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Prapas P, Anagnostouli M. Macrophages and HLA-Class II Alleles in Multiple Sclerosis: Insights in Therapeutic Dynamics. Int J Mol Sci 2024; 25:7354. [PMID: 39000461 PMCID: PMC11242320 DOI: 10.3390/ijms25137354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024] Open
Abstract
Antigen presentation is a crucial mechanism that drives the T cell-mediated immune response and the development of Multiple Sclerosis (MS). Genetic alterations within the highly variable Major Histocompatibility Complex Class II (MHC II) have been proven to result in significant changes in the molecular basis of antigen presentation and the clinical course of patients with both Adult-Onset MS (AOMS) and Pediatric-Onset MS (POMS). Among the numerous polymorphisms of the Human Leucocyte Antigens (HLA), within MHC II complex, HLA-DRB1*15:01 has been labeled, in Caucasian ethnic groups, as a high-risk allele for MS due to the ability of its structure to increase affinity to Myelin Basic Protein (MBP) epitopes. This characteristic, among others, in the context of the trimolecular complex or immunological synapsis, provides the foundation for autoimmunity triggered by environmental or endogenous factors. As with all professional antigen presenting cells, macrophages are characterized by the expression of MHC II and are often implicated in the formation of MS lesions. Increased presence of M1 macrophages in MS patients has been associated both with progression and onset of the disease, each involving separate but similar mechanisms. In this critical narrative review, we focus on macrophages, discussing how HLA genetic alterations can promote dysregulation of this population's homeostasis in the periphery and the Central Nervous System (CNS). We also explore the potential interconnection in observed pathological macrophage mechanisms and the function of the diverse structure of HLA alleles in neurodegenerative CNS, seen in MS, by comparing available clinical with molecular data through the prism of HLA-immunogenetics. Finally, we discuss available and experimental pharmacological approaches for MS targeting the trimolecular complex that are based on cell phenotype modulation and HLA genotype involvement and try to reveal fertile ground for the potential development of novel drugs.
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Affiliation(s)
- Petros Prapas
- Research Immunogenetics Laboratory, First Department of Neurology, Aeginition University Hospital, School of Medicine, National and Kapodistrian University of Athens, Vas. Sofias 72-74, 11528 Athens, Greece
| | - Maria Anagnostouli
- Research Immunogenetics Laboratory, First Department of Neurology, Aeginition University Hospital, School of Medicine, National and Kapodistrian University of Athens, Vas. Sofias 72-74, 11528 Athens, Greece
- Multiple Sclerosis and Demyelinating Diseases Unit, Center of Expertise for Rare Demyelinating and Autoimmune Diseases of CNS, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens NKUA, Aeginition University Hospital, Vas. Sofias 72-74, 11528 Athens, Greece
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2
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Eckert S, Jakimovski D, Zivadinov R, Hicar M, Weinstock-Guttman B. How to and should we target EBV in MS? Expert Rev Clin Immunol 2024; 20:703-714. [PMID: 38477887 DOI: 10.1080/1744666x.2024.2328739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
INTRODUCTION The etiology of multiple sclerosis (MS) remains unknown. Pathogenesis likely relies on a complex interaction between multiple environmental, genetic, and behavioral risk factors. However, a growing body of literature supports the role of a preceding Epstein-Barr virus (EBV) infection in the majority of cases. AREAS COVERED In this narrative review, we summarize the latest findings regarding the potential role of EBV as a predisposing event inducing new onset of MS. EBV interactions with the genetic background and other infectious agents such as human endogenous retrovirus are explored. Additional data regarding the role of EBV regarding the rate of mid- and long-term disease progression is also discussed. Lastly, the effect of currently approved disease-modifying therapies (DMT) for MS treatment on the EBV-based molecular mechanisms and the development of new EBV-specific therapies are further reviewed. EXPERT OPINION Recent strong epidemiological findings support that EBV may be the primary inducing event in certain individuals that shortly thereafter develop MS. More studies are needed in order to better understand the significant variability in susceptibility based on environmental factors such as EBV exposure. Future investigations should focus on determining the specific EBV-related risk antigen(s) and phenotyping people with likely EBV-induced MS. Targeting EBV via several different avenues, including development of an EBV vaccine, may become the mainstay of MS treatment in the future.
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Affiliation(s)
- Svetlana Eckert
- Jacobs Comprehensive MS Treatment and Research Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Dejan Jakimovski
- Jacobs Comprehensive MS Treatment and Research Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Robert Zivadinov
- Buffalo Neuroimaging Analysis Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
- Center for Biomedical Imaging at Clinical Translational Science Institute, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Mark Hicar
- Department of Pediatrics Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Bianca Weinstock-Guttman
- Jacobs Comprehensive MS Treatment and Research Center, Department of Neurology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, NY, USA
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Alade A, Mossey P, Awotoye W, Busch T, Oladayo AM, Aladenika E, Olujitan M, Wentworth E, Anand D, Naicker T, Gowans LJJ, Eshete MA, Adeyemo WL, Zeng E, Van Otterloo E, O'Rorke M, Adeyemo A, Murray JC, Cotney J, Lachke SA, Romitti P, Butali A. Rare variants analyses suggest novel cleft genes in the African population. Sci Rep 2024; 14:14279. [PMID: 38902479 PMCID: PMC11189897 DOI: 10.1038/s41598-024-65151-9] [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: 02/02/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
Non-syndromic orofacial clefts (NSOFCs) are common birth defects with a complex etiology. While over 60 common risk loci have been identified, they explain only a small proportion of the heritability for NSOFCs. Rare variants have been implicated in the missing heritability. Thus, our study aimed to identify genes enriched with nonsynonymous rare coding variants associated with NSOFCs. Our sample included 814 non-syndromic cleft lip with or without palate (NSCL/P), 205 non-syndromic cleft palate only (NSCPO), and 2150 unrelated control children from Nigeria, Ghana, and Ethiopia. We conducted a gene-based analysis separately for each phenotype using three rare-variants collapsing models: (1) protein-altering (PA), (2) missense variants only (MO); and (3) loss of function variants only (LOFO). Subsequently, we utilized relevant transcriptomics data to evaluate associated gene expression and examined their mutation constraint using the gnomeAD database. In total, 13 genes showed suggestive associations (p = E-04). Among them, eight genes (ABCB1, ALKBH8, CENPF, CSAD, EXPH5, PDZD8, SLC16A9, and TTC28) were consistently expressed in relevant mouse and human craniofacial tissues during the formation of the face, and three genes (ABCB1, TTC28, and PDZD8) showed statistically significant mutation constraint. These findings underscore the role of rare variants in identifying candidate genes for NSOFCs.
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Affiliation(s)
- Azeez Alade
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA.
- Department of Epidemiology, College of Public Health, University of Iowa, Butali Laboratory, ML2198, 500 Newton Road, Iowa City, IA, 52242, USA.
| | - Peter Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Waheed Awotoye
- Department of Orthodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Tamara Busch
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Abimbola M Oladayo
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Emmanuel Aladenika
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Mojisola Olujitan
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Emma Wentworth
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
- Graduate Program in Genetics and Developmental Biology, University of Connecticut School of Medicine, Farmington, CT, USA
| | - Deepti Anand
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
| | - Thirona Naicker
- Department of Paediatrics, Clinical Genetics, University of KwaZulu-Natal and Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Lord J J Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Mekonen A Eshete
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Idi-araba, Lagos, Nigeria
| | - Erliang Zeng
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
| | - Eric Van Otterloo
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA
- Department of Periodontics, College of Dentistry, University of Iowa, Iowa City, IA, USA
| | - Michael O'Rorke
- Department of Epidemiology, College of Public Health, University of Iowa, Butali Laboratory, ML2198, 500 Newton Road, Iowa City, IA, 52242, USA
| | | | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA
| | - Salil A Lachke
- Department of Biological Sciences, University of Delaware, Newark, DE, USA
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Paul Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Butali Laboratory, ML2198, 500 Newton Road, Iowa City, IA, 52242, USA
| | - Azeez Butali
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA, USA.
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Butali Laboratory, ML2198, 500 Newton Road, Iowa City, IA, 52242, USA.
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Yang Y, Bai Q, Liu F, Zhang S, Tang W, Liu L, Xing Z, Wang H, Zhang C, Yang Y, Fan H. Establishment of the Diagnostic Signature of Ferroptosis Genes in Multiple Sclerosis. Biochem Genet 2024:10.1007/s10528-024-10832-3. [PMID: 38886317 DOI: 10.1007/s10528-024-10832-3] [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: 01/17/2024] [Accepted: 05/08/2024] [Indexed: 06/20/2024]
Abstract
Ferroptosis is a novel form of membrane-dependent cell death that differs from other cell death modalities such as necrosis, apoptosis, and autophagy. Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system primarily affecting brain and spinal cord neurons. Although the pathogenesis of these two conditions may seem unrelated, recent studies have indicated a connection between ferroptosis and multiple sclerosis. In fact, ferroptosis plays a significant role in the development of MS, as evidenced by the presence of elevated iron levels and iron metabolism abnormalities in the brains, spinal cords, and other neurons of MS patients. These abnormalities disrupt iron homeostasis within cells, leading to the occurrence of ferroptosis. However, there is currently a lack of research on the diagnostic value of ferroptosis-related genes in multiple sclerosis. In this study, we employed bioinformatics methods to identify ferroptosis-related genes (ATM, GSK3B, HMGCR, KLF2, MAPK1, NFE2L1, NRAS, PCBP1, PIK3CA, RPL8, VDAC3) associated with the diagnosis of multiple sclerosis and constructed a diagnostic model. The results demonstrated that the diagnostic model accurately identified the patients' condition. Subsequently, subgroup analysis was performed based on the expression levels of ferroptosis-related genes, dividing patients into high and low expression groups. The results showed differences in immune function and immune cell infiltration between the two groups. Our study not only confirms the correlation between ferroptosis and multiple sclerosis but also demonstrates the diagnostic value of ferroptosis-related genes in the disease. This provides guidance for clinical practice and direction for further mechanistic research.
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Affiliation(s)
- Yang Yang
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Qianqian Bai
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Fangfei Liu
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Shumin Zhang
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Wenchao Tang
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Ling Liu
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Zhehua Xing
- Department of Trauma Center, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Hao Wang
- Department of Trauma Center, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Chi Zhang
- Department of Trauma Center, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China
| | - Yanhui Yang
- Department of Trauma Center, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China.
| | - Hua Fan
- Office of Research & Innovation, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471003, China.
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Neidhart S, Vlad B, Hilty M, Högelin KA, Ziegler M, Berenjeno-Correa E, Reichen I, Stridh P, Jelcic I, Khademi M, Kockum I, Sospedra M, Al Nimer F, Martin R, Jelcic I. HLA Associations of Intrathecal IgG Production against Specific Viruses in Multiple Sclerosis. Ann Neurol 2024; 95:1112-1126. [PMID: 38551149 DOI: 10.1002/ana.26921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/05/2024] [Accepted: 03/04/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVE Specific human leucocyte antigen (HLA) alleles are not only associated with higher risk to develop multiple sclerosis (MS) and other autoimmune diseases, but also with the severity of various viral and bacterial infections. Here, we analyzed the most specific biomarker for MS, that is, the polyspecific intrathecal IgG antibody production against measles, rubella, and varicella zoster virus (MRZ reaction), for possible HLA associations in MS. METHODS We assessed MRZ reaction from 184 Swiss patients with MS and clinically isolated syndrome (CIS) and 89 Swiss non-MS/non-CIS control patients, and performed HLA sequence-based typing, to check for associations of positive MRZ reaction with the most prevalent HLA alleles. We used a cohort of 176 Swedish MS/CIS patients to replicate significant findings. RESULTS Whereas positive MRZ reaction showed a prevalence of 38.0% in MS/CIS patients, it was highly specific (97.7%) for MS/CIS. We identified HLA-DRB1*15:01 and other tightly linked alleles of the HLA-DR15 haplotype as the strongest HLA-encoded risk factors for a positive MRZ reaction in Swiss MS/CIS (odds ratio [OR], 3.90, 95% confidence interval [CI] 2.05-7.46, padjusted = 0.0004) and replicated these findings in Swedish MS/CIS patients (OR 2.18, 95%-CI 1.16-4.02, padjusted = 0.028). In addition, female MS/CIS patients had a significantly higher probability for a positive MRZ reaction than male patients in both cohorts combined (padjusted <0.005). INTERPRETATION HLA-DRB1*15:01, the strongest genetic risk factor for MS, and female sex, 1 of the most prominent demographic risk factors for developing MS, predispose in MS/CIS patients for a positive MRZ reaction, the most specific CSF biomarker for MS. ANN NEUROL 2024;95:1112-1126.
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Affiliation(s)
- Stephan Neidhart
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Benjamin Vlad
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Marc Hilty
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Klara Asplund Högelin
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mario Ziegler
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Ernesto Berenjeno-Correa
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Ina Reichen
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Pernilla Stridh
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
| | - Mohsen Khademi
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mireia Sospedra
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
| | - Faiez Al Nimer
- Center for Molecular Medicine, Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Roland Martin
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
- Center for Molecular Medicine, Therapeutic Immune Design Unit, Department of Clinical Neuroscience, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ilijas Jelcic
- Neuroimmunology and Multiple Sclerosis Research Section, Department of Neurology, University of Zurich and University Hospital, Zurich, Switzerland
- Clinical Research Priority Program MS (CRPP) PrecisionMS of the University of Zurich, Zurich, Switzerland
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Rau CN, Severin ME, Lee PW, Deffenbaugh JL, Liu Y, Murphy SP, Petersen-Cherubini CL, Lovett-Racke AE. MicroRNAs targeting TGF-β signaling exacerbate central nervous system autoimmunity by disrupting regulatory T cell development and function. Eur J Immunol 2024; 54:e2350548. [PMID: 38634287 PMCID: PMC11156541 DOI: 10.1002/eji.202350548] [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: 04/27/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Transforming growth factor beta (TGF-β) signaling is essential for a balanced immune response by mediating the development and function of regulatory T cells (Tregs) and suppressing autoreactive T cells. Disruption of this balance can result in autoimmune diseases, including multiple sclerosis (MS). MicroRNAs (miRNAs) targeting TGF-β signaling have been shown to be upregulated in naïve CD4 T cells in MS patients, resulting in a limited in vitro generation of human Tregs. Utilizing the murine model experimental autoimmune encephalomyelitis, we show that perinatal administration of miRNAs, which target the TGF-β signaling pathway, enhanced susceptibility to central nervous system (CNS) autoimmunity. Neonatal mice administered with these miRNAs further exhibited reduced Treg frequencies with a loss in T cell receptor repertoire diversity following the induction of experimental autoimmune encephalomyelitis in adulthood. Exacerbated CNS autoimmunity as a result of miRNA overexpression in CD4 T cells was accompanied by enhanced Th1 and Th17 cell frequencies. These findings demonstrate that increased levels of TGF-β-associated miRNAs impede the development of a diverse Treg population, leading to enhanced effector cell activity, and contributing to an increased susceptibility to CNS autoimmunity. Thus, TGF-β-targeting miRNAs could be a risk factor for MS, and recovering optimal TGF-β signaling may restore immune homeostasis in MS patients.
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Affiliation(s)
- Christina N Rau
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Mary E Severin
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Priscilla W Lee
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Joshua L Deffenbaugh
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Yue Liu
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Shawn P Murphy
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
| | - Cora L Petersen-Cherubini
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Neuroscience Graduate Program, The Ohio State University, Columbus, Ohio, USA
| | - Amy E Lovett-Racke
- Department of Microbial Infection and Immunity, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
- Department of Neuroscience, Wexner Medical Center, The Ohio State University, Columbus, Ohio, USA
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7
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Skarlis C, Markoglou N, Gontika M, Artemiadis A, Pons MR, Stefanis L, Dalakas M, Chrousos G, Anagnostouli M. The impact of HLA-DRB1 alleles in a Hellenic, Pediatric-Onset Multiple Sclerosis cohort: Implications on clinical and neuroimaging profile. Neurol Sci 2024:10.1007/s10072-024-07619-0. [PMID: 38819529 DOI: 10.1007/s10072-024-07619-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Pediatric-Onset Multiple Sclerosis (POMS) is considered a complex disease entity and several genetic, hormonal, and environmental factors have been associated with disease pathogenesis. Linkage studies in Caucasians have consistently suggested the human leukocyte antigen (HLA) polymorphisms, as the genetic locus most strongly linked to MS, with the HLA-DRB1*15:01 allele, being associated with both adult and pediatric MS patients. Here we aim to investigate the prevalence of the HLA-DRB1 alleles among a Hellenic POMS cohort and any possible associations with clinical and imaging disease features. MATERIALS AND METHODS 100 POMS patients fulfilling the IPMSSG criteria, 168 Adult-Onset MS (AOMS) patients, and 246 Healthy Controls (HCs) have been enrolled. HLA genotyping was performed with a standard low-resolution sequence-specific oligonucleotide (SSO) technique. RESULTS POMS patients display a significantly increased HLA-DRB1*03 frequency compared to both HCs [24% vs. 12.6%, OR [95%CI]: 2.19 (1.21-3.97), p=0.016) and AOMS (24% vs. 13.1%, OR [95%CI]: 2.1 (1.1-3.98), p=0.034] respectively. HLA-DRB1*03-carriers display reduced risk for brainstem lesion development (OR [CI 95%]:0.19 (0.06-0.65), p=0.011). A significantly lower frequency of HLA-DRB1*07 (4% vs 13.4%, OR (95% CI): 0.27 (0.09-0.78), p= 0.017) and HLA-DRB1*11 (37% vs 52%, OR [95% CI]: 0.54 (0.34-0.87), p= 0.016) was observed in POMS compared to HCs. CONCLUSION The HLA-DRB1*03 allele was associated with a higher risk for POMS, replicating our previous findings, and with a lower risk for brainstem lesion development, a common clinical and neuroimaging feature in POMS, while HLA-DRB1*07 and HLA-DRB1*11 display a protective role. These findings expand the existing knowledge of HLA associations and POMS.
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Affiliation(s)
- Charalampos Skarlis
- Research Immunogenetics Laboratory, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
| | - Nikolaos Markoglou
- Research Immunogenetics Laboratory, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
- First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
| | - Maria Gontika
- Research Immunogenetics Laboratory, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
- Penteli Children's Hospital, Attiki, Greece
| | | | - Maria-Roser Pons
- First Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
| | - Leonidas Stefanis
- First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece
| | - Marinos Dalakas
- Neuroimmunology Laboratory, Department of Pathophysiology School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
- Clinical Neuroimmunology and Neuromuscular Diseases Department, Thomas Jefferson University of Philadelphia, Philadelphia, Pennsylvania, USA
| | - George Chrousos
- University Research Institute of Maternal, Child and Child Health Precision Medicine, Clinical and Translational Research Unit in Endocrinology, UNESCO Chair in Adolescent Health and Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Anagnostouli
- Research Immunogenetics Laboratory, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece.
- First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, Aeginition University Hospital, Vas. Sofias 72-74, 11528, Athens, Greece.
- Multiple Sclerosis and Demyelinating Diseases Unit, Center of Expertise for Rare Demyelinating and Autoimmune Diseases of CNS, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, NKUA, Aeginition University Hospital, Athens, Greece.
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8
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Johansson E, Alfredsson L, Strid P, Kockum I, Olsson T, Hedström AK. Head trauma results in manyfold increased risk of multiple sclerosis in genetically susceptible individuals. J Neurol Neurosurg Psychiatry 2024; 95:554-560. [PMID: 38212058 PMCID: PMC11103305 DOI: 10.1136/jnnp-2023-332643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/20/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Large register-based studies have reported an association between head trauma and increased risk of multiple sclerosis (MS). We aimed to investigate possible interactions between head trauma and MS-associated HLA genes in relation to MS risk. METHODS We used a Swedish population-based case-control study (2807 incident cases, 5950 matched controls with HLA genotypes available for 2057 cases, 2887 controls). Subjects with and without a history of self-reported head trauma were compared regarding MS risk, by calculating ORs with 95% CIs using logistic regression models. Additive interaction between head trauma, HLA-DRB1*1501 and absence of HLA-A*0201, was assessed by calculating the attributable proportion (AP) due to interaction. RESULTS A history of head trauma was associated with a 30% increased risk of subsequently developing MS (OR 1.34, 95% CI 1.17 to 1.53), with a trend showing increased risk of MS with increasing number of head impacts (p=0.03). We observed synergistic effects between recent head trauma and HLA-DRB1*15:01 as well as absence of HLA*02:01 in relation to MS risk (each AP 0.40, 95% CI 0.1 to 0.7). Recent head trauma in individuals with both genetic risk factors rendered an 18-fold increased risk of MS, compared with those with neither the genetic risk factors nor a history of head trauma (OR 17.7, 95% CI 7.13 to 44.1). CONCLUSIONS Our findings align with previous observations of a dose-dependent association between head trauma and increased risk of MS and add a novel aspect of this association by revealing synergistic effects between recent head trauma and MS-associated HLA genes.
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Affiliation(s)
- Eva Johansson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Strid
- Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Anna Karin Hedström
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
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9
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Boullerne AI, Goudey B, Paganini J, Erlichster M, Gaitonde S, Feinstein DL. Validation of tag SNPs for multiple sclerosis HLA risk alleles across the 1000 genomes panel. Hum Immunol 2024; 85:110790. [PMID: 38575482 DOI: 10.1016/j.humimm.2024.110790] [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: 09/12/2023] [Revised: 02/10/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
Currently, the genetic variants strongly associated with risk for Multiple Sclerosis (MS) are located in the Major Histocompatibility Complex. This includes DRB1*15:01 and DRB1*15:03 alleles at the HLA-DRB1 locus, the latter restricted to African populations; the DQB1*06:02 allele at the HLA-DQB1 locus which is in high linkage disequilibrium (LD) with DRB1*15:01; and protective allele A*02:01 at the HLA-A locus. HLA allele identification is facilitated by co-inherited ('tag') single nucleotide polymorphisms (SNPs); however, SNP validation is not typically done outside of the discovery population. We examined 19 SNPs reported to be in high LD with these alleles in 2,502 healthy subjects included in the 1000 Genomes panel having typed HLA data. Examination of 3 indices (LD R2 values, sensitivity and specificity, minor allele frequency) revealed few SNPs with high tagging performance. All SNPs examined that tag DRB1*15:01 were in perfect LD in the British population; three showed high tagging performance in 4 of the 5 European, and 2 of the 4 American populations. For DQB1*06:02, with no previously validated tag SNPs, we show that rs3135388 has high tagging performance in one South Asian, one American, and one European population. We identify for the first time that rs2844821 has high tagging performance for A*02:01 in 5 of 7 African populations including African Americans, and 4 of the 5 European populations. These results provide a basis for selecting SNPs with high tagging performance to assess HLA alleles across diverse populations, for MS risk as well as for other diseases and conditions.
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Affiliation(s)
- Anne I Boullerne
- Department of Anesthesiology, University Illinois, Chicago, IL, USA.
| | - Benjamin Goudey
- The Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michael Erlichster
- MX3 Diagnostics, Melbourne, Victoria, Australia; Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Sujata Gaitonde
- Department of Pathology, University Illinois, Chicago, IL, USA
| | - Douglas L Feinstein
- Department of Anesthesiology, University Illinois, Chicago, IL, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
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10
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Mentzer AJ, Dilthey AT, Pollard M, Gurdasani D, Karakoc E, Carstensen T, Muhwezi A, Cutland C, Diarra A, da Silva Antunes R, Paul S, Smits G, Wareing S, Kim H, Pomilla C, Chong AY, Brandt DYC, Nielsen R, Neaves S, Timpson N, Crinklaw A, Lindestam Arlehamn CS, Rautanen A, Kizito D, Parks T, Auckland K, Elliott KE, Mills T, Ewer K, Edwards N, Fatumo S, Webb E, Peacock S, Jeffery K, van der Klis FRM, Kaleebu P, Vijayanand P, Peters B, Sette A, Cereb N, Sirima S, Madhi SA, Elliott AM, McVean G, Hill AVS, Sandhu MS. High-resolution African HLA resource uncovers HLA-DRB1 expression effects underlying vaccine response. Nat Med 2024; 30:1384-1394. [PMID: 38740997 PMCID: PMC11108778 DOI: 10.1038/s41591-024-02944-5] [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: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 05/16/2024]
Abstract
How human genetic variation contributes to vaccine effectiveness in infants is unclear, and data are limited on these relationships in populations with African ancestries. We undertook genetic analyses of vaccine antibody responses in infants from Uganda (n = 1391), Burkina Faso (n = 353) and South Africa (n = 755), identifying associations between human leukocyte antigen (HLA) and antibody response for five of eight tested antigens spanning pertussis, diphtheria and hepatitis B vaccines. In addition, through HLA typing 1,702 individuals from 11 populations of African ancestry derived predominantly from the 1000 Genomes Project, we constructed an imputation resource, fine-mapping class II HLA-DR and DQ associations explaining up to 10% of antibody response variance in our infant cohorts. We observed differences in the genetic architecture of pertussis antibody response between the cohorts with African ancestries and an independent cohort with European ancestry, but found no in silico evidence of differences in HLA peptide binding affinity or breadth. Using immune cell expression quantitative trait loci datasets derived from African-ancestry samples from the 1000 Genomes Project, we found evidence of differential HLA-DRB1 expression correlating with inferred protection from pertussis following vaccination. This work suggests that HLA-DRB1 expression may play a role in vaccine response and should be considered alongside peptide selection to improve vaccine design.
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Affiliation(s)
- Alexander J Mentzer
- Centre for Human Genetics, University of Oxford, Oxford, UK.
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
| | - Alexander T Dilthey
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Medical Microbiology and Hospital Hygiene, University Hospital of Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | | | | | | | | | - Allan Muhwezi
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Clare Cutland
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Amidou Diarra
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | | | - Sinu Paul
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Gaby Smits
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Susan Wareing
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
| | | | | | - Amanda Y Chong
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Debora Y C Brandt
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California at Berkeley, California, CA, USA
| | - Samuel Neaves
- Avon Longitudinal Study of Parents and Children at University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicolas Timpson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Austin Crinklaw
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Anna Rautanen
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dennison Kizito
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Tom Parks
- Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Kate E Elliott
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Tara Mills
- Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Katie Ewer
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Nick Edwards
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Segun Fatumo
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- The Department of Non-communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine London, London, UK
| | - Emily Webb
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Sarah Peacock
- Tissue Typing Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Katie Jeffery
- Microbiology Department, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, UK
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | | | - Bjorn Peters
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | | | - Sodiomon Sirima
- Groupe de Recherche Action en Santé (GRAS) 06 BP 10248, Ouagadougou, Burkina Faso
| | - Shabir A Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Alison M Elliott
- Medical Research Council/Uganda Virus Research Institute and London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- MRC International Statistics and Epidemiology Group, London School of Hygiene and Tropical Medicine London, London, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Adrian V S Hill
- Centre for Human Genetics, University of Oxford, Oxford, UK
- The Jenner Institute, University of Oxford, Oxford, UK
| | - Manjinder S Sandhu
- Department of Epidemiology & Biostatistics, School of Public Health, Imperial College London, London, UK.
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11
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Bianco A, Di Sante G, Colò F, De Arcangelis V, Cicia A, Del Giacomo P, De Bonis M, Morganti TG, Carlomagno V, Lucchini M, Minucci A, Calabresi P, Mirabella M. Multiple Sclerosis Onset before and after COVID-19 Vaccination: Can HLA Haplotype Be Determinant? Int J Mol Sci 2024; 25:4556. [PMID: 38674141 PMCID: PMC11050425 DOI: 10.3390/ijms25084556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/13/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
A few cases of multiple sclerosis (MS) onset after COVID-19 vaccination have been reported, although the evidence is insufficient to establish causality. The aim of this study is to compare cases of newly diagnosed relapsing-remitting MS before and after the outbreak of the COVID-19 pandemic and the impact of COVID-19 vaccination. Potential environmental and genetic predisposing factors were also investigated, as well as clinical patterns. This is a single-centre retrospective cohort study including all patients who presented with relapsing-remitting MS onset between January 2018 and July 2022. Data on COVID-19 vaccination administration, dose, and type were collected. HLA-DRB1 genotyping was performed in three subgroups. A total of 266 patients received a new diagnosis of relapsing-remitting MS in our centre, 143 before the COVID-19 pandemic (until and including March 2020), and 123 during the COVID-19 era (from April 2020). The mean number of new MS onset cases per year was not different before and during the COVID-19 era and neither were baseline patients' characteristics, type of onset, clinical recovery, or radiological patterns. Fourteen (11.4%) patients who subsequently received a new diagnosis of MS had a history of COVID-19 vaccination within one month before symptoms onset. Patients' characteristics, type of onset, clinical recovery, and radiological patterns did not differ from those of patients with non-vaccine-related new diagnoses of MS. The allele frequencies of HLA-DRB1*15 were 17.6% and 22.2% in patients with non-vaccine-related disease onset before and during the COVID-19 era, respectively, while no case of HLA-DRB1*15 was identified among patients with a new diagnosis of MS post-COVID-19 vaccine. In contrast, HLA-DRB1*08+ or HLA-DRB1*10+ MS patients were present only in this subgroup. Although a causal link between COVID-19 vaccination and relapsing-remitting MS cannot be detected, it is interesting to note and speculate about the peculiarities and heterogeneities underlying disease mechanisms of MS, where the interactions of genetics and the environment could be crucial also for the follow-up and the evaluation of therapeutic options.
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Affiliation(s)
- Assunta Bianco
- Division of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 06123 Perugia, Italy
| | - Francesca Colò
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Valeria De Arcangelis
- Division of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Alessandra Cicia
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Paola Del Giacomo
- Department of Laboratory and Infectious Sciences, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Maria De Bonis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Tommaso Giuseppe Morganti
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Vincenzo Carlomagno
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Matteo Lucchini
- Division of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Paolo Calabresi
- Division of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
| | - Massimiliano Mirabella
- Division of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
- Department of Neurosciences, Centro di Ricerca per la Sclerosi Multipla “Anna Paola Batocchi”, Catholic University of Sacred Heart, 00168 Rome, Italy
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12
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Loginovic P, Wang F, Li J, Ferrat L, Mirshahi UL, Rao HS, Petzold A, Tyrrell J, Green HD, Weedon MN, Ganna A, Tuomi T, Carey DJ, Oram RA, Braithwaite T. Applying a genetic risk score model to enhance prediction of future multiple sclerosis diagnosis at first presentation with optic neuritis. Nat Commun 2024; 15:1415. [PMID: 38418465 PMCID: PMC10902342 DOI: 10.1038/s41467-024-44917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/09/2024] [Indexed: 03/01/2024] Open
Abstract
Optic neuritis (ON) is associated with numerous immune-mediated inflammatory diseases, but 50% patients are ultimately diagnosed with multiple sclerosis (MS). Differentiating MS-ON from non-MS-ON acutely is challenging but important; non-MS ON often requires urgent immunosuppression to preserve vision. Using data from the United Kingdom Biobank we showed that combining an MS-genetic risk score (GRS) with demographic risk factors (age, sex) significantly improved MS prediction in undifferentiated ON; one standard deviation of MS-GRS increased the Hazard of MS 1.3-fold (95% confidence interval 1.07-1.55, P < 0.01). Participants stratified into quartiles of predicted risk developed incident MS at rates varying from 4% (95%CI 0.5-7%, lowest risk quartile) to 41% (95%CI 33-49%, highest risk quartile). The model replicated across two cohorts (Geisinger, USA, and FinnGen, Finland). This study indicates that a combined model might enhance individual MS risk stratification, paving the way for precision-based ON treatment and earlier MS disease-modifying therapy.
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Affiliation(s)
- Pavel Loginovic
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Heavitree Road, Exeter, EX1 2HZ, UK
| | - Feiyi Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jiang Li
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Lauric Ferrat
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | | | - H Shanker Rao
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Axel Petzold
- Neuro-ophthalmology Expert Center, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Neuro-ophthalmology, The National Hospital for Neurology and Neurosurgery, Queen Square, UCL Institute of Neurology, London, UK
- Neuro-ophthalmology service, Moorfields Eye Hospital, London, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Harry D Green
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - David J Carey
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK.
- Academic Kidney Unit, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
| | - Tasanee Braithwaite
- King's College London, School of Immunology & Microbial Sciences and School of Life Course and Population Sciences, London, UK
- Medical Eye Unit, St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, Westminster Bridge Road, London, UK
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13
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Alade A, Mossey P, Awotoye W, Busch T, Oladayo A, Aladenika E, Olujitan M, Gowans JJL, Eshete MA, Adeyemo WL, Zeng E, Otterloo E, O'Rorke M, Adeyemo A, Murray JC, Cotney J, Lachke SA, Romitti P, Butali A, Wentworth E, Anand D, Naicker T. Rare Variants Analyses Suggest Novel Cleft Genes in the African Population. RESEARCH SQUARE 2024:rs.3.rs-3921355. [PMID: 38464065 PMCID: PMC10925394 DOI: 10.21203/rs.3.rs-3921355/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Non-syndromic orofacial clefts (NSOFCs) are common birth defects with a complex etiology. While over 60 common risk loci have been identified, they explain only a small proportion of the heritability for NSOFC. Rare variants have been implicated in the missing heritability. Thus, our study aimed to identify genes enriched with nonsynonymous rare coding variants associated with NSOFCs. Our sample included 814 non-syndromic cleft lip with or without palate (NSCL/P), 205 non-syndromic cleft palate only (NSCPO), and 2150 unrelated control children from Nigeria, Ghana, and Ethiopia. We conducted a gene-based analysis separately for each phenotype using three rare-variants collapsing models: (1) protein-altering (PA), (2) missense variants only (MO); and (3) loss of function variants only (LOFO). Subsequently, we utilized relevant transcriptomics data to evaluate associated gene expression and examined their mutation constraint using the gnomeAD database. In total, 13 genes showed suggestive associations (p = E-04). Among them, eight genes (ABCB1, ALKBH8, CENPF, CSAD, EXPH5, PDZD8, SLC16A9, and TTC28) were consistently expressed in relevant mouse and human craniofacial tissues during the formation of the face, and three genes (ABCB1, TTC28, and PDZD8) showed statistically significant mutation constraint. These findings underscore the role of rare variants in identifying candidate genes for NSOFCs.
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Affiliation(s)
| | | | | | | | | | | | | | - J J Lord Gowans
- Komfo Anokye Teaching Hospital and Kwame Nkrumah University of Science and Technology
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14
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Zhou H, McPeek MS. Overcoming the "feast or famine" effect: improved interaction testing in genome-wide association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580168. [PMID: 38405994 PMCID: PMC10888770 DOI: 10.1101/2024.02.13.580168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In genetic association analysis of complex traits, detection of interaction (either GxG or GxE) can help to elucidate the genetic architecture and biological mechanisms underlying the trait. Detection of interaction in a genome-wide association study (GWAS) can be methodologically challenging for various reasons, including a high burden of multiple comparisons when testing for epistasis between all possible pairs of a set of genomewide variants, as well as heteroscedasticity effects occurring in the presence of GxG or GxE interaction. In this paper, we address the problem of an even more striking phenomenon that we call the "feast or famine" effect that occurs when testing interaction in a genomewide context. As we verify, even in a simplified setting in which there is no interaction at all (and so no heteroscedasticity), in a GWAS to detect GxG or GxE interaction with a fixed genetic variant or environmental factor, the distribution of the genome-wide p-values under the null hypothesis is not the i.i.d. uniform one that is commonly assumed. Using standard methods, even if all SNPs are independent, some GWASs will have systematically underinflated p-values ("feast"), and others will have systematically overinflated p-values ("famine"), which can lead to false detection of interaction, reduced power, inconsistent results across studies, and failure to replicate true signal. This startling phenomenon is specific to detection of interaction in a GWAS, and it may partly explain why such detection has so far proved challenging and difficult to replicate. We show theoretically that the key cause of this phenomenon is which variables are conditioned on in the analysis, and this suggests an approach to correct the problem by changing the way the conditioning is done. Using this insight, we have developed the TINGA method to adjust the interaction test statistics to make their p-values closer to uniform under the null hypothesis. In simulations we show that TINGA both controls type 1 error and improves power. TINGA allows for covariates and population structure through use of a linear mixed model and accounts for heteroscedasticity. We apply TINGA to detection of epistasis in a study of flowering time in Arabidopsis thaliana.
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Affiliation(s)
- Huanlin Zhou
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
| | - Mary Sara McPeek
- Department of Statistics, The University of Chicago, Chicago, Illinois, U.S.A
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, U.S.A
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15
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Mohammadzamani M, Kazemzadeh K, Chand S, Thapa S, Ebrahimi N, Yazdan Panah M, Shaygannejad V, Mirmosayyeb O. Insights into the interplay between Epstein-Barr virus (EBV) and multiple sclerosis (MS): A state-of-the-art review and implications for vaccine development. Health Sci Rep 2024; 7:e1898. [PMID: 38361801 PMCID: PMC10867693 DOI: 10.1002/hsr2.1898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/12/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Background and Aims Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS). MS results from an inflammatory process leading to the loss of neural tissue and increased disability over time. The role of Epstein Barr Virus (EBV), as one of the most common global viruses, in MS development has been the subject of several studies. However, many related questions are still unanswered. This study aimed to review the connection between MS and EBV and provide a quick outline of MS prevention using EBV vaccination. Methods For this narrative review, an extensive literature search using specific terms was conducted across online databases, including PubMed/Medline, Scopus, Web of Science, and Google Scholar, to identify pertinent studies. Results Several studies proved that almost 100% of people with MS showed a history of EBV infection, and there was an association between high titers of EBV antibodies and an increased risk of MS development. Various hypotheses are proposed for how EBV may contribute to MS directly and indirectly: (1) Molecular Mimicry, (2) Mistaken Self, (3) Bystander Damage, and (4) Autoreactive B cells infected with EBV. Conclusion Given the infectious nature of EBV and its ability to elude the immune system, EBV emerges as a strong candidate for being the underlying cause of MS. The development of an EBV vaccine holds promise for preventing MS; however, overcoming the challenge of creating a safe and efficacious vaccine presents a significant obstacle.
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Affiliation(s)
- Mahtab Mohammadzamani
- Isfahan Neurosciences Research CenterIsfahan University of Medical SciencesIsfahanIran
| | - Kimia Kazemzadeh
- Students' Scientific Research CenterTehran University of Medical SciencesTehranIran
| | - Swati Chand
- Westchester Medical CenterNew York Medical CollegeValhallaNew YorkUSA
| | - Sangharsha Thapa
- Department of Neurology, Westchester Medical CenterNew York Medical CollegeValhallaUSA
| | - Narges Ebrahimi
- Isfahan Neurosciences Research CenterIsfahan University of Medical SciencesIsfahanIran
| | | | - Vahid Shaygannejad
- Isfahan Neurosciences Research CenterIsfahan University of Medical SciencesIsfahanIran
- Department of NeurologyIsfahan University of Medical SciencesIsfahanIran
| | - Omid Mirmosayyeb
- Isfahan Neurosciences Research CenterIsfahan University of Medical SciencesIsfahanIran
- Department of NeurologyIsfahan University of Medical SciencesIsfahanIran
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16
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Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
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Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
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17
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ElAbd H, Franke A. Mass Spectrometry-Based Immunopeptidomics of Peptides Presented on Human Leukocyte Antigen Proteins. Methods Mol Biol 2024; 2758:425-443. [PMID: 38549028 DOI: 10.1007/978-1-0716-3646-6_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Human leukocyte antigen (HLA) proteins are a group of glycoproteins that are expressed at the cell surface, where they present peptides to T cells through physical interactions with T-cell receptors (TCRs). Hence, characterizing the set of peptides presented by HLA proteins, referred to hereafter as the immunopeptidome, is fundamental for neoantigen identification, immunotherapy, and vaccine development. As a result, different methods have been used over the years to identify peptides presented by HLA proteins, including competition assays, peptide microarrays, and yeast display systems. Nonetheless, over the last decade, mass spectrometry-based immunopeptidomics (MS-immunopeptidomics) has emerged as the gold-standard method for identifying peptides presented by HLA proteins. MS-immunopeptidomics enables the direct identification of the immunopeptidome in different tissues and cell types in different physiological and pathological states, for example, solid tumors or virally infected cells. Despite its advantages, it is still an experimentally and computationally challenging technique with different aspects that need to be considered before planning an MS-immunopeptidomics experiment, while conducting the experiment and with analyzing and interpreting the results. Hence, we aim in this chapter to provide an overview of this method and discuss different practical considerations at different stages starting from sample collection until data analysis. These points should aid different groups aiming at utilizing MS-immunopeptidomics, as well as, identifying future research directions to improve the method.
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Affiliation(s)
- Hesham ElAbd
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany.
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18
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Jacobs BM, Tank P, Bestwick JP, Noyce AJ, Marshall CR, Mathur R, Giovannoni G, Dobson R. Modifiable risk factors for multiple sclerosis have consistent directions of effect across diverse ethnic backgrounds: a nested case-control study in an English population-based cohort. J Neurol 2024; 271:241-253. [PMID: 37676298 PMCID: PMC10769990 DOI: 10.1007/s00415-023-11971-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND Multiple sclerosis is a leading cause of non-traumatic neurological disability among young adults worldwide. Prior studies have identified modifiable risk factors for multiple sclerosis in cohorts of White ethnicity, such as infectious mononucleosis, smoking, and obesity during adolescence/early adulthood. It is unknown whether modifiable exposures for multiple sclerosis have a consistent impact on risk across ethnic groups. AIM To determine whether modifiable risk factors for multiple sclerosis have similar effects across diverse ethnic backgrounds. METHODS We conducted a nested case-control study using data from the UK Clinical Practice Research Datalink. Multiple sclerosis cases diagnosed from 2001 until 2022 were identified from electronic healthcare records and matched to unaffected controls based on year of birth. We used stratified logistic regression models and formal statistical interaction tests to determine whether the effect of modifiable risk factors for multiple sclerosis differed by ethnicity. RESULTS We included 9662 multiple sclerosis cases and 118,914 age-matched controls. The cohort was ethnically diverse (MS: 277 South Asian [2.9%], 251 Black [2.6%]; Controls: 5043 South Asian [5.7%], 4019 Black [4.5%]). The age at MS diagnosis was earlier in the Black (40.5 [SD 10.9]) and Asian (37.2 [SD 10.0]) groups compared with White cohort (46.1 [SD 12.2]). There was a female predominance in all ethnic groups; however, the relative proportion of males was higher in the South Asian population (proportion of women 60.3% vs 71% [White] and 75.7% [Black]). Established modifiable risk factors for multiple sclerosis-smoking, obesity, infectious mononucleosis, low vitamin D, and head injury-were consistently associated with multiple sclerosis in the Black and South Asian cohorts. The magnitude and direction of these effects were broadly similar across all ethnic groups examined. There was no evidence of statistical interaction between ethnicity and any tested exposure, and no evidence to suggest that differences in area-level deprivation modifies these risk factor-disease associations. These findings were robust to a range of sensitivity analyses. CONCLUSIONS AND RELEVANCE Established modifiable risk factors for multiple sclerosis are applicable across diverse ethnic backgrounds. Efforts to reduce the population incidence of multiple sclerosis by tackling these risk factors need to be inclusive of people from diverse ethnicities.
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Affiliation(s)
- Benjamin M Jacobs
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London, UK
| | - Pooja Tank
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
| | - Jonathan P Bestwick
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
| | - Alastair J Noyce
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London, UK
| | - Charles R Marshall
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London, UK
| | - Rohini Mathur
- Centre for Primary Care, Wolfson Institute of Population Health, Queen Mary University London, London, UK
| | - Gavin Giovannoni
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London, UK
- Blizard Institute, Queen Mary University London, London, UK
| | - Ruth Dobson
- Centre for Preventive Neurology, Wolfson Institute of Population Health, Queen Mary University London, London, EC1M 6BQ, UK.
- Department of Neurology, Royal London Hospital, London, UK.
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19
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Thomas OG, Olsson T. Mimicking the brain: Epstein-Barr virus and foreign agents as drivers of neuroimmune attack in multiple sclerosis. Front Immunol 2023; 14:1304281. [PMID: 38022632 PMCID: PMC10655090 DOI: 10.3389/fimmu.2023.1304281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
T cells have an essential role in adaptive immunity against pathogens and cancer, but failure of thymic tolerance mechanisms can instead lead to escape of T cells with the ability to attack host tissues. Multiple sclerosis (MS) occurs when structures such as myelin and neurons in the central nervous system (CNS) are the target of autoreactive immune responses, resulting in lesions in the brain and spinal cord which cause varied and episodic neurological deficits. A role for autoreactive T cell and antibody responses in MS is likely, and mounting evidence implicates Epstein-Barr virus (EBV) in disease mechanisms. In this review we discuss antigen specificity of T cells involved in development and progression of MS. We examine the current evidence that these T cells can target multiple antigens such as those from pathogens including EBV and briefly describe other mechanisms through which viruses could affect disease. Unravelling the complexity of the autoantigen T cell repertoire is essential for understanding key events in the development and progression of MS, with wider implications for development of future therapies.
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Affiliation(s)
- Olivia G. Thomas
- Therapeutic Immune Design, Centre for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
- Neuroimmunology Unit, Department of Clinical Neuroscience, Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Tomas Olsson
- Therapeutic Immune Design, Centre for Molecular Medicine, Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
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20
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Mehmood A, Shah S, Guo RY, Haider A, Shi M, Ali H, Ali I, Ullah R, Li B. Methyl-CpG-Binding Protein 2 Emerges as a Central Player in Multiple Sclerosis and Neuromyelitis Optica Spectrum Disorders. Cell Mol Neurobiol 2023; 43:4071-4101. [PMID: 37955798 DOI: 10.1007/s10571-023-01432-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/27/2023] [Indexed: 11/14/2023]
Abstract
MECP2 and its product methyl-CpG binding protein 2 (MeCP2) are associated with multiple sclerosis (MS) and neuromyelitis optica spectrum disorders (NMOSD), which are inflammatory, autoimmune, and demyelinating disorders of the central nervous system (CNS). However, the mechanisms and pathways regulated by MeCP2 in immune activation in favor of MS and NMOSD are not fully understood. We summarize findings that use the binding properties of MeCP2 to identify its targets, particularly the genes recognized by MeCP2 and associated with several neurological disorders. MeCP2 regulates gene expression in neurons, immune cells and during development by modulating various mechanisms and pathways. Dysregulation of the MeCP2 signaling pathway has been associated with several disorders, including neurological and autoimmune diseases. A thorough understanding of the molecular mechanisms underlying MeCP2 function can provide new therapeutic strategies for these conditions. The nervous system is the primary system affected in MeCP2-associated disorders, and other systems may also contribute to MeCP2 action through its target genes. MeCP2 signaling pathways provide promise as potential therapeutic targets in progressive MS and NMOSD. MeCP2 not only increases susceptibility and induces anti-inflammatory responses in immune sites but also leads to a chronic increase in pro-inflammatory cytokines gene expression (IFN-γ, TNF-α, and IL-1β) and downregulates the genes involved in immune regulation (IL-10, FoxP3, and CX3CR1). MeCP2 may modulate similar mechanisms in different pathologies and suggest that treatments for MS and NMOSD disorders may be effective in treating related disorders. MeCP2 regulates gene expression in MS and NMOSD. However, dysregulation of the MeCP2 signaling pathway is implicated in these disorders. MeCP2 plays a role as a therapeutic target for MS and NMOSD and provides pathways and mechanisms that are modulated by MeCP2 in the regulation of gene expression.
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Affiliation(s)
- Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Suleman Shah
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Health Science Center, Shenzhen University, Shenzhen, China
| | - Ruo-Yi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Arsalan Haider
- Key Lab of Health Psychology, Institute of Psychology, University of Chinese Academy of Sciences, Beijing, China
| | - Mengya Shi
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China
| | - Hamid Ali
- Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, 44000, Pakistan
| | - Ijaz Ali
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally, 32093, Kuwait
| | - Riaz Ullah
- Medicinal Aromatic and Poisonous Plants Research Center, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, Hebei, People's Republic of China.
- Key Laboratory of Neurology of Hebei Province, Shijiazhuang, 050000, Hebei, People's Republic of China.
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21
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Elsayed NS, Valenzuela RK, Kitchner T, Le T, Mayer J, Tang ZZ, Bayanagari VR, Lu Q, Aston P, Anantharaman K, Shukla SK. Genetic risk score in multiple sclerosis is associated with unique gut microbiome. Sci Rep 2023; 13:16269. [PMID: 37758833 PMCID: PMC10533555 DOI: 10.1038/s41598-023-43217-4] [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: 12/16/2022] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple sclerosis (MS) is a complex autoimmune disease in which both the roles of genetic susceptibility and environmental/microbial factors have been investigated. More than 200 genetic susceptibility variants have been identified along with the dysbiosis of gut microbiota, both independently have been shown to be associated with MS. We hypothesize that MS patients harboring genetic susceptibility variants along with gut microbiome dysbiosis are at a greater risk of exhibiting the disease. We investigated the genetic risk score for MS in conjunction with gut microbiota in the same cohort of 117 relapsing remitting MS (RRMS) and 26 healthy controls. DNA samples were genotyped using Illumina's Infinium Immuno array-24 v2 chip followed by calculating genetic risk score and the microbiota was determined by sequencing the V4 hypervariable region of the 16S rRNA gene. We identified two clusters of MS patients, Cluster A and B, both having a higher genetic risk score than the control group. However, the MS cases in cluster B not only had a higher genetic risk score but also showed a distinct gut microbiome than that of cluster A. Interestingly, cluster A which included both healthy control and MS cases had similar gut microbiome composition. This could be due to (i) the non-active state of the disease in that group of MS patients at the time of fecal sample collection and/or (ii) the restoration of the gut microbiome post disease modifying therapy to treat the MS. Our study showed that there seems to be an association between genetic risk score and gut microbiome dysbiosis in triggering the disease in a small cohort of MS patients. The MS Cluster A who have a higher genetic risk score but microbiome profile similar to that of healthy controls could be due to the remitting phase of the disease or due to the effect of disease modifying therapies.
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Affiliation(s)
- Noha S Elsayed
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
- Department of Pediatrics, Albert Einstein Medical College, New York, United States
| | - Robert K Valenzuela
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Terrie Kitchner
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
| | - Thao Le
- Integrated Research Development Laboratory, Marshfield Clinic Research Institute, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - John Mayer
- Office of Research Computing and Analytics, Marshfield Clinic Research Institute, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Vishnu R Bayanagari
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA
- Roger Williams Medical Center, Boston University School of Medicine, Providence, RI, 02908, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Paula Aston
- Department of Neurology, Marshfield Clinic Health System, Marshfield, WI, 54449, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sanjay K Shukla
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, 1000 N Oak Avenue # MLR, Marshfield, WI, 54449, USA.
- Computational and Informatics in Biology and Medicine Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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22
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Sherman MA, Pak K, Pinal-Fernandez I, Flegel WA, Targoff IN, Miller FW, Rider LG, Mammen AL. Autoantibodies Recognizing Specificity Protein 4 Co-occur With Anti-Transcription Intermediary Factor 1 and Are Associated With Distinct Clinical Features and Immunogenetic Risk Factors in Juvenile Myositis. Arthritis Rheumatol 2023; 75:1668-1677. [PMID: 36996276 PMCID: PMC10524257 DOI: 10.1002/art.42512] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 03/17/2023] [Accepted: 03/28/2023] [Indexed: 04/01/2023]
Abstract
OBJECTIVE Autoantibodies recognizing specificity protein 4 (Sp4) were recently discovered in adults with idiopathic inflammatory myopathies (IIM). Anti-Sp4 autoantibodies co-occurred in patients with anti-transcription intermediary factor 1 (anti-TIF1) autoantibody-positive dermatomyositis (DM) and were associated with a reduced risk of cancer. In the present study, the prevalence and clinical features associated with anti-Sp4 autoantibodies in juvenile-onset IIM were investigated. METHODS Serum samples from 336 patients with juvenile myositis in a cross-sectional cohort and 91 healthy controls were screened for anti-Sp4 autoantibodies using enzyme-linked immunosorbent assay. Clinical characteristics, outcomes, and HLA alleles of those with and those without anti-Sp4 autoantibodies were compared. RESULTS Anti-Sp4 autoantibodies were present in 23 patients (7%) with juvenile myositis and were not present in any of the controls. Anti-Sp4 autoantibodies were found among each clinical myositis subgroup. The frequency of TIF1 autoantibody positivity was significantly higher among those with anti-Sp4 autoantibodies (21 [91%] versus 92 [30%], P < 0.001). In the anti-TIF1 autoantibody-positive subgroup, Raynaud's phenomenon (8 [38%] versus 2 [2%], P < 0.001) was more common and peak aspartate aminotransferase was significantly lower in those with anti-Sp4 autoantibodies. None of the patients with anti-Sp4 autoantibodies required a wheelchair. Among White patients, DQA1*04 and DRB1*08 were associated with anti-Sp4 autoantibodies. CONCLUSION Anti-Sp4 autoantibodies were found in patients with juvenile-onset IIM, predominantly those with coexisting anti-TIF1 autoantibodies. Patients with anti-Sp4 autoantibodies represent a phenotypic subset of anti-TIF1 autoantibody-positive myositis characterized by frequent Raynaud's phenomenon and less pronounced muscle involvement, similar to adults with these autoantibodies. Novel immunogenetic risk factors for White patients with IIM were identified among juveniles with anti-Sp4 autoantibodies.
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Affiliation(s)
- Matthew A. Sherman
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Katherine Pak
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Iago Pinal-Fernandez
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Willy A. Flegel
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Ira N. Targoff
- Veteran’s Affairs Medical Center, University of Oklahoma Health Sciences Center, and Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Frederick W. Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa G. Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew L. Mammen
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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23
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Kalomoiri M, Prakash CR, Lagström S, Hauschulz K, Ewing E, Shchetynsky K, Kular L, Needhamsen M, Jagodic M. Simultaneous detection of DNA variation and methylation at HLA class II locus and immune gene promoters using targeted SureSelect Methyl-Sequencing. Front Immunol 2023; 14:1251772. [PMID: 37691926 PMCID: PMC10484099 DOI: 10.3389/fimmu.2023.1251772] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
The Human Leukocyte Antigen (HLA) locus associates with a variety of complex diseases, particularly autoimmune and inflammatory conditions. The HLA-DR15 haplotype, for example, confers the major risk for developing Multiple Sclerosis in Caucasians, pinpointing an important role in the etiology of this chronic inflammatory disease of the central nervous system. In addition to the protein-coding variants that shape the functional HLA-antigen-T cell interaction, recent studies suggest that the levels of HLA molecule expression, that are epigenetically controlled, also play a role in disease development. However, deciphering the exact molecular mechanisms of the HLA association has been hampered by the tremendous genetic complexity of the locus and a lack of robust approaches to investigate it. Here, we developed a method to specifically enrich the genomic DNA from the HLA class II locus (chr6:32,426,802-34,167,129) and proximal promoters of 2,157 immune-relevant genes, utilizing the Agilent RNA-based SureSelect Methyl-Seq Capture related method, followed by sequencing to detect genetic and epigenetic variation. We demonstrated successful simultaneous detection of the genetic variation and quantification of DNA methylation levels in HLA locus. Moreover, by the detection of differentially methylated positions in promoters of immune-related genes, we identified relevant pathways following stimulation of cells. Taken together, we present a method that can be utilized to study the interplay between genetic variance and epigenetic regulation in the HLA class II region, potentially, in a wide disease context.
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Affiliation(s)
- Maria Kalomoiri
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chandana Rao Prakash
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sonja Lagström
- Diagnostics and Genomics Group, Agilent Technologies Sweden AB, Sundbyberg, Sweden
| | - Kai Hauschulz
- Diagnostics and Genomics Group, Agilent Technologies Deutschland GmbH, Waldbronn, Germany
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klementy Shchetynsky
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
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24
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Hedström AK. Risk factors for multiple sclerosis in the context of Epstein-Barr virus infection. Front Immunol 2023; 14:1212676. [PMID: 37554326 PMCID: PMC10406387 DOI: 10.3389/fimmu.2023.1212676] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Compelling evidence indicates that Epstein Barr virus (EBV) infection is a prerequisite for multiple sclerosis (MS). The disease may arise from a complex interplay between latent EBV infection, genetic predisposition, and various environmental and lifestyle factors that negatively affect immune control of the infection. Evidence of gene-environment interactions and epigenetic modifications triggered by environmental factors in genetically susceptible individuals supports this view. This review gives a short introduction to EBV and host immunity and discusses evidence indicating EBV as a prerequisite for MS. The role of genetic and environmental risk factors, and their interactions, in MS pathogenesis is reviewed and put in the context of EBV infection. Finally, possible preventive measures are discussed based on the findings presented.
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Affiliation(s)
- Anna Karin Hedström
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
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25
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Fuh-Ngwa V, Charlesworth JC, Zhou Y, van der Mei I, Melton PE, Broadley SA, Ponsonby AL, Simpson-Yap S, Lechner-Scott J, Taylor BV. The association between disability progression, relapses, and treatment in early relapse onset MS: an observational, multi-centre, longitudinal cohort study. Sci Rep 2023; 13:11584. [PMID: 37463930 DOI: 10.1038/s41598-023-38415-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023] Open
Abstract
The indirect contribution of multiple sclerosis (MS) relapses to disability worsening outcomes, and vice-versa, remains unclear. Disease modifying therapies (DMTs) are potential modulators of this association. Understanding how these endo-phenotypes interact may provide insights into disease pathogenesis and treatment practice in relapse-onset MS (ROMS). Utilising a unique, prospectively collected clinical data from a longitudinal cohort of 279 first demyelinating event cases followed for up to 15 years post-onset, we examined indirect associations between relapses and treatment and the risk of disability worsening, and vice-versa. Indirect association parameters were estimated using joint models for longitudinal and survival data. Early relapses within 2.5 years of MS onset predicted early disability worsening outcomes (HR = 3.45, C.I 2.29-3.61) per relapse, but did not contribute to long-term disability worsening thereinafter (HR = 0.21, C.I 0.15-0.28). Conversely, disability worsening outcomes significantly contributed to relapse risk each year (HR = 2.96, C.I 2.91-3.02), and persisted over time (HR = 3.34, C.I 2.90-3.86), regardless of DMT treatments. The duration of DMTs significantly reduced the hazards of relapses (1st-line DMTs: HR = 0.68, C.I 0.58-0.79; 3rd-line DMTs: HR = 0.37, C.I 0.32-0.44) and disability worsening events (1st-line DMTs: HR = 0.74, C.I 0.69-0.79; 3rd-line DMTs: HR = 0.90, C.I 0.85-0.95), respectively. Results from time-dynamic survival probabilities further revealed individuals having higher risk of future relapses and disability worsening outcomes, respectively. The study provided evidence that in ROMS, relapses accrued within 2.5 years of MS onset are strong indicators of disability worsening outcomes, but late relapses accrued 2.5 years post onset are not overt risk factors for further disability worsening. In contrast, disability worsening outcomes are strong positive predictors of current and subsequent relapse risk. Long-term DMT use and older age strongly influence the individual outcomes and their associations.
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Affiliation(s)
- Valery Fuh-Ngwa
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia.
| | - Jac C Charlesworth
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Yuan Zhou
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Ingrid van der Mei
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Phillip E Melton
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia
| | - Simon A Broadley
- Menzies Health Institute Queensland and School of Medicine, Griffith University, Gold Coast, QLD, 4222, Australia
| | - Anne-Louise Ponsonby
- Florey Institute for Neuroscience and Mental Health, Parkville, VIC, 3052, Australia
| | - Steve Simpson-Yap
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia
- Neuroepidemiology Unit, Center for Epidemiology and Biostatistics, The University of Melbourne School of Population & Global Health, Melbourne, VIC, 3053, Australia
| | - Jeannette Lechner-Scott
- School of Medicine and Public Health New Lambton, Hunter New England Health, New Lambton Heights, NSW, Australia
- Department of Neurology, The University of Newcastle Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Bruce V Taylor
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool St, Hobart, TAS, 7000, Australia.
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26
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Sigurdsson AI, Louloudis I, Banasik K, Westergaard D, Winther O, Lund O, Ostrowski S, Erikstrup C, Pedersen O, Nyegaard M, Brunak S, Vilhjálmsson B, Rasmussen S. Deep integrative models for large-scale human genomics. Nucleic Acids Res 2023; 51:e67. [PMID: 37224538 PMCID: PMC10325897 DOI: 10.1093/nar/gkad373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/18/2023] [Accepted: 04/28/2023] [Indexed: 05/26/2023] Open
Abstract
Polygenic risk scores (PRSs) are expected to play a critical role in precision medicine. Currently, PRS predictors are generally based on linear models using summary statistics, and more recently individual-level data. However, these predictors mainly capture additive relationships and are limited in data modalities they can use. We developed a deep learning framework (EIR) for PRS prediction which includes a model, genome-local-net (GLN), specifically designed for large-scale genomics data. The framework supports multi-task learning, automatic integration of other clinical and biochemical data, and model explainability. When applied to individual-level data from the UK Biobank, the GLN model demonstrated a competitive performance compared to established neural network architectures, particularly for certain traits, showcasing its potential in modeling complex genetic relationships. Furthermore, the GLN model outperformed linear PRS methods for Type 1 Diabetes, likely due to modeling non-additive genetic effects and epistasis. This was supported by our identification of widespread non-additive genetic effects and epistasis in the context of T1D. Finally, we constructed PRS models that integrated genotype, blood, urine, and anthropometric data and found that this improved performance for 93% of the 290 diseases and disorders considered. EIR is available at https://github.com/arnor-sigurdsson/EIR.
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Affiliation(s)
- Arnór I Sigurdsson
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ioannis Louloudis
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - David Westergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Ole Winther
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen N, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
| | - Ole Lund
- Danish National Genome Center, Ørestads Boulevard 5, 2300 Copenhagen S, Denmark
- DTU Health Tech, Department of Health Technology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, 8000 Aarhus C, Denmark
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- Department of Clinical Immunology, Zealand University Hospital, 4600 Køge, Denmark
| | - Mette Nyegaard
- Department of Health Science and Technology, Aalborg University, DK- 9260 Gistrup, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Bjarni J Vilhjálmsson
- National Centre for Register-Based Research (NCRR), Aarhus University, 8000 Aarhus C, Denmark
- Lundbeck Foundation Initiative for Integrative Psychiatric Research (iPSYCH), 8210 Aarhus V, Denmark
- Bioinformatics Research Centre (BiRC), Aarhus University, 8000 Aarhus C, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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27
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Houwaart T, Scholz S, Pollock NR, Palmer WH, Kichula KM, Strelow D, Le DB, Belick D, Hülse L, Lautwein T, Wachtmeister T, Wollenweber TE, Henrich B, Köhrer K, Parham P, Guethlein LA, Norman PJ, Dilthey AT. Complete sequences of six major histocompatibility complex haplotypes, including all the major MHC class II structures. HLA 2023; 102:28-43. [PMID: 36932816 PMCID: PMC10986641 DOI: 10.1111/tan.15020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 02/10/2023] [Accepted: 02/24/2023] [Indexed: 03/19/2023]
Abstract
Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina, ultra-long Nanopore, and PacBio HiFi sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (GRCh38/hg38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.06%-0.49% in a 1000 Genomes Project read remapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.
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Affiliation(s)
- Torsten Houwaart
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Stephan Scholz
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Nicholas R. Pollock
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - William H. Palmer
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Katherine M. Kichula
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Daniel Strelow
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Duyen B. Le
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Lisanna Hülse
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tobias Lautwein
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Thorsten Wachtmeister
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Tassilo E. Wollenweber
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Karl Köhrer
- Biologisch‐Medizinisches‐Forschungszentrum (BMFZ)Genomics & Transcriptomics Laboratory, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Peter Parham
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Lisbeth A. Guethlein
- Department of Structural Biology, and Department of Microbiology and ImmunologyStanford UniversityStanfordCaliforniaUSA
| | - Paul J. Norman
- Department of Biomedical InformaticsAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
- Department of Immunology and MicrobiologyAnschutz Medical Campus, University of ColoradoAuroraColoradoUSA
| | - Alexander T. Dilthey
- Institute of Medical Microbiology and Hospital HygieneHeinrich Heine University DüsseldorfDüsseldorfGermany
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28
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Gurnari C, Pagliuca S, Maciejewski JP. Clonal evolution in aplastic anemia: failed tumor surveillance or maladaptive recovery? Leuk Lymphoma 2023; 64:1389-1399. [PMID: 37356012 PMCID: PMC11104022 DOI: 10.1080/10428194.2023.2215614] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 06/27/2023]
Abstract
Clonal evolution to secondary paroxysmal nocturnal hemoglobinuria (PNH) or myeloid neoplasia (MN) represents one of the long-term complications of patients with aplastic anemia (AA). The recent evidence in the field of immunology and the application of next-generation sequencing have shed light on the molecular underpinnings of these clonal complications, revealing clinical and molecular risk factors as well as potential immunological players. Particularly, whether MN evolution represents a failed tumor surveillance or a maladaptive recovery is still a matter of controversy in the field of bone marrow failure syndromes. However, recent studies have explored the precise dynamics of the immune-molecular forces governing such processes over time, generating knowledge useful for potential early therapeutic strategies. In this review, we will discuss the immune pathophysiology of AA and the emergence of clonal hematopoiesis with regard to the adaptive and maladaptive mechanisms at the basis of secondary evolution trajectories operating under the immune pressure.
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Affiliation(s)
- Carmelo Gurnari
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Biomedicine and Prevention, PhD in Immunology, Molecular Medicine and Applied Biotechnology, University of Rome Tor Vergata, Rome, Italy
| | - Simona Pagliuca
- Sérvice d‘hématologie Clinique, ChRu de Nancy, Nancy, France
- CNRS UMR 7365 IMoPa, Biopôle de l‘Université de Lorraine, France Vandœuvre-lès-Nancy
| | - Jaroslaw P. Maciejewski
- Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
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29
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Jacobs BM, Schalk L, Dunne A, Scalfari A, Nandoskar A, Gran B, Mein CA, Sellers C, Spilker C, Rog D, Visentin E, Bezzina EL, Uzochukwu E, Tallantyre E, Wozniak E, Sacre E, Hassan-Smith G, Ford HL, Harris J, Bradley J, Breedon J, Brooke J, Kreft KL, Tuite Dalton K, George K, Papachatzaki M, O'Malley M, Peter M, Mattoscio M, Rhule N, Evangelou N, Vinod N, Quinn O, Shamji R, Kaimal R, Boulton R, Tanveer R, Middleton R, Murray R, Bellfield R, Hoque S, Patel S, Raj S, Gumus S, Mitchell S, Sawcer S, Arun T, Pogreban T, Brown TL, Begum T, Antoine V, Rashid W, Noyce AJ, Silber E, Morris H, Giovannoni G, Dobson R. ADAMS project: a genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis based in the UK. BMJ Open 2023; 13:e071656. [PMID: 37197821 DOI: 10.1136/bmjopen-2023-071656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
PURPOSE Genetic studies of multiple sclerosis (MS) susceptibility and severity have focused on populations of European ancestry. Studying MS genetics in other ancestral groups is necessary to determine the generalisability of these findings. The genetic Association study in individuals from Diverse Ancestral backgrounds with Multiple Sclerosis (ADAMS) project aims to gather genetic and phenotypic data on a large cohort of ancestrally-diverse individuals with MS living in the UK. PARTICIPANTS Adults with self-reported MS from diverse ancestral backgrounds. Recruitment is via clinical sites, online (https://app.mantal.co.uk/adams) or the UK MS Register. We are collecting demographic and phenotypic data using a baseline questionnaire and subsequent healthcare record linkage. We are collecting DNA from participants using saliva kits (Oragene-600) and genotyping using the Illumina Global Screening Array V.3. FINDINGS TO DATE As of 3 January 2023, we have recruited 682 participants (n=446 online, n=55 via sites, n=181 via the UK MS Register). Of this initial cohort, 71.2% of participants are female, with a median age of 44.9 years at recruitment. Over 60% of the cohort are non-white British, with 23.5% identifying as Asian or Asian British, 16.2% as Black, African, Caribbean or Black British and 20.9% identifying as having mixed or other backgrounds. The median age at first symptom is 28 years, and median age at diagnosis is 32 years. 76.8% have relapsing-remitting MS, and 13.5% have secondary progressive MS. FUTURE PLANS Recruitment will continue over the next 10 years. Genotyping and genetic data quality control are ongoing. Within the next 3 years, we aim to perform initial genetic analyses of susceptibility and severity with a view to replicating the findings from European-ancestry studies. In the long term, genetic data will be combined with other datasets to further cross-ancestry genetic discoveries.
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Affiliation(s)
- Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Luisa Schalk
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Angie Dunne
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Antonio Scalfari
- Centre of Neuroscience, Department of Medicine, Imperial College London, London, UK
| | | | - Bruno Gran
- Department of Neurology, Nottingham University Hospitals NHS Trust, Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | - Charles A Mein
- Barts and the London Genome Centre, Queen Mary University of London, London, UK
| | - Charlotte Sellers
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Cord Spilker
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - David Rog
- Manchester Centre for Clinical Neurosciences, Northern Care Alliance NHS Trust, Manchester, UK
| | - Elisa Visentin
- Research and Innovation, Queen's Hospital, BHRUT, London, UK
| | | | - Emeka Uzochukwu
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Emma Tallantyre
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Department of Clinical Neurology, University Hospital of Wales, Cardiff, UK
| | - Eva Wozniak
- Barts and the London Genome Centre, Queen Mary University of London, London, UK
| | - Eve Sacre
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | | | - Helen L Ford
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Jade Harris
- Northern Care Alliance NHS Trust, Manchester, UK
| | | | - Joshua Breedon
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Karim L Kreft
- Department of Neurology, University Hospital of Wales, Cardiff, UK
| | | | - Katila George
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Martin O'Malley
- Leeds Centre for Neurosciences, Leeds teaching Hospitals NHS Trust, Leeds, UK
| | - Michelle Peter
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Miriam Mattoscio
- Department of neuroscience, Queen's Hospital, BHRUT NHS Trust, Romford, UK
| | - Neisha Rhule
- Queen Elizabeth Hospital (Lewisham and Greenwich NHS Trust), London, UK
| | - Nikos Evangelou
- Department of Neurology, Nottingham University Hospitals NHS Trust; Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | | | - Outi Quinn
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - Ramya Shamji
- Research and Innovation, Queen's Hospital, BHRUT, London, UK
| | - Rashmi Kaimal
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Rebecca Boulton
- Department of Neurology, Nottingham University Hospitals NHS Trust; Mental Health and Clinical Neuroscience Academic Unit, University of Nottingham School of Medicine, Nottingham, UK
| | - Riffat Tanveer
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Rod Middleton
- Population Data Science, Swansea University Medical School, Swansea, UK
| | - Roxanne Murray
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Ruth Bellfield
- Bradford Teaching Hospital Foundation Trust, Bradford, UK
| | - Sadid Hoque
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Shakeelah Patel
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Sonia Raj
- Lancashire Teaching Hospital NHS Foundation Trust, Preston, UK
| | - Stephanie Gumus
- Mid and South Essex NHS Foundation Trust, Southend-on-Sea, UK
| | | | - Stephen Sawcer
- University of Cambridge, Department of Clinical Neuroscience, Addenbrookes Hospital, Hills Road, Cambridge, UK
| | - Tarunya Arun
- University Hospitals of Coventry and Warwickshire, Coventry, UK
| | | | - Terri-Louise Brown
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Thamanna Begum
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Waqar Rashid
- St George's University Hospitals NHS Foundation Trust, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Eli Silber
- Kings College Hospital and Lewisham and Greenwich NHS Trusts, London, UK
| | - Huw Morris
- Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
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30
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Moore MZ, Pérez CA, Hutton GJ, Patel H, Cuascut FX. Health Disparities in Multiple Sclerosis among Hispanic and Black Populations in the United States. Biomedicines 2023; 11:biomedicines11041227. [PMID: 37189845 DOI: 10.3390/biomedicines11041227] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Multiple sclerosis (MS) is an acquired demyelinating disease of the central nervous system (CNS). Historically, research on MS has focused on White persons with MS. This preponderance of representation has important possible implications for minority populations with MS, from developing effective therapeutic agents to understanding the role of unique constellations of social determinants of health. A growing body of literature involving persons of historically underrepresented races and ethnicities in the field of multiple sclerosis is assembling. Our purpose in this narrative review is to highlight two populations in the United States: Black and Hispanic persons with multiple sclerosis. We will review the current understanding about the patterns of disease presentation, genetic considerations, response to treatment, roles of social determinants of health, and healthcare utilization. In addition, we explore future directions of inquiry as well as practical methods of meeting these challenges.
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Affiliation(s)
- Michael Z Moore
- Maxine Mesinger Multiple Sclerosis Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Carlos A Pérez
- Maxine Mesinger Multiple Sclerosis Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - George J Hutton
- Maxine Mesinger Multiple Sclerosis Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hemali Patel
- Maxine Mesinger Multiple Sclerosis Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fernando X Cuascut
- Maxine Mesinger Multiple Sclerosis Center, Baylor College of Medicine, Houston, TX 77030, USA
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31
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Fashina IA, McCoy CE, Furney SJ. In silico prioritisation of microRNA-associated common variants in multiple sclerosis. Hum Genomics 2023; 17:31. [PMID: 36991503 PMCID: PMC10061723 DOI: 10.1186/s40246-023-00478-4] [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: 02/14/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have highlighted over 200 autosomal variants associated with multiple sclerosis (MS). However, variants in non-coding regions such as those encoding microRNAs have not been explored thoroughly, despite strong evidence of microRNA dysregulation in MS patients and model organisms. This study explores the effect of microRNA-associated variants in MS, through the largest publicly available GWAS, which involved 47,429 MS cases and 68,374 controls. METHODS We identified SNPs within the coordinates of microRNAs, ± 5-kb microRNA flanking regions and predicted 3'UTR target-binding sites using miRBase v22, TargetScan 7.0 RNA22 v2.0 and dbSNP v151. We established the subset of microRNA-associated SNPs which were tested in the summary statistics of the largest MS GWAS by intersecting these datasets. Next, we prioritised those microRNA-associated SNPs which are among known MS susceptibility SNPs, are in strong linkage disequilibrium with the former or meet a microRNA-specific Bonferroni-corrected threshold. Finally, we predicted the effects of those prioritised SNPs on their microRNAs and 3'UTR target-binding sites using TargetScan v7.0, miRVaS and ADmiRE. RESULTS We have identified 30 candidate microRNA-associated variants which meet at least one of our prioritisation criteria. Among these, we highlighted one microRNA variant rs1414273 (MIR548AC) and four 3'UTR microRNA-binding site variants within SLC2A4RG (rs6742), CD27 (rs1059501), MMEL1 (rs881640) and BCL2L13 (rs2587100). We determined changes to the predicted microRNA stability and binding site recognition of these microRNA and target sites. CONCLUSIONS We have systematically examined the functional, structural and regulatory effects of candidate MS variants among microRNAs and 3'UTR targets. This analysis allowed us to identify candidate microRNA-associated MS SNPs and highlights the value of prioritising non-coding RNA variation in GWAS. These candidate SNPs could influence microRNA regulation in MS patients. Our study is the first thorough investigation of both microRNA and 3'UTR target-binding site variation in multiple sclerosis using GWAS summary statistics.
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Affiliation(s)
- Ifeolutembi A. Fashina
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- SFI Centre for Research Training in Genomics Data Sciences, University of Galway, H91 TK33 Galway, Ireland
- FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Claire E. McCoy
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Simon J. Furney
- Genomic Oncology Research Group, Department of Physiology & Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
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Sundaresan B, Shirafkan F, Ripperger K, Rattay K. The Role of Viral Infections in the Onset of Autoimmune Diseases. Viruses 2023; 15:v15030782. [PMID: 36992490 PMCID: PMC10051805 DOI: 10.3390/v15030782] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/31/2023] Open
Abstract
Autoimmune diseases (AIDs) are the consequence of a breach in immune tolerance, leading to the inability to sufficiently differentiate between self and non-self. Immune reactions that are targeted towards self-antigens can ultimately lead to the destruction of the host's cells and the development of autoimmune diseases. Although autoimmune disorders are comparatively rare, the worldwide incidence and prevalence is increasing, and they have major adverse implications for mortality and morbidity. Genetic and environmental factors are thought to be the major factors contributing to the development of autoimmunity. Viral infections are one of the environmental triggers that can lead to autoimmunity. Current research suggests that several mechanisms, such as molecular mimicry, epitope spreading, and bystander activation, can cause viral-induced autoimmunity. Here we describe the latest insights into the pathomechanisms of viral-induced autoimmune diseases and discuss recent findings on COVID-19 infections and the development of AIDs.
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Affiliation(s)
- Bhargavi Sundaresan
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Fatemeh Shirafkan
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Kevin Ripperger
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
| | - Kristin Rattay
- Institute of Pharmacology, Biochemical Pharmacological Center, University of Marburg, 35043 Marburg, Germany
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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: 57] [Impact Index Per Article: 57.0] [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.
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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.
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Jokubaitis VG. A role for HLA in mediating long-term multiple sclerosis outcomes? Mult Scler 2023; 29:314-316. [PMID: 36515360 DOI: 10.1177/13524585221139767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Brownlee WJ, Tur C, Manole A, Eshaghi A, Prados F, Miszkiel KA, Wheeler-Kingshott CAG, Houlden H, Ciccarelli O. HLA-DRB1*1501 influences long-term disability progression and tissue damage on MRI in relapse-onset multiple sclerosis. Mult Scler 2023; 29:333-342. [PMID: 36398585 DOI: 10.1177/13524585221130941] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Whether genetic factors influence the long-term course of multiple sclerosis (MS) is unresolved. OBJECTIVE To determine the influence of HLA-DRB1*1501 on long-term disease course in a homogeneous cohort of clinically isolated syndrome (CIS) patients. METHODS One hundred seven patients underwent clinical and MRI assessment at the time of CIS and after 1, 3, 5 and 15 years. HLA-DRB1*1501 status was determined using Sanger sequencing and tagging of the rs3135388 polymorphism. Linear/Poisson mixed-effects models were used to investigate rates of change in EDSS and MRI measures based on HLA-DRB1*1501 status. RESULTS HLA-DRB1*1501 -positive (n = 52) patients showed a faster rate of disability worsening compared with the HLA-DRB1*1501 -negative (n = 55) patients (annualised change in EDSS 0.14/year vs. 0.08/year, p < 0.025), and a greater annualised change in T2 lesion volume (adjusted difference 0.45 mL/year, p < 0.025), a higher number of gadolinium-enhancing lesions, and a faster rate of brain (adjusted difference -0.12%/year, p < 0.05) and spinal cord atrophy (adjusted difference -0.22 mm2/year, p < 0.05). INTERPRETATION These findings provide evidence that the HLA-DRB1*1501 allele plays a role in MS severity, as measured by long-term disability worsening and a greater extent of inflammatory disease activity and tissue loss. HLA-DRB1*1501 may provide useful information when considering prognosis and treatment decisions in early relapse-onset MS.
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Affiliation(s)
- Wallace J Brownlee
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK
| | - Carmen Tur
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK/UK e-Health Center, Universitat Oberta de Catalunya, Barcelona, Spain
| | - Andreea Manole
- Salk Institute for Biological Studies, San Diego, CA, USA
| | - Arman Eshaghi
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK
| | - Ferran Prados
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK/Centre for Medical Image Computing, Department of Medical Physics and Biomedical Engineering, University College London, London, UK
| | - Katherine A Miszkiel
- Lysholm Department of Neuroradiology, National Hospital for Neurology and Neurosurgery, London, UK
| | - Claudia Am Gandini Wheeler-Kingshott
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK/Brain Connectivity Center, C. Mondino National Neurological Institute, Pavia, Italy Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK/NIHR University College London Hospitals Biomedical Research Centre, London, UK
| | - Olga Ciccarelli
- NMR Research Unit, Queen Square MS Centre, Department of Neuroinflammation, UCL Institute of Neurology, London, UK/NIHR University College London Hospitals Biomedical Research Centre, London
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Breedon JR, Marshall CR, Giovannoni G, van Heel DA, Dobson R, Jacobs BM. Polygenic risk score prediction of multiple sclerosis in individuals of South Asian ancestry. Brain Commun 2023; 5:fcad041. [PMID: 37006331 PMCID: PMC10053643 DOI: 10.1093/braincomms/fcad041] [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: 07/25/2022] [Revised: 10/12/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
Polygenic risk scores aggregate an individual's burden of risk alleles to estimate the overall genetic risk for a specific trait or disease. Polygenic risk scores derived from genome-wide association studies of European populations perform poorly for other ancestral groups. Given the potential for future clinical utility, underperformance of polygenic risk scores in South Asian populations has the potential to reinforce health inequalities. To determine whether European-derived polygenic risk scores underperform at multiple sclerosis prediction in a South Asian-ancestry population compared with a European-ancestry cohort, we used data from two longitudinal genetic cohort studies: Genes & Health (2015-present), a study of ∼50 000 British-Bangladeshi and British-Pakistani individuals, and UK Biobank (2006-present), which is comprised of ∼500 000 predominantly White British individuals. We compared individuals with and without multiple sclerosis in both studies (Genes & Health: N Cases = 42, N Control = 40 490; UK Biobank: N Cases = 2091, N Control = 374 866). Polygenic risk scores were calculated using clumping and thresholding with risk allele effect sizes obtained from the largest multiple sclerosis genome-wide association study to date. Scores were calculated with and without the major histocompatibility complex region, the most influential locus in determining multiple sclerosis risk. Polygenic risk score prediction was evaluated using Nagelkerke's pseudo-R 2 metric adjusted for case ascertainment, age, sex and the first four genetic principal components. We found that, as expected, European-derived polygenic risk scores perform poorly in the Genes & Health cohort, explaining 1.1% (including the major histocompatibility complex) and 1.5% (excluding the major histocompatibility complex) of disease risk. In contrast, multiple sclerosis polygenic risk scores explained 4.8% (including the major histocompatibility complex) and 2.8% (excluding the major histocompatibility complex) of disease risk in European-ancestry UK Biobank participants. These findings suggest that polygenic risk score prediction of multiple sclerosis based on European genome-wide association study results is less accurate in a South Asian population. Genetic studies of ancestrally diverse populations are required to ensure that polygenic risk scores can be useful across ancestries.
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Affiliation(s)
- Joshua R Breedon
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
| | - Charles R Marshall
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
- Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - David A van Heel
- Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
| | - Benjamin M Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London EC1M 6BQ, UK
- Department of Neurology, Royal London Hospital, London E1 1FR, UK
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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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Confirmation of CD19+ B-Lymphocyte Depletion Prior to Intake of the Second Dose of Ocrelizumab in Multiple Sclerosis Patients. Biomedicines 2023; 11:biomedicines11020353. [PMID: 36830890 PMCID: PMC9953738 DOI: 10.3390/biomedicines11020353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
The aim of the retrospective study was to compare the immunophenotyping of T-lymphocytes, B-lymphocytes, and natural killer cells before the administration of the first and the second dose of ocrelizumab in 22 patients with multiple sclerosis in a three-year period (2019-2021) at the Department of Neurology of the University Hospital of Split. The values of cell immunophenotyping and protein electrophoresis, as well as laboratory parameters, were investigated. There was no significant decrease in serum albumin and globulins before the second dose of ocrelizumab (p > 0,05). A decrease in the number of T-lymphocytes before administration of the second dose of ocrelizumab was observed, but without statistical significance (p = 0.274). Significant depletion occurred in median CD19+ B-lymphocytes (p < 0.001) before the intake of the second dose of ocrelizumab confirming the primary action of ocrelizumab on the B cell lineage.
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Hedström AK, Segersson D, Hillert J, Stridh P, Kockum I, Olsson T, Bellander T, Alfredsson L. Association between exposure to combustion-related air pollution and multiple sclerosis risk. Int J Epidemiol 2023:6984751. [PMID: 36629499 DOI: 10.1093/ije/dyac234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Smoking and occupational pulmonary irritants contribute to multiple sclerosis (MS) development. We aimed to study the association between ambient air pollution and MS risk and potential interaction with the human leukocyte antigen (HLA)-DRB1*15:01 allele. METHODS Exposure to combustion-related air pollution was estimated as outdoor levels of nitrogen oxides (NOx) at the participants' residence locations, by spatially resolved dispersion modelling for the years 1990-18. Using two population-based case-control studies (6635 cases, 8880 controls), NOx levels were associated with MS risk by calculating odds ratios (OR) with 95% confidence intervals (CI) using logistic regression models. Interaction between high NOx levels and the HLA-DRB1*15:01 allele regarding MS risk was calculated by the attributable proportion due to interaction (AP). In addition, a register study was performed comprising all MS cases in Sweden who had received their diagnosis between 1993 and 2018 (n = 22 173), with 10 controls per case randomly selected from the National Population register. RESULTS Residential air pollution was associated with MS risk. NOx levels (3-year average) exceeding the 90th percentile (24.6 µg/m3) were associated with an OR of 1.37 (95% CI 1.10-1.76) compared with levels below the 25th percentile (5.9 µg/m3), with a trend of increasing risk of MS with increasing levels of NOx (P <0.0001). A synergistic effect was observed between high NOx levels (exceeding the lower quartile among controls) and the HLA-DRB1*15:01 allele regarding MS risk (AP 0.26, 95% CI 0.13-0.29). CONCLUSIONS Our findings indicate that moderate levels of combustion-related ambient air pollution may play a role in MS development.
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Affiliation(s)
- Anna Karin Hedström
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - David Segersson
- Air Quality Research Unit, Swedish Meteorological and Hydrological Institute, Norrköping, Sweden.,Department of Environmental Science, Stockholm University, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Pernilla Stridh
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Kockum
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Tom Bellander
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Center for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | - Lars Alfredsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Center for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
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Beecham AH, Amezcua L, Chinea A, Manrique CP, Gomez L, Martinez A, Beecham GW, Patsopoulos NA, Chitnis T, Weiner HL, De Jager PL, Burchard EG, Lund BT, Fitzgerald KC, Calabresi PA, Delgado SR, Oksenberg JR, McCauley JL. Ancestral risk modification for multiple sclerosis susceptibility detected across the Major Histocompatibility Complex in a multi-ethnic population. PLoS One 2022; 17:e0279132. [PMID: 36548255 PMCID: PMC9778564 DOI: 10.1371/journal.pone.0279132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The Major Histocompatibility Complex (MHC) makes the largest genetic contribution to multiple sclerosis (MS) susceptibility, with 32 independent effects across the region explaining 20% of the heritability in European populations. Variation is high across populations with allele frequency differences and population-specific risk alleles identified. We sought to identify MHC-specific MS susceptibility variants and assess the effect of ancestral risk modification within 2652 Latinx and Hispanic individuals as well as 2435 Black and African American individuals. We have identified several novel susceptibility alleles which are rare in European populations including HLA-B*53:01, and we have utilized the differing linkage disequilibrium patterns inherent to these populations to identify an independent role for HLA-DRB1*15:01 and HLA-DQB1*06:02 on MS risk. We found a decrease in Native American ancestry in MS cases vs controls across the MHC, peaking near the previously identified MICB locus with a decrease of ~5.5% in Hispanics and ~0.4% in African Americans. We have identified several susceptibility variants, including within the MICB gene region, which show global ancestry risk modification and indicate ancestral differences which may be due in part to correlated environmental factors. We have also identified several susceptibility variants for which MS risk is modified by local ancestry and indicate true ancestral genetic differences; including HLA-DQB1*06:02 for which MS risk for European allele carriers is almost two times the risk for African allele carriers. These results validate the importance of investigating MS susceptibility at an ancestral level and offer insight into the epidemiology of MS phenotypic diversity.
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Affiliation(s)
- Ashley H. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Lilyana Amezcua
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Angel Chinea
- San Juan MS Center, Guaynabo, Puerto Rico, United States of America
| | - Clara P. Manrique
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Andrea Martinez
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Gary W. Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Nikolaos A. Patsopoulos
- Ann Romney Center for Neurological Diseases, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Tanuja Chitnis
- Ann Romney Center for Neurological Diseases, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Howard L. Weiner
- Ann Romney Center for Neurological Diseases, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Philip L. De Jager
- Center For Translational & Computational Neuroimmunology and the Multiple Sclerosis Center, Department of Neurology, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Esteban G. Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America
| | - Brett T. Lund
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Kathryn C. Fitzgerald
- Department of Neurology and The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Peter A. Calabresi
- Department of Neurology and The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Silvia R. Delgado
- Multiple Sclerosis Division, Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, United States of America
| | - Jorge R. Oksenberg
- Department of Neurology, University of California, San Francisco, San Francisco, CA, United States of America
| | - Jacob L. McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
- Dr. John T. Macdonald Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, United States of America
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Trends in the environmental risks associated with earlier onset in multiple sclerosis. Mult Scler Relat Disord 2022; 68:104250. [PMID: 36544313 DOI: 10.1016/j.msard.2022.104250] [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: 06/13/2022] [Revised: 09/27/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND Several environmental and lifestyle factors relating to sunlight/vitamin D, body mass index (BMI), and smoking are associated with the risk of developing multiple sclerosis (MS). However, their relation to disease progression, particularly age at symptomatic onset, remains inconsistent, which may be the result of significant changes in human-environment interactions over the last century. This study investigates historical trends in the association between common MS environmental risk factors and age at disease onset. METHODS Using a narrative approach, we evaluated the current literature for published studies assessing the association between vitamin-D, BMI, and tobacco smoking exposures with the risk of early/pediatric-onset MS and direct correlations with age at MS onset using MEDLINE, EMBASE, and Web of Science. Measures were plotted by the average calendar year of disease onset for each cohort to examine trends over time. In total, 25, 9, and 11 articles were identified for vitamin D, BMI, and smoking-related exposures, respectively. RESULTS Higher sun exposure habits and residential solar radiation were associated with older age at onset. On the contrary, two studies observed a negative correlation between age at onset and serum 25-hydroxyvitamin D (25(OH)D) levels. Higher adolescent BMI was generally associated with younger age at onset, although genetic susceptibility for childhood obesity was not significantly associated. Tobacco smoking was associated with later disease onset, despite being a risk factor for MS. Association with age at onset was inflated for more recent studies relating to smoking, while often weaker for serum vitamin D and BMI. CONCLUSION Current findings indicate a likely association between age at onset and environmental risk factors, such as sun exposure, adolescent BMI, and tobacco smoking, in certain populations. However, findings are often inconsistent and assessment of the relationships and potential changes over time require further investigation.
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Attfield KE, Jensen LT, Kaufmann M, Friese MA, Fugger L. The immunology of multiple sclerosis. Nat Rev Immunol 2022; 22:734-750. [PMID: 35508809 DOI: 10.1038/s41577-022-00718-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2022] [Indexed: 12/11/2022]
Abstract
Our incomplete understanding of the causes and pathways involved in the onset and progression of multiple sclerosis (MS) limits our ability to effectively treat this complex neurological disease. Recent studies explore the role of immune cells at different stages of MS and how they interact with cells of the central nervous system (CNS). The findings presented here begin to question the exclusivity of an antigen-specific cause and highlight how seemingly distinct immune cell types can share common functions that drive disease. Innovative techniques further expose new disease-associated immune cell populations and reinforce how environmental context is critical to their phenotype and subsequent role in disease. Importantly, the differentiation of immune cells into a pathogenic state is potentially reversible through therapeutic manipulation. As such, understanding the mechanisms that provide plasticity to causal cell types is likely key to uncoupling these disease processes and may identify novel therapeutic targets that replace the need for cell ablation.
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Affiliation(s)
- Kathrine E Attfield
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Oxford University Hospitals, University of Oxford, Oxford, UK
| | - Lise Torp Jensen
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Max Kaufmann
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Manuel A Friese
- Institut für Neuroimmunologie und Multiple Sklerose, Zentrum für Molekulare Neurobiologie Hamburg, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Oxford University Hospitals, University of Oxford, Oxford, UK.
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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43
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Santoro S, Clarelli F, Preziosa P, Storelli L, Cannizzaro M, Mascia E, Esposito F, Rocca MA, Filippi M. Exploring the Association of HLA Genetic Risk Burden on Thalamic and Hippocampal Atrophy in Multiple Sclerosis Patients. Genes (Basel) 2022; 13:2136. [PMID: 36421810 PMCID: PMC9690825 DOI: 10.3390/genes13112136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 06/26/2024] Open
Abstract
Multiple sclerosis (MS) is a complex disease of the central nervous system for which human leukocyte antigen (HLA) alleles are major contributors to susceptibility. Several investigations have focused on the relationship between HLA and clinical parameters, while few studies have evaluated its correlation with brain magnetic resonance imaging (MRI) measures. We investigated the association between the HLA genetic burden (HLAGB), originating from the most updated HLA alleles associated with MS, and neuroimaging endophenotypes, with a specific focus on brain atrophy metrics. A monocentric Italian cohort of 334 MS patients with imputed HLA alleles and cross-sectional volumetric measures of white matter (WM), gray matter (GM), hippocampus, thalamus and T2-hyperintense lesions was investigated. Linear regression models with covariate adjustment were fitted for each metric. We detected no effect of HLAGB on WM and GM volumes. Interestingly, we found a marginal correlation between higher HLAGB and lower hippocampal volume (β = -0.142, p = 0.063) and a nominal association between higher HLAGB and lower thalamic volume (β = -0.299, p = 0.047). No association was found with T2 lesion volumes. The putative impact of higher HLAGB on hippocampus and thalamus suggests, if replicated in independent cohorts, a possible cumulative contribution of HLA risk loci on brain volumetric traits linked to clinical deficits in MS.
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Affiliation(s)
- Silvia Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Ferdinando Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Paolo Preziosa
- Unit of Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Loredana Storelli
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Miryam Cannizzaro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Unit of Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Elisabetta Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Federica Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Unit of Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Maria Assunta Rocca
- Unit of Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Massimo Filippi
- Unit of Neurology, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Neuroimaging Research Unit, Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Neurophysiology Service, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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44
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Leone P, Racanelli V. Editorial: Targeting antigen processing and presentation in autoimmune and autoinflammatory disorders. Front Immunol 2022; 13:1055152. [PMID: 36311705 PMCID: PMC9608642 DOI: 10.3389/fimmu.2022.1055152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
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45
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Jacobs BM, Peter M, Giovannoni G, Noyce AJ, Morris HR, Dobson R. Towards a global view of multiple sclerosis genetics. Nat Rev Neurol 2022; 18:613-623. [PMID: 36075979 DOI: 10.1038/s41582-022-00704-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a neuroimmunological disorder of the CNS with a strong heritable component. The genetic architecture of MS susceptibility is well understood in populations of European ancestry. However, the extent to which this architecture explains MS susceptibility in populations of non-European ancestry remains unclear. In this Perspective article, we outline the scientific arguments for studying MS genetics in ancestrally diverse populations. We argue that this approach is likely to yield insights that could benefit individuals with MS from all ancestral groups. We explore the logistical and theoretical challenges that have held back this field to date and conclude that, despite these challenges, inclusion of participants of non-European ancestry in MS genetics studies will ultimately be of value to all patients with MS worldwide.
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Affiliation(s)
- Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK. .,Department of Neurology, Royal London Hospital, London, UK.
| | - Michelle Peter
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Blizard Institute, Queen Mary University London, London, UK
| | - Alastair J Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK.,Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Huw R Morris
- Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
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46
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Jacobs BM, Watson C, Marshall C, Noyce A, Dobson R. No evidence for association between polygenic risk of multiple sclerosis and MRI phenotypes in ~30,000 healthy adult UK Biobank participants. Mult Scler 2022; 28:1656-1657. [PMID: 35293831 PMCID: PMC9315171 DOI: 10.1177/13524585221075744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
| | - Cameron Watson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
| | - Charles Marshall
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
| | - Alastair Noyce
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK.,Department of Neurology, Royal London Hospital, London, UK
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47
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Goris A, Vandebergh M, McCauley JL, Saarela J, Cotsapas C. Genetics of multiple sclerosis: lessons from polygenicity. Lancet Neurol 2022; 21:830-842. [PMID: 35963264 DOI: 10.1016/s1474-4422(22)00255-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022]
Abstract
Large-scale mapping studies have identified 236 independent genetic variants associated with an increased risk of multiple sclerosis. However, none of these variants are found exclusively in patients with multiple sclerosis. They are located throughout the genome, including 32 independent variants in the MHC and one on the X chromosome. Most variants are non-coding and seem to act through cell-specific effects on gene expression and splicing. The likely functions of these variants implicate both adaptive and innate immune cells in the pathogenesis of multiple sclerosis, provide pivotal biological insight into the causes and mechanisms of multiple sclerosis, and some of the variants implicated in multiple sclerosis also mediate risk of other autoimmune and inflammatory diseases. Genetics offers an approach to showing causality for environmental factors, through Mendelian randomisation. No single variant is necessary or sufficient to cause multiple sclerosis; instead, each increases total risk in an additive manner. This combined contribution from many genetic factors to disease risk, or polygenicity, has important consequences for how we interpret the epidemiology of multiple sclerosis and how we counsel patients on risk and prognosis. Ongoing efforts are focused on increasing cohort sizes, increasing diversity and detailed characterisation of study populations, and translating these associations into an understanding of the biology of multiple sclerosis.
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Affiliation(s)
- An Goris
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium.
| | - Marijne Vandebergh
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium
| | - Jacob L McCauley
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Janna Saarela
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway; Institute for Molecular Medicine Finland and Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Chris Cotsapas
- Departments of Neurology and Genetics, Yale School of Medicine, New Haven, CT, USA
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48
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Chang KJ, Wu HY, Yarmishyn AA, Li CY, Hsiao YJ, Chi YC, Lo TC, Dai HJ, Yang YC, Liu DH, Hwang DK, Chen SJ, Hsu CC, Kao CL. Genetics behind Cerebral Disease with Ocular Comorbidity: Finding Parallels between the Brain and Eye Molecular Pathology. Int J Mol Sci 2022; 23:ijms23179707. [PMID: 36077104 PMCID: PMC9456058 DOI: 10.3390/ijms23179707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Cerebral visual impairments (CVIs) is an umbrella term that categorizes miscellaneous visual defects with parallel genetic brain disorders. While the manifestations of CVIs are diverse and ambiguous, molecular diagnostics stand out as a powerful approach for understanding pathomechanisms in CVIs. Nevertheless, the characterization of CVI disease cohorts has been fragmented and lacks integration. By revisiting the genome-wide and phenome-wide association studies (GWAS and PheWAS), we clustered a handful of renowned CVIs into five ontology groups, namely ciliopathies (Joubert syndrome, Bardet–Biedl syndrome, Alstrom syndrome), demyelination diseases (multiple sclerosis, Alexander disease, Pelizaeus–Merzbacher disease), transcriptional deregulation diseases (Mowat–Wilson disease, Pitt–Hopkins disease, Rett syndrome, Cockayne syndrome, X-linked alpha-thalassaemia mental retardation), compromised peroxisome disorders (Zellweger spectrum disorder, Refsum disease), and channelopathies (neuromyelitis optica spectrum disorder), and reviewed several mutation hotspots currently found to be associated with the CVIs. Moreover, we discussed the common manifestations in the brain and the eye, and collated animal study findings to discuss plausible gene editing strategies for future CVI correction.
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Affiliation(s)
- Kao-Jung Chang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Hsin-Yu Wu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | | | - Cheng-Yi Li
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yu-Jer Hsiao
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chun Chi
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Tzu-Chen Lo
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - He-Jhen Dai
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Medical Research, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Yi-Chiang Yang
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Ding-Hao Liu
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - De-Kuang Hwang
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chih-Chien Hsu
- School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Correspondence: (C.-C.H.); (C.-L.K.); Tel.: +886-2-287-573-25 (C.-C.H.); +886-2-287-573-63 (C.-L.K.)
| | - Chung-Lan Kao
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Department of Physical Medicine and Rehabilitation, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Physical Medicine and Rehabilitation, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 300093, Taiwan
- Correspondence: (C.-C.H.); (C.-L.K.); Tel.: +886-2-287-573-25 (C.-C.H.); +886-2-287-573-63 (C.-L.K.)
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49
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Akel O, Zhao LP, Geraghty DE, Lind A. High-resolution HLA class II sequencing of Swedish multiple sclerosis patients. Int J Immunogenet 2022; 49:333-339. [PMID: 35959717 PMCID: PMC9545082 DOI: 10.1111/iji.12594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
Abstract
Multiple sclerosis (MS) is a chronic neurological disease believed to be caused by autoimmune pathogenesis. The aetiology is likely explained by a complex interplay between inherited and environmental factors. Genetic investigations into MS have been conducted for over 50 years, yielding >100 associations to date. Globally, the strongest linkage is with the human leukocyte antigen (HLA) HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype. Here, high-resolution sequencing of HLA was used to determine the alleles of DRB3, DRB4, DRB5, DRB1, DQA1, DQB1, DPA1 and DPB1 as well as their extended haplotypes and genotypes in 100 Swedish MS patients. Results were compared to 636 population controls. The heterogeneity in HLA associations with MS was demonstrated; among 100 patients, 69 extended HLA-DR-DQ genotypes were found. Three extended HLA-DR-DQ genotypes were found to be correlated to MS; HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype together with (A) HLA-DRB4*01:01:01//DRB4*01:01:01:01-DRB1*07:01:01-DQA1*02:01//02:01:01-DQB1*02:02:01, (B) HLA-DRBX*null-DRB1*08:01:01-DQA1*04:01:01-DQB1*04:02:01, and (C) HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01. At the allelic level, HLA-DRB3*01:01:02 was considered protective against MS. However, when combined with HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01, this extended haplotype was considered a predisposing risk factor. This highlights the limitations as included with investigations of single alleles relative to those of extended haplotypes/genotypes. In conclusion, with 69 genotypes presented among 100 patients, high-resolution sequencing was conducted to underscore the wide polymorphisms present among MS patients. Additional studies in larger cohorts will be of importance to define MS among the patient group not associated with HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01.
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Affiliation(s)
- Omar Akel
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
| | - Lue Ping Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexander Lind
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
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50
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HLA-DQB1*05:02, *05:03, and *03:01 alleles as risk factors for myasthenia gravis in a Spanish cohort. Neurol Sci 2022; 43:5057-5065. [DOI: 10.1007/s10072-022-06102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/25/2022] [Indexed: 11/27/2022]
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