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Nakamura H, Hikichi H, Seto S, Hijikata M, Keicho N. Transcriptional regulators SP110 and SP140 modulate inflammatory response genes in Mycobacterium tuberculosis-infected human macrophages. Microbiol Spectr 2024; 12:e0010124. [PMID: 39162523 PMCID: PMC11448263 DOI: 10.1128/spectrum.00101-24] [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: 01/15/2024] [Accepted: 07/16/2024] [Indexed: 08/21/2024] Open
Abstract
Understanding the functions of human transcriptional regulatory genes SP110 and SP140 during Mycobacterium tuberculosis infection is crucial; in a mouse model, homologous genes Sp110 and Sp140 have been shown to negatively regulate inflammatory response genes, including the type I interferon (IFN) response. The reduction of these genes in mice is associated with susceptibility to M. tuberculosis infection and the development of necrotizing granulomatous lesions. To investigate the involvement of SP110 and SP140 in human inflammatory response, we analyzed their regulatory manner in THP-1 macrophages infected with M. tuberculosis. Genome-wide transcriptional profiling revealed that the depletion of SP110 and/or SP140 impaired the induction of gene expression associated with inflammatory responses, including IFN response genes, although it had little effect on the intracellular proliferation of M. tuberculosis. By contrast, genes related to phosphorylation were upregulated in infected macrophages with SP110 and/or SP140 knockdown, but downregulated in infected control macrophages without their knockdown. Reverse transcription-quantitative PCR and ELISA further confirmed the impairment of the induction of IFN response genes by the depletion of SP110 and/or SP140 in M. tuberculosis-infected macrophages. These findings suggest that human SP110 and SP140 act as positive regulators for genes associated with inflammatory responses in M. tuberculosis-infected macrophages. IMPORTANCE Tuberculosis (TB) is one of the most serious infectious diseases, with high morbidity and mortality worldwide. C3HeB/FeJ mice are widely utilized for evaluating anti-TB drugs because their drug sensitivity and pathology during M. tuberculosis infection resemble those of human TB, including the development of necrotizing granulomas. Downregulation of the transcriptional regulatory genes Sp110 and Sp140 in C3HeB/FeJ mice has been demonstrated to activate gene expression associated with inflammatory responses during M. tuberculosis infection, resulting in susceptibility to the infection. Here, we examined the regulatory manner of SP110 and SP140 using transcriptomic analysis in M. tuberculosis-infected human macrophages. Depletion of SP110 and/or SP140 in M. tuberculosis-infected THP-1 macrophages impaired the induction of gene expression associated with inflammatory responses, including interferon response genes, compared with that in control macrophages. These results suggest that human SP110 and SP140 act as positive regulators for genes associated with inflammatory responses upon M. tuberculosis infection.
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Affiliation(s)
- Hajime Nakamura
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
- Department of Basic Mycobacteriosis, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Haruka Hikichi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
- Department of Basic Mycobacteriosis, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Naoto Keicho
- Department of Basic Mycobacteriosis, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
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2
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Sun D, Wang R, Du Q, Chen H, Shi Z, Zhang Y, Zhang N, Wang X, Zhou H. Integrating genetic and proteomic data to elucidate the association between immune system and blood-brain barrier dysfunction with multiple sclerosis risk and severity. J Affect Disord 2024; 362:652-660. [PMID: 39029667 DOI: 10.1016/j.jad.2024.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Immune system dysfunction and blood-brain barrier (BBB) impairment are implicated in multiple sclerosis (MS) risk and severity. However, the causal relationships and potential therapeutic targets remain unclear. METHODS Leveraging the MRC IEU OpenGWAS data infrastructure, we extracted 1254 peripheral immune systems and 792 BBB biomarkers as genetic instruments for exposure. MS risk data from the International Multiple Sclerosis Genetics Consortium (IMSGC) (47,429 MS cases, 68,374 controls) served as one outcome, replicated in FinnGen (1048 cases, 217,141 controls) and the UK Biobank (1679 cases, 461,254 controls). Genetic associations with MS severity derived from IMSGC and MultipleMS Consortium GWAS data (12,584 cases). Two-sample, bidirectional, and protein drug-target MR analyses were conducted, along with interaction analysis of identified proteins and druggability assessment. RESULTS Causal relationships between 45 immunological markers, 15 BBB markers, and MS risk were strongly supported. In peripheral immunity, the causal associations with MS are predominantly concentrated in CD4+ T cells and CD8+ T cells. Notably, anti-Epstein-Barr virus nuclear antigen (EBNA) IgG levels exhibited the most significant causal effect on MS risk (OR = 225.62, P = 5.63E-208), replicated in the MS severity (OR = 1.11, P = 0.04). Weak causal evidence was found between 62 immunological markers, 35 BBB markers, and MS severity. Reverse MR analysis suggested potential causal effects of MS risk on 8 markers. Drug-targeted MR analysis indicated potential therapeutic benefits in reducing MS risk for CD40 (OR = 0.71, P = 7.24E-13, PPH4 = 97.6 %), AHSG (OR = 0.88, P = 2.91E-05, PPH4 = 94.4 %), and FCRL3 (Sun BB et al.: OR = 0.83, P = 8.93E-09, PPH4 = 94.2 %, Suhre K et al.: OR = 0.88, P = 5.20E-08, PPH4 = 99.2 %). CONCLUSIONS This study provides evidence supporting the causal effects of immune system and BBB dysfunction on MS risk and severity. It emphasizes the significant role of anti-EBNA IgG levels, CD4+ T cells, and CD8+ T cells in MS, and delineates the potential therapeutic benefits of targeting three proteins associated with MS risk: CD40, AHSG, and FCRL3.
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Affiliation(s)
- Dongren Sun
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Rui Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Qin Du
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Hongxi Chen
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Ziyan Shi
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Yangyang Zhang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Nana Zhang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Xiaofei Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China.
| | - Hongyu Zhou
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China.
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3
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Becher B, Derfuss T, Liblau R. Targeting cytokine networks in neuroinflammatory diseases. Nat Rev Drug Discov 2024:10.1038/s41573-024-01026-y. [PMID: 39261632 DOI: 10.1038/s41573-024-01026-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2024] [Indexed: 09/13/2024]
Abstract
In neuroinflammatory diseases, systemic (blood-borne) leukocytes invade the central nervous system (CNS) and lead to tissue damage. A causal relationship between neuroinflammatory diseases and dysregulated cytokine networks is well established across several preclinical models. Cytokine dysregulation is also observed as an inadvertent effect of cancer immunotherapy, where it often leads to neuroinflammation. Neuroinflammatory diseases can be separated into those in which a pathogen is at the centre of the immune response and those of largely unknown aetiology. Here, we discuss the pathophysiology, cytokine networks and therapeutic landscape of 'sterile' neuroinflammatory diseases such as multiple sclerosis (MS), neuromyelitis optica spectrum disorder (NMOSD), neurosarcoidosis and immune effector cell-associated neurotoxicity syndrome (ICANS) triggered by cancer immunotherapy. Despite successes in targeting cytokine networks in preclinical models of neuroinflammation, the clinical translation of targeting cytokines and their receptors has shown mixed and often paradoxical responses.
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Affiliation(s)
- Burkhard Becher
- Institute of experimental Immunology, University of Zurich, Zurich, Switzerland.
| | - Tobias Derfuss
- Department of Neurology and Biomedicine, Research Center for Clinical Neuroimmunology and Neuroscience Basel (RC2NB), University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Roland Liblau
- Institute for inflammatory and infectious diseases, INSERM UMR1291 - CNRS UMR505, Toulouse, France.
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4
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Willis TW, Gkrania-Klotsas E, Wareham NJ, McKinney EF, Lyons PA, Smith KGC, Wallace C. Leveraging pleiotropy identifies common-variant associations with selective IgA deficiency. Clin Immunol 2024; 268:110356. [PMID: 39241920 DOI: 10.1016/j.clim.2024.110356] [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: 06/27/2024] [Revised: 08/22/2024] [Accepted: 08/31/2024] [Indexed: 09/09/2024]
Abstract
Selective IgA deficiency (SIgAD) is the most common inborn error of immunity (IEI). Unlike many IEIs, evidence of a role for highly penetrant rare variants in SIgAD is lacking. Previous SIgAD studies have had limited power to identify common variants due to their small sample size. We overcame this problem first through meta-analysis of two existing GWAS. This identified four novel common-variant associations and enrichment of SIgAD-associated variants in genes linked to Mendelian IEIs. SIgAD showed evidence of shared genetic architecture with serum IgA and a number of immune-mediated diseases. We leveraged this pleiotropy through the conditional false discovery rate procedure, conditioning our SIgAD meta-analysis on large GWAS of asthma and rheumatoid arthritis, and our own meta-analysis of serum IgA. This identified an additional 18 variants, increasing the number of known SIgAD-associated variants to 27 and strengthening the evidence for a polygenic, common-variant aetiology for SIgAD.
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Affiliation(s)
- Thomas W Willis
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
| | - Effrossyni Gkrania-Klotsas
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK; Department of Infectious Diseases, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Nicholas J Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Eoin F McKinney
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
| | - Kenneth G C Smith
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia; Department of Medical Biology, University of Melbourne, Melbourne, Australia
| | - Chris Wallace
- Medical Research Council Biostatistics Unit, University of Cambridge, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK; Department of Medicine, University of Cambridge, Cambridge, UK
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5
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Stevenson AW, Cadby G, Wallace HJ, Melton PE, Martin LJ, Wood FM, Fear MW. Genetic influence on scar vascularity after burn injury in individuals of European ancestry: A prospective cohort study. Burns 2024; 50:1871-1884. [PMID: 38902133 DOI: 10.1016/j.burns.2024.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/01/2024] [Accepted: 05/02/2024] [Indexed: 06/22/2024]
Abstract
After burn injury there is considerable variation in scar outcome, partially due to genetic factors. Scar vascularity is one characteristic that varies between individuals, and this study aimed to identify genetic variants contributing to different scar vascularity outcomes. An exome-wide array association study and gene pathway analysis was performed on a prospective cohort of 665 patients of European ancestry treated for burn injury, using their scar vascularity (SV) sub-score, part of the modified Vancouver Scar Scale (mVSS), as an outcome measure. DNA was genotyped using the Infinium HumanCoreExome-24 BeadChip, imputed to the Haplotype Reference Consortium panel. Associations between genetic variants (single nucleotide polymorphisms) and SV were estimated using an additive genetic model adjusting for sex, age, % total body surface area and number of surgical procedures, utilising linear and multinomial logistic regression. No individual genetic variants achieved the cut-off threshold for significance. Gene sets were also analysed using the Functional Mapping and Annotation (FUMA) platform, in which biological processes indirectly related to angiogenesis were significantly represented. This study suggests that SNPs in genes associated with angiogenesis may influence SV, but further studies with larger datasets are essential to validate these findings.
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Affiliation(s)
- Andrew W Stevenson
- Burn Injury Research Unit, School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia.
| | - Gemma Cadby
- School of Population and Global Health, The University of Western Australia, Perth, Australia
| | - Hilary J Wallace
- School of Population and Global Health, The University of Western Australia, Perth, Australia
| | - Phillip E Melton
- School of Population and Global Health, The University of Western Australia, Perth, Australia; Menzies Research Institute, University of Tasmania, Hobart, Tasmania, Australia
| | - Lisa J Martin
- Burn Injury Research Unit, School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia; Burns Service of Western Australia, Princess Margaret Hospital for Children and Fiona Stanley Hospital, Perth, Australia
| | - Fiona M Wood
- Burn Injury Research Unit, School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia; Burns Service of Western Australia, Princess Margaret Hospital for Children and Fiona Stanley Hospital, Perth, Australia
| | - Mark W Fear
- Burn Injury Research Unit, School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia
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Jordan MA, Gresle MM, Gemiarto AT, Stanley D, Smith LD, Laverick L, Spelman T, Stankovich J, Willson AM, Dinh XT, Johnson L, Robertson K, Reid CA, Field J, Butzkueven H, Baxter AG. Transcriptional network analysis of peripheral blood leukocyte subsets in multiple sclerosis identifies a pathogenic role for a cytotoxicity-associated gene network in myeloid cells. Immunol Cell Biol 2024; 102:702-720. [PMID: 38877291 DOI: 10.1111/imcb.12793] [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: 12/14/2023] [Revised: 05/17/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system affecting predominantly adults. It is a complex disease associated with both environmental and genetic risk factors. Although over 230 risk single-nucleotide polymorphisms have been associated with MS, all are common human variants. The mechanisms by which they increase the risk of MS, however, remain elusive. We hypothesized that a complex genetic phenotype such as MS could be driven by coordinated expression of genes controlled by transcriptional regulatory networks. We, therefore, constructed a gene coexpression network from microarray expression analyses of five purified peripheral blood leukocyte subsets of 76 patients with relapsing remitting MS and 104 healthy controls. These analyses identified a major network (or module) of expressed genes associated with MS that play key roles in cell-mediated cytotoxicity which was downregulated in monocytes of patients with MS. Manipulation of the module gene expression was achieved in vitro through small interfering RNA gene knockdown of identified drivers. In a mouse model, network gene knockdown modulated the autoimmune inflammatory MS model disease-experimental autoimmune encephalomyelitis. This research implicates a cytotoxicity-associated gene network in myeloid cells in the pathogenesis of MS.
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Affiliation(s)
- Margaret A Jordan
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | - Melissa M Gresle
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Adrian T Gemiarto
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | | | - Letitia D Smith
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | - Louise Laverick
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Tim Spelman
- Burnett Institute, Melbourne, VIC, Australia
| | - Jim Stankovich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Annie Ml Willson
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | - Xuyen T Dinh
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
- Hai Duong Medical Technical University, Hai Duong, Vietnam
| | - Laura Johnson
- The Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Kylie Robertson
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | - Christopher Ar Reid
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
| | | | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
- The Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Alan G Baxter
- Biomedical Sciences & Molecular Biology, CPHMVS, James Cook University, Townsville, QLD, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC, Australia
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7
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Brune Z, Lu A, Moss M, Brune L, Huang A, Matta B, Barnes BJ. IRF5 mediates adaptive immunity via altered glutamine metabolism, mTORC1 signaling and post-transcriptional regulation following T cell receptor activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.26.609422. [PMID: 39253451 PMCID: PMC11382993 DOI: 10.1101/2024.08.26.609422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Although dynamic alterations in transcriptional, translational, and metabolic programs have been described in T cells, the factors and pathways guiding these molecular shifts are poorly understood, with recent studies revealing a disassociation between transcriptional responses and protein expression following T cell receptor (TCR) stimulation. Previous studies identified interferon regulatory factor 5 (IRF5) in the transcriptional regulation of cytokines, chemotactic molecules and T effector transcription factors following TCR signaling. In this study, we identified T cell intrinsic IRF5 regulation of mTORC1 activity as a key modulator of CD40L protein expression. We further demonstrated a global shift in T cell metabolism, with alterations in glutamine metabolism accompanied by shifts in T cell populations at the single cell level due to loss of Irf5. T cell conditional Irf5 knockout mice in a murine model of experimental autoimmune encephalomyelitis (EAE) demonstrated protection from clinical disease with conserved defects in mTORC1 activity and glutamine regulation. Together, these findings expand our mechanistic understanding of IRF5 as an intrinsic regulator of T effector function(s) and support the therapeutic targeting of IRF5 in multiple sclerosis.
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Affiliation(s)
- Zarina Brune
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
| | - Ailing Lu
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Matthew Moss
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Leianna Brune
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Amanda Huang
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Bharati Matta
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Betsy J Barnes
- Center of Autoimmune, Musculoskeletal and Hematopoietic Diseases, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
- Departments of Molecular Medicine and Pediatrics, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11549, USA
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8
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Dziulko AK, Allen H, Chuong EB. An endogenous retrovirus regulates tumor-specific expression of the immune transcriptional regulator SP140. Hum Mol Genet 2024; 33:1454-1464. [PMID: 38751339 PMCID: PMC11305685 DOI: 10.1093/hmg/ddae084] [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: 02/27/2024] [Revised: 04/24/2024] [Accepted: 05/07/2024] [Indexed: 07/26/2024] Open
Abstract
Speckled Protein 140 (SP140) is a chromatin reader with critical roles regulating immune cell transcriptional programs, and SP140 splice variants are associated with immune diseases including Crohn's disease, multiple sclerosis, and chronic lymphocytic leukemia. SP140 expression is currently thought to be restricted to immune cells. However, by analyzing human transcriptomic datasets from a wide range of normal and cancer cell types, we found recurrent cancer-specific expression of SP140, driven by an alternative intronic promoter derived from an intronic endogenous retrovirus (ERV). The ERV belongs to the primate-specific LTR8B family and is regulated by oncogenic mitogen-activated protein kinase (MAPK) signaling. The ERV drives expression of multiple cancer-specific isoforms, including a nearly full-length isoform that retains all the functional domains of the full-length canonical isoform and is also localized within the nucleus, consistent with a role in chromatin regulation. In a fibrosarcoma cell line, silencing the cancer-specific ERV promoter of SP140 resulted in increased sensitivity to interferon-mediated cytotoxicity and dysregulation of multiple genes. Our findings implicate aberrant ERV-mediated SP140 expression as a novel mechanism contributing to immune gene dysregulation in a wide range of cancer cells.
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Affiliation(s)
- Adam K Dziulko
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Holly Allen
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Ave, JSC Biotech Bldg, Boulder, Colorado 80303, USA
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9
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Alakhras NS, Zhang W, Barros N, Sharma A, Ropa J, Priya R, Yang XF, Kaplan MH. An IL-23-STAT4 pathway is required for the proinflammatory function of classical dendritic cells during CNS inflammation. Proc Natl Acad Sci U S A 2024; 121:e2400153121. [PMID: 39088391 PMCID: PMC11317592 DOI: 10.1073/pnas.2400153121] [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: 01/03/2024] [Accepted: 06/11/2024] [Indexed: 08/03/2024] Open
Abstract
Although many cytokine pathways are important for dendritic cell (DC) development, it is less clear what cytokine signals promote the function of mature dendritic cells. The signal transducer and activator of transcription 4 (STAT4) promotes protective immunity and autoimmunity downstream of proinflammatory cytokines including IL-12 and IL-23. In experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), Stat4-/- mice are resistant to the development of inflammation and paralysis. To define whether STAT4 is required for intrinsic signaling in mature DC function, we used conditional mutant mice in the EAE model. Deficiency of STAT4 in CD11c-expressing cells resulted in decreased T cell priming and inflammation in the central nervous system. EAE susceptibility was recovered following adoptive transfer of wild-type bone marrow-derived DCs to mice with STAT4-deficient DCs, but not adoptive transfer of STAT4- or IL-23R-deficient DCs. Single-cell RNA-sequencing (RNA-seq) identified STAT4-dependent genes in DC subsets that paralleled a signature in MS patient DCs. Together, these data define an IL-23-STAT4 pathway in DCs that is key to DC function during inflammatory disease.
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Affiliation(s)
- Nada S. Alakhras
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Wenwu Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Nicolas Barros
- Department of Medicine, Division of Infectious Diseases Indiana University School of Medicine, Indianapolis, IN46202
| | - Anchal Sharma
- Advanced Analytics and Data Science, Eli Lilly and Company, New York, NY10016
| | - James Ropa
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Raj Priya
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
| | - Mark H. Kaplan
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN46202
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN46202
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10
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Montgomery TL, Peipert D, Krementsov DN. Modulation of multiple sclerosis risk and pathogenesis by the gut microbiota: Complex interactions between host genetics, bacterial metabolism, and diet. Immunol Rev 2024; 325:131-151. [PMID: 38717158 PMCID: PMC11338732 DOI: 10.1111/imr.13343] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
Abstract
Multiple sclerosis (MS) is an autoimmune disease of the central nervous system, affecting nearly 2 million people worldwide. The etiology of MS is multifactorial: Approximately 30% of the MS risk is genetic, which implies that the remaining ~70% is environmental, with a number of factors proposed. One recently implicated risk factor for MS is the composition of the gut microbiome. Numerous case-control studies have identified changes in gut microbiota composition of people with MS (pwMS) compared with healthy control individuals, and more recent studies in animal models have begun to identify the causative microbes and underlying mechanisms. Here, we review some of these mechanisms, with a specific focus on the role of host genetic variation, dietary inputs, and gut microbial metabolism, with a particular emphasis on short-chain fatty acid and tryptophan metabolism. We put forward a model where, in an individual genetically susceptible to MS, the gut microbiota and diet can synergize as potent environmental modifiers of disease risk and possibly progression, with diet-dependent gut microbial metabolites serving as a key mechanism. We also propose that specific microbial taxa may have divergent effects in individuals carrying distinct variants of MS risk alleles or other polymorphisms, as a consequence of host gene-by-gut microbiota interactions. Finally, we also propose that the effects of specific microbial taxa, especially those that exert their effects through metabolites, are highly dependent on the host dietary intake. What emerges is a complex multifaceted interaction that has been challenging to disentangle in human studies, contributing to the divergence of findings across heterogeneous cohorts with differing geography, dietary preferences, and genetics. Nonetheless, this provides a complex and individualized, yet tractable, model of how the gut microbiota regulate susceptibility to MS, and potentially progression of this disease. Thus, we conclude that prophylactic or therapeutic modulation of the gut microbiome to prevent or treat MS will require a careful and personalized consideration of host genetics, baseline gut microbiota composition, and dietary inputs.
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Affiliation(s)
- Theresa L. Montgomery
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Dan Peipert
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Dimitry N. Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
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11
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Hu H, Li H, Li R, Liu P, Liu H. Re-establishing immune tolerance in multiple sclerosis: focusing on novel mechanisms of mesenchymal stem cell regulation of Th17/Treg balance. J Transl Med 2024; 22:663. [PMID: 39010157 PMCID: PMC11251255 DOI: 10.1186/s12967-024-05450-x] [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: 01/23/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024] Open
Abstract
The T-helper 17 (Th17) cell and regulatory T cell (Treg) axis plays a crucial role in the development of multiple sclerosis (MS), which is regarded as an immune imbalance between pro-inflammatory cytokines and the maintenance of immune tolerance. Mesenchymal stem cell (MSC)-mediated therapies have received increasing attention in MS research. In MS and its animal model experimental autoimmune encephalomyelitis, MSC injection was shown to alter the differentiation of CD4+T cells. This alteration occurred by inducing anergy and reduction in the number of Th17 cells, stimulating the polarization of antigen-specific Treg to reverse the imbalance of the Th17/Treg axis, reducing the inflammatory cascade response and demyelination, and restoring an overall state of immune tolerance. In this review, we summarize the mechanisms by which MSCs regulate the balance between Th17 cells and Tregs, including extracellular vesicles, mitochondrial transfer, metabolic reprogramming, and autophagy. We aimed to identify new targets for MS treatment using cellular therapy by analyzing MSC-mediated Th17-to-Treg polarization.
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Affiliation(s)
- Huiru Hu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Hui Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Ruoyu Li
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Peidong Liu
- Department of Neurosurgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Translational Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
| | - Hongbo Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, 450000, Henan, China.
- Translational Medicine Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
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12
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Chen Y, Jiang B, Qu C, Jiang C, Zhang C, Wang Y, Chen F, Sun X, Su L, Luo Y. Genetically predicted metabolites mediate the causal associations between autoimmune thyroiditis and immune cells. Front Endocrinol (Lausanne) 2024; 15:1424957. [PMID: 39045270 PMCID: PMC11263034 DOI: 10.3389/fendo.2024.1424957] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/19/2024] [Indexed: 07/25/2024] Open
Abstract
Introduction We aimed to comprehensively investigate the causal relationship between 731 immune cell traits and autoimmune thyroiditis (AIT) and to identify and quantify the role of 1400 metabolic traits as potential mediators in between. Methods Using summary-level data from genome-wide association studies (GWAS) we performed a two-sample bidirectional Mendelian randomization (MR) analysis of genetically predicted AIT and 731 immune cell traits. Furthermore, we used a two-step MR analysis to quantify the proportion of the total effects (that the immune cells exerted on the risk of AIT) mediated by potential metabolites. Results We identified 24 immune cell traits (with odds ratio (OR) ranging from 1.3166 6 to 0.6323) and 10 metabolic traits (with OR ranging from 1.7954 to 0.6158) to be causally associated with AIT, respectively. Five immune cell traits (including CD38 on IgD+ CD24-, CD28 on CD28+ CD45RA+ CD8br, HLA DR+ CD4+ AC, TD CD4+ %CD4+, and CD8 on EM CD8br) were found to be associated with the risk of AIT, which were partially mediated by metabolites (including glycolithocholate sulfate, 5alpha-androstan-3alpha,17beta-diol disulfate, arachidonoylcholine, X-15486, and kynurenine). The proportion of genetically predicted AIT mediated by the identified metabolites could range from 5.58% to 17.7%. Discussion Our study identified causal associations between AIT and immune cells which were partially mediated by metabolites, thus providing guidance for future clinical and basic research.
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Affiliation(s)
- Yongzhao Chen
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Bo Jiang
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Cheng Qu
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Chaoyu Jiang
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Chen Zhang
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yanxue Wang
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Fei Chen
- General Surgery Center, Department of Thyroid Surgery, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xitai Sun
- Division of Pancreas and Metabolism Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Lei Su
- Department of General Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yuqian Luo
- Clinical Medicine Research Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
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13
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Nova A, Di Caprio G, Bernardinelli L, Fazia T. Genetic and early life factors influence on time-to-multiple sclerosis diagnosis: A UK Biobank study. Mult Scler 2024; 30:994-1003. [PMID: 38847449 DOI: 10.1177/13524585241257205] [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: 07/31/2024]
Abstract
BACKGROUND Previous investigations into multiple sclerosis (MS) risk factors predominantly relied on retrospective studies, which do not consider different follow-up times and assume a constant risk effect throughout lifetime. OBJECTIVE We aimed to evaluate the impact of genetic and early life factors on MS diagnosis by employing a time-to-event analysis in a prospective cohort. METHODS We used the UK Biobank data, considering the observation period from birth up to 31 December 2022. We considered genetic risk, using a multiple sclerosis polygenic risk score (MS-PRS), and various early life factors. Tobacco smoking and infectious mononucleosis diagnosis were also considered as time-varying variables along the follow-up. Using a Cox proportional hazards model, we examined the associations between these factors and MS diagnosis instantaneous risk. RESULTS We analyzed 345,027 participants, of which 1669 had an MS diagnosis. Our analysis revealed age-dependent effects for sex (females vs males) and higher MS-PRS, with greater hazard ratios observed in young adults. CONCLUSION The age-dependent effects suggest that retrospective studies could have underestimated sex and genetic variants' risk roles during younger ages. Therefore, we emphasize the importance of a time-to-event approach using longitudinal data to better characterize age-dependent risk effects.
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Affiliation(s)
- Andrea Nova
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Giovanni Di Caprio
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Luisa Bernardinelli
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
| | - Teresa Fazia
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
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14
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Papazian I, Kourouvani M, Dagkonaki A, Gouzouasis V, Dimitrakopoulou L, Markoglou N, Badounas F, Tselios T, Anagnostouli M, Probert L. Spontaneous human CD8 T cell and autoimmune encephalomyelitis-induced CD4/CD8 T cell lesions in the brain and spinal cord of HLA-DRB1*15-positive multiple sclerosis humanized immune system mice. eLife 2024; 12:RP88826. [PMID: 38900149 PMCID: PMC11189630 DOI: 10.7554/elife.88826] [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] [Indexed: 06/21/2024] Open
Abstract
Autoimmune diseases of the central nervous system (CNS) such as multiple sclerosis (MS) are only partially represented in current experimental models and the development of humanized immune mice is crucial for better understanding of immunopathogenesis and testing of therapeutics. We describe a humanized mouse model with several key features of MS. Severely immunodeficient B2m-NOG mice were transplanted with peripheral blood mononuclear cells (PBMCs) from HLA-DRB1-typed MS and healthy (HI) donors and showed rapid engraftment by human T and B lymphocytes. Mice receiving cells from MS patients with recent/ongoing Epstein-Barr virus reactivation showed high B cell engraftment capacity. Both HLA-DRB1*15 (DR15) MS and DR15 HI mice, not HLA-DRB1*13 MS mice, developed human T cell infiltration of CNS borders and parenchyma. DR15 MS mice uniquely developed inflammatory lesions in brain and spinal cord gray matter, with spontaneous, hCD8 T cell lesions, and mixed hCD8/hCD4 T cell lesions in EAE immunized mice, with variation in localization and severity between different patient donors. Main limitations of this model for further development are poor monocyte engraftment and lack of demyelination, lymph node organization, and IgG responses. These results show that PBMC humanized mice represent promising research tools for investigating MS immunopathology in a patient-specific approach.
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Affiliation(s)
- Irini Papazian
- Laboratory of Molecular Genetics, Hellenic Pasteur InstituteAthensGreece
| | - Maria Kourouvani
- Laboratory of Molecular Genetics, Hellenic Pasteur InstituteAthensGreece
- Athens International Master’s Programme in Neurosciences, Department of Biology, National and Kapodistrian University of AthensAthensGreece
| | | | - Vasileios Gouzouasis
- Laboratory of Molecular Genetics, Hellenic Pasteur InstituteAthensGreece
- Department of Molecular Biology and Genetics, Democritus University of ThraceAlexandroupolisGreece
| | - Lila Dimitrakopoulou
- Department of Hematology, Laiko General Hospital, National and Kapodistrian University of AthensAthensGreece
| | - Nikolaos Markoglou
- Research Immunogenetics Laboratory, Multiple Sclerosis and Demyelinating Diseases Unit, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, NKUA, Aeginition University HospitalAthensGreece
| | - Fotis Badounas
- Laboratory of Molecular Genetics, Hellenic Pasteur InstituteAthensGreece
- Transgenic Technology Unit, Hellenic Pasteur InstituteAthensGreece
| | | | - Maria Anagnostouli
- Research Immunogenetics Laboratory, Multiple Sclerosis and Demyelinating Diseases Unit, First Department of Neurology, School of Medicine, National and Kapodistrian University of Athens, NKUA, Aeginition University HospitalAthensGreece
| | - Lesley Probert
- Laboratory of Molecular Genetics, Hellenic Pasteur InstituteAthensGreece
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15
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Patel RA, Weiß CL, Zhu H, Mostafavi H, Simons YB, Spence JP, Pritchard JK. Conditional frequency spectra as a tool for studying selection on complex traits in biobanks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.15.599126. [PMID: 38948697 PMCID: PMC11212903 DOI: 10.1101/2024.06.15.599126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. To account for GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insight into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.
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Affiliation(s)
- Roshni A. Patel
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Clemens L. Weiß
- Stanford Cancer Institute Core, Stanford University School of Medicine, Stanford, CA
| | - Huisheng Zhu
- Department of Biology, Stanford University, Stanford, CA
| | - Hakhamanesh Mostafavi
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY
| | | | - Jeffrey P. Spence
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University School of Medicine, Stanford, CA
- Department of Biology, Stanford University, Stanford, CA
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16
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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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17
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Liu Q, Zheng Y, Sturmlechner I, Jain A, Own M, Yang Q, Zhang H, Pinto e Vairo F, Cerosaletti K, Buckner JH, Warrington KJ, Koster MJ, Weyand CM, Goronzy JJ. IKZF1 and UBR4 gene variants drive autoimmunity and Th2 polarization in IgG4-related disease. J Clin Invest 2024; 134:e178692. [PMID: 38885295 PMCID: PMC11324302 DOI: 10.1172/jci178692] [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: 12/26/2023] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
IgG4-related disease (IgG4-RD) is a systemic immune-mediated fibroinflammatory disease whose pathomechanisms remain poorly understood. Here, we identified gene variants in familial IgG4-RD and determined their functional consequences. All 3 affected members of the family shared variants of the transcription factor IKAROS, encoded by IKZF1, and the E3 ubiquitin ligase UBR4. The IKAROS variant increased binding to the FYN promoter, resulting in higher transcription of FYN in T cells. The UBR4 variant prevented the lysosomal degradation of the phosphatase CD45. In the presence of elevated FYN, CD45 functioned as a positive regulatory loop, lowering the threshold for T cell activation. Consequently, T cells from the affected family members were hyperresponsive to stimulation. When transduced with a low-avidity, autoreactive T cell receptor, their T cells responded to the autoantigenic peptide. In parallel, high expression of FYN in T cells biased their differentiation toward Th2 polarization by stabilizing the transcription factor JunB. This bias was consistent with the frequent atopic manifestations in patients with IgG4-RD, including the affected family members in the present study. Building on the functional consequences of these 2 variants, we propose a disease model that is not only instructive for IgG4-RD but also for atopic diseases and autoimmune diseases associated with an IKZF1 risk haplotype.
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Affiliation(s)
| | | | | | | | | | | | | | - Filippo Pinto e Vairo
- Center for Individualized Medicine and Department of Clinical Genomics, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
| | - Karen Cerosaletti
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
| | - Jane H. Buckner
- Center for Translational Immunology, Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
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18
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Salah S, Sadeq YI, Mosaad YM, Elmenshawi IEH, Tawhid ZME. Association of interleukin-17F (rs763780) single nucleotide polymorphism with multiple sclerosis and optic neuritis. Sci Rep 2024; 14:13643. [PMID: 38871733 PMCID: PMC11176185 DOI: 10.1038/s41598-024-62736-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 05/21/2024] [Indexed: 06/15/2024] Open
Abstract
IL-17F single nucleotide polymorphism (SNP) can affect IL-17F expression and activity and this can lead to the increased susceptibility to several autoimmune diseases. The aim was to investigate the association of IL-17F (rs763780) SNP with the development of multiple sclerosis (MS) in a cohort of Egyptian patients and to evaluate the effect of this polymorphism on the disease course. IL-17F (rs763780) gene polymorphisms was typed by TaqMan genotyping assay for 231 Egyptians divided into 102 MS patients and 129 healthy controls with matched age and sex. The IL-17F rs763780 C containing genotypes (CT+CC) and C allele have statistically significant increased frequency in MS patients when compared with controls (p = 0.005 and 0.004 respectively) especially in females' patients (p = 0.005 and 0.006 respectively). The heterozygous CT genotype was associated with the presence of optic neuritis (p = 0.038). The multivariable regression analysis revealed significant associations between smoking, the higher frequency of attacks and the prediction of higher EDSS score (p = 0.032, 0.049 respectively). It can be concluded that the IL-17F rs763780 C containing genotypes (CT and CC) and C allele may be risk factors for the development of MS in the studied Egyptian cohort by a gender-dependent mechanism that contributes to tendency for predisposition in females and optic neuritis is more common in patients carrying the CT heterozygous genotype.
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Affiliation(s)
- Shereen Salah
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Yousra I Sadeq
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Youssef M Mosaad
- Clinical Immunology Unit, Clinical Pathology Department and Mansoura Research Center for Cord Stem Cells (MARC_CSC), Faculty of Medicine, Mansoura University, Mansoura, 35111, Egypt.
| | - Ibrahim E H Elmenshawi
- Neurology Department, Mansoura Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Ziyad M E Tawhid
- Clinical Immunology Unit, Clinical Pathology Department, Faculty of Medicine, Mansoura University, Mansoura, Egypt
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19
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Li L, Zhang M, Gu M, Li J, Li Z, Zhang R, Du C, Lv Y. The causal relationship between autoimmune diseases and age-related macular degeneration: A two-sample mendelian randomization study. PLoS One 2024; 19:e0303170. [PMID: 38857222 PMCID: PMC11164335 DOI: 10.1371/journal.pone.0303170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 04/18/2024] [Indexed: 06/12/2024] Open
Abstract
OBJECTIVE The aim of this study is to investigate the potential causal relationship between autoimmune diseases, including systemic lupus erythematosus, rheumatoid arthritis, inflammatory bowel disease, multiple sclerosis, and Type 1 diabetes, and age-related macular degeneration (AMD). By utilizing the two-sample Mendelian Randomization (MR) approach, we endeavor to address this complex medical issue. METHODS Genome-wide association study (GWAS) data for autoimmune diseases and AMD were obtained from the IEU Open GWAS database and the FinnGen consortium. A series of stringent SNP filtering steps was applied to ensure the reliability of the genetic instruments. MR analyses were conducted using the TwoSampleMR and MR-PRESSO packages in R. The inverse-variance weighted (IVW) method served as the primary analysis, complemented by multiple supplementary analyses and sensitivity tests. RESULTS Within the discovery sample, only a statistically significant inverse causal relationship between multiple sclerosis (MS) and AMD was observed (OR = 0.92, 95% CI: 0.88-0.97, P = 0.003). This finding was confirmed in the replication sample (OR = 0.85, 95% CI: 0.80-0.89, P = 3.32×10-12). No statistically significant associations were detected between systemic lupus erythematosus, rheumatoid arthritis, inflammatory bowel disease, and Type 1 diabetes and AMD. CONCLUSION Strong evidence is provided by this study to support the existence of an inverse causal relationship between multiple sclerosis and age-related macular degeneration. However, no causal evidence was found linking other autoimmune diseases with AMD. These findings not only offer novel insights into the potential etiological mechanisms underlying AMD but also suggest possible directions for future clinical interventions.
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Affiliation(s)
- Linrui Li
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Mingyue Zhang
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Moxiu Gu
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Jun Li
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Zhiyuan Li
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Rong Zhang
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Chuanwang Du
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
| | - Yun Lv
- Department of Ophthalmology, Fushun People’s Hospital, Fushun, China. Sichuan Province, P.R. China
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20
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Chi J, Hu J, Wu N, Cai H, Lin C, Lai Y, Huang J, Li W, Su P, Li M, Xu L. Causal effects for neurodegenerative diseases on the risk of myocardial infarction: a two-sample Mendelian randomization study. Aging (Albany NY) 2024; 16:9944-9958. [PMID: 38850523 PMCID: PMC11210233 DOI: 10.18632/aging.205909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/03/2024] [Indexed: 06/10/2024]
Abstract
Several studies have demonstrated a correlation between neurodegenerative diseases (NDDs) and myocardial infarction (MI), yet the precise causal relationship between these remains elusive. This study aimed to investigate the potential causal associations of genetically predicted Alzheimer's disease (AD), dementia with Lewy bodies (DLB), Parkinson's disease (PD), and multiple sclerosis (MS) with MI using two-sample Mendelian randomization (TSMR). Various methods, including inverse variance weighted (IVW), weighted median (WM), MR-Egger regression, weighted mode, and simple mode, were employed to estimate the effects of genetically predicted NDDs on MI. To validate the analysis, we assessed pleiotropic effects, heterogeneity, and conducted leave-one-out sensitivity analysis. We identified that genetic predisposition to NDDs was suggestively associated with higher odds of MI (OR_IVW=1.07, OR_MR-Egger=1.08, OR_WM=1.07, OR_weighted mode=1.07, OR_simple mode=1.10, all P<0.05). Furthermore, we observed significant associations of genetically predicted DLB with MI (OR_IVW=1.07, OR_MR-Egger=1.11, OR_WM=1.09, OR_weighted mode=1.09, all P<0.05). However, there was no significant causal evidence of genetically predicted PD and MS in MI. Across all MR analyses, no horizontal pleiotropy or statistical heterogeneity was observed (all P>0.05). Additionally, results from MRPRESSO and leave-one-out sensitivity analysis confirmed the robustness of the causal effect estimations for genetically predicted AD, DLB, PD, and MS on MI. This study provides further support for the causal effects of AD on MI and, for the first time, establishes robust causal evidence for the detrimental effect of DLB on the risk of MI. Our findings emphasize the importance of monitoring the cardiovascular function of the elderly experiencing neurodegenerative changes.
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Affiliation(s)
- Jianing Chi
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Jiaman Hu
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Ningxia Wu
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hua Cai
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cailong Lin
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yingying Lai
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- School of Public Health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jianyu Huang
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
| | - Weihua Li
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
| | - Peng Su
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
| | - Min Li
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
| | - Lin Xu
- Department of Geriatric Cardiology, General Hospital of Southern Theater Command, Guangzhou, China
- Branch of National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Cardiac Rehabilitation, Guangzhou, China
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
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21
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Ferrari M, Vecchio D, D’Alfonso S, Gemma A, Marino F, Comi C, Cosentino M. Polymorphisms in the Dopaminergic Receptor D3 Gene Correlate with Disease Progression Rate in Relapsing-Remitting Multiple Sclerosis Patients. Genes (Basel) 2024; 15:736. [PMID: 38927672 PMCID: PMC11203028 DOI: 10.3390/genes15060736] [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: 04/25/2024] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a common chronic autoimmune disease of the central nervous system. In MS, disability progresses unpredictably. Dopamine (DA) is a modulator of immune functions, and compelling evidence supports its involvement in both pathogenesis and treatment of MS. Although single nucleotide polymorphisms (SNPs) in dopaminergic receptor (DR) genes have been extensively studied, their role in MS progression remains unexplored. Therefore, the aim of this explorative study is to investigate the potential association between functional SNPs in DR genes and MS progression. METHODS Caucasian patients with relapsing-remitting (RR) MS were enrolled, and disease progression assessed by the Multiple Sclerosis Severity Score (MSSS). RESULTS Out of the 59 RRMS patients enrolled, those with the G/G genotype for rs6280 and rs1800828 SNPs in DRD3 showed significantly higher MSSSs compared to those with ancestral and heterozygous genotypes. CONCLUSIONS If confirmed in a larger prospective study, the reported findings could contribute to a better understanding of MS pathophysiological mechanisms, opening the way for the identification of marker(s) for assessing MS progression as well as novel therapeutic strategies. A personalized approach to MS management has the potential to improve the overall well-being of MS patients and alleviate the burden on their caregivers.
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Affiliation(s)
- Marco Ferrari
- Center of Research in Medical Pharmacology, University of Insubria, 21100 Varese, Italy; (A.G.); (F.M.); (M.C.)
| | - Domizia Vecchio
- Neurology Unit, Department of Translational Medicine, Maggiore Della Carità Hospital, University of Piemonte Orientale, 28100 Novara, Italy; (D.V.); (C.C.)
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, 28100 Novara, Italy;
| | - Sandra D’Alfonso
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, 28100 Novara, Italy;
- Genetic Laboratory, Department of Translational Medicine, University of Piemonte Orientale (UPO), 28100 Novara, Italy
| | - Alessandra Gemma
- Center of Research in Medical Pharmacology, University of Insubria, 21100 Varese, Italy; (A.G.); (F.M.); (M.C.)
| | - Franca Marino
- Center of Research in Medical Pharmacology, University of Insubria, 21100 Varese, Italy; (A.G.); (F.M.); (M.C.)
| | - Cristoforo Comi
- Neurology Unit, Department of Translational Medicine, Maggiore Della Carità Hospital, University of Piemonte Orientale, 28100 Novara, Italy; (D.V.); (C.C.)
- Department of Health Sciences, Interdisciplinary Research Center of Autoimmune Diseases (IRCAD), University of Piemonte Orientale, 28100 Novara, Italy;
| | - Marco Cosentino
- Center of Research in Medical Pharmacology, University of Insubria, 21100 Varese, Italy; (A.G.); (F.M.); (M.C.)
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22
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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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23
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Wade KJ, Suseno R, Kizer K, Williams J, Boquett J, Caillier S, Pollock NR, Renschen A, Santaniello A, Oksenberg JR, Norman PJ, Augusto DG, Hollenbach JA. MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.20.595060. [PMID: 38826378 PMCID: PMC11142050 DOI: 10.1101/2024.05.20.595060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short read de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target-capture short read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short read data. MHConstructor facilitates wide-spread access to high quality, alignment-free MHC sequence analysis.
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Affiliation(s)
- Kristen J. Wade
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Rayo Suseno
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jacqueline Williams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Juliano Boquett
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stacy Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Nicholas R. Pollock
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Adam Renschen
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Paul J. Norman
- Department of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
- Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Danillo G. Augusto
- Department of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, United States
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, United States
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24
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Winschel I, Willing A, Engler JB, Walkenhorst M, Meurs N, Binkle-Ladisch L, Woo MS, Pfeffer LK, Sonner JK, Borgmeyer U, Hagen SH, Grünhagel B, Claussen JM, Altfeld M, Friese MA. Sex- and species-specific contribution of CD99 to T cell costimulation during multiple sclerosis. Biol Sex Differ 2024; 15:41. [PMID: 38750588 PMCID: PMC11097467 DOI: 10.1186/s13293-024-00618-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Differences in immune responses between women and men are leading to a strong sex bias in the incidence of autoimmune diseases that predominantly affect women, such as multiple sclerosis (MS). MS manifests in more than twice as many women, making sex one of the most important risk factor. However, it is incompletely understood which genes contribute to sex differences in autoimmune incidence. To address that, we conducted a gene expression analysis in female and male human spleen and identified the transmembrane protein CD99 as one of the most significantly differentially expressed genes with marked increase in men. CD99 has been reported to participate in immune cell transmigration and T cell regulation, but sex-specific implications have not been comprehensively investigated. METHODS In this study, we conducted a gene expression analysis in female and male human spleen using the Genotype-Tissue Expression (GTEx) project dataset to identify differentially expressed genes between women and men. After successful validation on protein level of human immune cell subsets, we assessed hormonal regulation of CD99 as well as its implication on T cell regulation in primary human T cells and Jurkat T cells. In addition, we performed in vivo assays in wildtype mice and in Cd99-deficient mice to further analyze functional consequences of differential CD99 expression. RESULTS Here, we found higher CD99 gene expression in male human spleens compared to females and confirmed this expression difference on protein level on the surface of T cells and pDCs. Androgens are likely dispensable as the cause shown by in vitro assays and ex vivo analysis of trans men samples. In cerebrospinal fluid, CD99 was higher on T cells compared to blood. Of note, male MS patients had lower CD99 levels on CD4+ T cells in the CSF, unlike controls. By contrast, both sexes had similar CD99 expression in mice and Cd99-deficient mice showed equal susceptibility to experimental autoimmune encephalomyelitis compared to wildtypes. Functionally, CD99 increased upon human T cell activation and inhibited T cell proliferation after blockade. Accordingly, CD99-deficient Jurkat T cells showed decreased cell proliferation and cluster formation, rescued by CD99 reintroduction. CONCLUSIONS Our results demonstrate that CD99 is sex-specifically regulated in healthy individuals and MS patients and that it is involved in T cell costimulation in humans but not in mice. CD99 could potentially contribute to MS incidence and susceptibility in a sex-specific manner.
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Affiliation(s)
- Ingo Winschel
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Willing
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jan Broder Engler
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mark Walkenhorst
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Meurs
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lars Binkle-Ladisch
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcel S Woo
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lena Kristina Pfeffer
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jana K Sonner
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Uwe Borgmeyer
- Center of Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Hendrik Hagen
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Benjamin Grünhagel
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Janna M Claussen
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Manuel A Friese
- Institute of Neuroimmunology and Multiple Sclerosis, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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25
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Kerns S, Owen KA, Schwalbe D, Grammer AC, Lipsky PE. Examination of the shared genetic architecture between multiple sclerosis and systemic lupus erythematosus facilitates discovery of novel lupus risk loci. Hum Genet 2024; 143:703-719. [PMID: 38609570 DOI: 10.1007/s00439-024-02672-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/24/2024] [Indexed: 04/14/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is an autoimmune disease with heterogeneous manifestations, including neurological and psychiatric symptoms. Genetic association studies in SLE have been hampered by insufficient sample size and limited power compared to many other diseases. Multiple Sclerosis (MS) is a chronic relapsing autoimmune disease of the central nervous system (CNS) that also manifests neurological and immunological features. Here, we identify a method of leveraging large-scale genome wide association studies (GWAS) in MS to identify novel genetic risk loci in SLE. Statistical genetic comparison methods including linkage disequilibrium score regression (LDSC) and cross-phenotype association analysis (CPASSOC) to identify genetic overlap in disease pathophysiology, traditional 2-sample and novel PPI-based mendelian randomization to identify causal associations and Bayesian colocalization were applied to association studies conducted in MS to facilitate discovery in the smaller, more limited datasets available for SLE. Pathway analysis using SNP-to-gene mapping identified biological networks composed of molecular pathways with causal implications for CNS disease in SLE specifically, as well as pathways likely causal of both pathologies, providing key insights for therapeutic selection.
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Affiliation(s)
- Sophia Kerns
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA.
- The RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Dana Schwalbe
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, 22902, USA
- The RILITE Research Institute, Charlottesville, VA, 22902, USA
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26
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Lincoln MR, Connally N, Axisa PP, Gasperi C, Mitrovic M, van Heel D, Wijmenga C, Withoff S, Jonkers IH, Padyukov L, Rich SS, Graham RR, Gaffney PM, Langefeld CD, Vyse TJ, Hafler DA, Chun S, Sunyaev SR, Cotsapas C. Genetic mapping across autoimmune diseases reveals shared associations and mechanisms. Nat Genet 2024; 56:838-845. [PMID: 38741015 DOI: 10.1038/s41588-024-01732-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/21/2024] [Indexed: 05/16/2024]
Abstract
Autoimmune and inflammatory diseases are polygenic disorders of the immune system. Many genomic loci harbor risk alleles for several diseases, but the limited resolution of genetic mapping prevents determining whether the same allele is responsible, indicating a shared underlying mechanism. Here, using a collection of 129,058 cases and controls across 6 diseases, we show that ~40% of overlapping associations are due to the same allele. We improve fine-mapping resolution for shared alleles twofold by combining cases and controls across diseases, allowing us to identify more expression quantitative trait loci driven by the shared alleles. The patterns indicate widespread sharing of pathogenic mechanisms but not a single global autoimmune mechanism. Our approach can be applied to any set of traits and is particularly valuable as sample collections become depleted.
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Affiliation(s)
- Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Division of Neurology at the Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada
| | - Noah Connally
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Mitja Mitrovic
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Faculty of Chemistry and Chemical Engineering, University of Maribor, Maribor, Slovenia
| | - David van Heel
- Blizard Institute, Queen Mary University of London, London, UK
| | - Cisca Wijmenga
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Iris H Jonkers
- Department of Genetics at the University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Leonid Padyukov
- Division of Rheumatology at the Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Robert R Graham
- Maze Therapeutics, South San Francisco, CA, USA
- Genentech, South San Francisco, CA, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, Kings College London, London, UK
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Sung Chun
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Vesalius Therapeutics, Cambridge, MA, USA.
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27
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Li J, Cheng C, Zhang J. Autoimmune diseases and the risk of bladder cancer: A Mendelian randomization analysis. J Autoimmun 2024; 146:103231. [PMID: 38692170 DOI: 10.1016/j.jaut.2024.103231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/25/2024] [Accepted: 04/16/2024] [Indexed: 05/03/2024]
Abstract
OBJECTIVE To investigate the association between autoimmune diseases (AIDs) and bladder cancer (BC) at the genetic level using Mendelian randomization (MR). METHODS Single nucleotide polymorphisms (SNPs) associated with the seven AIDs were extracted from the IEU GWAS database, and the SNPs were quality-controlled using strict screening criteria. The association between AIDs and BC risk was assessed by inverse-variance weighted (IVW), MR-Egger regression and Weighted median method. The heterogeneity of SNPs was evaluated by Cochran Q test. MR-Egger intercept test and MR-PRESSO global test were used to test the horizontal pleiotropy of SNPs. Both sides with potential causal associations were validated using the validation set. RESULTS Our result showed that genetically predicted RA was significantly associated with an increased risk of BC (IVW OR = 1.214, 95 % CI = 1.062-1.388, P = 0.005). MS nominally increased the risk of BC (IVW OR = 1.095, 95 % CI = 1.005-1.193, P = 0.037), consistent with the results of the MR analysis of the BC validation cohort. However SLE, T1D, UC, CD, and MG were not causally associated with BC risk (P > 0.05). The sensitivity analyses showed that there was no heterogeneity or horizontal pleiotropy in our findings. CONCLUSION This study provides evidence of a causal relationship between AIDs and BC risk at the genetic level, confirming a causal relationship between RA and MS in increasing the risk of BC.
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Affiliation(s)
- Jun Li
- Department of Urology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Cui Cheng
- Department of Urology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Jiajun Zhang
- Department of Urology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China.
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28
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Ren R, Jiang J, Li X, Zhang G. Research progress of autoimmune diseases based on induced pluripotent stem cells. Front Immunol 2024; 15:1349138. [PMID: 38720903 PMCID: PMC11076788 DOI: 10.3389/fimmu.2024.1349138] [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: 12/04/2023] [Accepted: 04/12/2024] [Indexed: 05/12/2024] Open
Abstract
Autoimmune diseases can damage specific or multiple organs and tissues, influence the quality of life, and even cause disability and death. A 'disease in a dish' can be developed based on patients-derived induced pluripotent stem cells (iPSCs) and iPSCs-derived disease-relevant cell types to provide a platform for pathogenesis research, phenotypical assays, cell therapy, and drug discovery. With rapid progress in molecular biology research methods including genome-sequencing technology, epigenetic analysis, '-omics' analysis and organoid technology, large amount of data represents an opportunity to help in gaining an in-depth understanding of pathological mechanisms and developing novel therapeutic strategies for these diseases. This paper aimed to review the iPSCs-based research on phenotype confirmation, mechanism exploration, drug discovery, and cell therapy for autoimmune diseases, especially multiple sclerosis, inflammatory bowel disease, and type 1 diabetes using iPSCs and iPSCs-derived cells.
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Affiliation(s)
| | | | | | - Guirong Zhang
- Shandong Yinfeng Academy of Life Science, Jinan, Shandong, China
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29
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Saadh MJ, Ahmed HM, Alani ZK, Al Zuhairi RAH, Almarhoon ZM, Ahmad H, Ubaid M, Alwan NH. The Role of Gut-derived Short-Chain Fatty Acids in Multiple Sclerosis. Neuromolecular Med 2024; 26:14. [PMID: 38630350 DOI: 10.1007/s12017-024-08783-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 03/08/2024] [Indexed: 04/19/2024]
Abstract
Multiple sclerosis (MS) is a chronic condition affecting the central nervous system (CNS), where the interplay of genetic and environmental factors influences its pathophysiology, triggering immune responses and instigating inflammation. Contemporary research has been notably dedicated to investigating the contributions of gut microbiota and their metabolites in modulating inflammatory reactions within the CNS. Recent recognition of the gut microbiome and dietary patterns as environmental elements impacting MS development emphasizes the potential influence of small, ubiquitous molecules from microbiota, such as short-chain fatty acids (SCFAs). These molecules may serve as vital molecular signals or metabolic substances regulating host cellular metabolism in the intricate interplay between microbiota and the host. A current emphasis lies on optimizing the health-promoting attributes of colonic bacteria to mitigate urinary tract issues through dietary management. This review aims to spotlight recent investigations on the impact of SCFAs on immune cells pivotal in MS, the involvement of gut microbiota and SCFAs in MS development, and the considerable influence of probiotics on gastrointestinal disruptions in MS. Comprehending the gut-CNS connection holds promise for the development of innovative therapeutic approaches, particularly probiotic-based supplements, for managing MS.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | - Hani Moslem Ahmed
- Department of Dental Industry Techniques, Al-Noor University College, Nineveh, Iraq
| | - Zaid Khalid Alani
- College of Health and Medical Technical, Al-Bayan University, Baghdad, Iraq
| | | | - Zainab M Almarhoon
- Department of Chemistry, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Hijaz Ahmad
- Section of Mathematics, International Telematic University Uninettuno, Corso Vittorio Emanuele II, 39, 00186, Rome, Italy.
- Center for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Mubarak Al-Abdullah, Kuwait.
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
| | - Mohammed Ubaid
- Medical Technical College, Al-Farahidi University, Baghdad, Iraq
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Yu X, Chen Y, Chen J, Fan Y, Lu H, Wu D, Xu Y. Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis. BMC Med 2024; 22:161. [PMID: 38616254 PMCID: PMC11017616 DOI: 10.1186/s12916-024-03385-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/08/2024] [Indexed: 04/16/2024] Open
Abstract
BACKGROUND To study the shared genetic structure between autoimmune diseases and B-cell acute lymphoblastic leukemia (B-ALL) and identify the shared risk loci and genes and genetic mechanisms involved. METHODS Based on large-scale genome-wide association study (GWAS) summary-level data sets, we observed genetic overlaps between autoimmune diseases and B-ALL, and cross-trait pleiotropic analysis was performed to detect shared pleiotropic loci and genes. A series of functional annotation and tissue-specific analysis were performed to determine the influence of pleiotropic genes. The heritability enrichment analysis was used to detect crucial immune cells and tissues. Finally, bidirectional Mendelian randomization (MR) methods were utilized to investigate the casual associations. RESULTS Our research highlighted shared genetic mechanisms between seven autoimmune disorders and B-ALL. A total of 73 pleiotropic loci were identified at the genome-wide significance level (P < 5 × 10-8), 16 of which had strong evidence of colocalization. We demonstrated that several loci have been previously reported (e.g., 17q21) and discovered some novel loci (e.g., 10p12, 5p13). Further gene-level identified 194 unique pleiotropic genes, for example IKZF1, GATA3, IKZF3, GSDMB, and ORMDL3. Pathway analysis determined the key role of cellular response to cytokine stimulus, B cell activation, and JAK-STAT signaling pathways. SNP-level and gene-level tissue enrichment suggested that crucial role pleiotropic mechanisms involved in the spleen, whole blood, and EBV-transformed lymphocytes. Also, hyprcoloc and stratified LD score regression analyses revealed that B cells at different developmental stages may be involved in mechanisms shared between two different diseases. Finally, two-sample MR analysis determined causal effects of asthma and rheumatoid arthritis on B-ALL. CONCLUSIONS Our research proved shared genetic architecture between autoimmune disorders and B-ALL and shed light on the potential mechanism that might involve in.
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Affiliation(s)
- Xinghao Yu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Yiyin Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China
| | - Jia Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yi Fan
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Huimin Lu
- Department of Outpatient and Emergency, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China.
- Collaborative Innovation Center of Hematology, Institute of Blood and Marrow Transplantation, Soochow University, Suzhou, China.
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases. HGG ADVANCES 2024; 5:100279. [PMID: 38389303 PMCID: PMC10943488 DOI: 10.1016/j.xhgg.2024.100279] [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: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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Su Y, Zhang Y, Chai Y, Xu J. Autoimmune diseases and their genetic link to bronchiectasis: insights from a genetic correlation and Mendelian randomization study. Front Immunol 2024; 15:1343480. [PMID: 38660310 PMCID: PMC11039849 DOI: 10.3389/fimmu.2024.1343480] [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: 11/23/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Background Previous studies have demonstrated that autoimmune diseases are closely associated with bronchiectasis (BE). However, the causal effects between autoimmune diseases and BE remain elusive. Methods All summary-level data were obtained from large-scale Genome-Wide Association Studies (GWAS). The univariate Mendelian randomization (UVMR) was utilized to investigate the genetic causal correlation (rg) of 12 autoimmune diseases and bronchiectasis, The Multivariable Mendelian Randomization (MVMR) method was used to explore the effects of the confounding factors. Further investigation was conducted to identify potential intermediate factors using mediation analysis. Finally, the linkage disequilibrium score regression (LDSC) method was used to identify genetic correlations among complex traits. A series of sensitivity analyses was performed to validate the robustness of the results. Results The LDSC analysis revealed significant genetic correlations between BE and Crohn's disease (CD) (rg = 0.220, P = 0.037), rheumatoid arthritis (RA) (rg = 0.210, P = 0.021), and ulcerative colitis (UC) (rg = 0.247, P = 0.023). However, no genetic correlation was found with other autoimmune diseases (P > 0.05). The results of the primary IVW analysis suggested that for every SD increase in RA, there was a 10.3% increase in the incidence of BE (odds ratio [OR] = 1.103, 95% confidence interval [CI] 1.055-1.154, P = 1.75×10-5, FDR = 5.25×10-5). Furthermore, for every standard deviation (SD) increase in celiac disease (CeD), the incidence of BE reduced by 5.1% (OR = 0.949, 95% CI 0.902-0.999, P = 0.044, FDR = 0.044). We also observed suggestive evidence corresponding to a 3% increase in BE incidence with T1DM (OR = 1.033, 95% CI 1.001-1.066, P = 0.042, FDR = 0.063). Furthermore, MVMR analysis showed that RA was an independent risk factor for BE, whereas mediator MR analysis did not identify any mediating factors. The sensitivity analyses corroborated the robustness of these findings. Conclusion LDSC analysis revealed significant genetic correlations between several autoimmune diseases and BE, and further MVMR analysis showed that RA is an independent risk factor for BE.
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Affiliation(s)
- Yue Su
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Youqian Zhang
- Health Science Center, Yangtze University, Jingzhou, Hubei, China
| | - Yanhua Chai
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jinfu Xu
- Department of Respiratory and Critical Care Medicine, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Gedvilaite G, Pileckaite E, Ramanauskas I, Kriauciuniene L, Balnyte R, Liutkeviciene R. Investigating the Potential Influence of TAS2R16 Genetic Variants and Protein Levels on Multiple Sclerosis Development. J Pers Med 2024; 14:402. [PMID: 38673029 PMCID: PMC11051568 DOI: 10.3390/jpm14040402] [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: 03/07/2024] [Revised: 04/04/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
The study aimed to investigate the association between the TAS2R16 gene (rs860170, rs978739, rs1357949), TAS2R16 serum levels, and multiple sclerosis (MS). A total of 265 healthy control subjects and 218 MS patients were included in the study. Single nucleotide polymorphisms (SNPs) were tested by real-time polymerase chain reaction (RT-PCR). The serum concentration of TAS2R16 was measured using the ELISA method. Analyses revealed that the TAS2R16 rs860170 TT genotype was statistically significantly less frequent in the MS group than in the control group (p = 0.041), and the CC genotype was statistically significantly more frequent in the MS group than in the control group (p < 0.001). In the most robust (codominant) model, the CC genotype was found to increase the odds of MS by ~27-fold (p = 0.002), and each C allele increased the odds of MS by 1.8-fold (p < 0.001). Haplotype analysis of the rs860170, rs978739, and rs1357949 polymorphisms showed that the C-C-A haplotype was associated with a ~12-fold increased odds of MS occurrence (p = 0.02). Serum TAS2R16 levels were elevated in the MS group compared to control subjects (p = 0.014). Conclusions: The rs860170, rs978739, and rs1357949 polymorphisms demonstrated that the C-C-A haplotype and elevated TAS2R16 serum levels can promote the development of MS. These preliminary findings underscore the importance of specific genetic variants, such as rs860170, rs978739, and rs1357949, in MS risk. Additionally, elevated TAS2R16 serum levels in MS patients suggest a potential role in MS pathogenesis. These findings provide insights into the genetic and molecular mechanisms underlying MS and pave the way for personalized diagnostic and therapeutic strategies. Integrating genetic and serum biomarker data in MS research offers promising avenues for improving clinical outcomes and advancing precision medicine approaches in the future.
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Affiliation(s)
- Greta Gedvilaite
- Neuroscience Institute, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (G.G.); (L.K.); (R.L.)
- Medical Faculty, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Enrika Pileckaite
- Neuroscience Institute, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (G.G.); (L.K.); (R.L.)
- Medical Faculty, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Ignas Ramanauskas
- Medical Faculty, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Loresa Kriauciuniene
- Neuroscience Institute, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (G.G.); (L.K.); (R.L.)
| | - Renata Balnyte
- Department of Neurology, Medical Academy, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania;
| | - Rasa Liutkeviciene
- Neuroscience Institute, Lithuanian University of Health Sciences, LT-50161 Kaunas, Lithuania; (G.G.); (L.K.); (R.L.)
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Wang Z, Guo Z, Wang X, Chen F, Wang Z, Wang Z. ASSESSING THE CAUSAL RELATIONSHIP BETWEEN SEPSIS AND AUTOIMMUNE: A MENDELIAN RANDOMIZATION STUDY. Shock 2024; 61:564-569. [PMID: 37856654 DOI: 10.1097/shk.0000000000002246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
ABSTRACT Objective : Numerous epidemiological studies have identified a potential link between sepsis and a variety of autoimmune disorders. The primary objective of this study is to delve deeper into this connection, investigating the potential causal relationship between sepsis and autoimmune disorders through the application of Mendelian randomization (MR). Methods : To assess the potential genetic impact on sepsis risk relating to susceptibility toward immune-related outcomes, we used summary data from the largest European genome-wide association studies (GWAS) on these conditions using a two-sample MR framework. Single nucleotide polymorphisms-which had strong associations with the nine traits-were extracted from the GWAS and examined their effects in an extensive European sepsis GWAS (486,484 cases and 474,841 controls). We used inverse-variance weighted MR, weighted median, and MR Egger for analyses, supplementing these with sensitivity analyses and assessing level pleiotropy using MR methodologies. We also executed a reverse MR analysis to test sepsis' causal effects on the designated autoimmune traits. Results : With primary sclerosing cholangitis being the exception, our MR analysis suggests that susceptibility toward most autoimmune diseases does not affect sepsis risks. The reverse MR analysis did not validate any influence of sepsis susceptibility over other autoimmune diseases. Our primary inverse-variance weighted MR analysis outcomes found general confirmation through our sensitivity MR examinations. Variance in the exposures, as dictated by the single nucleotide polymorphism sets used as MR instruments, ranged between 4.88 × 10 -5 to 0.005. Conclusion : Our MR research, centered on a European population, does not validate a correlation between susceptibility to the majority of autoimmune disorders and sepsis risk. Associations discerned in epidemiological studies may owe partly to shared biological or environmental confounders. The risk susceptibility for primary sclerosing cholangitis does relate to sepsis risk, opening doors for personalized precision treatments in the future.
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Affiliation(s)
- Ziyi Wang
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People's Republic of China
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35
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Caldwell BA, Li L. Epigenetic regulation of innate immune dynamics during inflammation. J Leukoc Biol 2024; 115:589-606. [PMID: 38301269 PMCID: PMC10980576 DOI: 10.1093/jleuko/qiae026] [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: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.
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Affiliation(s)
- Blake A. Caldwell
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
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36
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Dressman D, Tasaki S, Yu L, Schneider J, Bennett DA, Elyaman W, Vardarajan B. Polygenic risk associated with Alzheimer's disease and other traits influences genes involved in T cell signaling and activation. Front Immunol 2024; 15:1337831. [PMID: 38590520 PMCID: PMC10999606 DOI: 10.3389/fimmu.2024.1337831] [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: 11/13/2023] [Accepted: 02/22/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction T cells, known for their ability to respond to an enormous variety of pathogens and other insults, are increasingly recognized as important mediators of pathology in neurodegeneration and other diseases. T cell gene expression phenotypes can be regulated by disease-associated genetic variants. Many complex diseases are better represented by polygenic risk than by individual variants. Methods We first compute a polygenic risk score (PRS) for Alzheimer's disease (AD) using genomic sequencing data from a cohort of Alzheimer's disease (AD) patients and age-matched controls, and validate the AD PRS against clinical metrics in our cohort. We then calculate the PRS for several autoimmune disease, neurological disorder, and immune function traits, and correlate these PRSs with T cell gene expression data from our cohort. We compare PRS-associated genes across traits and four T cell subtypes. Results Several genes and biological pathways associated with the PRS for these traits relate to key T cell functions. The PRS-associated gene signature generally correlates positively for traits within a particular category (autoimmune disease, neurological disease, immune function) with the exception of stroke. The trait-associated gene expression signature for autoimmune disease traits was polarized towards CD4+ T cell subtypes. Discussion Our findings show that polygenic risk for complex disease and immune function traits can have varying effects on T cell gene expression trends. Several PRS-associated genes are potential candidates for therapeutic modulation in T cells, and could be tested in in vitro applications using cells from patients bearing high or low polygenic risk for AD or other conditions.
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Affiliation(s)
- Dallin Dressman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Shinya Tasaki
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Julie Schneider
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
- Department of Pathology, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Wassim Elyaman
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Badri Vardarajan
- Department of Neurology, Columbia University, New York, NY, United States
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University, New York, NY, United States
- College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, The Gertrude H. Sergievsky Center, New York, NY, United States
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Caratis F, Opiełka M, Hausmann M, Velasco-Estevez M, Rojek B, de Vallière C, Seuwen K, Rogler G, Karaszewski B, Rutkowska A. The proton-sensing receptors TDAG8 and GPR4 are differentially expressed in human and mouse oligodendrocytes: Exploring their role in neuroinflammation and multiple sclerosis. PLoS One 2024; 19:e0283060. [PMID: 38527054 PMCID: PMC10962805 DOI: 10.1371/journal.pone.0283060] [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: 02/27/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Acidosis is one of the hallmarks of demyelinating central nervous system (CNS) lesions in multiple sclerosis (MS). The response to acidic pH is primarily mediated by a family of G protein-coupled proton-sensing receptors: OGR1, GPR4 and TDAG8. These receptors are inactive at alkaline pH, reaching maximal activation at acidic pH. Genome-wide association studies have identified a locus within the TDAG8 gene associated with several autoimmune diseases, including MS. Accordingly, we here found that expression of TDAG8, as opposed to GPR4 or OGR1, is upregulated in MS plaques. This led us to investigate the expression of TDAG8 in oligodendrocytes using mouse and human in vitro and in vivo models. We observed significant upregulation of TDAG8 in human MO3.13 oligodendrocytes during maturation and in response to acidic conditions. However, its deficiency did not impact normal myelination in the mouse CNS, and its expression remained unaltered under demyelinating conditions in mouse organotypic cerebellar slices. Notably, our data revealed no expression of TDAG8 in primary mouse oligodendrocyte progenitor cells (OPCs), in contrast to its expression in primary human OPCs. Our investigations have revealed substantial species differences in the expression of proton-sensing receptors in oligodendrocytes, highlighting the limitations of the employed experimental models in fully elucidating the role of TDAG8 in myelination and oligodendrocyte biology. Consequently, the study does not furnish robust evidence for the role of TDAG8 in such processes. Nonetheless, our findings tentatively point towards a potential association between TDAG8 and myelination processes in humans, hinting at a potential link between TDAG8 and the pathophysiology of MS and warrants further research.
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Affiliation(s)
- Fionä Caratis
- Brain Diseases Centre, Medical University of Gdansk, Gdansk, Poland
- Department of Anatomy and Neurobiology, Medical University of Gdansk, Gdansk, Poland
| | - Mikołaj Opiełka
- Brain Diseases Centre, Medical University of Gdansk, Gdansk, Poland
| | - Martin Hausmann
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Maria Velasco-Estevez
- H12O-CNIO Hematological Malignancies Group, Clinical Research Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain
| | - Bartłomiej Rojek
- Department of Adult Neurology, Medical University of Gdansk & University Clinical Centre, Gdansk, Poland
| | - Cheryl de Vallière
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Klaus Seuwen
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Bartosz Karaszewski
- Brain Diseases Centre, Medical University of Gdansk, Gdansk, Poland
- Department of Adult Neurology, Medical University of Gdansk & University Clinical Centre, Gdansk, Poland
| | - Aleksandra Rutkowska
- Brain Diseases Centre, Medical University of Gdansk, Gdansk, Poland
- Department of Anatomy and Neurobiology, Medical University of Gdansk, Gdansk, Poland
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Andorra M, Freire A, Zubizarreta I, de Rosbo NK, Bos SD, Rinas M, Høgestøl EA, de Rodez Benavent SA, Berge T, Brune-Ingebretse S, Ivaldi F, Cellerino M, Pardini M, Vila G, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer S, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Brandt A, Saez-Rodriguez J, Alexopoulos LG, Paul F, Harbo HF, Shams H, Oksenberg J, Uccelli A, Baeza-Yates R, Villoslada P. Predicting disease severity in multiple sclerosis using multimodal data and machine learning. J Neurol 2024; 271:1133-1149. [PMID: 38133801 PMCID: PMC10896787 DOI: 10.1007/s00415-023-12132-z] [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: 06/24/2023] [Revised: 10/28/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Multiple sclerosis patients would benefit from machine learning algorithms that integrates clinical, imaging and multimodal biomarkers to define the risk of disease activity. METHODS We have analysed a prospective multi-centric cohort of 322 MS patients and 98 healthy controls from four MS centres, collecting disability scales at baseline and 2 years later. Imaging data included brain MRI and optical coherence tomography, and omics included genotyping, cytomics and phosphoproteomic data from peripheral blood mononuclear cells. Predictors of clinical outcomes were searched using Random Forest algorithms. Assessment of the algorithm performance was conducted in an independent prospective cohort of 271 MS patients from a single centre. RESULTS We found algorithms for predicting confirmed disability accumulation for the different scales, no evidence of disease activity (NEDA), onset of immunotherapy and the escalation from low- to high-efficacy therapy with intermediate to high-accuracy. This accuracy was achieved for most of the predictors using clinical data alone or in combination with imaging data. Still, in some cases, the addition of omics data slightly increased algorithm performance. Accuracies were comparable in both cohorts. CONCLUSION Combining clinical, imaging and omics data with machine learning helps identify MS patients at risk of disability worsening.
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Affiliation(s)
- Magi Andorra
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Ana Freire
- School of Management, Pompeu Fabra University, Barcelona, Spain
- UPF Barcelona School of Management, Balmes 132, 08008, Barcelona, Spain
| | - Irati Zubizarreta
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Nicole Kerlero de Rosbo
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Steffan D Bos
- University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Melanie Rinas
- Institute for Computational Biomedicine, Heidelberg University Hospital, and Heidelberg University, Heidelberg, Germany
| | - Einar A Høgestøl
- University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | | | - Tone Berge
- Oslo University Hospital, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | | | - Federico Ivaldi
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Maria Cellerino
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Matteo Pardini
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gemma Vila
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Irene Pulido-Valdeolivas
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Elena H Martinez-Lapiscina
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Sara Llufriu
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Albert Saiz
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Yolanda Blanco
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Eloy Martinez-Heras
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | - Elisabeth Solana
- Institut d'Investigacions Biomediques August Pi Sunyer (IDIBAPS) and Hospital Clinic Barcelona, Barcelona, Spain
| | | | | | | | - Susanna Asseyer
- Charité Universitaetsmedizin Berlin, Berlin, Germany
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | | | - Claudia Chien
- Charité Universitaetsmedizin Berlin, Berlin, Germany
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Hanna Zimmermann
- Charité Universitaetsmedizin Berlin, Berlin, Germany
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | | | | | - Alex Brandt
- Charité Universitaetsmedizin Berlin, Berlin, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Heidelberg University Hospital, and Heidelberg University, Heidelberg, Germany
| | - Leonidas G Alexopoulos
- ProtATonce Ltd, Athens, Greece
- School of Mechanical Engineering, National Technical University of Athens, Zografou, Greece
| | - Friedemann Paul
- Charité Universitaetsmedizin Berlin, Berlin, Germany
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Hanne F Harbo
- University of Oslo, Oslo, Norway
- Oslo University Hospital, Oslo, Norway
| | - Hengameh Shams
- Department of Neurology, University of California, San Francisco, USA
| | - Jorge Oksenberg
- Department of Neurology, University of California, San Francisco, USA
| | - Antonio Uccelli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Pablo Villoslada
- Department of Medicine and Life Sciences, Pompeu Fabra University, Barcelona, Spain.
- Hospital del Mar Research Institute, Barcelona, Spain.
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Binder MD, Nwoke EC, Morwitch E, Dwyer C, Li V, Xavier A, Lea RA, Lechner-Scott J, Taylor BV, Ponsonby AL, Kilpatrick TJ. HLA-DRB1*15:01 and the MERTK Gene Interact to Selectively Influence the Profile of MERTK-Expressing Monocytes in Both Health and MS. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200190. [PMID: 38150649 PMCID: PMC10752576 DOI: 10.1212/nxi.0000000000200190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/31/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND AND OBJECTIVES HLA-DRB1*15:01 (DR15) and MERTK are 2 risk genes for multiple sclerosis (MS). The variant rs7422195 is an expression quantitative trait locus for MERTK in CD14+ monocytes; cells with phagocytic and immunomodulatory potential. We aimed to understand how drivers of disease risk and pathogenesis vary with HLA and MERTK genotype and disease activity. METHODS We investigated how proportions of monocytes vary with HLA and MERTK genotype and disease activity in MS. CD14+ monocytes were isolated from patients with MS at relapse (n = 40) and 3 months later (n = 23). Healthy controls (HCs) underwent 2 blood collections 3 months apart. Immunophenotypic profiling of monocytes was performed by flow cytometry. Methylation of 35 CpG sites within and near the MERTK gene was assessed in whole blood samples of individuals experiencing their first episode of clinical CNS demyelination (n = 204) and matched HCs (n = 345) using an Illumina EPIC array. RESULTS DR15-positive patients had lower proportions of CD14+ MERTK+ monocytes than DR15-negative patients, independent of genotype at the MERTK SNP rs7422195. Proportions of CD14+ MERTK+ monocytes were further reduced during relapse in DR15-positive but not DR15-negative patients. Patients homozygous for the major G allele at rs7422195 exhibited higher proportions of CD14+ MERTK+ monocytes at both relapse and remission compared with controls. We observed that increased methylation of the MERTK gene was significantly associated with the presence of DR15. DISCUSSION DR15 and MERTK genotype independently influence proportions of CD14+ MERTK+ monocytes in MS. We confirmed previous observations that the MERTK risk SNP rs7422195 is associated with altered MERTK expression in monocytes. We identified that expression of MERTK is stratified by disease in people homozygous for the major G allele of rs7422195. The finding that the proportion of CD14+ MERTK+ monocytes is reduced in DR15-positive individuals supports prior data identifying genetic links between these 2 loci in influencing MS risk. DR15 genotype-dependent alterations in methylation of the MERTK gene provides a molecular link between these loci and identifies a potential mechanism by which MERTK expression is influenced by DR15. This links DR15 haplotype to MS susceptibility beyond direct influence on antigen presentation and suggests the need for HLA-based stratification of approaches to MERTK as a therapeutic target.
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Affiliation(s)
- Michele D Binder
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Eze C Nwoke
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Ellen Morwitch
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Chris Dwyer
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Vivien Li
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Alexandre Xavier
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Rodney A Lea
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Jeannette Lechner-Scott
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Bruce V Taylor
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Anne-Louise Ponsonby
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
| | - Trevor J Kilpatrick
- From the Florey Institute of Neuroscience and Mental Health (M.D.B., E.C.N., E.M., C.D., V.L., A.-L.P., T.J.K.); Department of Anatomy and Physiology (M.D.B.), University of Melbourne, Parkville; Crux Biolabs (E.C.N.), Bayswater; Department of Neurology (C.D.), Royal Melbourne Hospital, Parkville; Department of Neurology (A.X., J.L.-S.), John Hunter Hospital, Newcastle; Hunter Medical Research Institute (A.X., J.L.-S.), University of Newcastle, New South Wales Genomics Research Centre (R.A.L.), Centre of Genomics and Personalised Health, Queensland University of Technology; and Menzies Institute for Medical Research (B.V.T.), University of Tasmania, Hobart, Australia
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Hawiger D. Emerging T cell immunoregulatory mechanisms in multiple sclerosis and Alzheimer's disease. Front Aging Neurosci 2024; 16:1350240. [PMID: 38435400 PMCID: PMC10904586 DOI: 10.3389/fnagi.2024.1350240] [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: 12/05/2023] [Accepted: 01/31/2024] [Indexed: 03/05/2024] Open
Abstract
Multiple sclerosis (MS) and Alzheimer's disease (AD) are neuroinflammatory and neurodegenerative diseases with considerable socioeconomic impacts but without definitive treatments. AD and MS have multifactorial pathogenesis resulting in complex cognitive and neurologic symptoms and growing evidence also indicates key functions of specific immune cells. Whereas relevant processes dependent on T cells have been elucidated in both AD and MS, mechanisms that can control such immune responses still remain elusive. Here, a brief overview of select recent findings clarifying immunomodulatory mechanisms specifically induced by tolerogenic dendritic cells to limit the activation and functions of neurodegenerative T cells is presented. These insights could become a foundation for new cutting-edge research as well as therapeutic strategies.
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Affiliation(s)
- Daniel Hawiger
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, United States
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Min H, O’Neil SM, Xu L, Moseman EA, Kurtzberg J, Filiano AJ. Mural cells interact with macrophages in the dura mater to regulate CNS immune surveillance. J Exp Med 2024; 221:e20230326. [PMID: 38193859 PMCID: PMC10783178 DOI: 10.1084/jem.20230326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 09/07/2023] [Accepted: 12/13/2023] [Indexed: 01/10/2024] Open
Abstract
The central nervous system (CNS) tightly regulates access of circulating immune cells. Immunosurveillance is therefore managed in the meninges at the borders of the CNS. Here, we demonstrated that mural cells, which include pericytes and smooth muscle cells, decreased coverage around blood vessels in the dura, the outermost layer of the meninges, and upregulated gene pathways involved in leukocyte migration in presymptomatic experimental autoimmune encephalomyelitis (EAE). Partially depleting mural cells promoted the trafficking of CNS antigen-specific T cells to the dura in a process that depended on resident antigen-presenting cells, thereby increasing susceptibility to passive EAE. Mechanistically, mural cells physically contacted macrophages in the dura and transferred cytoplasmic components, including processing bodies (RNA granules shown to reprogram transcriptomes), which were critical to suppress antigen-dependent T helper (TH) cell activation and TH17 differentiation. Our study revealed a mechanism by which mural cell-macrophage interactions regulate the trafficking of CNS antigen-specific T cells to the dura.
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Affiliation(s)
- Hyunjung Min
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Shane M. O’Neil
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC, USA
| | - Li Xu
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC, USA
| | - E. Ashley Moseman
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Joanne Kurtzberg
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC, USA
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Anthony J. Filiano
- Marcus Center for Cellular Cures, Duke University School of Medicine, Durham, NC, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
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Qiu X, Huang MN, Ping S. Genetic susceptibility and causal pathway analysis of eye disorders coexisting in multiple sclerosis. Front Immunol 2024; 15:1337528. [PMID: 38375484 PMCID: PMC10875133 DOI: 10.3389/fimmu.2024.1337528] [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: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/21/2024] Open
Abstract
Introduction The comorbidity of optic neuritis with multiple sclerosis has been well recognized. However, the causal association between multiple sclerosis and optic neuritis, as well as other eye disorders, remains incompletely understood. To address these gaps, we investigated the genetically relationship between multiple sclerosis and eye disorders, and explored potential drugs. Methods In order to elucidate the genetic susceptibility and causal links between multiple sclerosis and eye disorders, we performed two-sample Mendelian randomization analyses to examine the causality between multiple sclerosis and eye disorders. Additionally, causal single-nucleotide polymorphisms were annotated and searched for expression quantitative trait loci data. Pathway enrichment analysis was performed to identify the possible mechanisms responsible for the eye disorders coexisting with multiple sclerosis. Potential therapeutic chemicals were also explored using the Cytoscape. Results Mendelian randomization analysis revealed that multiple sclerosis increased the incidence of optic neuritis while reducing the likelihood of concurrent of cataract and macular degeneration. Gene Ontology enrichment analysis implicated that lymphocyte proliferation, activation and antigen processing as potential contributors to the pathogenesis of eye disorders coexisting with multiple sclerosis. Furthermore, pharmaceutical agents traditionally employed for allograft rejection exhibited promising therapeutic potential for the eye disorders coexisting with multiple sclerosis. Discussion Multiple sclerosis genetically contributes to the development of optic neuritis while mitigating the concurrent occurrence of cataract and macular degeneration. Further research is needed to validate these findings and explore additional mechanisms underlying the comorbidity of multiple sclerosis and eye disorders.
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Affiliation(s)
- Xuecheng Qiu
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Research Center for Biochemistry and Molecular Biology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Mi Ni Huang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, China
| | - Suning Ping
- Department of Histology and Embryology, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, China
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Shenzhen, Guangdong, China
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Kennedy KE, Kerlero de Rosbo N, Uccelli A, Cellerino M, Ivaldi F, Contini P, De Palma R, Harbo HF, Berge T, Bos SD, Høgestøl EA, Brune-Ingebretsen S, de Rodez Benavent SA, Paul F, Brandt AU, Bäcker-Koduah P, Behrens J, Kuchling J, Asseyer S, Scheel M, Chien C, Zimmermann H, Motamedi S, Kauer-Bonin J, Saez-Rodriguez J, Rinas M, Alexopoulos LG, Andorra M, Llufriu S, Saiz A, Blanco Y, Martinez-Heras E, Solana E, Pulido-Valdeolivas I, Martinez-Lapiscina EH, Garcia-Ojalvo J, Villoslada P. Multiscale networks in multiple sclerosis. PLoS Comput Biol 2024; 20:e1010980. [PMID: 38329927 PMCID: PMC10852301 DOI: 10.1371/journal.pcbi.1010980] [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: 02/25/2023] [Accepted: 12/12/2023] [Indexed: 02/10/2024] Open
Abstract
Complex diseases such as Multiple Sclerosis (MS) cover a wide range of biological scales, from genes and proteins to cells and tissues, up to the full organism. In fact, any phenotype for an organism is dictated by the interplay among these scales. We conducted a multilayer network analysis and deep phenotyping with multi-omics data (genomics, phosphoproteomics and cytomics), brain and retinal imaging, and clinical data, obtained from a multicenter prospective cohort of 328 patients and 90 healthy controls. Multilayer networks were constructed using mutual information for topological analysis, and Boolean simulations were constructed using Pearson correlation to identified paths within and among all layers. The path more commonly found from the Boolean simulations connects protein MK03, with total T cells, the thickness of the retinal nerve fiber layer (RNFL), and the walking speed. This path contains nodes involved in protein phosphorylation, glial cell differentiation, and regulation of stress-activated MAPK cascade, among others. Specific paths identified were subsequently analyzed by flow cytometry at the single-cell level. Combinations of several proteins (GSK3AB, HSBP1 or RS6) and immune cells (Th17, Th1 non-classic, CD8, CD8 Treg, CD56 neg, and B memory) were part of the paths explaining the clinical phenotype. The advantage of the path identified from the Boolean simulations is that it connects information about these known biological pathways with the layers at higher scales (retina damage and disability). Overall, the identified paths provide a means to connect the molecular aspects of MS with the overall phenotype.
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Affiliation(s)
- Keith E. Kennedy
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nicole Kerlero de Rosbo
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
- TomaLab, Institute of Nanotechnology, Consiglio Nazionale delle Ricerche (CNR), Rome, Italy
| | - Antonio Uccelli
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Maria Cellerino
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Federico Ivaldi
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Paola Contini
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Raffaele De Palma
- Department of Neurology, Ospedale Policlinico San Martino-IRCCS and Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa Italy
| | - Hanne F. Harbo
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Oslo Metropolitan University, Oslo, Norway
| | - Steffan D. Bos
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Einar A. Høgestøl
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Synne Brune-Ingebretsen
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Sigrid A. de Rodez Benavent
- Department of Neurology, University of Oslo, Oslo, Norway
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Friedemann Paul
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Alexander U. Brandt
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
- Department of Neurology, University of California, Irvine, California, United States of America
| | - Priscilla Bäcker-Koduah
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Janina Behrens
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Joseph Kuchling
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Susanna Asseyer
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Michael Scheel
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Claudia Chien
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Hanna Zimmermann
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Seyedamirhosein Motamedi
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Josef Kauer-Bonin
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, and Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Melanie Rinas
- Institute for Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Leonidas G. Alexopoulos
- ProtATonce Ltd, Athens, Greece
- School of Mechanical Engineering, National Technical University of Athens, Zografou, Greece
| | - Magi Andorra
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Sara Llufriu
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Albert Saiz
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Yolanda Blanco
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Eloy Martinez-Heras
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elisabeth Solana
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Irene Pulido-Valdeolivas
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Elena H. Martinez-Lapiscina
- Center of Neuroimmunology, Hospital Clinic Barcelona, and Institut d’Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Pablo Villoslada
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
- Department of Neurology, Hospital del Mar Research Institute, Barcelona, Spain
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Ishikawa Y, Tanaka N, Asano Y, Kodera M, Shirai Y, Akahoshi M, Hasegawa M, Matsushita T, Saito K, Motegi SI, Yoshifuji H, Yoshizaki A, Kohmoto T, Takagi K, Oka A, Kanda M, Tanaka Y, Ito Y, Nakano K, Kasamatsu H, Utsunomiya A, Sekiguchi A, Niiro H, Jinnin M, Makino K, Makino T, Ihn H, Yamamoto M, Suzuki C, Takahashi H, Nishida E, Morita A, Yamamoto T, Fujimoto M, Kondo Y, Goto D, Sumida T, Ayuzawa N, Yanagida H, Horita T, Atsumi T, Endo H, Shima Y, Kumanogoh A, Hirata J, Otomo N, Suetsugu H, Koike Y, Tomizuka K, Yoshino S, Liu X, Ito S, Hikino K, Suzuki A, Momozawa Y, Ikegawa S, Tanaka Y, Ishikawa O, Takehara K, Torii T, Sato S, Okada Y, Mimori T, Matsuda F, Matsuda K, Amariuta T, Imoto I, Matsuo K, Kuwana M, Kawaguchi Y, Ohmura K, Terao C. GWAS for systemic sclerosis identifies six novel susceptibility loci including one in the Fcγ receptor region. Nat Commun 2024; 15:319. [PMID: 38296975 PMCID: PMC10830486 DOI: 10.1038/s41467-023-44541-z] [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: 03/20/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
Here we report the largest Asian genome-wide association study (GWAS) for systemic sclerosis performed to date, based on data from Japanese subjects and comprising of 1428 cases and 112,599 controls. The lead SNP is in the FCGR/FCRL region, which shows a penetrating association in the Asian population, while a complete linkage disequilibrium SNP, rs10917688, is found in a cis-regulatory element for IRF8. IRF8 is also a significant locus in European GWAS for systemic sclerosis, but rs10917688 only shows an association in the presence of the risk allele of IRF8 in the Japanese population. Further analysis shows that rs10917688 is marked with H3K4me1 in primary B cells. A meta-analysis with a European GWAS detects 30 additional significant loci. Polygenic risk scores constructed with the effect sizes of the meta-analysis suggest the potential portability of genetic associations beyond populations. Prioritizing the top 5% of SNPs of IRF8 binding sites in B cells improves the fitting of the polygenic risk scores, underscoring the roles of B cells and IRF8 in the development of systemic sclerosis. The results also suggest that systemic sclerosis shares a common genetic architecture across populations.
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Affiliation(s)
- Yuki Ishikawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Nao Tanaka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
- Department of Rheumatology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoshihide Asano
- Department of Dermatology, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Masanari Kodera
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yuichiro Shirai
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Mitsuteru Akahoshi
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
- Department of Rheumatology, Saga University Hospital, Saga, Japan
| | - Minoru Hasegawa
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Takashi Matsushita
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Kazuyoshi Saito
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Sei-Ichiro Motegi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ayumi Yoshizaki
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Kohmoto
- Aichi Cancer Center Research Institute, Division of Molecular Genetics, Nagoya, Japan
| | - Kae Takagi
- Tokyo Women's Medical University, Adachi Medical Center, Tokyo, Japan
| | - Akira Oka
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Miho Kanda
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yoshihito Tanaka
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Yumi Ito
- Department of Dermatology, Chukyo Hospital, Japan Community Health Care Organization, Nagoya, Japan
| | - Kazuhisa Nakano
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Hiroshi Kasamatsu
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Akira Utsunomiya
- Faculty of Medical Sciences, Department of Dermatology, University of Fukui, Fukui, Japan
| | - Akiko Sekiguchi
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Hiroaki Niiro
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Masatoshi Jinnin
- Department of Dermatology, Wakayama Medical University Graduate School of Medicine, Wakayama, Japan
| | - Katsunari Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takamitsu Makino
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hironobu Ihn
- Department of Dermatology and Plastic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Motohisa Yamamoto
- Department of Rheumatology and Allergy, IMSUT Hospital, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Chisako Suzuki
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroki Takahashi
- Department of Rheumatology and Clinical Immunology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Emi Nishida
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
- Department of Dermatology, Okazaki City Hospital, Okazaki, Japan
| | - Akimichi Morita
- Department of Geriatric and Environmental Dermatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Toshiyuki Yamamoto
- Department of Dermatology, Fukushima Medical University, School of Medicine, Fukushima, Japan
| | - Manabu Fujimoto
- Department of Dermatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuya Kondo
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Daisuke Goto
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takayuki Sumida
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naho Ayuzawa
- Department of Clinical Immunology, National Hospital Organization, Utano National Hospital, Kyoto, Japan
| | - Hidetoshi Yanagida
- Department of Clinical Immunology, National Hospital Organization, Utano National Hospital, Kyoto, Japan
| | - Tetsuya Horita
- Faculty of Medicine and Graduate School of Medicine, Department of Rheumatology, Endocrinology and Nephrology, Hokkaido University, Sapporo, Japan
| | - Tatsuya Atsumi
- Faculty of Medicine and Graduate School of Medicine, Department of Rheumatology, Endocrinology and Nephrology, Hokkaido University, Sapporo, Japan
| | - Hirahito Endo
- Omori Medical Center, Toho University, Rheumatic Disease Center, Tokyo, Japan
| | - Yoshihito Shima
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jun Hirata
- Immunology Frontier Center, Osaka University, Statistical Immunology, Osaka, Japan
| | - Nao Otomo
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Hiroyuki Suetsugu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Yoshinao Koike
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Kohei Tomizuka
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Soichiro Yoshino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Shuji Ito
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan
| | - Keiko Hikino
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Pharmacogenomics, Yokohama, Japan
| | - Akari Suzuki
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Autoimmune Diseases, Yokohama, Japan
| | - Yukihide Momozawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Genotyping Development, Yokohama, Japan
| | - Shiro Ikegawa
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Bone and Joint Diseases, Yokohama, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Osamu Ishikawa
- Department of Dermatology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kazuhiko Takehara
- Department of Dermatology, Faculty of Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Shinichi Sato
- Department of Dermatology, The University of Tokyo, Tokyo, Japan
| | - Yukinori Okada
- Immunology Frontier Center, Osaka University, Statistical Immunology, Osaka, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Ijinkai Takeada General Hospital, Kyoto, Japan
| | - Fumihiko Matsuda
- Graduate School of Medicine, Kyoto University, Center for Genomic Medicine, Kyoto, Japan
| | - Koichi Matsuda
- Institute of Medical Science, The University of Tokyo, Laboratory of Genome Technology, Human Genome Center, Tokyo, Japan
- Department of Computational Biology and Medical Sciences, Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Graduate School of Arts and Sciences, Harvard University, Cambridge, MA, USA
| | - Issei Imoto
- Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Keitaro Matsuo
- Aichi Cancer Center Research Institute, Division of Cancer Epidemiology and Prevention, Nagoya, Japan
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, Tokyo, Japan
| | - Yasushi Kawaguchi
- Tokyo Women's Medical University, Division of Rheumatology, Department of Internal Medicine, Tokyo, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, The Laboratory for Statistical and Translational Genetics, Yokohama, Japan.
- Shizuoka General Hospital, The Clinical Research Center, Shizuoka, Japan.
- The Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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Hou Y, Si K, Yang J, Liu T, Abdelazeem B, Theerasuwipakorn N, Zhao J, Shen Z. Association between regulatory T cells and ischemic heart disease: a Mendelian randomization study. J Thorac Dis 2024; 16:564-572. [PMID: 38410592 PMCID: PMC10894418 DOI: 10.21037/jtd-23-1790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
Background An imbalance of innate and acquired immune responses is significantly involved in the pathophysiology of coronary atherosclerosis and the occurrence of ischemic heart disease (IHD). Regulatory T cells (Tregs) play an essential regulatory role in atherosclerotic plaque formation and maintenance; therefore, dysfunction of Tregs triggers the formation of atherosclerotic plaques and accelerates their progression. However, due to the inherent limitations of observational research, clinical evidence is limited concerning the relationship between the variation in peripheral Tregs and the risk of IHD, and the cause-and-effect relationship between these factors is unclear. Mendelian randomization (MR) uses genetic variation as a proxy for exposure and can be used to inferentially determine the causal effect of exposure on outcomes. We thus used MR analysis to investigate whether there is a causal relationship between the biomarkers of Tregs and IHD. Methods Selected genetic variants (P<5.00E-08) from the summary data of a genome-wide association study (GWAS) were used to conduct a two-sample bidirectional MR analysis. The analysis included 51 extensive Treg subtypes involving 3,757 individuals from the general population. Summary statistics of IHD were obtained from the IEU open GWAS project, which contains 30,952 cases and 187,845 controls. The populations in both GWAS studies were of European ancestry. Results We identified a set of 197 single-nucleotide polymorphisms (SNPs) that served as instrumental variables (IVs) for evaluating 51 Treg subtypes. Thirteen significant variables were found to be potentially associated with IHD. After false-discovery rate (FDR) adjustment, we identified four Treg subtypes to be causally protective for IHD risk: CD28 on activated & secreting CD4 Tregs [odds ratio (OR) =0.89; 95% confidence interval (CI): 0.82-0.96; P=3.10E-03; adjusted P=0.04], CD28 on activated CD4 Tregs (OR =0.87; 95% CI: 0.80-0.95; P=3.10E-03; adjusted P=0.04), CD28 on CD4 Tregs (OR =0.87; 95% CI: 0.80-0.96; P=3.41E-03; adjusted P=0.04), and CD28 on resting CD4 Treg cell (OR =0.91; 95% CI: 0.85-0.97; P=3.48E-03; adjusted P=0.04). Reverse MR analysis found eight potential causal variables, but these associations were nonsignificant after FDR correction (all adjusted P values >0.05). Conclusions This study identified the significance of elevated CD28 expression on CD4 Tregs as a novel molecular modifier that may influence IHD occurrence, suggesting that targeting CD28 expression on CD4 Tregs could offer a promising therapeutic approach for IHD.
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Affiliation(s)
- Yucheng Hou
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Ke Si
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jingyue Yang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Tan Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Basel Abdelazeem
- Department of Cardiology, West Virginia University, Morgantown, WV, USA
| | - Nonthikorn Theerasuwipakorn
- Division of Cardiovascular Medicine, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Cardiac Center, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Jingwei Zhao
- Department of General Surgery, Xinhua Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine & Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai, China
| | - Zhenya Shen
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
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Tang C, Lei X, Ding Y, Yang S, Ma Y, He D. Causal relationship between immune cells and neurodegenerative diseases: a two-sample Mendelian randomisation study. Front Immunol 2024; 15:1339649. [PMID: 38348026 PMCID: PMC10859421 DOI: 10.3389/fimmu.2024.1339649] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
Background There is increasing evidence that the types of immune cells are associated with various neurodegenerative diseases. However, it is currently unclear whether these associations reflect causal relationships. Objective To elucidate the causal relationship between immune cells and neurodegenerative diseases, we conducted a two-sample Mendelian randomization (MR) analysis. Materials and methods The exposure and outcome GWAS data used in this study were obtained from an open-access database (https://gwas.mrcieu.ac.uk/), the study employed two-sample MR analysis to assess the causal relationship between 731 immune cell features and four neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and multiple sclerosis (MS). All immune cell data was obtained from Multiple MR methods were used to minimize bias and obtain reliable estimates of the causal relationship between the variables of interest and the outcomes. Instrumental variable selection criteria were restricted to ensure the accuracy and effectiveness of the causal relationship between species of immune cells and the risk of these neurodegenerative diseases. Results The study identified potential causal relationships between various immune cells and different neurodegenerative diseases. Specifically, we found that 8 different types of immune cells have potential causal relationships with AD, 1 type of immune cells has potential causal relationships with PD, 6 different types of immune cells have potential causal relationships with ALS, and 6 different types of immune cells have potential causal relationships with MS. Conclusion Our study, through genetic means, demonstrates close causal associations between the specific types of immune cells and AD, PD, ALS and MS, providing useful guidance for future clinical researches.
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Affiliation(s)
| | | | | | | | | | - Dian He
- Department of Neurology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
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Sun D, Wang R, Du Q, Zhang Y, Chen H, Shi Z, Wang X, Zhou H. Causal relationship between multiple sclerosis and cortical structure: a Mendelian randomization study. J Transl Med 2024; 22:83. [PMID: 38245759 PMCID: PMC10800041 DOI: 10.1186/s12967-024-04892-7] [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: 06/29/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND Observational studies have suggested an association between multiple sclerosis (MS) and cortical structure, but the results have been inconsistent. OBJECTIVE We used two-sample Mendelian randomization (MR) to assess the causal relationship between MS and cortical structure. METHODS MS data as the exposure trait, including 14,498 cases and 24,091 controls, were obtained from the International Multiple Sclerosis Genetics Consortium. Genome-wide association study (GWAS) data for cortical surface area (SAw/nw) and thickness (THw/nw) in 51,665 individuals of European ancestry were obtained from the ENIGMA Consortium. The inverse-variance weighted (IVW) method was used as the primary analysis for MR. Sensitivity analyses were conducted to evaluate heterogeneity and pleiotropy. Enrichment analysis was performed on MR analyses filtered by sensitivity analysis. RESULTS After IVW and sensitivity analysis filtering, only six surviving MR results provided suggestive evidence supporting a causal relationship between MS and cortical structure, including lingual SAw (p = .0342, beta (se) = 5.7127 (2.6969)), parahippocampal SAw (p = .0224, beta (se) = 1.5577 (0.6822)), rostral middle frontal SAw (p = .0154, beta (se) = - 9.0301 (3.7281)), cuneus THw (p = .0418, beta (se) = - 0.0020 (0.0010)), lateral orbitofrontal THw (p = .0281, beta (se) = 0.0025 (0.0010)), and lateral orbitofrontal THnw (p = .0417, beta (se) = 0.0029 (0.0014)). Enrichment analysis suggested that leukocyte cell-related pathways, JAK-STAT signaling pathway, NF-kappa B signaling pathway, cytokine-cytokine receptor interaction, and prolactin signaling pathway may be involved in the effect of MS on cortical morphology. CONCLUSION Our results provide evidence supporting a causal relationship between MS and cortical structure. Enrichment analysis suggests that the pathways mediating brain morphology abnormalities in MS patients are mainly related to immune and inflammation-driven pathways.
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Affiliation(s)
- Dongren Sun
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Rui Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Qin Du
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Ying Zhang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Hongxi Chen
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Ziyan Shi
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China
| | - Xiaofei Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China.
| | - Hongyu Zhou
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang #37, Chengdu, 610041, China.
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Lee CY, Chan KH. Personalized Use of Disease-Modifying Therapies in Multiple Sclerosis. Pharmaceutics 2024; 16:120. [PMID: 38258130 PMCID: PMC10820407 DOI: 10.3390/pharmaceutics16010120] [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: 12/01/2023] [Revised: 01/05/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Multiple sclerosis is an important neurological disease affecting millions of young patients globally. It is encouraging that more than ten disease-modifying drugs became available for use in the past two decades. These disease-modifying therapies (DMTs) have different levels of efficacy, routes of administration, adverse effect profiles and concerns for pregnancy. Much knowledge and caution are needed for their appropriate use in MS patients who are heterogeneous in clinical features and severity, lesion load on magnetic resonance imaging and response to DMT. We aim for an updated review of the concept of personalization in the use of DMT for relapsing MS patients. Shared decision making with consideration for the preference and expectation of patients who understand the potential efficacy/benefits and risks of DMT is advocated.
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Affiliation(s)
- Chi-Yan Lee
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 405B, 4/F, Professorial Block, 102 Pokfulam Road, Hong Kong
- Neuroimmunology and Neuroinflammation Research Laboratory, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Koon-Ho Chan
- Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, 405B, 4/F, Professorial Block, 102 Pokfulam Road, Hong Kong
- Neuroimmunology and Neuroinflammation Research Laboratory, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
- Research Center of Heart, Brain, Hormone and Healthy Aging, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong
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Shim G, Romero-Morales AI, Sripathy SR, Maher BJ. Utilizing hiPSC-derived oligodendrocytes to study myelin pathophysiology in neuropsychiatric and neurodegenerative disorders. Front Cell Neurosci 2024; 17:1322813. [PMID: 38273973 PMCID: PMC10808804 DOI: 10.3389/fncel.2023.1322813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Oligodendrocytes play a crucial role in our central nervous system (CNS) by myelinating axons for faster action potential conduction, protecting axons from degeneration, structuring the position of ion channels, and providing nutrients to neurons. Oligodendrocyte dysfunction and/or dysmyelination can contribute to a range of neurodegenerative diseases and neuropsychiatric disorders such as Multiple Sclerosis (MS), Leukodystrophy (LD), Schizophrenia (SCZ), and Autism Spectrum Disorder (ASD). Common characteristics identified across these disorders were either an inability of oligodendrocytes to remyelinate after degeneration or defects in oligodendrocyte development and maturation. Unfortunately, the causal mechanisms of oligodendrocyte dysfunction are still uncertain, and therapeutic targets remain elusive. Many studies rely on the use of animal models to identify the molecular and cellular mechanisms behind these disorders, however, such studies face species-specific challenges and therefore lack translatability. The use of human induced pluripotent stem cells (hiPSCs) to model neurological diseases is becoming a powerful new tool, improving our understanding of pathophysiology and capacity to explore therapeutic targets. Here, we focus on the application of hiPSC-derived oligodendrocyte model systems to model disorders caused by oligodendrocyte dysregulation.
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Affiliation(s)
- Gina Shim
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Alejandra I. Romero-Morales
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Srinidhi R. Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Psychiatry and Behavioral Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
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50
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Lei Z, Lin W. Mechanisms Governing Oligodendrocyte Viability in Multiple Sclerosis and Its Animal Models. Cells 2024; 13:116. [PMID: 38247808 PMCID: PMC10814231 DOI: 10.3390/cells13020116] [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: 12/14/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune inflammatory demyelinating disease of the central nervous system (CNS), which is triggered by an autoimmune assault targeting oligodendrocytes and myelin. Recent research indicates that the demise of oligodendrocytes due to an autoimmune attack contributes significantly to the pathogenesis of MS and its animal model experimental autoimmune encephalomyelitis (EAE). A key challenge in MS research lies in comprehending the mechanisms governing oligodendrocyte viability and devising therapeutic approaches to enhance oligodendrocyte survival. Here, we provide an overview of recent findings that highlight the contributions of oligodendrocyte death to the development of MS and EAE and summarize the current literature on the mechanisms governing oligodendrocyte viability in these diseases.
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Affiliation(s)
- Zhixin Lei
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China;
| | - Wensheng Lin
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
- Institute for Translational Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
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