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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.
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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.
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Gakis G, Angelopoulos I, Panagoulias I, Mouzaki A. Current knowledge on multiple sclerosis pathophysiology, disability progression assessment and treatment options, and the role of autologous hematopoietic stem cell transplantation. Autoimmun Rev 2024; 23:103480. [PMID: 38008300 DOI: 10.1016/j.autrev.2023.103480] [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: 10/31/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system (CNS) that affects nearly 2.8 million people each year. MS distinguishes three main types: relapsing-remitting MS (RRMS), secondary progressive MS (SPMS) and primary progressive MS (PPMS). RRMS is the most common type, with the majority of patients eventually progressing to SPMS, in which neurological development is constant, whereas PPMS is characterized by a progressive course from disease onset. New or additional insights into the role of effector and regulatory cells of the immune and CNS systems, Epstein-Barr virus (EBV) infection, and the microbiome in the pathophysiology of MS have emerged, which may lead to the development of more targeted therapies that can halt or reverse neurodegeneration. Depending on the type and severity of the disease, various disease-modifying therapies (DMTs) are currently used for RRMS/SPMS and PPMS. As a last resort, and especially in highly active RRMS that does not respond to DMTs, autologous hematopoietic stem cell transplantation (AHSCT) is performed and has shown good results in reducing neuroinflammation. Nevertheless, the question of its potential role in preventing disability progression remains open. The aim of this review is to provide a comprehensive update on MS pathophysiology, assessment of MS disability progression and current treatments, and to examine the potential role of AHSCT in preventing disability progression.
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Affiliation(s)
- Georgios Gakis
- Laboratory of Immunohematology, Medical School, University of Patras, Patras, Greece
| | - Ioannis Angelopoulos
- Laboratory of Immunohematology, Medical School, University of Patras, Patras, Greece
| | - Ioannis Panagoulias
- Laboratory of Immunohematology, Medical School, University of Patras, Patras, Greece
| | - Athanasia Mouzaki
- Laboratory of Immunohematology, Medical School, University of Patras, Patras, Greece.
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Du Y, Zhang Y, Diao J, Fu P, Jiang R, Wang P, Yang H, Zheng X, Zhang L, Bi J, Zhou Q. Decoding the diagnostic potential of T cell repertoires in peripheral blood of patients from amnestic mild cognitive impairment to Alzheimer's disease. FASEB J 2024; 38:e23317. [PMID: 38095240 DOI: 10.1096/fj.202301485r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/13/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023]
Abstract
Alzheimer's disease (AD) is currently an incurable neurodegenerative disorder and is the most common etiological cause of dementia. Consequently, it has severe burden on its patients and on their caregivers and represents a global health concern. Clinical investigations have indicated that a dysregulation of peripheral T cell immune homeostasis may be involved in the pathogenesis of AD, as well as in the early stages of AD, characterized by mild cognitive impairment (MCI). However, the characteristics and concomitant feasibility of the use of T-cell receptor (TCR) typing for disease diagnosis remains largely unknown. We employed a high-throughput sequencing and multidimensional bioinformatics analyses for the identification of TCR repertoires present in peripheral blood samples of 10 patients with amnestic MCI (aMCI), 10 patients with AD, and 10 healthy controls (HCs). Based on the characteristics of the TCR repertoires in the amount and diversity of combinations of V-J, the spectrum of immune defense, and differentially expressed genes (DEGs), single and specific TCR profiles were observed in the patient samples of aMCI and AD compared to profiles of HCs. In particular, the diversity of TCR clonotypes manifested a pattern of "decreased first and then increased" pattern during the progression from aMCI to AD, a pattern that was not observed in HC samples. Additionally, a total of 46 and 35 amino acid CDR3 sequences with consistent and reverse expressive abundance with diversity of TCR clonotypes were identified, respectively. Taken together, we provide novel and essential preliminary evidence demonstrating the presence of diversity of T cell repertoires from differentially expressed V-J gene segments and amino acid clonotypes using peripheral blood samples from patients with AD, aMCI, and from HC. Such findings have the potential to reveal potential mechanisms through which aMCI progresses to AD and provide a reference for the future development of immune-related diagnoses and therapies for AD.
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Affiliation(s)
- Yansheng Du
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yichen Zhang
- Department of Critical Care Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jiuzhou Diao
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Pengrui Fu
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Runze Jiang
- Department of Translational Medicine Research Institute, Shandong Jingwei Biotechnology Co. Ltd, Jinan, China
| | - Ping Wang
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hui Yang
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaolei Zheng
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Leisheng Zhang
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province & NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, China
- Key Laboratory of Radiation Technology and Biophysics, Hefei Institute of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Jianzhong Bi
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qingbo Zhou
- Department of Neurology Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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Hu J, Yang X, Ren J, Zhong S, Fan Q, Li W. Identification and verification of characteristic differentially expressed ferroptosis-related genes in osteosarcoma using bioinformatics analysis. Toxicol Mech Methods 2023; 33:781-795. [PMID: 37488941 DOI: 10.1080/15376516.2023.2240879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND This study identified and verified the characteristic differentially expressed ferroptosis-related genes (CDEFRGs) in osteosarcoma (OS). METHODS We extracted ferroptosis-related genes (FRGs), identified differentially expressed FRGs (DEFRGs) in OS, and conducted correlation analysis between DEFRGs. Next, we conducted GO and KEGG analyses to explore the biological functions and pathways of DEFRGs. Furthermore, we used LASSO and SVM-RFE algorithms to screen CDEFRGs, and evaluated its accuracy in diagnosing OS through ROC curves. Then, we demonstrated the molecular function and pathway enrichment of CDEFRGs through GSEA analysis. In addition, we evaluated the differences in immune cell infiltration between OS and NC groups, as well as the correlation between CDEFRGs expressions and immune cell infiltrations. Finally, the expression of CDEFRGs was verified through qRT-PCR, western blotting, and immunohistochemistry experiments. RESULTS We identified 51 DEFRGs and the expression relationship between them. GO and KEGG analysis revealed their key functions and important pathways. Based on four CDEFRGs (PEX3, CPEB1, NOX1, and ALOX5), we built the OS diagnostic model, and verified its accuracy. GSEA analysis further revealed the important functions and pathways of CDEFRGs. In addition, there were differences in immune cell infiltration between OS group and NC group, and CDEFRGs showed significant correlation with certain infiltrating immune cells. Finally, we validated the differential expression levels of four CDEFRGs through external experiments. CONCLUSIONS This study has shed light on the molecular pathological mechanism of OS and has offered novel perspectives for the early diagnosis and immune-targeted therapy of OS patients.
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Affiliation(s)
- Jianhua Hu
- Department of Orthopedic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, P. R. China
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, P. R. China
| | - Xi Yang
- Department of Orthopedic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, P. R. China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, P. R. China
| | - Jing Ren
- Department of Spinal Surgery, Qujing No. 1 Hospital, Affiliated Qujing Hospital of Kunming Medical University, Qujing, P. R. China
| | - Shixiao Zhong
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, P. R. China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, P. R. China
| | - Qianbo Fan
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, P. R. China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, P. R. China
| | - Weichao Li
- Department of Orthopedic Surgery, The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, P. R. China
- Faculty of Medical Science, Kunming University of Science and Technology, Kunming, P. R. China
- Yunnan Key Laboratory of Digital Orthopaedics, Kunming, P. R. China
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Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023; 14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
T cell receptors (TCR) play a vital role in the immune system's ability to recognize and respond to foreign antigens, relying on the highly polymorphic rearrangement of TCR genes. The recognition of autologous peptides by adaptive immunity may lead to the development and progression of autoimmune diseases. Understanding the specific TCR involved in this process can provide insights into the autoimmune process. RNA-seq (RNA sequencing) is a valuable tool for studying TCR repertoires by providing a comprehensive and quantitative analysis of the RNA transcripts. With the development of RNA technology, transcriptomic data must provide valuable information to model and predict TCR and antigen interaction and, more importantly, identify or predict neoantigens. This review provides an overview of the application and development of bulk RNA-seq and single-cell (SC) RNA-seq to examine the TCR repertoires. Furthermore, discussed here are bioinformatic tools that can be applied to study the structural biology of peptide/TCR/MHC (major histocompatibility complex) and predict antigenic epitopes using advanced artificial intelligence tools.
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Affiliation(s)
- Yiran Shen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Xuebing Leng
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Amy A. Rodriguez
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, United States
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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.
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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.
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Høye E, Dagenborg VJ, Torgunrud A, Lund-Andersen C, Fretland ÅA, Lorenz S, Edwin B, Hovig E, Fromm B, Inderberg EM, Greiff V, Ree AH, Flatmark K. T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases. Gigascience 2022; 12:giad032. [PMID: 37161965 PMCID: PMC10170408 DOI: 10.1093/gigascience/giad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite-stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumor-infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T-cell infiltration in CLM using T-cell receptor (TCR) repertoire sequencing. Eighty-five resected CLMs from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T-cell fractions were calculated, repertoire clonality was analyzed based on Hill evenness curves, and TCR sequence convergence was assessed using network analysis. RESULTS Increased T-cell fractions (10.6% vs. 6.3%) were detected in CLMs exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT-exposed tumors independently of the timing of NACT administration and surgery. While private clones made up >90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence. CONCLUSIONS TCR repertoire sequencing can be used to quantify T-cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T-cell clonal expansion in CLM in a clinical context.
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Affiliation(s)
- Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
| | - Vegar J Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Department of Gastroenterological Surgery, The Norwegian Radium Hospital, 0379 Oslo, Norway
| | - Annette Torgunrud
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Christin Lund-Andersen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
| | - Åsmund A Fretland
- The Intervention Centre, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
- Department of Hepato-Pancreato-Biliary Surgery, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Bjørn Edwin
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- The Intervention Centre, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
- Department of Hepato-Pancreato-Biliary Surgery, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Else M Inderberg
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, 0379 Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Anne H Ree
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- Department of Oncology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- Department of Gastroenterological Surgery, The Norwegian Radium Hospital, 0379 Oslo, Norway
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Ruder J, Docampo MJ, Rex J, Obahor S, Naghavian R, Müller AM, Schanz U, Jelcic I, Martin R. Dynamics of T cell repertoire renewal following autologous hematopoietic stem cell transplantation in multiple sclerosis. Sci Transl Med 2022; 14:eabq1693. [DOI: 10.1126/scitranslmed.abq1693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Autologous hematopoietic stem cell transplantation (aHSCT) is a highly effective treatment of multiple sclerosis (MS). It depletes autoreactive cells and subsequently renews adaptive immune cells. The possible proinflammatory potential of surviving T cells early after aHSCT has not been studied. Here, we examined the dynamics of new and surviving T cells in 27 patients after aHSCT by multidimensional flow cytometry, T cell receptor (TCR) sequencing, specificity testing, telomere length profiling, and HLA genotyping. Early after aHSCT, naïve T cells are barely detectable, whereas effector memory (EM) T cells quickly reconstitute to pre-aHSCT values. EM CD4+T cells early after aHSCT have shorter telomeres, have higher expression of senescence and exhaustion markers, and proliferate less than those before aHSCT. We find a median TCR repertoire overlap of 26% between the early post-aHSCT EM CD4+T cells and pre-aHSCT, indicating persistence of EM CD4+T cells early after transplantation. The EM CD4+TCR repertoire overlap declines to 15% at 12 months after aHSCT, whereas the naïve TCR repertoire entirely renews. HLA-DR–associated EM CD4+T cell reactivity toward MS-related antigens decreased after aHSCT, whereas reactivity toward EBV increased. Our data show substantial survival of pre-aHSCT EM CD4+T cells early after transplantation but complete renewal of the T cell repertoire by nascent T cells later.
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Affiliation(s)
- Josefine Ruder
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - María José Docampo
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jordan Rex
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Simon Obahor
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Reza Naghavian
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Antonia M.S. Müller
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Urs Schanz
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ilijas Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section (NIMS), Department of Neurology, University and University Hospital Zurich, 8091 Zurich, Switzerland
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Willison AG, Meuth SG. [Multiple sclerosis: interventions to halt disease : Which patients can be considered for autologous stem cell transplantation]. DER NERVENARZT 2022; 93:987-999. [PMID: 35951049 DOI: 10.1007/s00115-022-01358-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/28/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Autologous hematopoietic stem cell transplantation (aHSCT) for treatment of multiple sclerosis (MS) is gaining increasing prominence in the therapeutic landscape. This review article focuses on describing the evidence and European guidelines for aHSCT so that neurologists in Germany can consider this treatment option for appropriate MS patients. In this context, it must be taken into consideration that in every case a cost transfer must be individually applied for. AIM To provide information for neurologists considering aHSCT for patients with MS. MATERIAL AND METHODS In this narrative review articles from PubMed were pooled and analyzed. RESULTS AND DISCUSSION High quality data from randomized, controlled clinical trials are required to compare the efficacy of aHSCT to the currently available highly effective disease-modifying therapies (DMT) so that reliable conclusions can be drawn regarding the relationship between the risks and benefits of aHSCT in MS; however, the studies discussed in this review provide important points of reference for patient selection and the transplantation protocol. Further advice is available from the European Society for Blood and Marrow Transplantation (EBMT) for experienced centers considering aHSCT. The available data and the European guidelines suggest that patients aged less than 45 years, an expanded disability status scale (EDSS) ≤ 5.5, highly active MS, a disease duration of less than 10 years, an ineffective course of DMT or rapidly progressive MS may be eligible for aHSCT and should be referred to an experienced center for further assessment.
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Affiliation(s)
- A G Willison
- Klinik für Neurologie, Universitätsklinikum Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Deutschland.
| | - S G Meuth
- Klinik für Neurologie, Universitätsklinikum Düsseldorf, Moorenstraße 5, 40225, Düsseldorf, Deutschland.
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Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022; 2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
B and T cell receptor (immune) repertoires can represent an individual's immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters. Here, we introduce immuneREF: a quantitative multidimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2,400 datasets from individuals with varying immune states (healthy, [autoimmune] disease, and infection). We discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF enables the population-wide study of adaptive immune response similarity across immune states.
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Affiliation(s)
- Cédric R. Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen, China
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Philippe A. Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain
| | - Geir K. Sandve
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
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11
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Relevance of Pathogenetic Mechanisms to Clinical Effectiveness of B-Cell-Depleting Monoclonal Antibodies in Multiple Sclerosis. J Clin Med 2022; 11:jcm11154288. [PMID: 35893382 PMCID: PMC9332715 DOI: 10.3390/jcm11154288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/17/2022] [Accepted: 07/19/2022] [Indexed: 01/27/2023] Open
Abstract
Evidence of the effectiveness of B-cell-depleting monoclonal antibodies (mAbs) in multiple sclerosis (MS) prompted a partial revisitation of the pathogenetic paradigm of the disease, which was, so far, considered a T-cell-mediated autoimmune disorder. Mechanisms underlying the efficacy of B-cell-depleting mAbs in MS are still unknown. However, they likely involve the impairment of pleiotropic B-cell functions different from antibody secretion, such as their role as antigen-presenting cells during both the primary immune response in the periphery and the secondary response within the central nervous system (CNS). A potential impact of B-cell-depleting mAbs on inflammation compartmentalised within the CNS was also suggested, but little is known about the mechanism underlying this latter phenomenon as no definite evidence was provided so far on the ability of mAbs to cross the blood–brain barrier and reliable biomarkers of compartmentalised inflammation are lacking. The present paper briefly summarises the immunopathogenesis of MS with a focus on onset of autoimmunity and compartmentalisation of the immune response; mechanisms mediating B-cell depletion and underlying the effectiveness of B-cell-depleting mAbs are also discussed.
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12
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Towlerton AMH, Ravishankar S, Coffey DG, Puronen CE, Warren EH. Serial Analysis of the T-Cell Receptor β-Chain Repertoire in People Living With HIV Reveals Incomplete Recovery After Long-Term Antiretroviral Therapy. Front Immunol 2022; 13:879190. [PMID: 35585986 PMCID: PMC9108698 DOI: 10.3389/fimmu.2022.879190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
Long-term antiretroviral therapy (ART) in people living with HIV (PLHIV) is associated with sustained increases in CD4+ T-cell count, but its effect on the peripheral blood T-cell repertoire has not been comprehensively evaluated. In this study, we performed serial profiling of the composition and diversity of the T-cell receptor β-chain (TRB) repertoire in 30 adults with HIV infection before and after the initiation of ART to define its long-term impact on the TRB repertoire. Serially acquired blood samples from 30 adults with HIV infection collected over a mean of 6 years (range, 1-12) years, with 1-4 samples collected before and 2-8 samples collected after the initiation of ART, were available for analysis. TRB repertoires were characterized via high-throughput sequencing of the TRB variable region performed on genomic DNA extracted from unsorted peripheral blood mononuclear cells. Additional laboratory and clinical metadata including serial measurements of HIV viral load and CD4 + T-cell count were available for all individuals in the cohort. A previously published control group of 189 TRB repertoires from peripheral blood samples of adult bone marrow transplant donors was evaluated for comparison. ART initiation in PLHIV was associated with a sustained reduction in viral load and a significant increase in TRB repertoire diversity. However, repertoire diversity in PLHIV remained significantly lower than in the control group even after long-term ART. The composition of TRB repertoires of PLHIV after ART also remained perturbed compared to the control cohort, as evidenced by large persistent private clonal expansions, reduced efficiency in the generation of TRB CDR3 amino acid sequences, and a narrower range of CDR3 lengths. Network analysis revealed an antigen-experienced structure in the TRB repertoire of PLHIV both before and after ART initiation that was quite distinct from the structure of control repertoires, with a slight shift toward a more naïve structure observed after ART initiation. Though we observe significant improvement in TRB repertoire diversity with durable viral suppression in PLHIV on long-term ART, the composition and structure of these repertoires remain significantly perturbed compared to the control cohort of adult bone marrow transplant donors.
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Affiliation(s)
- Andrea M. H. Towlerton
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Shashidhar Ravishankar
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - David G. Coffey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
- Division of Hematology, University of Miami, Miami, FL, United States
| | - Camille E. Puronen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
| | - Edus H. Warren
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Division of Medical Oncology, University of Washington, Seattle, WA, United States
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13
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The current standing of autologous haematopoietic stem cell transplantation for the treatment of multiple sclerosis. J Neurol 2022; 269:3937-3958. [PMID: 35399125 PMCID: PMC8995166 DOI: 10.1007/s00415-022-11063-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/02/2022] [Accepted: 03/03/2022] [Indexed: 11/01/2022]
Abstract
AbstractAutologous haematopoietic stem cell transplantation (aHSCT) is gaining traction as a valuable treatment option for patients affected by severe multiple sclerosis (MS), particularly the relapsing–remitting form. We describe the current literature in terms of clinical trials, observational and retrospective studies, as well as immune reconstitution following transplantation, with a focus on the conditioning regimens used for transplantation. The evidence base predominantly consists of non-randomised, uncontrolled clinical trials or data from retrospective or observational cohorts, i.e. very few randomised or controlled trials. Most often, intermediate-intensity conditioning regimens are used, with promising results from both myeloablative and lymphoablative strategies, as well as from regimens that are low and high intensity. Efficacy of transplantation, which is likely secondary to immune reconstitution and restored immune tolerance, is, therefore, not clearly dependent on the intensity of the conditioning regimen. However, the conditioning regimen may well influence the immune response to transplantation. Heterogeneity of conditioning regimens among studies hinders synthesis of the articles assessing post-aHSCT immune system changes. Factors associated with better outcomes were lower Kurtzke Expanded Disability Status Scale, relapsing–remitting MS, younger age, and shorter disease duration at baseline, which supports the guidance for patient selection proposed by the European Society for Blood and Marrow Transplantation. Interestingly, promising outcomes were described for patients with secondary progressive MS by some studies, which may be worth taking into account when considering treatment options for patients with active, progressive disease. Of note, a significant proportion of patients develop autoimmune disease following transplantation, with alemtuzumab-containing regimens associated with the highest incidence.
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14
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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.
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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
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15
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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.
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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
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16
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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).
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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.
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17
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Kubick N, Klimovich P, Flournoy PH, Bieńkowska I, Łazarczyk M, Sacharczuk M, Bhaumik S, Mickael ME, Basu R. Interleukins and Interleukin Receptors Evolutionary History and Origin in Relation to CD4+ T Cell Evolution. Genes (Basel) 2021; 12:genes12060813. [PMID: 34073576 PMCID: PMC8226699 DOI: 10.3390/genes12060813] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022] Open
Abstract
Understanding the evolution of interleukins and interleukin receptors is essential to control the function of CD4+ T cells in various pathologies. Numerous aspects of CD4+ T cells’ presence are controlled by interleukins including differentiation, proliferation, and plasticity. CD4+ T cells have emerged during the divergence of jawed vertebrates. However, little is known about the evolution of interleukins and their origin. We traced the evolution of interleukins and their receptors from Placozoa to primates. We performed phylogenetic analysis, ancestral reconstruction, HH search, and positive selection analysis. Our results indicated that various interleukins’ emergence predated CD4+ T cells divergence. IL14 was the most ancient interleukin with homologs in fungi. Invertebrates also expressed various interleukins such as IL41 and IL16. Several interleukin receptors also appeared before CD4+ T cells divergence. Interestingly IL17RA and IL17RD, which are known to play a fundamental role in Th17 CD4+ T cells first appeared in mollusks. Furthermore, our investigations showed that there is not any single gene family that could be the parent group of interleukins. We postulate that several groups have diverged from older existing cytokines such as IL4 from TGFβ, IL10 from IFN, and IL28 from BCAM. Interleukin receptors were less divergent than interleukins. We found that IL1R, IL7R might have diverged from a common invertebrate protein that contained TIR domains, conversely, IL2R, IL4R and IL6R might have emerged from a common invertebrate ancestor that possessed a fibronectin domain. IL8R seems to be a GPCR that belongs to the rhodopsin-like family and it has diverged from the Somatostatin group. Interestingly, several interleukins that are known to perform a critical function for CD4+ T cells such as IL6, IL17, and IL1B have gained new functions and evolved under positive selection. Overall evolution of interleukin receptors was not under significant positive selection. Interestingly, eight interleukin families appeared in lampreys, however, only two of them (IL17B, IL17E) evolved under positive selection. This observation indicates that although lampreys have a unique adaptive immune system that lacks CD4+ T cells, they could be utilizing interleukins in homologous mode to that of the vertebrates’ immune system. Overall our study highlights the evolutionary heterogeneity within the interleukins and their receptor superfamilies and thus does not support the theory that interleukins evolved solely in jawed vertebrates to support T cell function. Conversely, some of the members are likely to play conserved functions in the innate immune system.
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Affiliation(s)
- Norwin Kubick
- Institute of Biochemistry, Molecular Cell Biology, University Clinic Hamburg-Eppendorf, 0251 Hamburg, Germany;
| | - Pavel Klimovich
- PM Research Center, 20 Kaggeholm, Ekerö, 178 54 Stockholm, Sweden; (P.K.); (P.H.F.)
| | | | - Irmina Bieńkowska
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, ul. Postepu 36A, Jastrzebiec, 05-552 Magdalenka, Poland; (I.B.); (M.Ł.); (M.S.)
| | - Marzena Łazarczyk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, ul. Postepu 36A, Jastrzebiec, 05-552 Magdalenka, Poland; (I.B.); (M.Ł.); (M.S.)
| | - Mariusz Sacharczuk
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, ul. Postepu 36A, Jastrzebiec, 05-552 Magdalenka, Poland; (I.B.); (M.Ł.); (M.S.)
| | - Suniti Bhaumik
- Bevill Biomedical Sciences Research Building, The University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA;
| | - Michel-Edwar Mickael
- PM Research Center, 20 Kaggeholm, Ekerö, 178 54 Stockholm, Sweden; (P.K.); (P.H.F.)
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, ul. Postepu 36A, Jastrzebiec, 05-552 Magdalenka, Poland; (I.B.); (M.Ł.); (M.S.)
- Correspondence: (M.-E.M.); (R.B.)
| | - Rajatava Basu
- Bevill Biomedical Sciences Research Building, The University of Alabama at Birmingham, Birmingham, AL 35294-2170, USA;
- Correspondence: (M.-E.M.); (R.B.)
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18
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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.
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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
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19
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Jaime-Pérez JC, Turrubiates-Hernández GA, López-Silva LJ, Salazar-Riojas R, Gómez-Almaguer D. Early changes in IL-21, IL-22, CCL2, and CCL4 serum cytokines after outpatient autologous transplantation for multiple sclerosis: A proof of concept study. Clin Transplant 2020; 34:e14114. [PMID: 33048389 DOI: 10.1111/ctr.14114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/18/2020] [Accepted: 09/24/2020] [Indexed: 12/11/2022]
Abstract
Changes in serum cytokines after autologous hematopoietic stem cell transplantation (AHSCT) in multiple sclerosis (MS) patients were documented. Thirty-six consecutive MS patients who had their Expanded Disability Status Scale (EDSS) scored before AHSCT were prospectively enrolled. Cyclophosphamide (Cy) was infused at 200 mg/kg in two administrations given 10 days apart: the first dose for mobilization, the second as the conditioning regimen. Patients were mobilized with 10 µg/kg/day subcutaneous G-CSF. Serum was collected 14 days before and 14 after AHSCT. IL-6, IL-9, IL-10, IL 17-A, IL-21, IL-22, IL-23, TNF-A, CCL2, CCL3, and CCL4 were measured by magnetic bead-based immunoassay. t Test and Wilcoxon test were used to compare cytokine levels before and after AHSCT. There were 28 women and 8 men with a median age of 46 (15-62) years, median duration of MS was 9.5 (1-32) years, and EDSS score was 5.7 (1.5-8.0). Patients had a decrement of pro-inflammatory IL-21 and IL-22 (p = .003 and p = .028) and an increment of anti-inflammatory CCL2 and CCL4 (p < .001 and p = .039) after AHSCT. Decrease of IL-21 and IL-22 coupled with an increment of CCL2 and CCL4 could reflect the immunomodulatory effect of auto-HSCT and be an early indicator of its efficacy.
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Affiliation(s)
- José C Jaime-Pérez
- Department of Hematology, Internal Medicine Division, Dr. José Eleuterio González University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Grecia A Turrubiates-Hernández
- Department of Hematology, Internal Medicine Division, Dr. José Eleuterio González University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Leslie J López-Silva
- Department of Hematology, Internal Medicine Division, Dr. José Eleuterio González University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Rosario Salazar-Riojas
- Department of Hematology, Internal Medicine Division, Dr. José Eleuterio González University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - David Gómez-Almaguer
- Department of Hematology, Internal Medicine Division, Dr. José Eleuterio González University Hospital and School of Medicine, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
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Different T-cell subsets in glioblastoma multiforme and targeted immunotherapy. Cancer Lett 2020; 496:134-143. [PMID: 33022290 DOI: 10.1016/j.canlet.2020.09.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022]
Abstract
Glioblastoma multiforme (GBM) is a brain tumor with a high mortality rate. Surgical resection combined with radiotherapy and chemotherapy is the standard treatment for GBM patients, but the 5-year survival rate of patients despite this treatment is low. Immunotherapy has attracted increasing attention in recent years. As the pioneer and the main effector cells of immunotherapy, T cells play a key role in tumor immunotherapy. However, the T cells in GBM microenvironment are inhibited by the highly immunosuppressive environment of GBM, posing huge challenges to T cell-based GBM immunotherapy. This review summarizes the effects of the GBM microenvironment on the infiltration and function of different T-cell subsets and the possible strategies to overcome immunosuppression, and thus enhance the effectiveness of GBM immunotherapy.
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