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Loginovic P, Wang F, Li J, Ferrat L, Mirshahi UL, Rao HS, Petzold A, Tyrrell J, Green HD, Weedon MN, Ganna A, Tuomi T, Carey DJ, Oram RA, Braithwaite T. Applying a genetic risk score model to enhance prediction of future multiple sclerosis diagnosis at first presentation with optic neuritis. Nat Commun 2024; 15:1415. [PMID: 38418465 PMCID: PMC10902342 DOI: 10.1038/s41467-024-44917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/09/2024] [Indexed: 03/01/2024] Open
Abstract
Optic neuritis (ON) is associated with numerous immune-mediated inflammatory diseases, but 50% patients are ultimately diagnosed with multiple sclerosis (MS). Differentiating MS-ON from non-MS-ON acutely is challenging but important; non-MS ON often requires urgent immunosuppression to preserve vision. Using data from the United Kingdom Biobank we showed that combining an MS-genetic risk score (GRS) with demographic risk factors (age, sex) significantly improved MS prediction in undifferentiated ON; one standard deviation of MS-GRS increased the Hazard of MS 1.3-fold (95% confidence interval 1.07-1.55, P < 0.01). Participants stratified into quartiles of predicted risk developed incident MS at rates varying from 4% (95%CI 0.5-7%, lowest risk quartile) to 41% (95%CI 33-49%, highest risk quartile). The model replicated across two cohorts (Geisinger, USA, and FinnGen, Finland). This study indicates that a combined model might enhance individual MS risk stratification, paving the way for precision-based ON treatment and earlier MS disease-modifying therapy.
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Affiliation(s)
- Pavel Loginovic
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Heavitree Road, Exeter, EX1 2HZ, UK
| | - Feiyi Wang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jiang Li
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Lauric Ferrat
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | | | - H Shanker Rao
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Axel Petzold
- Neuro-ophthalmology Expert Center, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Neuro-ophthalmology, The National Hospital for Neurology and Neurosurgery, Queen Square, UCL Institute of Neurology, London, UK
- Neuro-ophthalmology service, Moorfields Eye Hospital, London, UK
| | - Jessica Tyrrell
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, EX2 5DW, UK
| | - Harry D Green
- Exeter Centre of Excellence for Diabetes Research (EXCEED), University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Abdominal Center, Endocrinology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - David J Carey
- Weis Center for Research, Geisinger, Danville, PA, USA
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, St Luke's Campus, University of Exeter, Heavitree Road, Exeter, Devon, EX1 2LU, UK.
- Academic Kidney Unit, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK.
| | - Tasanee Braithwaite
- King's College London, School of Immunology & Microbial Sciences and School of Life Course and Population Sciences, London, UK
- Medical Eye Unit, St Thomas' Hospital, Guy's and St Thomas' NHS Foundation Trust, Westminster Bridge Road, London, UK
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Shams H, Shao X, Santaniello A, Kirkish G, Harroud A, Ma Q, Isobe N, Schaefer CA, McCauley JL, Cree BAC, Didonna A, Baranzini SE, Patsopoulos NA, Hauser SL, Barcellos LF, Henry RG, Oksenberg JR. Polygenic risk score association with multiple sclerosis susceptibility and phenotype in Europeans. Brain 2023; 146:645-656. [PMID: 35253861 PMCID: PMC10169285 DOI: 10.1093/brain/awac092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/29/2022] [Accepted: 02/15/2022] [Indexed: 11/13/2022] Open
Abstract
Polygenic inheritance plays a pivotal role in driving multiple sclerosis susceptibility, an inflammatory demyelinating disease of the CNS. We developed polygenic risk scores (PRS) of multiple sclerosis and assessed associations with both disease status and severity in cohorts of European descent. The largest genome-wide association dataset for multiple sclerosis to date (n = 41 505) was leveraged to generate PRS scores, serving as an informative susceptibility marker, tested in two independent datasets, UK Biobank [area under the curve (AUC) = 0.73, 95% confidence interval (CI): 0.72-0.74, P = 6.41 × 10-146] and Kaiser Permanente in Northern California (KPNC, AUC = 0.8, 95% CI: 0.76-0.82, P = 1.5 × 10-53). Individuals within the top 10% of PRS were at higher than 5-fold increased risk in UK Biobank (95% CI: 4.7-6, P = 2.8 × 10-45) and 15-fold higher risk in KPNC (95% CI: 10.4-24, P = 3.7 × 10-11), relative to the median decile. The cumulative absolute risk of developing multiple sclerosis from age 20 onwards was significantly higher in genetically predisposed individuals according to PRS. Furthermore, inclusion of PRS in clinical risk models increased the risk discrimination by 13% to 26% over models based only on conventional risk factors in UK Biobank and KPNC, respectively. Stratifying disease risk by gene sets representative of curated cellular signalling cascades, nominated promising genetic candidate programmes for functional characterization. These pathways include inflammatory signalling mediation, response to viral infection, oxidative damage, RNA polymerase transcription, and epigenetic regulation of gene expression to be among significant contributors to multiple sclerosis susceptibility. This study also indicates that PRS is a useful measure for estimating susceptibility within related individuals in multicase families. We show a significant association of genetic predisposition with thalamic atrophy within 10 years of disease progression in the UCSF-EPIC cohort (P < 0.001), consistent with a partial overlap between the genetics of susceptibility and end-organ tissue injury. Mendelian randomization analysis suggested an effect of multiple sclerosis susceptibility on thalamic volume, which was further indicated to be through horizontal pleiotropy rather than a causal effect. In summary, this study indicates important, replicable associations of PRS with enhanced risk assessment and radiographic outcomes of tissue injury, potentially informing targeted screening and prevention strategies.
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Affiliation(s)
- Hengameh Shams
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.,Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Xiaorong Shao
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Gina Kirkish
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Adil Harroud
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Qin Ma
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Noriko Isobe
- Department of Neurology, Graduate School of medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | | | | | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA.,Dr. John T. Macdonald Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Alessandro Didonna
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.,Department of Anatomy and Cell Biology, East Carolina University, Greenville, NC 27834, USA
| | - Sergio E Baranzini
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Nikolaos A Patsopoulos
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women's Hospital, Boston, 02115 MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen L Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Lisa F Barcellos
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Roland G Henry
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Jorge R Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
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Kanchan K, Shankar G, Huffaker MF, Bahnson HT, Chinthrajah RS, Sanda S, Manohar M, Ling H, Paschall JE, Toit GD, Ruczinski I, Togias A, Lack G, Nadeau KC, Jones SM, Nepom GT, Mathias RA. HLA-associated outcomes in peanut oral immunotherapy trials identify mechanistic and clinical determinants of therapeutic success. Front Immunol 2022; 13:941839. [PMID: 36466872 PMCID: PMC9717393 DOI: 10.3389/fimmu.2022.941839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022] Open
Abstract
Rationale Previous studies identified an interaction between HLA and oral peanut exposure. HLA-DQA1*01:02 had a protective role with the induction of Ara h 2 epitope-specific IgG4 associated with peanut consumption during the LEAP clinical trial for prevention of peanut allergy, while it was a risk allele for peanut allergy in the peanut avoidance group. We have now evaluated this gene-environment interaction in two subsequent peanut oral immunotherapy (OIT) trials - IMPACT and POISED - to better understand the potential for the HLA-DQA1*01:02 allele as an indicator of higher likelihood of desensitization, sustained unresponsiveness, and peanut allergy remission. Methods We determined HLA-DQA1*01:02 carrier status using genome sequencing from POISED (N=118, age: 7-55yr) and IMPACT (N=126, age: 12-<48mo). We tested for association with remission, sustained unresponsiveness (SU), and desensitization in the OIT groups, as well as peanut component specific IgG4 (psIgG4) using generalized linear models and adjusting for relevant covariates and ancestry. Results While not quite statistically significant, a higher proportion of HLA-DQA1*01:02 carriers receiving OIT in IMPACT were desensitized (93%) compared to non-carriers (78%); odds ratio (OR)=5.74 (p=0.06). In this sample we also observed that a higher proportion of carriers achieved remission (35%) compared to non-carriers (22%); OR=1.26 (p=0.80). In POISED, carriers more frequently attained continued desensitization (80% versus 61% among non-carriers; OR=1.28, p=0.86) and achieved SU (52% versus 31%; OR=2.32, p=0.19). psIgG4 associations with HLA-DQA1*01:02 in the OIT arm of IMPACT which included younger study subjects recapitulated patterns noted in LEAP, but no associations of note were observed in the older POISED study subjects. Conclusions Findings across three clinical trials show a pattern of a gene environment interaction between HLA and oral peanut exposure. Age, and prior sensitization contribute additional determinants of outcomes, consistent with a mechanism of restricted antigen recognition fundamental to driving protective immune responses to OIT.
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Affiliation(s)
- Kanika Kanchan
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Gautam Shankar
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | | | - Henry T. Bahnson
- The Immune Tolerance Network, Seattle, WA, United States,Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - R Sharon Chinthrajah
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, CA, United States
| | - Srinath Sanda
- The Immune Tolerance Network, San Francisco, CA, United States
| | - Monali Manohar
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, CA, United States
| | - Hua Ling
- Institute of Genetic Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Justin E. Paschall
- Institute of Genetic Medicine, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - George Du Toit
- The Department of Pediatric Allergy, Division of Asthma, Allergy and Lung Biology, King’s College London, and Guy’s and St Thomas’ National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Alkis Togias
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States
| | - Gideon Lack
- The Department of Pediatric Allergy, Division of Asthma, Allergy and Lung Biology, King’s College London, and Guy’s and St Thomas’ National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Kari C. Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University, Palo Alto, CA, United States
| | - Stacie M. Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, AR, United States
| | - Gerald T. Nepom
- The Immune Tolerance Network, Seattle, WA, United States,Benaroya Research Institute at Virginia Mason, Seattle, WA, United States
| | - Rasika A. Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States,*Correspondence: Rasika Mathias,
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Goris A, Vandebergh M, McCauley JL, Saarela J, Cotsapas C. Genetics of multiple sclerosis: lessons from polygenicity. Lancet Neurol 2022; 21:830-842. [PMID: 35963264 DOI: 10.1016/s1474-4422(22)00255-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/07/2022] [Accepted: 04/12/2022] [Indexed: 11/27/2022]
Abstract
Large-scale mapping studies have identified 236 independent genetic variants associated with an increased risk of multiple sclerosis. However, none of these variants are found exclusively in patients with multiple sclerosis. They are located throughout the genome, including 32 independent variants in the MHC and one on the X chromosome. Most variants are non-coding and seem to act through cell-specific effects on gene expression and splicing. The likely functions of these variants implicate both adaptive and innate immune cells in the pathogenesis of multiple sclerosis, provide pivotal biological insight into the causes and mechanisms of multiple sclerosis, and some of the variants implicated in multiple sclerosis also mediate risk of other autoimmune and inflammatory diseases. Genetics offers an approach to showing causality for environmental factors, through Mendelian randomisation. No single variant is necessary or sufficient to cause multiple sclerosis; instead, each increases total risk in an additive manner. This combined contribution from many genetic factors to disease risk, or polygenicity, has important consequences for how we interpret the epidemiology of multiple sclerosis and how we counsel patients on risk and prognosis. Ongoing efforts are focused on increasing cohort sizes, increasing diversity and detailed characterisation of study populations, and translating these associations into an understanding of the biology of multiple sclerosis.
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Affiliation(s)
- An Goris
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium.
| | - Marijne Vandebergh
- KU Leuven, Leuven Brain Institute, Department of Neurosciences, Laboratory for Neuroimmunology, Leuven, Belgium
| | - Jacob L McCauley
- John P Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Janna Saarela
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway; Institute for Molecular Medicine Finland and Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Chris Cotsapas
- Departments of Neurology and Genetics, Yale School of Medicine, New Haven, CT, USA
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