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Liang H, Sedillo JC, Schrodi SJ, Ikeda A. Structural variants in linkage disequilibrium with GWAS-significant SNPs. Heliyon 2024; 10:e32053. [PMID: 38882374 PMCID: PMC11177133 DOI: 10.1016/j.heliyon.2024.e32053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/17/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
With the recent expansion of structural variant identification in the human genome, understanding the role of these impactful variants in disease architecture is critically important. Currently, a large proportion of genome-wide-significant genome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are functionally unresolved, raising the possibility that some of these SNPs are associated with disease through linkage disequilibrium with causal structural variants. Hence, understanding the linkage disequilibrium between newly discovered structural variants and statistically significant SNPs may provide a resource for further investigation into disease-associated regions in the genome. Here we present a resource cataloging structural variant-significant SNP pairs in high linkage disequilibrium. The database is composed of (i) SNPs that have exhibited genome-wide significant association with traits, primarily disease phenotypes, (ii) newly released structural variants (SVs), and (iii) linkage disequilibrium values calculated from unphased data. All data files including those detailing SV and GWAS SNP associations and results of GWAS-SNP-SV pairs are available at the SV-SNP LD Database and can be accessed at 'https://github.com/hliang-SchrodiLab/SV_SNPs. Our analysis results represent a useful fine mapping tool for interrogating SVs in linkage disequilibrium with disease-associated SNPs. We anticipate that this resource may play an important role in subsequent studies which investigate incorporating disease causing SVs into disease risk prediction models.
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Affiliation(s)
- Hao Liang
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Joni C Sedillo
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Steven J Schrodi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
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2
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Evans F, Alí-Ruiz D, Rego N, Negro-Demontel ML, Lago N, Cawen FA, Pannunzio B, Sanchez-Molina P, Reyes L, Paolino A, Rodríguez-Duarte J, Pérez-Torrado V, Chicote-González A, Quijano C, Marmisolle I, Mulet AP, Schlapp G, Meikle MN, Bresque M, Crispo M, Savio E, Malagelada C, Escande C, Peluffo H. CD300f immune receptor contributes to healthy aging by regulating inflammaging, metabolism, and cognitive decline. Cell Rep 2023; 42:113269. [PMID: 37864797 DOI: 10.1016/j.celrep.2023.113269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023] Open
Abstract
Emerging evidence suggests that immune receptors may participate in many aging-related processes such as energy metabolism, inflammation, and cognitive decline. CD300f, a TREM2-like lipid-sensing immune receptor, is an exceptional receptor as it integrates activating and inhibitory cell-signaling pathways that modulate inflammation, efferocytosis, and microglial metabolic fitness. We hypothesize that CD300f can regulate systemic aging-related processes and ultimately healthy lifespan. We closely followed several cohorts of two strains of CD300f-/- and WT mice of both sexes for 30 months and observed an important reduction in lifespan and healthspan in knockout mice. This was associated with systemic inflammaging, increased cognitive decline, reduced brain glucose uptake observed by 18FDG PET scans, enrichment in microglial aging/neurodegeneration phenotypes, proteostasis alterations, senescence, increased frailty, and sex-dependent systemic metabolic changes. Moreover, the absence of CD300f altered macrophage immunometabolic phenotype. Taken together, we provide strong evidence suggesting that myeloid cell CD300f immune receptor contributes to healthy aging.
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Affiliation(s)
- Frances Evans
- Department of Histology and Embryology, Faculty of Medicine, UDELAR, Montevideo, Uruguay; Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Daniela Alí-Ruiz
- Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay; Faculty of Sciences, UDELAR, Montevideo, Uruguay
| | - María Luciana Negro-Demontel
- Department of Histology and Embryology, Faculty of Medicine, UDELAR, Montevideo, Uruguay; Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Natalia Lago
- Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Fabio Andrés Cawen
- Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Bruno Pannunzio
- Department of Histology and Embryology, Faculty of Medicine, UDELAR, Montevideo, Uruguay; Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Paula Sanchez-Molina
- Department of Cell Biology, Physiology and Immunology, and Institute of Neuroscience, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laura Reyes
- Uruguayan Center for Molecular Imaging (CUDIM), Montevideo, Uruguay
| | - Andrea Paolino
- Uruguayan Center for Molecular Imaging (CUDIM), Montevideo, Uruguay
| | - Jorge Rodríguez-Duarte
- Laboratory of Vascular Biology and Drug Development, INDICYO Program, Institut Pasteur Montevideo, Montevideo, Uruguay
| | - Valentina Pérez-Torrado
- Metabolic Diseases and Aging Laboratory, INDICYO Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Almudena Chicote-González
- Unitat de Bioquímica i Biologia Molecular, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Neurociències, Universitat de Barcelona (UB), Barcelona, Spain
| | - Celia Quijano
- Departamento de Bioquímica y Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Inés Marmisolle
- Departamento de Bioquímica y Centro de Investigaciones Biomédicas (CEINBIO), Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ana Paula Mulet
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Geraldine Schlapp
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María Noel Meikle
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Mariana Bresque
- Metabolic Diseases and Aging Laboratory, INDICYO Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Martina Crispo
- Unidad de Biotecnología en Animales de Laboratorio, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Eduardo Savio
- Uruguayan Center for Molecular Imaging (CUDIM), Montevideo, Uruguay
| | - Cristina Malagelada
- Unitat de Bioquímica i Biologia Molecular, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Neurociències, Universitat de Barcelona (UB), Barcelona, Spain
| | - Carlos Escande
- Metabolic Diseases and Aging Laboratory, INDICYO Program, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Hugo Peluffo
- Department of Histology and Embryology, Faculty of Medicine, UDELAR, Montevideo, Uruguay; Neuroinflammation and Gene Therapy Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay; Unitat de Bioquímica i Biologia Molecular, Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain; Institut de Neurociències, Universitat de Barcelona (UB), Barcelona, Spain.
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3
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Papiri G, D’Andreamatteo G, Cacchiò G, Alia S, Silvestrini M, Paci C, Luzzi S, Vignini A. Multiple Sclerosis: Inflammatory and Neuroglial Aspects. Curr Issues Mol Biol 2023; 45:1443-1470. [PMID: 36826039 PMCID: PMC9954863 DOI: 10.3390/cimb45020094] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Multiple sclerosis (MS) represents the most common acquired demyelinating disorder of the central nervous system (CNS). Its pathogenesis, in parallel with the well-established role of mechanisms pertaining to autoimmunity, involves several key functions of immune, glial and nerve cells. The disease's natural history is complex, heterogeneous and may evolve over a relapsing-remitting (RRMS) or progressive (PPMS/SPMS) course. Acute inflammation, driven by infiltration of peripheral cells in the CNS, is thought to be the most relevant process during the earliest phases and in RRMS, while disruption in glial and neural cells of pathways pertaining to energy metabolism, survival cascades, synaptic and ionic homeostasis are thought to be mostly relevant in long-standing disease, such as in progressive forms. In this complex scenario, many mechanisms originally thought to be distinctive of neurodegenerative disorders are being increasingly recognized as crucial from the beginning of the disease. The present review aims at highlighting mechanisms in common between MS, autoimmune diseases and biology of neurodegenerative disorders. In fact, there is an unmet need to explore new targets that might be involved as master regulators of autoimmunity, inflammation and survival of nerve cells.
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Affiliation(s)
- Giulio Papiri
- Neurology Unit, Ospedale Provinciale “Madonna del Soccorso”, 63074 San Benedetto del Tronto, Italy
| | - Giordano D’Andreamatteo
- Neurology Unit, Ospedale Provinciale “Madonna del Soccorso”, 63074 San Benedetto del Tronto, Italy
| | - Gabriella Cacchiò
- Neurology Unit, Ospedale Provinciale “Madonna del Soccorso”, 63074 San Benedetto del Tronto, Italy
| | - Sonila Alia
- Section of Biochemistry, Biology and Physics, Department of Clinical Sciences, Università Politecnica delle Marche, 60100 Ancona, Italy
| | - Mauro Silvestrini
- Neurology Unit, Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60100 Ancona, Italy
| | - Cristina Paci
- Neurology Unit, Ospedale Provinciale “Madonna del Soccorso”, 63074 San Benedetto del Tronto, Italy
| | - Simona Luzzi
- Neurology Unit, Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, 60100 Ancona, Italy
| | - Arianna Vignini
- Section of Biochemistry, Biology and Physics, Department of Clinical Sciences, Università Politecnica delle Marche, 60100 Ancona, Italy
- Correspondence:
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4
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Pragya SU, Pragya SC, Griswold AJ, Gu E, Mehta ND, Uddin P, Veeramachaneni P, Mehta N, Mehta D, Abomoelak B. Preksha Dhyāna Meditation Effect on the DNA Methylation Signature in College Students. JOURNAL OF INTEGRATIVE AND COMPLEMENTARY MEDICINE 2023; 29:224-233. [PMID: 36749149 DOI: 10.1089/jicm.2022.0713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: The stress and psychological factors affect the human transcriptomic and epigenomic landscapes. Preksha Dhyana meditation (PM) was found to be effective, in novice healthy college student meditators, at the cognitive skills and transcriptomic levels. Recently published data showed that PM induced alterations at the transcriptome level in healthy and novice college students. Methods: To decipher potential mechanisms underlying the PM effect at the cellular level, array-based methylation analyses in peripheral blood were performed at baseline and 8 weeks postintervention in 34 participants. Results: Overall, 470 CpG sites were nominally differentially methylated (p ≤ 0.05 and change magnitude from ≥3% to ≤ -3%) between baseline and 8 weeks postintervention with 180 sites hypermethylated and 290 sites hypomethylated. Pathway analysis of the genes linked to the differentially methylated sites revealed the enrichment of several molecular and cellular signaling pathways, especially metabolic and brain function signaling pathways. Conclusions: Besides its beneficial effects on cognitive skills and transcriptome alterations, the current data indicate that PM meditation also affects the DNA methylation profile of novice and healthy college students 8 weeks postintervention. Clinical Trial Registration number: NCT03779269.
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Affiliation(s)
- Samani U Pragya
- Department of Religions and Philosophies, University of London, London, United Kingdom
| | - Samani C Pragya
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Esther Gu
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Neelam D Mehta
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Parvin Uddin
- College of Arts, Sciences and Education, Florida International University, Miami, FL, USA
| | | | - Naina Mehta
- Neurodevelopmental Pediatrician, Behavioral and Developmental Center, Orlando Health, Orlando, FL, USA
| | - Devendra Mehta
- Gastrointestinal Translational Laboratory, Arnold Palmer Hospital for Children, Orlando, FL, USA
| | - Bassam Abomoelak
- Gastrointestinal Translational Laboratory, Arnold Palmer Hospital for Children, Orlando, FL, USA
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5
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Investigating the shared genetic architecture between multiple sclerosis and inflammatory bowel diseases. Nat Commun 2021; 12:5641. [PMID: 34561436 PMCID: PMC8463615 DOI: 10.1038/s41467-021-25768-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/31/2021] [Indexed: 12/15/2022] Open
Abstract
An epidemiological association between multiple sclerosis (MS) and inflammatory bowel disease (IBD) is well established, but whether this reflects a shared genetic aetiology, and whether consistent genetic relationships exist between MS and the two predominant IBD subtypes, ulcerative colitis (UC) and Crohn’s disease (CD), remains unclear. Here, we use large-scale genome-wide association study summary data to investigate the shared genetic architecture between MS and IBD overall and UC and CD independently. We find a significantly greater genetic correlation between MS and UC than between MS and CD, and identify three SNPs shared between MS and IBD (rs13428812), UC (rs116555563) and CD (rs13428812, rs9977672) in cross-trait meta-analyses. We find suggestive evidence for a causal effect of MS on UC and IBD using Mendelian randomization, but no or weak and inconsistent evidence for a causal effect of IBD or UC on MS. We observe largely consistent patterns of tissue-specific heritability enrichment for MS and IBDs in lung, spleen, whole blood and small intestine, and identify cell-type-specific enrichment for MS and IBDs in CD4+ T cells in lung and CD8+ cytotoxic T cells in lung and spleen. Our study sheds light on the biological basis of comorbidity between MS and IBD. An epidemiological association between multiple sclerosis (MS) and inflammatory bowel disease (IBD) is well-established, but a genetic link is unclear. Here, the authors investigate the shared genetic architecture between MS and IBD to shed light on the biological basis of comorbidity.
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6
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Lim WY, Lee H, Cho YS. Identification of genetic variants for blood insulin level in sex-stratified Korean population and evaluation of the causal relationship between blood insulin level and polycystic ovary syndrome. Genes Genomics 2021; 43:1105-1117. [PMID: 34304350 DOI: 10.1007/s13258-021-01134-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 06/24/2021] [Indexed: 01/06/2023]
Abstract
BACKGROUND Blood insulin level is an important risk factor for numerous disorders. Individual blood insulin level is known to be substantially influenced by genetic factors. Several genetic association studies identified a number of genetic variants for blood insulin level, but none of them was from a sex-stratified population. OBJECTIVE This study aimed to identify male- and female-specific genetic variants related to blood insulin level and to evaluate the causal relationship between blood insulin level and polycystic ovary syndrome (PCOS) that is likely caused by high insulin in Korean women. METHODS A genome-wide association study was conducted to identify genetic variants influencing blood insulin level in males (N = 4183) and females (N = 4659) in the Korean population. Two-sample Mendelian randomization (MR) analysis was used to investigate the causal effects of the insulin variants identified from GWAS on PCOS in Korean women. Genetic association data for PCOS were obtained from a PCOS study cohort (946 cases, 976 controls) in Ewha Womans University Hospital. RESULTS GWAS linear regression analysis identified 13 female-specific SNPs and 13 male-specific SNPs showing suggestive associations (P < 10-5) with blood insulin level. The results from two-sample MR analysis using the GWAS variants for PCOS indicated that genetically determined insulin level was not associated with the risk of PCOS in Korean women. CONCLUSION This study identified sex-specific genetic variants showing associations with insulin for the first time in East Asian populations. In addition, MR analysis using variants discovered from Korean women revealed that genetically determined high level of insulin is not the cause of PCOS.
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Affiliation(s)
- Woo Young Lim
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea
| | - Hyejin Lee
- Department of Internal Medicine, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Yoon Shin Cho
- Department of Biomedical Science, Hallym University, Chuncheon, Gangwon-do, 24252, Republic of Korea.
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7
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Yazdanpanah M, Jalilian N, Abdollah Zadeh R, Sahraian MA, Noori-Daloii MR. Investigating the association of polymorphisms of ANKRD55 and MMEL1 with susceptibility to multiple sclerosis in Iranian population. Int J Neurosci 2021; 132:1037-1042. [PMID: 33491520 DOI: 10.1080/00207454.2020.1860964] [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] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Multiple sclerosis (MS) is an autoimmune neurological disability in which immune cells attack the myelin sheaths that protect nerve fibers. The pathogenesis of the disease involves both complex genetic effects as well as multifaceted gene-environment interactions. In the present study, we examined the association of two Single nucleotide polymorphisms (SNPs) in ANKRD55 (rs6859219) and MMEL (rs3748816) with MS in the Iranian population. ANKRD55 is specifically expressed in human peripheral blood mononuclear cells and CD4 + T cells, while MMEL1is involved in the degradation of both neuropeptides and β-amyloid. METHODS In this case-control study, 110 patients with MS and 110 matched healthy controls were enrolled. The Participants were genotyped for ANKRD55 and MMEL1 SNPs using PCR-RFLP and Real-Time TaqMan SNP Genotyping respectively. The results were finally analyzed using SPSS software version 22. RESULTS Our results did not show significant differences in allelic frequencies of two SNPs among cases and controls (P-Value >0.05). However, for ANKRD55 (rs6859219), CA genotype was shown to have a protective effect (p = 0.035 and OR = 0.55), while CC genotype was a susceptive genotype to MS (p = 0.036 and OR = 1.8). There was no significant difference in genotypic frequencies of SNP rs3748816 in MMEL1. CONCLUSION We could successfully replicate the association of ANKRD55 (rs6859219) with susceptibility to MS in the Iranian population. Our result can provide an insight into better understanding the pathogenesis of MS and also improve the genetic counseling for patients affected with multiple sclerosis in Iran.
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Affiliation(s)
- Mahboobeh Yazdanpanah
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nazanin Jalilian
- Department of Clinical Biochemistry, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Rasoul Abdollah Zadeh
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Sahraian
- MS Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
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8
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CD300f immunoreceptor is associated with major depressive disorder and decreased microglial metabolic fitness. Proc Natl Acad Sci U S A 2020; 117:6651-6662. [PMID: 32152116 DOI: 10.1073/pnas.1911816117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A role for microglia in neuropsychiatric diseases, including major depressive disorder (MDD), has been postulated. Regulation of microglial phenotype by immune receptors has become a central topic in many neurological conditions. We explored preclinical and clinical evidence for the role of the CD300f immune receptor in the fine regulation of microglial phenotype and its contribution to MDD. We found that a prevalent nonsynonymous single-nucleotide polymorphism (C/T, rs2034310) of the human CD300f receptor cytoplasmic tail inhibits the protein kinase C phosphorylation of a threonine and is associated with protection against MDD, mainly in women. Interestingly, CD300f-/- mice displayed several characteristic MDD traits such as augmented microglial numbers, increased interleukin 6 and interleukin 1 receptor antagonist messenger RNA, alterations in synaptic strength, and noradrenaline-dependent and persistent depressive-like and anhedonic behaviors in females. This behavioral phenotype could be potentiated inducing the lipopolysaccharide depression model. RNA sequencing and biochemical studies revealed an association with impaired microglial metabolic fitness. In conclusion, we report a clear association that links the function of the CD300f immune receptor with MDD in humans, depressive-like and anhedonic behaviors in female mice, and altered microglial metabolic reprogramming.
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9
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Sharma A, Liu X, Hadley D, Hagopian W, Chen WM, Onengut-Gumuscu S, Törn C, Steck AK, Frohnert BI, Rewers M, Ziegler AG, Lernmark Å, Toppari J, Krischer JP, Akolkar B, Rich SS, She JX. Identification of non-HLA genes associated with development of islet autoimmunity and type 1 diabetes in the prospective TEDDY cohort. J Autoimmun 2018; 89:90-100. [PMID: 29310926 PMCID: PMC5902429 DOI: 10.1016/j.jaut.2017.12.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/28/2022]
Abstract
Traditional linkage analysis and genome-wide association studies have identified HLA and a number of non-HLA genes as genetic factors for islet autoimmunity (IA) and type 1 diabetes (T1D). However, the relative risk associated with previously identified non-HLA genes is usually very small as measured in cases/controls from mixed populations. Genetic associations for IA and T1D may be more accurately assessed in prospective cohorts. In this study, 5806 subjects from the TEDDY (The Environmental Determinants of Diabetes in the Young) study, an international prospective cohort study, were genotyped for 176,586 SNPs on the ImmunoChip. Cox proportional hazards analyses were performed to discover the SNPs associated with the risk for IA, T1D, or both. Three regions were associated with the risk of developing any persistent confirmed islet autoantibody: one known region near SH2B3 (HR = 1.35, p = 3.58 × 10-7) with Bonferroni-corrected significance and another known region near PTPN22 (HR = 1.46, p = 2.17 × 10-6) and one novel region near PPIL2 (HR = 2.47, p = 9.64 × 10-7) with suggestive evidence (p < 10-5). Two known regions (PTPN22: p = 2.25 × 10-6, INS; p = 1.32 × 10-7) and one novel region (PXK/PDHB: p = 8.99 × 10-6) were associated with the risk for multiple islet autoantibodies. First appearing islet autoantibodies differ with respect to association. Two regions (INS: p = 5.67 × 10-6 and TTC34/PRDM16: 6.45 × 10-6) were associated if the fist appearing autoantibody was IAA and one region (RBFOX1: p = 8.02 × 10-6) was associated if the first appearing autoantibody was GADA. The analysis of T1D identified one region already known to be associated with T1D (INS: p = 3.13 × 10-7) and three novel regions (RNASET2, PLEKHA1, and PPIL2; 5.42 × 10-6 > p > 2.31 × 10-6). These results suggest that a number of low frequency variants influence the risk of developing IA and/or T1D and these variants can be identified by large prospective cohort studies using a survival analysis approach.
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Affiliation(s)
- Ashok Sharma
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA; Division of Biostatistics and Data Science, Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Xiang Liu
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - David Hadley
- Division of Population Health Sciences and Education, St George's University of London, London, United Kingdom
| | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Carina Törn
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO, USA
| | - Brigitte I Frohnert
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO, USA
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich-Neuherberg, Germany; Klinikum rechts der Isar, Technische Universität München, Munich-Neuherberg, Germany; Forschergruppe Diabetes e.V., Munich-Neuherberg, Germany
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Beena Akolkar
- National Institutes of Diabetes and Digestive and Kidney Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA.
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11
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Tian L, Choi SC, Lee HN, Murakami Y, Qi CF, Sengottuvelu M, Voss O, Krzewski K, Coligan JE. Enhanced efferocytosis by dendritic cells underlies memory T-cell expansion and susceptibility to autoimmune disease in CD300f-deficient mice. Cell Death Differ 2016; 23:1086-96. [PMID: 26768664 DOI: 10.1038/cdd.2015.161] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/20/2015] [Accepted: 11/19/2015] [Indexed: 12/27/2022] Open
Abstract
Homeostasis requires the immunologically silent clearance of apoptotic cells before they become pro-inflammatory necrotic cells. CD300f (CLM-1) is a phosphatidylserine receptor known to positively regulate efferocytosis by macrophages, and CD300f gene-deficient mice are predisposed to develop a lupus-like disease. Here we show that, in contrast to CD300f function in macrophages, its expression inhibits efferocytosis by DC, and its deficiency leads to enhanced antigen processing and T-cell priming by these DC. The consequences are the expansion of memory T cells and increased ANA levels in aged CD300f-deficient mice, which predispose CD300f-deficient mice to develop an overt autoimmune disease when exposed to an overload of apoptotic cells, or an exacerbated autoimmunity when combined with FcγRIIB deficiency. Thus, our data demonstrates that CD300f helps to maintain immune homeostasis by promoting macrophage clearance of self-antigens, while conversely inhibiting DC uptake and presentation of self-antigens.
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Affiliation(s)
- L Tian
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - S-C Choi
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - H-N Lee
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - Y Murakami
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - C-F Qi
- Pathology Core, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - M Sengottuvelu
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - O Voss
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - K Krzewski
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
| | - J E Coligan
- Receptor Cell Biology Section, Laboratory of Immunogenetics, NIAID, NIH, Rockville, MD, USA
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12
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Replication of GWAS Coding SNPs Implicates MMEL1 as a Potential Susceptibility Locus among Saudi Arabian Celiac Disease Patients. DISEASE MARKERS 2015; 2015:351673. [PMID: 26843707 PMCID: PMC4710944 DOI: 10.1155/2015/351673] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023]
Abstract
Celiac disease (CD), a gluten intolerance disorder, was implicated to have 57 genetic susceptibility loci for Europeans but not for culturally and geographically distinct ethnic populations like Saudi Arabian CD patients. Therefore, we genotyped Saudi CD patients and healthy controls for three polymorphisms, that is, Phe196Ser in IRAK1, Trp262Arg in SH2B3, and Met518Thr in MMEL1 genes. Single locus analysis identified that carriers of the 518 Thr/Thr (MMEL1) genotype conferred a 1.6-fold increased disease risk compared to the noncarriers (OR = 2.6; 95% CI: 1.22-5.54; P < 0.01). This significance persisted even under allelic (OR = 1.55; 95% CI: 1.05-2.28; P = 0.02) and additive (OR = 0.35; 95% CI: 0.17-0.71; P = 0.03) genetic models. However, frequencies for Trp262Arg (SH2B3) and Phe196Ser (IRAK1) polymorphisms were not significantly different between patients and controls. The overall best MDR model included Met518Thr and Trp262Arg polymorphisms, with a maximal testing accuracy of 64.1% and a maximal cross-validation consistency of 10 out of 10 (P = 0.0156). Allelic distribution of the 518 Thr/Thr polymorphism in MMEL1 primarily suggests its independent and synergistic contribution towards CD susceptibility among Saudi patients. Lack of significant association of IRAK and SH2B3 gene polymorphisms in Saudi patients but their association in European groups suggests the genetic heterogeneity of CD.
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13
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Dankowski T, Buck D, Andlauer TFM, Antony G, Bayas A, Bechmann L, Berthele A, Bettecken T, Chan A, Franke A, Gold R, Graetz C, Haas J, Hecker M, Herms S, Infante-Duarte C, Jöckel KH, Kieseier BC, Knier B, Knop M, Kümpfel T, Lichtner P, Lieb W, Lill CM, Limmroth V, Linker RA, Loleit V, Meuth SG, Moebus S, Müller-Myhsok B, Nischwitz S, Nöthen MM, Paul F, Pütz M, Ruck T, Salmen A, Stangel M, Stellmann JP, Strauch K, Stürner KH, Tackenberg B, Then Bergh F, Tumani H, Waldenberger M, Weber F, Wiendl H, Wildemann B, Zettl UK, Ziemann U, Zipp F, Hemmer B, Ziegler A. Successful Replication of GWAS Hits for Multiple Sclerosis in 10,000 Germans Using the Exome Array. Genet Epidemiol 2015; 39:601-8. [PMID: 26497834 DOI: 10.1002/gepi.21933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) successfully identified various chromosomal regions to be associated with multiple sclerosis (MS). The primary aim of this study was to replicate reported associations from GWAS using an exome array in a large German study. German MS cases (n = 4,476) and German controls (n = 5,714) were genotyped using the Illumina HumanExome v1-Chip. Genotype calling was performed with the Illumina Genome Studio(TM) Genotyping Module, followed by zCall. Single-nucleotide polymorphisms (SNPs) in seven regions outside the human leukocyte antigen (HLA) region showed genome-wide significant associations with MS (P values < 5 × 10(-8) ). These associations have been reported previously. In addition, SNPs in three previously reported regions outside the HLA region yielded P values < 10(-5) . The effect of nine SNPs in the HLA region remained (P < 10(-5) ) after adjustment for other significant SNPs in the HLA region. All of these findings have been reported before or are driven by known risk loci. In summary, findings from previous GWAS for MS could be successfully replicated. We conclude that the regions identified in previous GWAS are also associated in the German population. This reassures the need for detailed investigations of the functional mechanisms underlying the replicated associations.
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Affiliation(s)
- Theresa Dankowski
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Dorothea Buck
- Department of Neurology, Technische Universität München, Munich, Germany
| | | | - Gisela Antony
- Central Information Office (CIO), Philipps University Marburg, Marburg, Germany
| | - Antonios Bayas
- Department of Neurology, Klinikum Augsburg, Augsburg, Germany
| | - Lukas Bechmann
- Department of Neurology, University of Leipzig, Leipzig, Germany.,Institute of Medical Microbiology, Otto-von-Guericke University, Magdeburg, Germany
| | - Achim Berthele
- Department of Neurology, Technische Universität München, Munich, Germany
| | | | - Andrew Chan
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Ralf Gold
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Christiane Graetz
- Department of Neurology, University Medical Center Mainz, Mainz, Germany
| | - Jürgen Haas
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Hecker
- Department of Neurology, University of Rostock, Rostock, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Division of Medical Genetics, University Hospital, Basel, Switzerland.,Human Genetics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Bernd C Kieseier
- Department of Neurology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin Knier
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Matthias Knop
- Department of Neurology, MPI of Psychiatry, Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, Ludwigs-Maximilians-Universität, Munich, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank popgen, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Christina M Lill
- Department of Neurology, University Medical Center Mainz, Mainz, Germany.,Platform for Genome Analytics, Institutes of Neurogenetics, & for Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Volker Limmroth
- Department of Neurology, Hospital Köln-Merheim, Köln, Germany
| | - Ralf A Linker
- Department of Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Verena Loleit
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Sven G Meuth
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Friedemann Paul
- Department of Neurology, Charité University Medicine Berlin, Berlin, Germany.,NeuroCure Clinical Research Center, Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Pütz
- Department of Neurology, Philipps-University of Marburg, Marburg, Germany
| | - Tobias Ruck
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Anke Salmen
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Martin Stangel
- Clinical Neuroimmunology and Neurochemistry, Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Jan-Patrick Stellmann
- Department of Neurology and, Institute of Neuroimmunology and MS (INIMS), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Klarissa H Stürner
- Department of Neurology and, Institute of Neuroimmunology and MS (INIMS), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Tackenberg
- Department of Neurology, Philipps-University of Marburg, Marburg, Germany
| | - Florian Then Bergh
- Department of Neurology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | | | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank Weber
- Department of Neurology, MPI of Psychiatry, Munich, Germany.,Neurological Clinic, Medical Park, Bad Camberg, Germany
| | - Heinz Wiendl
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Brigitte Wildemann
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Uwe K Zettl
- Department of Neurology, University of Rostock, Rostock, Germany
| | - Ulf Ziemann
- Department of Neurology, University Hospital, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
| | - Frauke Zipp
- Department of Neurology, University Medical Center Mainz, Mainz, Germany
| | - Bernhard Hemmer
- Department of Neurology, Technische Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,Zentrum für Klinische Studien, Universität zu Lübeck, Lübeck, Germany.,School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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14
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Goodin DS, Khankhanian P. Single nucleotide polymorphism (SNP)-strings: an alternative method for assessing genetic associations. PLoS One 2014; 9:e90034. [PMID: 24727690 PMCID: PMC3984082 DOI: 10.1371/journal.pone.0090034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 01/30/2014] [Indexed: 12/21/2022] Open
Abstract
Background Genome-wide association studies (GWAS) identify disease-associations for single-nucleotide-polymorphisms (SNPs) from scattered genomic-locations. However, SNPs frequently reside on several different SNP-haplotypes, only some of which may be disease-associated. This circumstance lowers the observed odds-ratio for disease-association. Methodology/Principal Findings Here we develop a method to identify the two SNP-haplotypes, which combine to produce each person’s SNP-genotype over specified chromosomal segments. Two multiple sclerosis (MS)-associated genetic regions were modeled; DRB1 (a Class II molecule of the major histocompatibility complex) and MMEL1 (an endopeptidase that degrades both neuropeptides and β-amyloid). For each locus, we considered sets of eleven adjacent SNPs, surrounding the putative disease-associated gene and spanning ∼200 kb of DNA. The SNP-information was converted into an ordered-set of eleven-numbers (subject-vectors) based on whether a person had zero, one, or two copies of particular SNP-variant at each sequential SNP-location. SNP-strings were defined as those ordered-combinations of eleven-numbers (0 or 1), representing a haplotype, two of which combined to form the observed subject-vector. Subject-vectors were resolved using probabilistic methods. In both regions, only a small number of SNP-strings were present. We compared our method to the SHAPEIT-2 phasing-algorithm. When the SNP-information spanning 200 kb was used, SHAPEIT-2 was inaccurate. When the SHAPEIT-2 window was increased to 2,000 kb, the concordance between the two methods, in both of these eleven-SNP regions, was over 99%, suggesting that, in these regions, both methods were quite accurate. Nevertheless, correspondence was not uniformly high over the entire DNA-span but, rather, was characterized by alternating peaks and valleys of concordance. Moreover, in the valleys of poor-correspondence, SHAPEIT-2 was also inconsistent with itself, suggesting that the SNP-string method is more accurate across the entire region. Conclusions/Significance Accurate haplotype identification will enhance the detection of genetic-associations. The SNP-string method provides a simple means to accomplish this and can be extended to cover larger genomic regions, thereby improving a GWAS’s power, even for those published previously.
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Affiliation(s)
- Douglas S. Goodin
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
- UCSF Multiple Sclerosis Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| | - Pouya Khankhanian
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
- UCSF Multiple Sclerosis Center, University of California San Francisco, San Francisco, California, United States of America
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15
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Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TMC, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BAC, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 2013; 45:1353-60. [PMID: 24076602 PMCID: PMC3832895 DOI: 10.1038/ng.2770] [Citation(s) in RCA: 995] [Impact Index Per Article: 90.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022]
Abstract
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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16
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Baranzini S, Khankhanian P, Patsopoulos N, Li M, Stankovich J, Cotsapas C, Søndergaard H, Ban M, Barizzone N, Bergamaschi L, Booth D, Buck D, Cavalla P, Celius E, Comabella M, Comi G, Compston A, Cournu-Rebeix I, D’alfonso S, Damotte V, Din L, Dubois B, Elovaara I, Esposito F, Fontaine B, Franke A, Goris A, Gourraud PA, Graetz C, Guerini F, Guillot-Noel L, Hafler D, Hakonarson H, Hall P, Hamsten A, Harbo H, Hemmer B, Hillert J, Kemppinen A, Kockum I, Koivisto K, Larsson M, Lathrop M, Leone M, Lill C, Macciardi F, Martin R, Martinelli V, Martinelli-Boneschi F, McCauley J, Myhr KM, Naldi P, Olsson T, Oturai A, Pericak-Vance M, Perla F, Reunanen M, Saarela J, Saker-Delye S, Salvetti M, Sellebjerg F, Sørensen P, Spurkland A, Stewart G, Taylor B, Tienari P, Winkelmann J, Zipp F, Ivinson A, Haines J, Sawcer S, DeJager P, Hauser S, Oksenberg J. Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls. Am J Hum Genet 2013; 92:854-65. [PMID: 23731539 PMCID: PMC3958952 DOI: 10.1016/j.ajhg.2013.04.019] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/04/2013] [Accepted: 04/23/2013] [Indexed: 02/03/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory CNS disease with a substantial genetic component, originally mapped to only the human leukocyte antigen (HLA) region. In the last 5 years, a total of seven genome-wide association studies and one meta-analysis successfully identified 57 non-HLA susceptibility loci. Here, we merged nominal statistical evidence of association and physical evidence of interaction to conduct a protein-interaction-network-based pathway analysis (PINBPA) on two large genetic MS studies comprising a total of 15,317 cases and 29,529 controls. The distribution of nominally significant loci at the gene level matched the patterns of extended linkage disequilibrium in regions of interest. We found that products of genome-wide significantly associated genes are more likely to interact physically and belong to the same or related pathways. We next searched for subnetworks (modules) of genes (and their encoded proteins) enriched with nominally associated loci within each study and identified those modules in common between the two studies. We demonstrate that these modules are more likely to contain genes with bona fide susceptibility variants and, in addition, identify several high-confidence candidates (including BCL10, CD48, REL, TRAF3, and TEC). PINBPA is a powerful approach to gaining further insights into the biology of associated genes and to prioritizing candidates for subsequent genetic studies of complex traits.
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17
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Identity-by-descent mapping to detect rare variants conferring susceptibility to multiple sclerosis. PLoS One 2013; 8:e56379. [PMID: 23472070 PMCID: PMC3589405 DOI: 10.1371/journal.pone.0056379] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/08/2013] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified around 60 common variants associated with multiple sclerosis (MS), but these loci only explain a fraction of the heritability of MS. Some missing heritability may be caused by rare variants that have been suggested to play an important role in the aetiology of complex diseases such as MS. However current genetic and statistical methods for detecting rare variants are expensive and time consuming. ‘Population-based linkage analysis’ (PBLA) or so called identity-by-descent (IBD) mapping is a novel way to detect rare variants in extant GWAS datasets. We employed BEAGLE fastIBD to search for rare MS variants utilising IBD mapping in a large GWAS dataset of 3,543 cases and 5,898 controls. We identified a genome-wide significant linkage signal on chromosome 19 (LOD = 4.65; p = 1.9×10−6). Network analysis of cases and controls sharing haplotypes on chromosome 19 further strengthened the association as there are more large networks of cases sharing haplotypes than controls. This linkage region includes a cluster of zinc finger genes of unknown function. Analysis of genome wide transcriptome data suggests that genes in this zinc finger cluster may be involved in very early developmental regulation of the CNS. Our study also indicates that BEAGLE fastIBD allowed identification of rare variants in large unrelated population with moderate computational intensity. Even with the development of whole-genome sequencing, IBD mapping still may be a promising way to narrow down the region of interest for sequencing priority.
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18
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Harbo HF, Lorentzen AR, Lie BA, Celius EG, Spurkland A. [New gene map for multiple sclerosis]. TIDSSKRIFT FOR DEN NORSKE LEGEFORENING 2011; 131:2126-30. [PMID: 22048209 DOI: 10.4045/tidsskr.10.0823] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Multiple sclerosis (MS) is a demyelinating, inflammatory disease of the central nervous system which affects young adults with a relapsing or progressive disease course. The etiology of the disease is unknown, but both environmental and genetic factors contribute to the risk of developing MS. MATERIAL AND METHODS We give an overview of new knowledge of the genetic risk factors for MS, based on our own work as well as on literature in this field. RESULTS Through genome-wide association studies and subsequent replication studies a series of novel MS genes have recently been identified, in addition to the HLA association previously described. The International MS Genetics Consortium in collaboration with the Wellcome Trust Case Control Consortium recently published a genome-wide study of 9,722 MS patients and 17,376 controls. Genome-wide significant association (p < 10-8) was observed for 29 new as well as 23 previously identified gene regions, in addition to the HLA-DRB1 and -A loci .The majority of these MS-associated regions encode immune-related molecules. CONCLUSION Genetic studies of large patient and control samples obtained through international and national collaborations have identified a list of more than 50 MS risk-gene regions, in addition to HLA-DRB1 and -A loci. The risk associated with each of these loci is low, however, they collectively point to the importance of immune-related pathways in the etiology of MS.
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Affiliation(s)
- Hanne F Harbo
- Nevrologisk avdeling, Oslo universitetssykehus, Ullevål, Norway.
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19
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Zuvich RL, Bush WS, McCauley JL, Beecham AH, De Jager PL, Ivinson AJ, Compston A, Hafler DA, Hauser SL, Sawcer SJ, Pericak-Vance MA, Barcellos LF, Mortlock DP, Haines JL. Interrogating the complex role of chromosome 16p13.13 in multiple sclerosis susceptibility: independent genetic signals in the CIITA-CLEC16A-SOCS1 gene complex. Hum Mol Genet 2011; 20:3517-24. [PMID: 21653641 PMCID: PMC3153306 DOI: 10.1093/hmg/ddr250] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/17/2011] [Accepted: 05/31/2011] [Indexed: 11/12/2022] Open
Abstract
Multiple sclerosis (MS) is a neurodegenerative, autoimmune disease of the central nervous system, and numerous studies have shown that MS has a strong genetic component. Independent studies to identify MS-associated genes have often indicated multiple signals in physically close genomic regions, although by their proximity it is not always clear if these data indicate redundant or truly independent genetic signals. Recently, three MS study samples were genotyped in parallel using an Illumina Custom BeadChip. These revealed multiple significantly associated single-nucleotide polymorphisms within a 600 kb stretch on chromosome 16p13. Here we present a detailed analysis of variants in this region that clarifies the independent nature of these signals. The linkage disequilibrium patterns in the region and logistic regression analysis of the associations suggest that this region likely harbors three independent MS disease loci. Further, we examined cis-expression QTLs, histone modifications and CCCTC-binding factor (CTCF) binding data in the region. We also tested for correlated expression of the genes from the region using whole-genome expression array data from lymphoblastoid cell lines. Three of the genes show expression correlations across loci. Furthermore, in the GM12878 lymphoblastoid cell line, these three genes are in a continuous region devoid of H3K27 methylation, suggesting an open chromatin configuration. This region likely only contributes minimal risk to MS; however, investigation of this region will undoubtedly provide insight into the functional mechanisms of these genes. These data highlight the importance of taking a closer look at the expression and function of chromosome 16p13 in the pathogenesis of MS.
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Affiliation(s)
- Rebecca L Zuvich
- Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN 37232-0700, USA.
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20
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Suzuki A, Kochi Y, Okada Y, Yamamoto K. Insight from genome-wide association studies in rheumatoid arthritis and multiple sclerosis. FEBS Lett 2011; 585:3627-32. [PMID: 21600898 DOI: 10.1016/j.febslet.2011.05.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/07/2011] [Accepted: 05/09/2011] [Indexed: 12/25/2022]
Abstract
Autoimmune diseases are caused by multiple genes and environmental effects. In addition, genetic contributions and the number of associated genes differ among different diseases and ethnic populations. Genome-wide association studies (GWAS) on rheumatoid arthritis (RA) and multiple sclerosis (MS) show that these diseases share many genetic factors. Recently, in addition to the major histocompatibility complex (MHC) gene, other genetic loci have been found to be associated with the risk for autoimmune diseases. This review focuses on the search for genetic variants that influence the susceptibility to RA and MS as typical autoimmune diseases and discusses the future of GWAS.
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Affiliation(s)
- Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Tsurumi-ku, Yokohama City, Kanagawa, Japan
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Kemppinen A, Sawcer S, Compston A. Genome-wide association studies in multiple sclerosis: lessons and future prospects. Brief Funct Genomics 2011; 10:61-70. [PMID: 21310812 DOI: 10.1093/bfgp/elr004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory neurodegenerative disease with complex aetiology. A haplotype within the major histocompatibility region is the major risk factor for MS, but despite clear evidence for a genetic component additional risk variants were not identified until the recent advent of genome-wide association studies (GWAS). At present, 10 GWAS have been conducted in MS, and together with follow-up studies these have confirmed 16 loci with genome-wide significance. Many of these common risk variants are located at or near genes with central immunological functions and the majority are associated with other autoimmune diseases. However, evidence from pathway analyses on more modestly associated variants also supports the involvement of neurological genes. Although the mechanisms by which the associated variants exert their effects are still poorly understood, some have been shown to correlate with expression of nearby genes. Further studies are required to define the functionally relevant variants in the identified regions and to investigate their effects at the molecular and cellular level. Finally, many genetic risk variants for MS remain to be identified. In order to expose some of the loci with more modest effects, a GWAS in nearly 10,000 MS patients has recently been completed.
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Affiliation(s)
- Anu Kemppinen
- Neurology Unit, Department of Clinical Neurosciences, University of Cambridge, UK.
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