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Kuczynski AM, Jones A, Kimbrough D, Muccilli A, Roy-Hewitson C, Okuda DT, Baral S, Oh J. Clinical characteristics and disease burden of African, Caribbean, and Black people with multiple sclerosis in Toronto, Canada. Mult Scler Relat Disord 2024; 90:105802. [PMID: 39126938 DOI: 10.1016/j.msard.2024.105802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/24/2024] [Accepted: 08/03/2024] [Indexed: 08/12/2024]
Abstract
BACKGROUND Different racial and ethnic groups have demonstrated heterogeneity in the clinical course of multiple sclerosis(MS). OBJECTIVE We aimed to evaluate disease characteristics in African, Caribbean, and Black people with MS(ACB-MS) followed at a single centre in Toronto, Canada. METHODS ACB-MS were compared with age- and sex-matched people with MS (pwMS) of European descent(EUR-MS) identified through the clinic registry. RESULTS 344 PwMS were included(n = 172 ACB-MS, n = 172 EUR-MS; mean age 43 years, 68 % female). Baseline mean Expanded disability status scale (EDSS) scores (ACB-MS 2.3 ± 2.3 vs. EUR-MS 2.2 ± 2.0, p = 0.38) and subsequent clinical and radiological measures of disease activity were similar between groups, including annualized relapse rate (ARR)(ACB-MS 0.47 ± 0.47 vs. EUR-MS 0.41 ± 0.34, p = 0.2) and most recent EDSS (ACB-MS 2.7 ± 2.2 vs. EUR-MS 2.3 ± 2.1, p = 0.10). However, the proportion of MRI brain demonstrating new disease activity was higher(37% vs. 26 %, p < 0.05) and disability progression greater in ACB-MS vs. EUR-MS(43% vs. 33 %,p < 0.05) but measures of disease severity including MS Severity Score(3.17 vs. 2.58, p = 0.3) and Progression Index(PI) (0.27 vs. 0.30, p = 0.5) were comparable. CONCLUSION Disability progression was seen more commonly in ACB-MS, though clinical disease activity and severity were generally comparable between ACB-MS and EUR-MS patients in Toronto, Canada. These findings partially differ from prior studies demonstrating more overtly aggressive MS disease courses in Black and African American PwMS, necessitating further studies to understand how structural determinants of health drive these disparities.
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Affiliation(s)
- Andrea M Kuczynski
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Ashley Jones
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Dorlan Kimbrough
- Department of Neurology, Duke University, Durham, North Carolina, USA
| | - Alexandra Muccilli
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | | | - Darin T Okuda
- Department of Neurology, University of Texas Southwestern Medical Centre, Dallas, Texas, USA
| | - Stefan Baral
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Jiwon Oh
- Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Boullerne AI, Goudey B, Paganini J, Erlichster M, Gaitonde S, Feinstein DL. Validation of tag SNPs for multiple sclerosis HLA risk alleles across the 1000 genomes panel. Hum Immunol 2024; 85:110790. [PMID: 38575482 DOI: 10.1016/j.humimm.2024.110790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/10/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
Currently, the genetic variants strongly associated with risk for Multiple Sclerosis (MS) are located in the Major Histocompatibility Complex. This includes DRB1*15:01 and DRB1*15:03 alleles at the HLA-DRB1 locus, the latter restricted to African populations; the DQB1*06:02 allele at the HLA-DQB1 locus which is in high linkage disequilibrium (LD) with DRB1*15:01; and protective allele A*02:01 at the HLA-A locus. HLA allele identification is facilitated by co-inherited ('tag') single nucleotide polymorphisms (SNPs); however, SNP validation is not typically done outside of the discovery population. We examined 19 SNPs reported to be in high LD with these alleles in 2,502 healthy subjects included in the 1000 Genomes panel having typed HLA data. Examination of 3 indices (LD R2 values, sensitivity and specificity, minor allele frequency) revealed few SNPs with high tagging performance. All SNPs examined that tag DRB1*15:01 were in perfect LD in the British population; three showed high tagging performance in 4 of the 5 European, and 2 of the 4 American populations. For DQB1*06:02, with no previously validated tag SNPs, we show that rs3135388 has high tagging performance in one South Asian, one American, and one European population. We identify for the first time that rs2844821 has high tagging performance for A*02:01 in 5 of 7 African populations including African Americans, and 4 of the 5 European populations. These results provide a basis for selecting SNPs with high tagging performance to assess HLA alleles across diverse populations, for MS risk as well as for other diseases and conditions.
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Affiliation(s)
- Anne I Boullerne
- Department of Anesthesiology, University Illinois, Chicago, IL, USA.
| | - Benjamin Goudey
- The Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, Australia; Centre for Epidemiology and Biostatistics, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Michael Erlichster
- MX3 Diagnostics, Melbourne, Victoria, Australia; Centre for Neural Engineering, University of Melbourne, Melbourne, Victoria, Australia; Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
| | - Sujata Gaitonde
- Department of Pathology, University Illinois, Chicago, IL, USA
| | - Douglas L Feinstein
- Department of Anesthesiology, University Illinois, Chicago, IL, USA; Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
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Behr M, Kumbier K, Cordova-Palomera A, Aguirre M, Ronen O, Ye C, Ashley E, Butte AJ, Arnaout R, Brown B, Priest J, Yu B. Learning epistatic polygenic phenotypes with Boolean interactions. PLoS One 2024; 19:e0298906. [PMID: 38625909 PMCID: PMC11020961 DOI: 10.1371/journal.pone.0298906] [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: 01/26/2023] [Accepted: 01/31/2024] [Indexed: 04/18/2024] Open
Abstract
Detecting epistatic drivers of human phenotypes is a considerable challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Predictability, Computability, Stability (PCS) framework, we introduce the epiTree pipeline to extract higher-order interactions from genomic data using tree-based models. The epiTree pipeline first selects a set of variants derived from tissue-specific estimates of gene expression. Next, it uses iterative random forests (iRF) to search training data for candidate Boolean interactions (pairwise and higher-order). We derive significance tests for interactions, based on a stabilized likelihood ratio test, by simulating Boolean tree-structured null (no epistasis) and alternative (epistasis) distributions on hold-out test data. Finally, our pipeline computes PCS epistasis p-values that probabilisticly quantify improvement in prediction accuracy via bootstrap sampling on the test set. We validate the epiTree pipeline in two case studies using data from the UK Biobank: predicting red hair and multiple sclerosis (MS). In the case of predicting red hair, epiTree recovers known epistatic interactions surrounding MC1R and novel interactions, representing non-linearities not captured by logistic regression models. In the case of predicting MS, a more complex phenotype than red hair, epiTree rankings prioritize novel interactions surrounding HLA-DRB1, a variant previously associated with MS in several populations. Taken together, these results highlight the potential for epiTree rankings to help reduce the design space for follow up experiments.
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Affiliation(s)
- Merle Behr
- Faculty of Informatics and Data Science, University of Regensburg, Regensburg, Germany
| | - Karl Kumbier
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America
| | | | - Matthew Aguirre
- Department of Pediatrics, Stanford Medicine, Stanford, CA, United States of America
- Department of Biomedical Data Science, Stanford Medicine, Stanford, CA, United States of America
| | - Omer Ronen
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
| | - Chengzhong Ye
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
| | - Euan Ashley
- Division of Cardiovascular Medicine, Stanford Medicine, Stanford, CA, United States of America
| | - Atul J. Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States of America
| | - Rima Arnaout
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA, United States of America
- Division of Cardiology, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States of America
| | - Ben Brown
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
- Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - James Priest
- Department of Pediatrics, Stanford Medicine, Stanford, CA, United States of America
| | - Bin Yu
- Department of Statistics, University of California at Berkeley, Berkeley, CA, United States of America
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California at Berkeley, Berkeley, CA, United States of America
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Marzouka NAD, Alnaqbi H, Al-Aamri A, Tay G, Alsafar H. Investigating the genetic makeup of the major histocompatibility complex (MHC) in the United Arab Emirates population through next-generation sequencing. Sci Rep 2024; 14:3392. [PMID: 38337023 PMCID: PMC10858242 DOI: 10.1038/s41598-024-53986-1] [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: 11/26/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
The Human leukocyte antigen (HLA) molecules are central to immune response and have associations with the phenotypes of various diseases and induced drug toxicity. Further, the role of HLA molecules in presenting antigens significantly affects the transplantation outcome. The objective of this study was to examine the extent of the diversity of HLA alleles in the population of the United Arab Emirates (UAE) using Next-Generation Sequencing methodologies and encompassing a larger cohort of individuals. A cohort of 570 unrelated healthy citizens of the UAE volunteered to provide samples for Whole Genome Sequencing and Whole Exome Sequencing. The definition of the HLA alleles was achieved through the application of the bioinformatics tools, HLA-LA and xHLA. Subsequently, the findings from this study were compared with other local and international datasets. A broad range of HLA alleles in the UAE population, of which some were previously unreported, was identified. A comparison with other populations confirmed the current population's unique intertwined genetic heritage while highlighting similarities with populations from the Middle East region. Some disease-associated HLA alleles were detected at a frequency of > 5%, such as HLA-B*51:01, HLA-DRB1*03:01, HLA-DRB1*15:01, and HLA-DQB1*02:01. The increase in allele homozygosity, especially for HLA class I genes, was identified in samples with a higher level of genome-wide homozygosity. This highlights a possible effect of consanguinity on the HLA homozygosity. The HLA allele distribution in the UAE population showcases a unique profile, underscoring the need for tailored databases for traditional activities such as unrelated transplant matching and for newer initiatives in precision medicine based on specific populations. This research is part of a concerted effort to improve the knowledge base, particularly in the fields of transplant medicine and investigating disease associations as well as in understanding human migration patterns within the Arabian Peninsula and surrounding regions.
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Affiliation(s)
- Nour Al Dain Marzouka
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Alnaqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Amira Al-Aamri
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan Tay
- Division of Psychiatry, Faculty of Health and Medical Sciences, Medical School, The University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
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Ryapolova A, Minskaia E, Gasanov N, Moroz V, Krapivin B, Egorov AD, Laktyushkin V, Zhuravleva S, Nagornych M, Subcheva E, Malogolovkin A, Ivanov R, Karabelsky A. Development of Recombinant Oncolytic rVSV-mIL12-mGMCSF for Cancer Immunotherapy. Int J Mol Sci 2023; 25:211. [PMID: 38203382 PMCID: PMC10779112 DOI: 10.3390/ijms25010211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Anti-cancer therapy based on oncolytic viruses (OVs) is a targeted approach that takes advantage of OVs' ability to selectively infect and replicate in tumor cells, activate the host immune response, and destroy malignant cells over healthy ones. Vesicular stomatitis virus (VSV) is known for its wide range of advantages: a lack of pre-existing immunity, a genome that is easily amenable to manipulation, and rapid growth to high titers in a broad range of cell lines, to name a few. VSV-induced tumor immunity can be enhanced by the delivery of immunostimulatory cytokines. The targeted cytokine delivery to tumors avoids the significant toxicity associated with systemic delivery while also boosting the immune response. To demonstrate this enhanced effect on both tumor growth and survival, a novel recombinant VSV (rVSV)-mIL12-mGMCSF, co-expressing mouse IL-12 (interleukin-12) and GM-CSF (granulocyte-macrophage colony-stimulating factor), was tested alongside rVSV-dM51-GFP (rVSV-GFP) that was injected intratumorally in a syngeneic in vivo C57BL/6 mouse model infused subcutaneously with B16-F10 melanoma cells. The pilot study tested the effect of two viral injections 4 days apart and demonstrated that treatment with the two rVSVs resulted in partial inhibition of tumor growth (TGII of around 40%) and an increased survival rate in animals from the treatment groups. The effect of the two VSVs on immune cell populations will be investigated in future in vivo studies with an optimized experimental design with multiple higher viral doses, as a lack of this information presents a limitation of this study.
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Affiliation(s)
- Anastasia Ryapolova
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Ekaterina Minskaia
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Nizami Gasanov
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Vasiliy Moroz
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Bogdan Krapivin
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Alexander D. Egorov
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Victor Laktyushkin
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Sofia Zhuravleva
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Maksim Nagornych
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Elena Subcheva
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Alexander Malogolovkin
- Department of Molecular Virology, First Moscow State Medical University (Sechenov University), 20 Pirogovskaya, 119991 Moscow, Russia;
| | - Roman Ivanov
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
| | - Alexander Karabelsky
- Department of Gene Therapy, Sirius University of Science and Technology, Olympic Avenue, 1, 354340 Sochi, Russia; (A.R.); (N.G.); (V.M.); (B.K.); (A.D.E.); (V.L.); (S.Z.); (M.N.); (E.S.); (R.I.); (A.K.)
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Moglan AM, Albaradie OA, Alsayegh FF, Alharbi HM, Samman YM, Jalal MM, Saeedi NH, Mahmoud AB, Alkayyal AA. Preclinical efficacy of oncolytic VSV-IFNβ in treating cancer: A systematic review. Front Immunol 2023; 14:1085940. [PMID: 37063914 PMCID: PMC10104167 DOI: 10.3389/fimmu.2023.1085940] [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: 10/31/2022] [Accepted: 03/17/2023] [Indexed: 04/03/2023] Open
Abstract
BackgroundCancer incidence and mortality are increasing rapidly worldwide, necessitating further investigation into developing and optimizing emergent cancer therapies. Oncolytic viruses such as vesicular stomatitis virus encoding interferon β (VSV-IFNβ) have attracted considerable attention, as they offer great efficacy and safety profiles. This systematic review aimed to determine and compare the efficacy profile between VSV-IFNβ and non-treatment controls in preclinical cancer models.MethodologyThe Embase and Medline databases were systematically searched for relevant studies using related key terms and Medical Subject Headings (MeSH). Titles, abstracts, and full texts were screened, and data from eligible articles were extracted by two groups independently and in duplicate (two reviewers per group). Disagreements were resolved by a fifth independent reviewer. The included articles were all preclinical (translational) in vivo English studies that investigated and compared the efficacy profile between VSV-IFNβ and non-treatment controls in animal models. The risk of bias among the studies was assessed by two reviewers independently and in duplicate using SYRCLE’s risk-of-bias tool for animal studies; disparities were addressed by a third independent reviewer.ResultsAfter employing relevant MeSH and key terms, we identified 1598 articles. A total of 87 articles were either duplicates or conference proceedings and were thus excluded. Following title and abstract screening, 37 articles were included in the full-text assessment. Finally, 14 studies met the eligibility criteria. Forty-two experiments from the included studies examined the potential efficacy of VSV-IFNβ through different routes of administration, including intratumoral, intraperitoneal, and intravenous routes. Thirty-seven experiments reported positive outcomes. Meanwhile, five experiments reported negative outcomes, three and two of which examined intratumoral and intravenous VSV-IFNβ administration, respectively.ConclusionAlthough the majority of the included studies support the promising potential of VSV-IFNβ as an oncolytic virus, further research is necessary to ensure a safe and efficacious profile to translate its application into clinical trials.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/, identifier CRD42022335418.
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Affiliation(s)
- Abdulaziz Molham Moglan
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Omar A. Albaradie
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Fares Fayez Alsayegh
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Hussam Mohsen Alharbi
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Yahya Marwan Samman
- College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
| | - Mohammed M. Jalal
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Nizar H. Saeedi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- Department of Medical Laboratory Technology, College of Applied Medical Sciences, Taibah University, Almadinah Almunwarah, Saudi Arabia
- Strategic Research and Innovation Laboratories, Taibah University, Almadinah Almunwarah, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- *Correspondence: Ahmad Bakur Mahmoud, ; Almohanad A. Alkayyal,
| | - Almohanad A. Alkayyal
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- *Correspondence: Ahmad Bakur Mahmoud, ; Almohanad A. Alkayyal,
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Akel O, Zhao LP, Geraghty DE, Lind A. High-resolution HLA class II sequencing of Swedish multiple sclerosis patients. Int J Immunogenet 2022; 49:333-339. [PMID: 35959717 PMCID: PMC9545082 DOI: 10.1111/iji.12594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
Abstract
Multiple sclerosis (MS) is a chronic neurological disease believed to be caused by autoimmune pathogenesis. The aetiology is likely explained by a complex interplay between inherited and environmental factors. Genetic investigations into MS have been conducted for over 50 years, yielding >100 associations to date. Globally, the strongest linkage is with the human leukocyte antigen (HLA) HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype. Here, high-resolution sequencing of HLA was used to determine the alleles of DRB3, DRB4, DRB5, DRB1, DQA1, DQB1, DPA1 and DPB1 as well as their extended haplotypes and genotypes in 100 Swedish MS patients. Results were compared to 636 population controls. The heterogeneity in HLA associations with MS was demonstrated; among 100 patients, 69 extended HLA-DR-DQ genotypes were found. Three extended HLA-DR-DQ genotypes were found to be correlated to MS; HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype together with (A) HLA-DRB4*01:01:01//DRB4*01:01:01:01-DRB1*07:01:01-DQA1*02:01//02:01:01-DQB1*02:02:01, (B) HLA-DRBX*null-DRB1*08:01:01-DQA1*04:01:01-DQB1*04:02:01, and (C) HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01. At the allelic level, HLA-DRB3*01:01:02 was considered protective against MS. However, when combined with HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01, this extended haplotype was considered a predisposing risk factor. This highlights the limitations as included with investigations of single alleles relative to those of extended haplotypes/genotypes. In conclusion, with 69 genotypes presented among 100 patients, high-resolution sequencing was conducted to underscore the wide polymorphisms present among MS patients. Additional studies in larger cohorts will be of importance to define MS among the patient group not associated with HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01.
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Affiliation(s)
- Omar Akel
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
| | - Lue Ping Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexander Lind
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
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Liver kinase B1 rs9282860 polymorphism and risk for multiple sclerosis in White and Black Americans. Mult Scler Relat Disord 2021; 55:103185. [PMID: 34371271 DOI: 10.1016/j.msard.2021.103185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/12/2021] [Accepted: 07/31/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND We previously reported that the single nucleotide polymorphism (SNP) rs9282860 in serine threonine kinase 11 (STK11) gene which codes for liver kinase B1 (LKB1) has higher prevalence in White relapsing-remitting multiple sclerosis (RRMS) patients than controls. However it is not known if this SNP is a risk factor for MS in other populations. METHODS We assessed the prevalence of the STK11 SNP in samples collected from African American (AA) persons with MS (PwMS) and controls at multiple Veterans Affairs (VA) Medical Centers and from a network of academic MS centers. Genotyping was carried out using a specific Taqman assay. Comparisons of SNP frequencies were made using Fisher's exact test to determine significance and odds ratios. Group means were compared by appropriate t-tests based on normality and variance using SPSS V27. RESULTS There were no significant differences in average age at first symptom onset, age at diagnosis, disease duration, or disease severity between RRMS patients recruited from VAMCs versus non-VAMCs. The SNP was more prevalent in AA than White PwMS, however only in secondary progressive MS (SPMS) patients was that difference statistically significant. AA SPMS patients had higher STK11 SNP prevalence than controls; and in that cohort the SNP was associated with older age at symptom onset and at diagnosis. CONCLUSIONS The results suggest that the STK11 SNP represents a risk factor for SPMS in AA patients, and can influence both early (onset) and later (conversion to SPMSS) events.
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Vinoy N, Sheeja N, Kumar S, Biswas L. Class II HLA (DRB1, & DQB1) alleles and IL7R (rs6897932) variants and the risk for Multiple Sclerosis in Kerala, India. Mult Scler Relat Disord 2021; 50:102848. [PMID: 33657520 DOI: 10.1016/j.msard.2021.102848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Different human leukocyte antigen (HLA) variants are known to modulate the risk of multiple sclerosis. The main objective of this study was to identify HLA-DRB1 and HLA-DQB1 alleles and Non -HLA gene IL7R (rs6897932) variants associated with MS. METHODS Patients attending the MS clinic, diagnosed with Multiple Sclerosis as per Mc Donald diagnostic criteria were the subjects in the study. The association of the highly polymorphic HLA-DRB1 and HLA-DQB1 loci was determined by high resolution tissue typing and the genotyping of the IL7R (rs6897932) variants was performed by Sanger sequencing in MS patients (n = 81) and healthy individuals (n = 82). RESULTS HLA-DRB1*15:01/15:02 alleles (OR = 3.65; p< 0.0001) and HLA-DQB1*06:02 (OR=4.19, p<0.0001) were found to be positively associated while HLA-DRB1*14:04:01 (OR = 0.21; p = 0.0009) was found to be negatively associated with MS. The most significant predisposing HLA haplotype was found to be DRB1*15:01-DQB1*06:02 (OR=5.69, p<0.0001). Univariate analysis of IL7R SNP (rs6897932) showed no significant association with MS in our population whereas analysis of HLA-DRB1 alleles and IL7R (rs6897932) genotypes showed significant association between the HLA-DRB1*15:01/15:02 and the IL7R (rs6897932) CC genotype (OR = 3.58, p = 0.0002). CONCLUSION HLA-DRB1*15:01, 15:02 and DQB1*06:02 are the predisposing alleles while HLA-DRB1*14:04 is the protective allele for MS in our population.
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Affiliation(s)
- Navia Vinoy
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India
| | - Neethu Sheeja
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India
| | - Suresh Kumar
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, Kerala 682041, India.
| | - Lalitha Biswas
- Centre for Nanosciences and Molecular Medicine, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala 682041, India.
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10
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Review: Reversed low-rank ANOVA model for transforming high dimensional genetic data into low dimension. J Korean Stat Soc 2019. [DOI: 10.1016/j.jkss.2018.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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11
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Goodin DS, Khankhanian P, Gourraud PA, Vince N. Highly conserved extended haplotypes of the major histocompatibility complex and their relationship to multiple sclerosis susceptibility. PLoS One 2018; 13:e0190043. [PMID: 29438392 PMCID: PMC5810982 DOI: 10.1371/journal.pone.0190043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 12/07/2017] [Indexed: 12/03/2022] Open
Abstract
Objective To determine the relationship between highly-conserved extended-haplotypes (CEHs) in the major histocompatibility complex (MHC) and MS-susceptibility. Background Among the ~200 MS-susceptibility regions, which are known from genome-wide analyses of single nucleotide polymorphisms (SNPs), the MHC accounts for roughly a third of the currently explained variance and the strongest MS-associations are for certain Class II alleles (e.g., HLA-DRB1*15:01; HLA-DRB1*03:01; and HLA-DRB1*13:03), which frequently reside on CEHs within the MHC. Design/Methods Autosomal SNPs (441,547) from 11,376 MS cases and 18,872 controls in the WTCCC dataset were phased. The most significant MS associated SNP haplotype was composed of 11 SNPs in the MHC Class II region surrounding the HLA-DRB1 gene. We also phased alleles at the HLA-A, HLA-C, HLA-B, HLA-DRB1, and HLA-DQB1 loci. This data was used to probe the relationship between CEHs and MS susceptibility. Results We phased a total of 59,884 extended haplotypes (HLA-A, HLA-C, HLA-B, HLA-DRB1, HLA-DQB1 and SNP haplotypes) from 29,942 individuals. Of these, 10,078 unique extended haplotypes were identified. The 10 most common CEHs accounted for 22% (13,302) of the total. By contrast, the 8,446 least common extended haplotypes also accounted for approximately 20% (12,298) of the total. This extreme frequency-disparity among extended haplotypes necessarily complicates interpretation of reported disease-associations with specific HLA alleles. In particular, the HLA motif HLA-DRB1*15:01~HLA-DQB1*06:02 is strongly associated with MS risk. Nevertheless, although this motif is almost always found on the a1 SNP haplotype, it can rarely be found on others (e.g., a27 and a36), and, in these cases, it seems to have no apparent disease-association (OR = 0.7; CI = 0.3–1.3 and OR = 0.7; CI = 0.2–2.2, respectively). Furthermore, single copy carriers of the a1 SNP-haplotype without this HLA motif still have an increased disease risk (OR = 2.2; CI = 1.2–3.8). In addition, even among the set of CEHs, which carry the Class II motif of HLA-DRB1*15:01~HLA-DQB1*06:02~a1, different CEHs have differing strengths in their MS-associations. Conclusions The MHC in diverse human populations consists, primarily, of a very small collection of very highly-selected CEHs. Our findings suggest that the MS-association with the HLA-DRB1*15:01~HLA-DQB1*06:02 haplotype may be due primarily to the combined attributes of the CEHs on which this particular HLA-motif often resides.
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Affiliation(s)
- Douglas S. Goodin
- Department of Neurology, University of California, San Francisco, CA, United States of America
- * E-mail:
| | - Pouya Khankhanian
- Center for Neuro-engineering and Therapeutics, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Pierre-Antoine Gourraud
- Department of Neurology, University of California, San Francisco, CA, United States of America
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
| | - Nicolas Vince
- Centre de Recherche en Transplantation et Immunologie UMR 1064, INSERM, Université de Nantes, Nantes, France
- Institut de Transplantation Urologie Néphrologie (ITUN), CHU Nantes, Nantes, France
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12
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Wang QS, Xiao HQ, Chen HX, Liu YP, Ding XD. The single nucleotide polymorphism site of aquaporin-4 gene in patients with neuromyelitis optica. Exp Ther Med 2017; 14:6017-6021. [PMID: 29285152 PMCID: PMC5740579 DOI: 10.3892/etm.2017.5267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 09/21/2017] [Indexed: 11/06/2022] Open
Abstract
The single nucleotide polymorphism (SNP) site within the aquaporin (AQP)-4 gene exons and its possible role in the pathogenesis of neuromyelitis optica (NMO) were studied. From March 2010 to June 2012, 72 patients with NMO from Xiangyang No. 1 People's Hospital, Hubei University of Medicine were enrolled in the NMO group. At the same time, 80 patients with multiple sclerosis (MS) were enrolled in our study as the MS group. Blood samples were collected and DNA was extracted for analysis of SNP sites of AQP4 gene. Specific site-directed mutagenesis method was used for site-directed mutagenesis on plasmid enhanced green fluorescence protein carrying AQP4 gene. Mutant plasmids were constructed and used for transfecting cell lines. The differences of anti-AQP4 antibody level in the cell line were analyzed. The possible correlation between AQP4 gene SNP sites and the pathogenesis of NMO were analyzed. In the NMO group, 6 SNP sites in AQP4 gene were located in exons 2 and 5. These included R108T, I110N, E280R, D281R, P295R and E317M. There was no SNP site in exons 1, 3 and 4. In the MS group, no SNP site was found in AQP4 gene. R108T, I110N, R108T/I110N, E280R/D281R, P295R and E317M cell lines were constructed in the NMO group, and anti-AQP4 antibody in the serum was compared between R108T/I110N, E280R/D281R and E317M cell lines and the original HEK293T cell line. The difference was statistically significant (P<0.05). The positive rate of anti-AQP4 antibody titer in serum was compared between R108T, I110N, R108T/I110N, E280R/D281R, P295R and E317M cell lines in the NMO group and the original cell line in the MS group. In conclusion, SNP sites in AQP4 gene in patients with NMO may lead to some conformational changes in AQP4 protein. This affects the antigenicity of AQP4 protein. The different intensity of antigen-antibody reaction may cause the differences of titer observed between the different mutant cell lines.
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Affiliation(s)
- Qing-Song Wang
- Department of Rehabilitation Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Hong-Qiong Xiao
- Department of Rehabilitation Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Hua-Xian Chen
- Department of Rehabilitation Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Yan-Ping Liu
- Department of Rehabilitation Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Xu-Dong Ding
- Department of Rehabilitation Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
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Al-Kawaz M, Monohan E, Morris E, Perumal JS, Nealon N, Vartanian T, Gauthier SA. Differential Impact of Multiple Sclerosis on Cortical and Deep Gray Matter Structures in African Americans and Caucasian Americans. J Neuroimaging 2016; 27:333-338. [PMID: 27634620 DOI: 10.1111/jon.12393] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 08/10/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND African Americans with multiple sclerosis (AAwMS) have different disease phenotypes when compared to Caucasians Americans with MS (CAwMS). The pathologic basis of this difference in disease presentation is unknown. METHODS Fifty-Four AAwMS and 54 CAwMS were appropriately matched for age, gender, treatment duration, and disease duration. FreeSurfer was used to segment brain white matter and gray matter from T1 images and compute thalamic volume. Regional cortical thickness was calculated using QDEC. RESULTS The 2 matched cohorts differed in disability, with AAwMS demonstrating significantly higher EDSS scores (2.3±2.2 vs. 1.3±1.5, P < .009), yet the 2 populations had similar T2 hyperintense lesion volumes (P = .35). AAwMS had a significantly lower total global cortical thickness when compared to CAwMS (P = .03). Controlling for EDSS, AAwMS showed multiple cortical regions to be significantly thinner than CAwMS; these included areas within the temporal, parietal and occipital lobes, as well as the precentral and postcentral gyrus. Middletemporal cortex was most affected in AAwMS in the left hemisphere (P = .009), while the superiortemporal cortex was most affected in the right hemisphere (P = .0001). In contrast, thalamic volume was significantly reduced in CAwMS when compared to AAwMS (P = .01). In both groups, worse disability was associated with lower total thalamic volume percentage. CONCLUSION AAwMS and CAwMS patients differ with regard to global and regional cortical thickness and thalamic volume. This diverging pattern of gray matter volumetrics among otherwise matched patients suggests that racial-specific disease differences may exist.
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Affiliation(s)
- Mais Al-Kawaz
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY
| | - Elizabeth Monohan
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY
| | - Eric Morris
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY
| | - Jai S Perumal
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY.,Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY
| | - Nancy Nealon
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY.,Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY
| | - Timothy Vartanian
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY.,Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY
| | - Susan A Gauthier
- Department of Neurology, New York Presbyterian Hospital/ Weill Cornell, New York, NY.,Brain and Mind Research Institute, Weill Cornell Medical College, New York, NY
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14
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van Rensburg SJ, van Toorn R, Moremi KE, Peeters AV, Oguniyi A, Kotze MJ. Multiple sclerosis-like diagnosis as a complication of previously treated malaria in an iron and vitamin D deficient Nigerian patient. Metab Brain Dis 2016; 31:197-204. [PMID: 26746433 DOI: 10.1007/s11011-015-9788-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 12/28/2015] [Indexed: 02/06/2023]
Abstract
In contrast to malaria, multiple sclerosis (MS) is infrequently found in Black Africans. We describe a 29 year old Nigerian female who developed an MS-like condition with symptoms similar to relapsing-remitting MS following malaria infection, leading to a diagnosis of MS. However, absence of hyperintense lesions in the brain and spinal cord presented a conundrum since not all the diagnostic criteria for MS were met. Pathology supported genetic testing (PSGT) was applied to combine family and personal medical history, lifestyle factors, and biochemical test results for interpretation of genetic findings. This approach provides a means of identifying risk factors for different subtypes of demyelinating disease. The patient was subsequently treated according to an individualised intervention program including nutritional supplementation as well as a change in diet and lifestyle. Deficiencies of vitamin B12, iron and vitamin D were addressed. Genetic analysis revealed absence of the HLA DRB1*1501 allele, considered to be the most prominent genetic risk factor for MS. Extended mutation analysis identified variations in three genes in the folate-vitamin B12 metabolic pathway, which could have increased the patient's sensitivity to the antifolate drugs used to treat the malaria. A glutathione-S-transferase GSTM1 null allele, previously associated with neurological complications of malaria, was also detected. Furthermore, a heterozygous variation in the iron-related transmembrane protease serine 6 (TMPRSS6) gene, rs855791 was found, which could have impacted the patient's iron status following two successive blood donations and exposure to malaria preceding the MS diagnosis. PSGT identifies relevant risk factors for demyelinating disorders resembling MS and uses the data for individualised treatment programs, and to systematically build a database that can provide evidence in large patient cohorts. Follow-up investigations may be suggested, such as whole exome sequencing in selected cases, to ensure that remyelination and restoration of function are achieved.
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Affiliation(s)
- Susan J van Rensburg
- Chemical Pathology, National Health Laboratory Service (NHLS) and Stellenbosch University, Cape Town, South Africa.
| | - Ronald van Toorn
- Paediatric Medicine and Child Health, Stellenbosch University, Cape Town, South Africa
| | - Kelebogile E Moremi
- Chemical Pathology, National Health Laboratory Service (NHLS) and Stellenbosch University, Cape Town, South Africa
| | - Armand V Peeters
- Anatomical Pathology, Stellenbosch University, Cape Town, South Africa
| | - Adesola Oguniyi
- Department of Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Maritha J Kotze
- Anatomical Pathology, Stellenbosch University, Cape Town, South Africa
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15
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Nicholas RS, Kostadima V, Hanspal M, Wakerley BR, Sergeant R, Decuypere S, Malik O, Boyton RJ, Altmann DM. MS in South Asians in England: early disease onset and novel pattern of myelin autoimmunity. BMC Neurol 2015; 15:72. [PMID: 25935418 PMCID: PMC4429974 DOI: 10.1186/s12883-015-0324-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidemiological studies describe a latitude gradient for increased MS prevalence and a preponderance of disease in Caucasian individuals. However, individuals from other ethnic backgrounds and low-risk regions can acquire a raised risk through migration. Nearly a fifth of the London population is of Asian/Asian-British origin and a significant proportion of referrals are from this group. METHODS We investigated whether there were differences in timing, presentation, severity, and immunology of disease (with respect to CD4 myelin epitope recognition) between individuals in London with MS who were either of S. Asian or Caucasian origin. Individuals of S. Asian origin with MS were compared with healthy S. Asian controls, individuals with MS and of Caucasian origin and Caucasian controls. RESULTS Age at MS onset is significantly lower in the S. Asian group, attributable to earlier onset specifically in UK-born individuals, though clinical presentation is similar. Analysis of CD4 autoimmunity to myelin antigens shows disease in S. Asian individuals to encompass recognition of novel epitopes; immunity to MBP116-130 in S. Asian individuals was highly disease-specific. CONCLUSIONS These findings emphasize the need to define disease profiles across ethnicities and identify environmental triggers conferring acquired risk. Such findings must inform choices for immunotherapeutic interventions suitable for all, across ethnicities.
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Affiliation(s)
- Richard S Nicholas
- Department of Clinical Neurosciences, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK.
| | - Vassiliki Kostadima
- Department of Medicine, Imperial College, Du Cane Road, London, W12 0NN, UK. .,Department of Clinical Neurosciences, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK.
| | - Maya Hanspal
- Department of Clinical Neurosciences, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK.
| | - Benjamin R Wakerley
- Department of Medicine, Imperial College, Du Cane Road, London, W12 0NN, UK. .,Department of Neurology, John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | - Ruhena Sergeant
- H & I Laboratory, Hammersmith Hospital Imperial College NHS trust, Du Cane Road, W12 0HS, London, UK.
| | - Saskia Decuypere
- Telethon Kids Institute, PO Box 855, West Perth, Western Australia, Australia.
| | - Omar Malik
- Department of Clinical Neurosciences, Imperial College Healthcare NHS Trust, Fulham Palace Road, London, W6 8RF, UK.
| | - Rosemary J Boyton
- Department of Medicine, Imperial College, Du Cane Road, London, W12 0NN, UK.
| | - Daniel M Altmann
- Department of Medicine, Imperial College, Du Cane Road, London, W12 0NN, UK.
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Abstract
One of the most consistent findings in multiple sclerosis (MS) is that development of MS is linked with carriage of the class II human leucocyte antigen (HLA) molecule HLA-DRB1*15:01; around 60 % of Caucasian MS patients carry this allele compared to 25-30 % of ethnically matched healthy individuals. However, other HLA molecules have also been linked to the development of MS. In this chapter, the association between different HLA types and susceptibility to MS will be reviewed, and other linkages between the carriage of specific HLA molecules and clinical and experimental findings in MS will be considered.
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Affiliation(s)
- Judith M Greer
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Riyal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia.
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17
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Jung Y, Huang JZ, Hu J. Biomarker Detection in Association Studies: Modeling SNPs Simultaneously via Logistic ANOVA. J Am Stat Assoc 2014; 109:1355-1367. [PMID: 25642005 DOI: 10.1080/01621459.2014.928217] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
In genome-wide association studies, the primary task is to detect biomarkers in the form of Single Nucleotide Polymorphisms (SNPs) that have nontrivial associations with a disease phenotype and some other important clinical/environmental factors. However, the extremely large number of SNPs comparing to the sample size inhibits application of classical methods such as the multiple logistic regression. Currently the most commonly used approach is still to analyze one SNP at a time. In this paper, we propose to consider the genotypes of the SNPs simultaneously via a logistic analysis of variance (ANOVA) model, which expresses the logit transformed mean of SNP genotypes as the summation of the SNP effects, effects of the disease phenotype and/or other clinical variables, and the interaction effects. We use a reduced-rank representation of the interaction-effect matrix for dimensionality reduction, and employ the L1-penalty in a penalized likelihood framework to filter out the SNPs that have no associations. We develop a Majorization-Minimization algorithm for computational implementation. In addition, we propose a modified BIC criterion to select the penalty parameters and determine the rank number. The proposed method is applied to a Multiple Sclerosis data set and simulated data sets and shows promise in biomarker detection.
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Affiliation(s)
- Yoonsuh Jung
- Department of Statistics, Univerisity of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Jianhua Z Huang
- Department of Statistics, Texas A&M University, College Station, TX, USA, and Special Term Professor at ISEM, Captial University of Economics and Business, Beijing, China
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Gourraud PA, Khankhanian P, Cereb N, Yang SY, Feolo M, Maiers M, D. Rioux J, Hauser S, Oksenberg J. HLA diversity in the 1000 genomes dataset. PLoS One 2014; 9:e97282. [PMID: 24988075 PMCID: PMC4079705 DOI: 10.1371/journal.pone.0097282] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 04/17/2014] [Indexed: 12/20/2022] Open
Abstract
The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation by sequencing at a level that should allow the genome-wide detection of most variants with frequencies as low as 1%. However, in the major histocompatibility complex (MHC), only the top 10 most frequent haplotypes are in the 1% frequency range whereas thousands of haplotypes are present at lower frequencies. Given the limitation of both the coverage and the read length of the sequences generated by the 1000 Genomes Project, the highly variable positions that define HLA alleles may be difficult to identify. We used classical Sanger sequencing techniques to type the HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genes in the available 1000 Genomes samples and combined the results with the 103,310 variants in the MHC region genotyped by the 1000 Genomes Project. Using pairwise identity-by-descent distances between individuals and principal component analysis, we established the relationship between ancestry and genetic diversity in the MHC region. As expected, both the MHC variants and the HLA phenotype can identify the major ancestry lineage, informed mainly by the most frequent HLA haplotypes. To some extent, regions of the genome with similar genetic or similar recombination rate have similar properties. An MHC-centric analysis underlines departures between the ancestral background of the MHC and the genome-wide picture. Our analysis of linkage disequilibrium (LD) decay in these samples suggests that overestimation of pairwise LD occurs due to a limited sampling of the MHC diversity. This collection of HLA-specific MHC variants, available on the dbMHC portal, is a valuable resource for future analyses of the role of MHC in population and disease studies.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Pouya Khankhanian
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Nezih Cereb
- Histogenetics Inc., Ossining, New York, United States of America
| | - Soo Young Yang
- Histogenetics Inc., Ossining, New York, United States of America
| | - Michael Feolo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Martin Maiers
- National Marrow Donor Program, Minneapolis, Minnesota, United States of America
| | - John D. Rioux
- Université de Montréal Institut de Cardiologie de Montréal, Montréal, Quebec, Canada
| | - Stephen Hauser
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Jorge Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
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19
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Novel insights into autoimmune liver diseases provided by genome-wide association studies. J Autoimmun 2013; 46:41-54. [DOI: 10.1016/j.jaut.2013.07.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 12/14/2022]
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20
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Isobe N, Gourraud PA, Harbo HF, Caillier SJ, Santaniello A, Khankhanian P, Maiers M, Spellman S, Cereb N, Yang S, Pando MJ, Piccio L, Cross AH, De Jager PL, Cree BAC, Hauser SL, Oksenberg JR. Genetic risk variants in African Americans with multiple sclerosis. Neurology 2013; 81:219-27. [PMID: 23771490 PMCID: PMC3770164 DOI: 10.1212/wnl.0b013e31829bfe2f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/04/2013] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES To assess the association of established multiple sclerosis (MS) risk variants in 3,254 African Americans (1,162 cases and 2,092 controls). METHODS Human leukocyte antigen (HLA)-DRB1, HLA-DQB1, and HLA-A alleles were typed by molecular techniques. Single nucleotide polymorphism (SNP) genotyping was conducted for 76 MS-associated SNPs and 52 ancestry informative marker SNPs selected throughout the genome. Self-declared ancestry was refined by principal component analysis of the ancestry informative marker SNPs. An ancestry-adjusted multivariate model was applied to assess genetic associations. RESULTS The following major histocompatibility complex risk alleles were replicated: HLA-DRB1*15:01 (odds ratio [OR] = 2.02 [95% confidence interval: 1.54-2.63], p = 2.50e-07), HLA-DRB1*03:01 (OR = 1.58 [1.29-1.94], p = 1.11e-05), as well as HLA-DRB1*04:05 (OR = 2.35 [1.26-4.37], p = 0.007) and the African-specific risk allele of HLA-DRB1*15:03 (OR = 1.26 [1.05-1.51], p = 0.012). The protective association of HLA-A*02:01 was confirmed (OR = 0.72 [0.55-0.93], p = 0.013). None of the HLA-DQB1 alleles were associated with MS. Using a significance threshold of p < 0.01, outside the major histocompatibility complex region, 8 MS SNPs were also found to be associated with MS in African Americans. CONCLUSION MS genetic risk in African Americans only partially overlaps with that of Europeans and could explain the difference of MS prevalence between populations.
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Affiliation(s)
- Noriko Isobe
- Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
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Goris A, Pauwels I, Dubois B. Progress in multiple sclerosis genetics. Curr Genomics 2013; 13:646-63. [PMID: 23730204 PMCID: PMC3492804 DOI: 10.2174/138920212803759695] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 09/20/2012] [Accepted: 09/24/2012] [Indexed: 01/06/2023] Open
Abstract
A genetic component in the susceptibility to multiple sclerosis (MS) has long been known, and the first and major genetic risk factor, the HLA region, was identified in the 1970’s. However, only with the advent of genome-wide association studies in the past five years did the list of risk factors for MS grow from 1 to over 50. In this review, we summarize the search for MS risk genes and the latest results. Comparison with data from other autoimmune and neurological diseases and from animal models indicates parallels and differences between diseases. We discuss how these translate into an improved understanding of disease mechanisms, and address current challenges such as genotype-phenotype correlations, functional mechanisms of risk variants and the missing heritability.
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Affiliation(s)
- An Goris
- Laboratory for Neuroimmunology, Section of Experimental Neurology, KU Leuven, Leuven, Belgium
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Gourraud PA, Harbo HF, Hauser SL, Baranzini SE. The genetics of multiple sclerosis: an up-to-date review. Immunol Rev 2012. [PMID: 22725956 DOI: 10.1111/j.1600-065x.2012.01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Multiple sclerosis (MS) is a prevalent inflammatory disease of the central nervous system that often leads to disability in young adults. Treatment options are limited and often only partly effective. The disease is likely caused by a complex interaction between multiple genes and environmental factors, leading to inflammatory-mediated central nervous system deterioration. A series of genomic studies have confirmed a central role for the immune system in the development of MS, including genetic association studies that have now dramatically expanded the roster of MS susceptibility genes beyond the longstanding human leukocyte antigen (HLA) association in MS first identified nearly 40 years ago. Advances in technology together with novel models for collaboration across research groups have enabled the discovery of more than 50 non-HLA genetic risk factors associated with MS. However, with a large proportion of the disease heritability still unaccounted for, current studies are now geared towards identification of causal alleles, associated pathways, epigenetic mechanisms, and gene-environment interactions. This article reviews recent efforts in addressing the genetics of MS and the challenges posed by an ever increasing amount of analyzable data, which is spearheading development of novel statistical methods necessary to cope with such complexity.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143-0435, USA
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Wallin MT, Culpepper WJ, Coffman P, Pulaski S, Maloni H, Mahan CM, Haselkorn JK, Kurtzke JF. The Gulf War era multiple sclerosis cohort: age and incidence rates by race, sex and service. ACTA ACUST UNITED AC 2012; 135:1778-85. [PMID: 22628389 DOI: 10.1093/brain/aws099] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We characterize here a new nationwide incident cohort of multiple sclerosis from the US military-veteran population. This cohort provides an update to the only other US nationwide incidence study of multiple sclerosis performed during the 1970s. Medical records and data from the Department of Defense and Department of Veterans Affairs for cases of multiple sclerosis who served in the military between 1990, the start of the Gulf War era, and 2007 and who were service-connected for this disorder by the Department of Veterans Affairs from 1990 on, were reviewed. A total of 2691 patients were confirmed as having multiple sclerosis: 2288 definite, 190 possible, 207 clinically isolated syndrome and six neuromyelitis optica. Overall racial categories were White, Black and other, which included all Hispanics. There were 1278 White males and 556 females; 360 Black males and 296 females; and 200 others, 153 (77%) of whom were Hispanic. Mean age at onset of 30.7 years did not differ significantly by race or sex. Age at onset was 17-50 years in 99%, the same age range as 99% of the military. Average annual age specific (age 17-50 years) incidence rates per 100 000 for the entire series were 9.6 with 95% confidence interval of 9.3-10.0. Rates for Blacks were highest at 12.1 with confidence interval 11.2-13.1, Whites were 9.3 (interval 8.9-9.8) and others 6.9 (interval 6.0-7.9). For 83 Hispanics defined for 2000-07, the rate was 8.2 (interval 6.5-10.1). Much smaller numbers gave rates of 3.3 for Asian/Pacific Islanders and 3.1 for native Americans. Rates by sex for Whites were 7.3 and 25.8 male and female, respectively, for Blacks 8.4 and 26.3, and for Hispanics 6.6 and 17.0. Rates by service were high for Air Force (10.9) and Army (10.6), medium for Navy (9.1) and Coast Guard (7.9), and low for Marines (5.3). Relative risk of multiple sclerosis was 3.39 female:male and 1.27 Black:White. These new findings indicate that females of all races now have incidence rates for multiple sclerosis some three times those of their male counterparts and that among these groups, Blacks have the highest and others (probably including Hispanics) the lowest incidence rates regardless of sex or service. The low rate for Marines is unexplained. This Gulf War era multiple sclerosis cohort provides a unique resource for further study.
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Affiliation(s)
- Mitchell T Wallin
- Neurology Service, Department of Veterans Affairs Medical Centre, Washington, DC 20422, USA.
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Abstract
Multiple sclerosis (MS) is a prevalent inflammatory disease of the central nervous system that often leads to disability in young adults. Treatment options are limited and often only partly effective. The disease is likely caused by a complex interaction between multiple genes and environmental factors, leading to inflammatory-mediated central nervous system deterioration. A series of genomic studies have confirmed a central role for the immune system in the development of MS, including genetic association studies that have now dramatically expanded the roster of MS susceptibility genes beyond the longstanding human leukocyte antigen (HLA) association in MS first identified nearly 40 years ago. Advances in technology together with novel models for collaboration across research groups have enabled the discovery of more than 50 non-HLA genetic risk factors associated with MS. However, with a large proportion of the disease heritability still unaccounted for, current studies are now geared towards identification of causal alleles, associated pathways, epigenetic mechanisms, and gene-environment interactions. This article reviews recent efforts in addressing the genetics of MS and the challenges posed by an ever increasing amount of analyzable data, which is spearheading development of novel statistical methods necessary to cope with such complexity.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
| | - Hanne F. Harbo
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Stephen L. Hauser
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
| | - Sergio E. Baranzini
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
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Alcina A, Abad-Grau MDM, Fedetz M, Izquierdo G, Lucas M, Fernández Ó, Ndagire D, Catalá-Rabasa A, Ruiz A, Gayán J, Delgado C, Arnal C, Matesanz F. Multiple sclerosis risk variant HLA-DRB1*1501 associates with high expression of DRB1 gene in different human populations. PLoS One 2012; 7:e29819. [PMID: 22253788 PMCID: PMC3258250 DOI: 10.1371/journal.pone.0029819] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 12/06/2011] [Indexed: 01/19/2023] Open
Abstract
The human leukocyte antigen (HLA) DRB1*1501 has been consistently associated with multiple sclerosis (MS) in nearly all populations tested. This points to a specific antigen presentation as the pathogenic mechanism though this does not fully explain the disease association. The identification of expression quantitative trait loci (eQTL) for genes in the HLA locus poses the question of the role of gene expression in MS susceptibility. We analyzed the eQTLs in the HLA region with respect to MS-associated HLA-variants obtained from genome-wide association studies (GWAS). We found that the Tag of DRB1*1501, rs3135388 A allele, correlated with high expression of DRB1, DRB5 and DQB1 genes in a Caucasian population. In quantitative terms, the MS-risk AA genotype carriers of rs3135388 were associated with 15.7-, 5.2- and 8.3-fold higher expression of DQB1, DRB5 and DRB1, respectively, than the non-risk GG carriers. The haplotype analysis of expression-associated variants in a Spanish MS cohort revealed that high expression of DRB1 and DQB1 alone did not contribute to the disease. However, in Caucasian, Asian and African American populations, the DRB1*1501 allele was always highly expressed. In other immune related diseases such as type 1 diabetes, inflammatory bowel disease, ulcerative colitis, asthma and IgA deficiency, the best GWAS-associated HLA SNPs were also eQTLs for different HLA Class II genes. Our data suggest that the DR/DQ expression levels, together with specific structural properties of alleles, seem to be the causal effect in MS and in other immunopathologies rather than specific antigen presentation alone.
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Affiliation(s)
- Antonio Alcina
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
- * E-mail: (FM); (AA)
| | - María del Mar Abad-Grau
- Departamento de Lenguajes y Sistemas Informáticos, CITIC, Universidad de Granada, Granada, Spain
| | - María Fedetz
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | | | - Miguel Lucas
- Servicio de Biología Molecular, Hospital Virgen Macarena, Sevilla, Spain
| | - Óscar Fernández
- Servicio de Neurología, Instituto de Neurociencias Clínicas, Hospital Carlos Haya, Málaga, Spain
| | - Dorothy Ndagire
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Antonio Catalá-Rabasa
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Agustín Ruiz
- Departamento de Genómica Estructural, Neocodex, Sevilla, Spain
| | - Javier Gayán
- Departamento de Genómica Estructural, Neocodex, Sevilla, Spain
| | | | - Carmen Arnal
- Servicio de Neurología, Hospital Virgen de las Nieves, Granada, Spain
| | - Fuencisla Matesanz
- Instituto de Parasitología y Biomedicina “López Neyra”, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
- Unidad de Esclerosis Múltiple, Hospital Virgen Macarena, Sevilla, Spain
- * E-mail: (FM); (AA)
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Folseraas T, Melum E, Franke A, Karlsen TH. Genetics in primary sclerosing cholangitis. Best Pract Res Clin Gastroenterol 2011; 25:713-26. [PMID: 22117637 DOI: 10.1016/j.bpg.2011.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Accepted: 09/30/2011] [Indexed: 01/31/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a chronic and severe inflammatory disease leading to fibrotic bile duct destruction and in most cases liver cirrhosis. As in other complex genetic diseases, the sibling risk of PSC is more than ten times that of the general population. Recent genome-wide association studies have consistently identified several genetic susceptibility loci. The overlap of these loci with susceptibility loci in other chronic inflammatory diseases is considerable, and offers intriguing opportunities for transfer of pathogenetic knowledge and potentially treatment options. In the present article we summarise the present knowledge on PSC genetics with a particular emphasis on the major histocompatibility complex (MHC). We discuss the clinical relevance of the risk loci and elaborate on the insight that may be obtained from associated inflammatory conditions and existing murine knock-out models.
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Affiliation(s)
- Trine Folseraas
- Norwegian PSC Research Center, Clinic for Specialized Medicine and Surgery, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway
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McElroy JP, Isobe N, Gourraud PA, Caillier SJ, Matsushita T, Kohriyama T, Miyamoto K, Nakatsuji Y, Miki T, Hauser SL, Oksenberg JR, Kira J. SNP-based analysis of the HLA locus in Japanese multiple sclerosis patients. Genes Immun 2011; 12:523-30. [PMID: 21654846 DOI: 10.1038/gene.2011.25] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Although several major histocompatibility complex (MHC)-wide single-nucleotide polymorphism (SNP) studies have been performed in populations of European descent, none have been performed in Asian populations. The objective of this study was to identify human leukocyte antigen (HLA) loci associated with multiple sclerosis (MS) in a Japanese population genotyped for 3534 MHC region SNPs. Using a logistic regression model, two SNPs (MHC Class III SNP rs422951 in the NOTCH4 gene and MHC Class II SNP rs3997849, susceptible alleles A and G, respectively) were independently associated with MS susceptibility (204 patients; 280 controls), two (MHC Class II SNP rs660895 and MHC Class I SNP rs2269704 in the NRM gene, susceptible alleles G and G, respectively) with aquaporin-4- (AQP4-) MS susceptibility (149 patients; 280 controls) and a single SNP (MHC Class II SNP rs1694112, susceptible allele G) was significant when contrasting AQP4+ against AQP4- patients. Haplotype analysis revealed a large susceptible association, likely DRB1*04 or a locus included in the DRB1*04 haplotype, with AQP4- MS, which excluded DRB1*15:01. This study is the largest study of the HLA's contribution to MS in Japanese individuals.
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Affiliation(s)
- J P McElroy
- Department of Neurology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA.
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Meyer NJ, Li M, Feng R, Bradfield J, Gallop R, Bellamy S, Fuchs BD, Lanken PN, Albelda SM, Rushefski M, Aplenc R, Abramova H, Atochina-Vasserman EN, Beers MF, Calfee CS, Cohen MJ, Pittet JF, Christiani DC, O'Keefe GE, Ware LB, May AK, Wurfel MM, Hakonarson H, Christie JD. ANGPT2 genetic variant is associated with trauma-associated acute lung injury and altered plasma angiopoietin-2 isoform ratio. Am J Respir Crit Care Med 2011; 183:1344-53. [PMID: 21257790 DOI: 10.1164/rccm.201005-0701oc] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RATIONALE Acute lung injury (ALI) acts as a complex genetic trait, yet its genetic risk factors remain incompletely understood. Large-scale genotyping has not previously been reported for ALI. OBJECTIVES To identify ALI risk variants after major trauma using a large-scale candidate gene approach. METHODS We performed a two-stage genetic association study. We derived findings in an African American cohort (n = 222) using a cardiopulmonary disease-centric 50K single nucleotide polymorphism (SNP) array. Genotype and haplotype distributions were compared between subjects with ALI and without ALI, with adjustment for clinical factors. Top performing SNPs (P < 10(-4)) were tested in a multicenter European American trauma-associated ALI case-control population (n = 600 ALI; n = 2,266 population-based control subjects) for replication. The ALI-associated genomic region was sequenced, analyzed for in silico prediction of function, and plasma was assayed by ELISA and immunoblot. MEASUREMENTS AND MAIN RESULTS Five SNPs demonstrated a significant association with ALI after adjustment for covariates in Stage I. Two SNPs in ANGPT2 (rs1868554 and rs2442598) replicated their significant association with ALI in Stage II. rs1868554 was robust to multiple comparison correction: odds ratio 1.22 (1.06-1.40), P = 0.0047. Resequencing identified predicted novel splice sites in linkage disequilibrium with rs1868554, and immunoblots showed higher proportion of variant angiopoietin-2 (ANG2) isoform associated with rs1868554T (0.81 vs. 0.48; P = 0.038). CONCLUSIONS An ANGPT2 region is associated with both ALI and variation in plasma angiopoietin-2 isoforms. Characterization of the variant isoform and its genetic regulation may yield important insights about ALI pathogenesis and susceptibility.
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Affiliation(s)
- Nuala J Meyer
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.
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A polymorphism in the HLA-DPB1 gene is associated with susceptibility to multiple sclerosis. PLoS One 2010; 5:e13454. [PMID: 21049023 PMCID: PMC2964313 DOI: 10.1371/journal.pone.0013454] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 08/26/2010] [Indexed: 01/10/2023] Open
Abstract
We conducted an association study across the human leukocyte antigen (HLA) complex to identify loci associated with multiple sclerosis (MS). Comparing 1927 SNPs in 1618 MS cases and 3413 controls of European ancestry, we identified seven SNPs that were independently associated with MS conditional on the others (each P ≤ 4 x 10(-6)). All associations were significant in an independent replication cohort of 2212 cases and 2251 controls (P ≤ 0.001) and were highly significant in the combined dataset (P ≤ 6 x 10(-8)). The associated SNPs included proxies for HLA-DRB1*15:01 and HLA-DRB1*03:01, and SNPs in moderate linkage disequilibrium (LD) with HLA-A*02:01, HLA-DRB1*04:01 and HLA-DRB1*13:03. We also found a strong association with rs9277535 in the class II gene HLA-DPB1 (discovery set P = 9 x 10(-9), replication set P = 7 x 10(-4), combined P = 2 x 10(-10)). HLA-DPB1 is located centromeric of the more commonly typed class II genes HLA-DRB1, -DQA1 and -DQB1. It is separated from these genes by a recombination hotspot, and the association is not affected by conditioning on genotypes at DRB1, DQA1 and DQB1. Hence rs9277535 represents an independent MS-susceptibility locus of genome-wide significance. It is correlated with the HLA-DPB1*03:01 allele, which has been implicated previously in MS in smaller studies. Further genotyping in large datasets is required to confirm and resolve this association.
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Maugeri N, Radhakrishnan J, Knight JC. Genetic determinants of HSP70 gene expression following heat shock. Hum Mol Genet 2010; 19:4939-47. [PMID: 20876613 PMCID: PMC2989893 DOI: 10.1093/hmg/ddq418] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The regulation of heat shock protein expression is of significant physiological and pathophysiological significance. Here we show that genetic diversity is an important determinant of heat shock protein 70 expression involving local, likely cis-acting, polymorphisms. We define DNA sequence variation for the highly homologous HSPA1A and HSPA1B genes in the major histocompatibility complex on chromosome 6p21 and establish quantitative and specific assays for determining transcript abundance. We show for lymphoblastoid cell lines established from individuals of African ancestry that following heat shock, expression of HSPA1B is associated with rs400547 (P 3.88 × 10−8) and linked single nucleotide polymorphisms (SNPs) located 62–93 kb telomeric to HSPA1B. This association was found to explain 31 and 29% of the variance in HSPA1B expression following heat shock or in resting cells, respectively. The associated SNPs show marked variation in minor allele frequency among populations, being more common in individuals of African ancestry, and are located in a region showing population-specific haplotypic block structure. The work illustrates how analysis of a heritable induced expression phenotype can be highly informative in defining functionally important genetic variation.
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Affiliation(s)
- Narelle Maugeri
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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