: 10.1371/journal.pntd.0008896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 10/15/2020] [Indexed: 11/19/2022] Open
Abstract
Zika virus (ZIKV) is a significant global health threat due to its potential for rapid emergence and association with severe congenital malformations during infection in pregnancy. Despite the urgent need, accurate diagnosis of ZIKV infection is still a major hurdle that must be overcome. Contributing to the inaccuracy of most serologically-based diagnostic assays for ZIKV, is the substantial geographic and antigenic overlap with other flaviviruses, including the four serotypes of dengue virus (DENV). Within this study, we have utilized a novel T cell receptor (TCR) sequencing platform to distinguish between ZIKV and DENV infections. Using high-throughput TCR sequencing of lymphocytes isolated from DENV and ZIKV infected mice, we were able to develop an algorithm which could identify virus-associated TCR sequences uniquely associated with either a prior ZIKV or DENV infection in mice. Using this algorithm, we were then able to separate mice that had been exposed to ZIKV or DENV infection with 97% accuracy. Overall this study serves as a proof-of-principle that T cell receptor sequencing can be used as a diagnostic tool capable of distinguishing between closely related viruses. Our results demonstrate the potential for this innovative platform to be used to accurately diagnose Zika virus infection and potentially the next emerging pathogen(s). Diagnostic differentiation between dengue virus and Zika virus infections is a challenge due to serological cross-reactivity. In this study, we used a novel T cell receptor sequencing platform to identify T cell receptor sequences significantly associated with either dengue or Zika virus infection in HLA-A2 transgenic mice. These libraries were used to computationally train diagnostic classifiers which were capable of distinguishing between dengue and Zika virus in independent cohorts of infected mice.
Collapse
|
37
|
Chase Huizar C, Raphael I, Forsthuber TG. Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. Cell Immunol 2020; 358:104219. [PMID: 33039896 PMCID: PMC7927152 DOI: 10.1016/j.cellimm.2020.104219] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 09/13/2020] [Accepted: 09/16/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disorder characterized by autoimmune-mediated inflammatory lesions in CNS leading to myelin damage and axonal loss. MS is a heterogenous disease with variable and unpredictable disease course. Due to its complex nature, MS is difficult to diagnose and responses to specific treatments may vary between individuals. Therefore, there is an indisputable need for biomarkers for early diagnosis, prediction of disease exacerbations, monitoring the progression of disease, and for measuring responses to therapy. Genomic and proteomic studies have sought to understand the molecular basis of MS and find biomarker candidates. Advances in next-generation sequencing and mass-spectrometry techniques have yielded an unprecedented amount of genomic and proteomic data; yet, translation of the results into the clinic has been underwhelming. This has prompted the development of novel data science techniques for exploring these large datasets to identify biologically relevant relationships and ultimately point towards useful biomarkers. Herein we discuss optimization of omics study designs, advances in the generation of omics data, and systems biology approaches aimed at improving biomarker discovery and translation to the clinic for MS.
Collapse
Affiliation(s)
- Carol Chase Huizar
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Itay Raphael
- Department of Neurological Surgery, University of Pittsburgh, UPMC Children's Hospital, Pittsburgh, PA, USA.
| | - Thomas G Forsthuber
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA.
| |
Collapse
|
38
|
Tfh Cells in Health and Immunity: Potential Targets for Systems Biology Approaches to Vaccination. Int J Mol Sci 2020; 21:ijms21228524. [PMID: 33198297 PMCID: PMC7696930 DOI: 10.3390/ijms21228524] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 12/16/2022] Open
Abstract
T follicular helper (Tfh) cells are a specialised subset of CD4+ T cells that play a significant role in the adaptive immune response, providing critical help to B cells within the germinal centres (GC) of secondary lymphoid organs. The B cell receptors of GC B cells undergo multiple rounds of somatic hypermutation and affinity maturation within the GC response, a process dependent on cognate interactions with Tfh cells. B cells that receive sufficient help from Tfh cells form antibody-producing long-lived plasma and memory B cells that provide the basis of decades of effective and efficient protection and are considered the gold standard in correlates of protection post-vaccination. However, the T cell response to vaccination has been understudied, and over the last 10 years, exponential improvements in the technological underpinnings of sampling techniques, experimental and analytical tools have allowed multidisciplinary characterisation of the role of T cells and the immune system as a whole. Of particular interest to the field of vaccinology are GCs and Tfh cells, representing a unique target for improving immunisation strategies. Here, we discuss recent insights into the unique journey of Tfh cells from thymus to lymph node during differentiation and their role in the production of high-quality antibody responses as well as their journey back to the periphery as a population of memory cells. Further, we explore their function in health and disease and the power of next-generation sequencing techniques to uncover their potential as modulators of vaccine-induced immunity.
Collapse
|
39
|
Basu S, Elkington P, Rao NA. Pathogenesis of ocular tuberculosis: New observations and future directions. Tuberculosis (Edinb) 2020; 124:101961. [PMID: 33010848 DOI: 10.1016/j.tube.2020.101961] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/22/2020] [Accepted: 06/03/2020] [Indexed: 01/01/2023]
Abstract
Ocular tuberculosis (OTB) encompasses all forms of intra- and extra-ocular inflammation associated with Mycobacterium tuberculosis (Mtb) infection. However, the organism is rarely found in ocular fluid samples of diseased eyes, rendering the pathomechanisms of the disease unclear. This confounds clinical decision-making in diagnosis and treatment of OTB. Here, we critically review existing human and animal data related to ocular inflammation and TB pathogenesis to unravel likely pathomechanisms of OTB. Broadly there appear to be two fundamental mechanisms that may underlie the development of TB-associated ocular inflammation: a. inflammatory response to live/replicating Mtb in the eye, and b. immune mediated ocular inflammation induced by non-viable Mtb or its components in the eye. This distinction is significant as in direct Mtb-driven mechanisms, diagnosis and treatment would be aimed at detection of Mtb-infection and its elimination; while indirect mechanisms would primarily require anti-inflammatory therapy with adjunctive anti-TB therapy. Further, we discuss how that most clinical phenotypes of OTB likely represent a combination of both mechanisms, with one being predominant than the other.
Collapse
Affiliation(s)
- Soumyava Basu
- Retina and Uveitis Service, L V Prasad Eye Institute (Mithu Tulsi Chanrai Campus), Bhubaneswar, India.
| | - Paul Elkington
- NIHR Biomedical Research Centre, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, UK
| | - Narsing A Rao
- USC-Roski Eye Institute, Department of Ophthalmology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
40
|
Smolders J, Fransen NL, Hsiao CC, Hamann J, Huitinga I. Perivascular tissue resident memory T cells as therapeutic target in multiple sclerosis. Expert Rev Neurother 2020; 20:835-848. [PMID: 32476499 DOI: 10.1080/14737175.2020.1776609] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Multiple sclerosis (MS) is characterized by inflammatory attacks of infiltrating leukocytes at onset but evolves into a smoldering, progressive disease within the central nervous system at its later stages. The authors discuss the contribution of white matter lesions to the pathology of advanced MS, thereby paying particular attention to the role of T cells. AREAS COVERED Diagnostic biopsy and autopsy studies of white matter lesions in early MS show different pathological patterns of demyelination and leukocyte infiltration. Brain autopsies from advanced MS display substantial inflammation without distinct patterns and suggest a role for perivascular CD8+ tissue-resident memory T (TRM) cells in active and mixed active/inactive MS white matter lesions. When compared to control and normal-appearing white matter, these lesions are enriched for parenchymal CD8+ T cells. In the perivascular space, cuffs containing CD8+ TRM cells are observed also in progressive MS, and could be sites of local reactivation. EXPERT OPINION Recent findings point toward the perivascular space as an immunological hotspot, which could be targeted in order to suppress a contribution of TRM cells to ongoing white matter lesion activity in advanced progressive MS. The authors discuss approaches, which may be explored to suppress TRM-cell reactivation in the perivascular space.
Collapse
Affiliation(s)
- Joost Smolders
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience , Amsterdam, The Netherlands.,MS Center ErasMS, Departments of Neurology and Immunology, Erasmus Medical Center , Rotterdam, The Netherlands
| | - Nina L Fransen
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience , Amsterdam, The Netherlands
| | - Cheng-Chih Hsiao
- Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers , Amsterdam, The Netherlands
| | - Jörg Hamann
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience , Amsterdam, The Netherlands.,Department of Experimental Immunology, Amsterdam Infection & Immunity Institute, Amsterdam University Medical Centers , Amsterdam, The Netherlands
| | - Inge Huitinga
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience , Amsterdam, The Netherlands
| |
Collapse
|
41
|
Amoriello R, Greiff V, Aldinucci A, Bonechi E, Carnasciali A, Peruzzi B, Repice AM, Mariottini A, Saccardi R, Mazzanti B, Massacesi L, Ballerini C. The TCR Repertoire Reconstitution in Multiple Sclerosis: Comparing One-Shot and Continuous Immunosuppressive Therapies. Front Immunol 2020; 11:559. [PMID: 32328061 PMCID: PMC7160336 DOI: 10.3389/fimmu.2020.00559] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 03/11/2020] [Indexed: 11/13/2022] Open
Abstract
Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the post-treatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naïve and memory CD4+ and CD8+) across 15 RRMS patients before and after two years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRß sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRß repertoire dynamics with respect to clonal expansion, clonal diversity and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multi-dimensional computational immunology to a TCRß dataset of treated MS patients, we show that qualitative changes of TCRß repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis and treatment regimes. Natalizumab (NTZ) and autologous hematopoietic stem cell transplantation (AHSCT) are two successful treatments for relapsing-remitting multiple sclerosis (RRMS), an autoimmune T-cell-driven disorder affecting the central nervous system that is characterized by relapses interspersed with periods of complete or partial recovery. Both RRMS treatments have been documented to impact T-cell subpopulations and the T-cell receptor (TCR) repertoire in terms of clone frequency, but, so far, the link between T-cell naive and memory populations, autoimmunity, and treatment outcome has not yet been established hindering insight into the posttreatment TCR landscape of MS patients. To address this important knowledge gap, we tracked peripheral T-cell subpopulations (naive and memory CD4+ and CD8+) across 15 RRMS patients before and after 2 years of continuous treatment (NTZ) and a single treatment course (AHSCT) by high-throughput TCRβ sequencing. We found that the two MS treatments left treatment-specific multidimensional traces in patient TCRβ repertoire dynamics with respect to clonal expansion, clonal diversity, and repertoire architecture. Comparing MS TCR sequences with published datasets suggested that the majority of public TCRs belonged to virus-associated sequences. In summary, applying multidimensional computational immunology to a TCRβ dataset of treated MS patients, we show that qualitative changes of TCRβ repertoires encode treatment-specific information that may be relevant for future clinical trials monitoring and personalized MS follow-up, diagnosis, and treatment regimens.
Collapse
Affiliation(s)
- Roberta Amoriello
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Alessandra Aldinucci
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Elena Bonechi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alberto Carnasciali
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Benedetta Peruzzi
- Centro Diagnostico di Citofluorimetria e Immunoterapia, Careggi University Hospital, Florence, Italy
| | - Anna Maria Repice
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Alice Mariottini
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Riccardo Saccardi
- SODc Terapie Cellulari e Medicina Trasfusionale, Careggi University Hospital, Florence, Italy
| | - Benedetta Mazzanti
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
| | - Luca Massacesi
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco e Salute del Bambino (NEUROFARBA), University of Florence, Florence, Italy
| | - Clara Ballerini
- Dipartimento di Medicina Sperimentale e Clinica (DMSC), University of Florence, Florence, Italy
| |
Collapse
|
42
|
Meyer Zu Hörste G, Gross CC, Klotz L, Schwab N, Wiendl H. Next-Generation Neuroimmunology: New Technologies to Understand Central Nervous System Autoimmunity. Trends Immunol 2020; 41:341-354. [PMID: 32147112 DOI: 10.1016/j.it.2020.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/11/2022]
Abstract
Understanding neuroimmunological disorders is essential for developing new diagnostic and therapeutic strategies. Rodent models have provided valuable insights, but are sometimes equated with their human counterparts. Here, we summarize how novel technologies may enable an improved human-focused view of immune mechanisms. Recent studies have applied these new technologies to the brain parenchyma, its surrounding cerebrospinal fluid, and peripheral immune compartments. Therapeutic interventions have also facilitated translational understanding in a reverse way. However, with improved technology, access to patient samples remains a rate-limiting step in translational research. We anticipate that next-generation neuroimmunology is likely to integrate, in the immediate future, diverse technical tools for optimal diagnosis, prognosis, and treatment of neuroimmunological disorders.
Collapse
Affiliation(s)
- Gerd Meyer Zu Hörste
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Münster, Germany.
| |
Collapse
|
43
|
Harris KM, Lim N, Lindau P, Robins H, Griffith LM, Nash RA, Turka LA, Muraro PA. Extensive intrathecal T cell renewal following hematopoietic transplantation for multiple sclerosis. JCI Insight 2020; 5:127655. [PMID: 31877116 DOI: 10.1172/jci.insight.127655] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 12/18/2019] [Indexed: 12/16/2022] Open
Abstract
A recent study of autologous hematopoietic stem cell transplantation (AHSCT) for active relapsing-remitting multiple sclerosis (RRMS) showed efficacy in preventing disease worsening. However, the immunologic basis for efficacy remains poorly defined. Multiple sclerosis pathology is known to be driven by inflammatory T cells that infiltrate the CNS. Therefore, we hypothesized that the preexisting T cell repertoire in the intrathecal compartment of active RRMS participants was ablated and replaced with new clones following AHSCT. T cell repertoires were assessed using high-throughput TCRβ chain sequencing in paired cerebrospinal fluid (CSF) and peripheral blood CD4+ and CD8+ T cells from participants that underwent AHSCT, before and up to 4 years following transplantation. More than 90% of the preexisting CSF repertoire in participants with active RRMS was removed following AHSCT and replaced with clonotypes predominantly generated from engrafted autologous stem cells. Of the preexisting clones in CSF, approximately 60% were also detected in blood before therapy, and concordant treatment effects were observed for clonotypes in both compartments following AHSCT. These results indicate that replacement of the preexisting TCR repertoire in active RRMS is a mechanism for AHSCT efficacy and suggest that peripheral blood could serve as a surrogate for CSF to define mechanisms associated with efficacy in future studies of AHSCT.
Collapse
Affiliation(s)
| | - Noha Lim
- Immune Tolerance Network, Bethesda, Maryland, USA
| | - Paul Lindau
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Harlan Robins
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Adaptive Biotechnologies, Seattle, Washington, USA
| | - Linda M Griffith
- Division of Allergy, Immunology and Transplantation, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Richard A Nash
- Colorado Blood Cancer Institute, Presbyterian/St. Luke's, Denver, Colorado, USA
| | - Laurence A Turka
- Immune Tolerance Network, Bethesda, Maryland, USA.,Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Paolo A Muraro
- Department of Brain Sciences, Imperial College London, London, United Kingdom
| |
Collapse
|
44
|
Mohammed EM. Environmental Influencers, MicroRNA, and Multiple Sclerosis. J Cent Nerv Syst Dis 2020; 12:1179573519894955. [PMID: 32009827 PMCID: PMC6971968 DOI: 10.1177/1179573519894955] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a complex neurological disorder characterized by an aberrant immune system that affects patients' quality of life. Several environmental factors have previously been proposed to associate with MS pathophysiology, including vitamin D deficiency, Epstein-Barr virus (EBV) infection, and cigarette smoking. These factors may influence cellular molecularity, interfering with cellular proliferation, differentiation, and apoptosis. This review argues that small noncoding RNA named microRNA (miRNA) influences these factors' mode of action. Dysregulation in the miRNAs network may deeply impact cellular hemostasis, thereby possibly resulting in MS pathogenicity. This article represents a literature review and an author's theory of how environmental factors may induce dysregulations in the miRNAs network, which could ultimately affect MS pathogenicity.
Collapse
|
45
|
Gross CC, Meyer C, Bhatia U, Yshii L, Kleffner I, Bauer J, Tröscher AR, Schulte-Mecklenbeck A, Herich S, Schneider-Hohendorf T, Plate H, Kuhlmann T, Schwaninger M, Brück W, Pawlitzki M, Laplaud DA, Loussouarn D, Parratt J, Barnett M, Buckland ME, Hardy TA, Reddel SW, Ringelstein M, Dörr J, Wildemann B, Kraemer M, Lassmann H, Höftberger R, Beltrán E, Dornmair K, Schwab N, Klotz L, Meuth SG, Martin-Blondel G, Wiendl H, Liblau R. CD8 + T cell-mediated endotheliopathy is a targetable mechanism of neuro-inflammation in Susac syndrome. Nat Commun 2019; 10:5779. [PMID: 31852955 PMCID: PMC6920411 DOI: 10.1038/s41467-019-13593-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/11/2019] [Indexed: 12/19/2022] Open
Abstract
Neuroinflammation is often associated with blood-brain-barrier dysfunction, which contributes to neurological tissue damage. Here, we reveal the pathophysiology of Susac syndrome (SuS), an enigmatic neuroinflammatory disease with central nervous system (CNS) endotheliopathy. By investigating immune cells from the blood, cerebrospinal fluid, and CNS of SuS patients, we demonstrate oligoclonal expansion of terminally differentiated activated cytotoxic CD8+ T cells (CTLs). Neuropathological data derived from both SuS patients and a newly-developed transgenic mouse model recapitulating the disease indicate that CTLs adhere to CNS microvessels in distinct areas and polarize granzyme B, which most likely results in the observed endothelial cell injury and microhemorrhages. Blocking T-cell adhesion by anti-α4 integrin-intervention ameliorates the disease in the preclinical model. Similarly, disease severity decreases in four SuS patients treated with natalizumab along with other therapy. Our study identifies CD8+ T-cell-mediated endotheliopathy as a key disease mechanism in SuS and highlights therapeutic opportunities.
Collapse
Affiliation(s)
- Catharina C Gross
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
| | - Céline Meyer
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
| | - Urvashi Bhatia
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Lidia Yshii
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
| | - Ilka Kleffner
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Department of Neurology, University Hospital Knappschaftskrankenhaus Bochum, Ruhr University Bochum, In der Schornau 23-25, 44892, Bochum, Germany
| | - Jan Bauer
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Anna R Tröscher
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Andreas Schulte-Mecklenbeck
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Sebastian Herich
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Tilman Schneider-Hohendorf
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Henrike Plate
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Tanja Kuhlmann
- Institute of Neuropathology, University Hospital Münster, University of Münster, Pottkamp 2, 48149, Münster, Germany
| | - Markus Schwaninger
- Institute of Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Wolfgang Brück
- Institute of Neuropathology, University Medical Center Göttingen, Robert-Koch-Straße 40, 37099, Göttingen, Germany
| | - Marc Pawlitzki
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - David-Axel Laplaud
- UMR 1064, INSERM, Centre de Recherche en Transplantation et Immunologie, Université de Nantes, CHU Nantes - Hôtel Dieu Bd Jean Monnet, 44093, Nantes Cedex 01, France
- Service Neurologie, CHU Nantes, Nantes, France
| | - Delphine Loussouarn
- Service d'Anatomo-Pathologie, CHU Nantes, Hôtel-Dieu, rez-de-jardin, 44093, Nantes Cedex 1, France
| | - John Parratt
- Department of Neurology, Royal North Shore Hospital, Sydney, Australia
- Australia Northern Clinical School, University of Sydney, Reserve Road, St Leonards, Sydney, NSW, 2065, Australia
| | - Michael Barnett
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
| | - Michael E Buckland
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neuropathology, Royal Prince Alfred Hospital, 94, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
| | - Todd A Hardy
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neurology, Concord Hospital, University of Sydney, Sydney, NSW, 2139, Australia
| | - Stephen W Reddel
- Brain and Mind Centre, Medical Faculty, University of Sydney, Mallett Street, Camperdown, Sydney, NSW, 2050, Australia
- Department of Neurology, Concord Hospital, University of Sydney, Sydney, NSW, 2139, Australia
| | - Marius Ringelstein
- Department of Neurology, Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Department of Neurology, Center of Neurology und Neuropsychiatry, LVR-Klinikum, Heinrich Heine University Düsseldorf, Bergische Landstraße 2, 40629, Düsseldorf, Germany
| | - Jan Dörr
- Max Delbrueck Center for Molecular Medicine and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, NeuroCure, Experimental and Clinical Research Center, Charitéplatz 1, 10117, Berlin, Germany
| | - Brigitte Wildemann
- Molecular Neuroimmunology Group, Department of Neurology, University of Heidelberg, Im Neuenheimer Feld 400, 69120, Heidelberg, Germany
| | - Markus Kraemer
- Department of Neurology, Medical Faculty, Heinrich Heine University, Moorenstraße 5, 40225, Düsseldorf, Germany
- Department of Neurology, Alfried Krupp Hospital, Alfried-Krupp-Strasse 21, 45130, Essen, Germany
| | - Hans Lassmann
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Romana Höftberger
- Institute of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Eduardo Beltrán
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians-University Munich, Großhaderner Straße 9, Martinsried, 82152, Munich, Germany
| | - Klaus Dornmair
- Institute of Clinical Neuroimmunology, Biomedical Center and Hospital of the Ludwig-Maximilians-University Munich, Großhaderner Straße 9, Martinsried, 82152, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Nicholas Schwab
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Luisa Klotz
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
| | - Sven G Meuth
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany
- Cells in Motion (CiM), Münster, Germany
| | - Guillaume Martin-Blondel
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France
- Department of Infectious and Tropical Diseases, Toulouse University Hospital, Toulouse, France
| | - Heinz Wiendl
- Department of Neurology with Institute of Translational Neurology, University Hospital Münster, University of Münster, Albert-Schweitzer-Campus 1, 48149, Münster, Germany.
- Australia Northern Clinical School, University of Sydney, Reserve Road, St Leonards, Sydney, NSW, 2065, Australia.
- Cells in Motion (CiM), Münster, Germany.
| | - Roland Liblau
- Centre de Physiopathologie Toulouse-Purpan (CPTP), Université de Toulouse, CNRS, Inserm, UPS, CHU Purpan - BP 3028 - 31024, Toulouse Cedex 3, Toulouse, France.
| |
Collapse
|
46
|
Wolf K, Hether T, Gilchuk P, Kumar A, Rajeh A, Schiebout C, Maybruck J, Buller RM, Ahn TH, Joyce S, DiPaolo RJ. Identifying and Tracking Low-Frequency Virus-Specific TCR Clonotypes Using High-Throughput Sequencing. Cell Rep 2019; 25:2369-2378.e4. [PMID: 30485806 PMCID: PMC7770954 DOI: 10.1016/j.celrep.2018.11.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 09/18/2018] [Accepted: 10/31/2018] [Indexed: 12/30/2022] Open
Abstract
Tracking antigen-specific T cell responses over time within individuals is difficult because of lack of knowledge of antigen-specific TCR sequences, limitations in sample size, and assay sensitivities. We hypothesized that analyses of high-throughput sequencing of TCR clonotypes could provide functional readouts of individuals' immunological histories. Using high-throughput TCR sequencing, we develop a database of TCRβ sequences from large cohorts of mice before (naive) and after smallpox vaccination. We computationally identify 315 vaccine-associated TCR sequences (VATS) that are used to train a diagnostic classifier that distinguishes naive from vaccinated samples in mice up to 9 months post-vaccination with >99% accuracy. We determine that the VATS library contains virus-responsive TCRs by in vitro expansion assays and virus-specific tetramer sorting. These data outline a platform for advancing our capabilities to identify pathogen-specific TCR sequences, which can be used to identify and quantitate low-frequency pathogen-specific TCR sequences in circulation over time with exceptional sensitivity.
Collapse
Affiliation(s)
- Kyle Wolf
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO 63104, USA
| | - Tyler Hether
- Adaptive Biotechnologies, Seattle, WA 98102, USA
| | - Pavlo Gilchuk
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Amrendra Kumar
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Ahmad Rajeh
- Program in Bioinformatics and Computational Biology, Saint Louis University, Saint Louis, MO 63104, USA
| | - Courtney Schiebout
- Program in Bioinformatics and Computational Biology, Saint Louis University, Saint Louis, MO 63104, USA
| | - Julie Maybruck
- Federal Bureau of Investigation, Washington, DC 20535, USA
| | - R Mark Buller
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO 63104, USA
| | - Tae-Hyuk Ahn
- Department of Computer Science, Saint Louis University, Saint Louis, MO 63104, USA; Program in Bioinformatics and Computational Biology, Saint Louis University, Saint Louis, MO 63104, USA
| | - Sebastian Joyce
- Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN 37212, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, TN 37232, USA
| | - Richard J DiPaolo
- Department of Molecular Microbiology and Immunology, Saint Louis University, Saint Louis, MO 63104, USA.
| |
Collapse
|
47
|
Epstein-Barr Virus-Specific CD8 T Cells Selectively Infiltrate the Brain in Multiple Sclerosis and Interact Locally with Virus-Infected Cells: Clue for a Virus-Driven Immunopathological Mechanism. J Virol 2019; 93:JVI.00980-19. [PMID: 31578295 PMCID: PMC6880158 DOI: 10.1128/jvi.00980-19] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
EBV establishes a lifelong and asymptomatic infection in most individuals and more rarely causes infectious mononucleosis and malignancies, like lymphomas. The virus is also strongly associated with MS, a chronic neuroinflammatory disease with unknown etiology. Infectious mononucleosis increases the risk of developing MS, and immune reactivity toward EBV is higher in persons with MS, indicating inadequate control of the virus. Previous studies have suggested that persistent EBV infection in the CNS stimulates an immunopathological response, causing bystander neural cell damage. To verify this, we need to identify the immune culprits responsible for the detrimental antiviral response in the CNS. In this study, we analyzed postmortem brains donated by persons with MS and show that CD8 cytotoxic T cells recognizing EBV enter the brain and interact locally with the virus-infected cells. This antiviral CD8 T cell-mediated immune response likely contributes to MS pathology. Epstein-Barr virus (EBV) is a ubiquitous herpesvirus strongly associated with multiple sclerosis (MS), a chronic inflammatory disease of the central nervous system (CNS). However, the mechanisms linking EBV infection to MS pathology are uncertain. Neuropathological and immunological studies suggest that a persistent EBV infection in the CNS can stimulate a CD8 T-cell response aimed at clearing the virus but inadvertently causing CNS injury. Inasmuch as in situ demonstration of EBV-specific CD8 T cells and their effector function is missing, we searched for EBV-specific CD8 T cells in MS brain tissue using the pentamer technique. Postmortem brain samples from 12 donors with progressive MS and known HLA class I genotype were analyzed. Brain sections were stained with HLA-matched pentamers coupled with immunogenic peptides from EBV-encoded proteins, control virus (cytomegalovirus and influenza A virus) proteins, and myelin basic protein. CD8 T cells recognizing proteins expressed in the latent and lytic phases of the EBV life cycle were visualized in white matter lesions and/or meninges of 11/12 MS donors. The fraction (median value) of CD8 T cells recognizing individual EBV epitopes ranged from 0.5 to 2.5% of CNS-infiltrating CD8 T cells. Cytomegalovirus-specific CD8 T cells were detected at a lower frequency (≤0.3%) in brain sections from 4/12 MS donors. CNS-infiltrating EBV-specific CD8 T cells were CD107a positive, suggesting a cytotoxic phenotype, and stuck to EBV-infected cells. Together with local EBV dysregulation, selective enrichment of EBV-specific CD8 T cells in the MS brain supports the notion that skewed immune responses toward EBV contribute to inflammation causing CNS injury. IMPORTANCE EBV establishes a lifelong and asymptomatic infection in most individuals and more rarely causes infectious mononucleosis and malignancies, like lymphomas. The virus is also strongly associated with MS, a chronic neuroinflammatory disease with unknown etiology. Infectious mononucleosis increases the risk of developing MS, and immune reactivity toward EBV is higher in persons with MS, indicating inadequate control of the virus. Previous studies have suggested that persistent EBV infection in the CNS stimulates an immunopathological response, causing bystander neural cell damage. To verify this, we need to identify the immune culprits responsible for the detrimental antiviral response in the CNS. In this study, we analyzed postmortem brains donated by persons with MS and show that CD8 cytotoxic T cells recognizing EBV enter the brain and interact locally with the virus-infected cells. This antiviral CD8 T cell-mediated immune response likely contributes to MS pathology.
Collapse
|
48
|
TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. Nat Immunol 2019; 20:1692-1699. [PMID: 31745340 DOI: 10.1038/s41590-019-0544-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/21/2019] [Indexed: 01/14/2023]
Abstract
High-throughput 3' single-cell RNA-sequencing (scRNA-seq) allows cost-effective, detailed characterization of individual immune cells from tissues. Current techniques, however, are limited in their ability to elucidate essential immune cell features, including variable sequences of T cell antigen receptors (TCRs) that confer antigen specificity. Here, we present a strategy that enables simultaneous analysis of TCR sequences and corresponding full transcriptomes from 3'-barcoded scRNA-seq samples. This approach is compatible with common 3' scRNA-seq methods, and adaptable to processed samples post hoc. We applied the technique to identify transcriptional signatures associated with T cells sharing common TCRs from immunized mice and from patients with food allergy. We observed preferential phenotypes among subsets of expanded clonotypes, including type 2 helper CD4+ T cell (TH2) states associated with food allergy. These results demonstrate the utility of our method when studying diseases in which clonotype-driven responses are critical to understanding the underlying biology.
Collapse
|
49
|
Bertoli D, Sottini A, Capra R, Scarpazza C, Bresciani R, Notarangelo LD, Imberti L. Lack of specific T- and B-cell clonal expansions in multiple sclerosis patients with progressive multifocal leukoencephalopathy. Sci Rep 2019; 9:16605. [PMID: 31719595 PMCID: PMC6851145 DOI: 10.1038/s41598-019-53010-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 10/26/2019] [Indexed: 01/11/2023] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is a rare, potentially devastating myelin-degrading disease caused by the JC virus. PML occurs preferentially in patients with compromised immune system, but has been also observed in multiple sclerosis (MS) patients treated with disease-modifying drugs. We characterized T and B cells in 5 MS patients that developed PML, 4 during natalizumab therapy and one after alemtuzumab treatment, and in treated patients who did not develop the disease. Results revealed that: i) thymic and bone marrow output was impaired in 4 out 5 patients at the time of PML development; ii) T-cell repertoire was restricted; iii) clonally expanded T cells were present in all patients. However, common usage or pairings of T-cell receptor beta variable or joining genes, specific clonotypes or obvious “public” T-cell response were not detected at the moment of PML onset. Similarly, common restrictions were not found in the immunoglobulin heavy chain repertoire. The data indicate that no JCV-related specific T- and B-cell expansions were mounted at the time of PML. The current results enhance our understanding of JC virus infection and PML, and should be taken into account when choosing targeted therapies.
Collapse
Affiliation(s)
- Diego Bertoli
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy.,Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Alessandra Sottini
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy
| | - Ruggero Capra
- Multiple Sclerosis Center, ASST Spedali Civili, Brescia, Italy
| | - Cristina Scarpazza
- Multiple Sclerosis Center, ASST Spedali Civili, Brescia, Italy.,Department of General Psychology, University of Padova, Padova, Italy
| | - Roberto Bresciani
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Luisa Imberti
- Centro di Ricerca Emato-oncologica AIL (CREA), Diagnostic Department, ASST Spedali Civili, Brescia, Italy.
| |
Collapse
|
50
|
López-Valencia D, Medina-Ortega Á, Hoyos-Samboní DF, Saavedra-Torres JS, Salguero C. Epstein-Barr virus infection as a predisposing factor for multiple sclerosis. An update from molecular biology, immunology and epidemiology. REVISTA DE LA FACULTAD DE MEDICINA 2019. [DOI: 10.15446/revfacmed.v67n3.70149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introduction: Epstein-Barr virus is an infectious agent used to immortalize and induce polyclonal activation of B cells. It has been widely described that this virus produces changes in the cells it infects and in the immune response, and stimulates the development of autoimmune diseases.Objective: To characterize the association between Epstein-Barr virus and multiple sclerosis described in current scientific literature.Materials and methods: A 59-years range literature search was conducted in the PubMed, ScienceDirect, Redalyc and SciELO databases using the following MeSH terms: “Epstein-Barr virus, multiple sclerosis autoimmune diseases, autoimmune diseases of the nervous system”.Results: Many studies describe the association between Epstein-Barr virus and multiple sclerosis. It is believed that acute infection and viral reactivation promote the development of multiple sclerosis.Conclusions: It is necessary to conduct further research on the pathogenesis and morphophysiological and neuroimmunological changes –at the ecological, molecular, cellular, tissue, organic and systemic level– induced by the immune response and that favor the development of multiple sclerosis.
Collapse
|