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Zhuo J, Wu Y, Li W, Li Z, Ding Y, Jin T. Missense Variant rs28362680 in BTNL2 Reduces Risk of Coronary Heart Disease. Pharmgenomics Pers Med 2022; 15:449-464. [PMID: 35572349 PMCID: PMC9091699 DOI: 10.2147/pgpm.s353085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Background The pathological basis of coronary heart disease (CHD) is atherosclerosis. BTNL2 can inhibit the activation of T cells. We aimed to explore the association between BTNL2 genetic variants and CHD risk in the southern Chinese Han population. Methods We recruited 1419 participants to perform an association analysis between missense variants in BTNL2 and CHD risk through SNPStats online software. Genotyping of all candidate SNPs were completed by the Agena MassARRAY. In addition, we used false-positive report probability analysis to detect whether the positive findings were noteworthy observations. We also used Haploview 4.2 software and SNPStats online software to conduct the haplotype analysis and analysis of linkage disequilibrium (LD). Finally, the interaction of SNP-SNP in CHD risk was evaluated by multi-factor dimensionality reduction (MDR). Results The results showed that BTNL2-rs35624343, -rs117896888, -rs41441651, -rs41417449, -rs28362680 and -rs2076523 were significantly associated with the CHD susceptibility. Especially for BTNL2-rs28362680, the allele A (OR = 0.68, p < 0.0001), genotype AA (OR = 0.40, p = 0.001) or GA (OR = 0.68, p < 0.0001) were associated with the reducing CHD risk. And -rs28362680 significantly reduced the CHD risk under all genetic models (dominant: OR = 0.64, p < 0.0001; recessive: OR = 0.47, p = 0.003; overdominant: OR = 0.73, p = 0.004; log-additive: OR = 0.66, p < 0.0001). And -rs28362680 was also closely associated with CHD risk reduction in all stratified analyses (age, gender, smoking, drinking, hypertension and diabetes). In addition, haplotype analysis showed that the “Crs117896888Crs41441651Trs41417449Ars28362680” (OR = 0.65, p < 0.0001) and “Grs117896888Trs41441651Crs41417449Ars28362680” (OR = 0.68, p = 0.013) may reduce CHD risk. Conclusion Missense variants (rs35624343, rs117896888, rs41441651, rs41417449, rs28362680, rs2076523) may be protective factors for the CHD risk. In particular, there were sufficient evidences that BTNL2-rs28362680 can protective CHD risk.
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Affiliation(s)
- Jian Zhuo
- Department of Emergency Service, People’s Hospital of Wanning, Wanning, Hainan, 571500, People’s Republic of China
| | - Yingchun Wu
- Department of Intensive Care Unit, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, 570311, Hainan, People’s Republic of China
| | - Wei Li
- Department of Emergency Service, People’s Hospital of Wanning, Wanning, Hainan, 571500, People’s Republic of China
| | - Zerong Li
- Department of Emergency Service, People’s Hospital of Wanning, Wanning, Hainan, 571500, People’s Republic of China
| | - Yipeng Ding
- Department of General Practice, Hainan General Hospital, Hainan affiliated Hospital of Hainan Medical University, Haikou, 570311, Hainan, People’s Republic of China
- Correspondence: Yipeng Ding, Department of General Practice, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, No. 19, Xinhua Road, Xiuying District, Haikou, 570311, Hainan, People’s Republic of China, Tel +86-18976335858, Email
| | - Tianbo Jin
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi‘an, Shaanxi, 710069, People’s Republic of China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi’an, People’s Republic of China
- Tianbo Jin, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, #229 Taibai North Road, Xi’an, 710069, Shaanxi, People’s Republic of China, Tel/Fax +86-29-88895902, Email
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2
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Dolatkhah K, Alizadeh N, Mohajjel-Shoja H, Abdoli Shadbad M, Hajiasgharzadeh K, Aghebati-Maleki L, Baghbanzadeh A, Hosseinkhani N, Karim Ahangar N, Baradaran B. B7 immune checkpoint family members as putative therapeutics in autoimmune disease: An updated overview. Int J Rheum Dis 2022; 25:259-271. [PMID: 34994525 DOI: 10.1111/1756-185x.14273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/11/2021] [Accepted: 12/18/2021] [Indexed: 12/23/2022]
Abstract
Autoimmune diseases, especially among young people in the US, are one of the leading causes of morbidity and death. The immune responses are the fundamental pathogenicity of autoimmune disorders. The equilibrium between stimulatory and inhibitory signals is critical for the stimulation, migration, survival, and T cell-related immune responses. The B7 family can substantially regulate T cell-mediated immune responses. Nevertheless, recent breakthroughs in immune checkpoint blockade in cancer immunotherapy have facilitated autoimmune diseases, especially among the prone populations. In the current study, we tried to concisely review the role of the B7 family in regulating immune reactions and the influence of immune checkpoint inhibitors on autoimmunity development.
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Affiliation(s)
- Katayoun Dolatkhah
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazila Alizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hanieh Mohajjel-Shoja
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | | | | | - Amir Baghbanzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Negar Hosseinkhani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Noora Karim Ahangar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Pharmaceutical Analysis Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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3
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Johnson SB, Lynch KF, Roth R, Lundgren M, Parikh HM, Akolkar B, Hagopian W, Krischer J, Rewers M, She JX, Toppari J, Ziegler AG, Lernmark Å. First-appearing islet autoantibodies for type 1 diabetes in young children: maternal life events during pregnancy and the child's genetic risk. Diabetologia 2021; 64:591-602. [PMID: 33404683 PMCID: PMC7880544 DOI: 10.1007/s00125-020-05344-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/19/2020] [Indexed: 10/22/2022]
Abstract
AIMS/HYPOTHESIS Psychological stress has long been considered a possible trigger of type 1 diabetes, although prospective studies examining the link between psychological stress or life events during pregnancy and the child's type 1 diabetes risk are rare. The objective of this study was to examine the association between life events during pregnancy and first-appearing islet autoantibodies (IA) in young children, conditioned by the child's type 1 diabetes-related genetic risk. METHODS The IA status of 7317 genetically at-risk The Environmental Determinants of Diabetes in the Young (TEDDY) participants was assessed every 3 months from 3 months to 4 years, and bi-annually thereafter. Reports of major life events during pregnancy were collected at study inception when the child was 3 months of age and placed into one of six categories. Life events during pregnancy were examined for association with first-appearing insulin (IAA) (N = 222) or GAD (GADA) (N = 209) autoantibodies in the child until 6 years of age using proportional hazard models. Relative excess risk due to interaction (RERI) by the child's HLA-DR and SNP profile was estimated. RESULTS Overall, 65% of mothers reported a life event during pregnancy; disease/injury (25%), serious interpersonal (28%) and job-related (25%) life events were most common. The association of life events during pregnancy differed between IAA and GADA as the first-appearing autoantibody. Serious interpersonal life events correlated with increased risk of GADA-first only in HLA-DR3 children with the BACH2-T allele (HR 2.28, p < 0.0001), an additive interaction (RERI 1.87, p = 0.0004). Job-related life events were also associated with increased risk of GADA-first among HLA-DR3/4 children (HR 1.53, p = 0.04) independent of serious interpersonal life events (HR 1.90, p = 0.002), an additive interaction (RERI 1.19, p = 0.004). Job-related life events correlated with reduced risk of IAA-first (HR 0.55, p = 0.004), particularly in children with the BTNL2-GG allele (HR 0.48; 95% CI 0.31, 0.76). CONCLUSIONS/INTERPRETATION Specific life events during pregnancy are differentially related to IAA vs GADA as first-appearing IA and interact with different HLA and non-HLA genetic factors, supporting the concept of different endotypes underlying type 1 diabetes. However, the mechanisms underlying these associations remain to be discovered. Life events may be markers for other yet-to-be-identified factors important to the development of first-appearing IA.
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Affiliation(s)
- Suzanne Bennett Johnson
- Department of Behavioral Sciences and Social Medicine, Florida State University, Tallahassee, FL, USA.
| | - Kristian F Lynch
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Roswith Roth
- Institute for Psychology, Graz University, Graz, Austria
| | - Markus Lundgren
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | | | - Jeffrey Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische Universität München, and Forschergruppe Diabetes e.V., Neuherberg, Germany
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
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4
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Li R, Duan R, Zhang X, Lumley T, Pendergrass S, Bauer C, Hakonarson H, Carrell DS, Smoller JW, Wei WQ, Carroll R, Velez Edwards DR, Wiesner G, Sleiman P, Denny JC, Mosley JD, Ritchie MD, Chen Y, Moore JH. Lossless integration of multiple electronic health records for identifying pleiotropy using summary statistics. Nat Commun 2021; 12:168. [PMID: 33420026 PMCID: PMC7794298 DOI: 10.1038/s41467-020-20211-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 11/13/2020] [Indexed: 11/22/2022] Open
Abstract
Increasingly, clinical phenotypes with matched genetic data from bio-bank linked electronic health records (EHRs) have been used for pleiotropy analyses. Thus far, pleiotropy analysis using individual-level EHR data has been limited to data from one site. However, it is desirable to integrate EHR data from multiple sites to improve the detection power and generalizability of the results. Due to privacy concerns, individual-level patients' data are not easily shared across institutions. As a result, we introduce Sum-Share, a method designed to efficiently integrate EHR and genetic data from multiple sites to perform pleiotropy analysis. Sum-Share requires only summary-level data and one round of communication from each site, yet it produces identical test statistics compared with that of pooled individual-level data. Consequently, Sum-Share can achieve lossless integration of multiple datasets. Using real EHR data from eMERGE, Sum-Share is able to identify 1734 potential pleiotropic SNPs for five cardiovascular diseases.
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Affiliation(s)
- Ruowang Li
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Rui Duan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xinyuan Zhang
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Sarah Pendergrass
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | - Christopher Bauer
- Biomedical and Translational Informatics Institute, Geisinger, Danville, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - David S Carrell
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Robert Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Digna R Velez Edwards
- Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Georgia Wiesner
- Clinical and Translational Hereditary Cancer Program, Division of Genetic Medicine, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Patrick Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Josh C Denny
- Department of Biomedical Informatics, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Jonathan D Mosley
- Department of Biomedical Informatics, Vanderbilt University Medical Centre, Nashville, TN, USA
| | - Marylyn D Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yong Chen
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jason H Moore
- Department of Biostatistics, Epidemiology & Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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5
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DNA methylation profiles are associated with complex regional pain syndrome after traumatic injury. Pain 2020; 160:2328-2337. [PMID: 31145213 DOI: 10.1097/j.pain.0000000000001624] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Factors contributing to development of complex regional pain syndrome (CRPS) are not fully understood. This study examined possible epigenetic mechanisms that may contribute to CRPS after traumatic injury. DNA methylation profiles were compared between individuals developing CRPS (n = 9) and those developing non-CRPS neuropathic pain (n = 38) after undergoing amputation following military trauma. Linear Models for Microarray (LIMMA) analyses revealed 48 differentially methylated cytosine-phosphate-guanine dinucleotide (CpG) sites between groups (unadjusted P's < 0.005), with the top gene COL11A1 meeting Bonferroni-adjusted P < 0.05. The second largest differential methylation was observed for the HLA-DRB6 gene, an immune-related gene linked previously to CRPS in a small gene expression study. For all but 7 of the significant CpG sites, the CRPS group was hypomethylated. Numerous functional Gene Ontology-Biological Process categories were significantly enriched (false discovery rate-adjusted q value <0.15), including multiple immune-related categories (eg, activation of immune response, immune system development, regulation of immune system processes, and antigen processing and presentation). Differentially methylated genes were more highly connected in human protein-protein networks than expected by chance (P < 0.05), supporting the biological relevance of the findings. Results were validated in an independent sample linking a DNA biobank with electronic health records (n = 126 CRPS phenotype, n = 19,768 non-CRPS chronic pain phenotype). Analyses using PrediXcan methodology indicated differences in the genetically determined component of gene expression in 7 of 48 genes identified in methylation analyses (P's < 0.02). Results suggest that immune- and inflammatory-related factors might confer risk of developing CRPS after traumatic injury. Validation findings demonstrate the potential of using electronic health records linked to DNA for genomic studies of CRPS.
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6
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Yoshida K, Yokota K, Kutsuwada Y, Nakayama K, Watanabe K, Matsumoto A, Miyashita H, Khor SS, Tokunaga K, Kawai Y, Nagasaki M, Iwamoto S. Genome-Wide Association Study of Lean Nonalcoholic Fatty Liver Disease Suggests Human Leukocyte Antigen as a Novel Candidate Locus. Hepatol Commun 2020; 4:1124-1135. [PMID: 32766473 PMCID: PMC7395061 DOI: 10.1002/hep4.1529] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/10/2020] [Accepted: 04/14/2020] [Indexed: 12/28/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is supposed to manifest its metabolic phenotype in the liver, but it is common to have lean individuals diagnosed with NAFLD, known as lean NAFLD. We conducted a two-stage analysis to identify NAFLD-associated loci in Japanese patients. In stage I, 275 metabolically healthy normal-weight patients with NAFLD were compared with 1,411 non-NAFLD controls adjusted for age, sex, and alcohol consumption by a genome-wide association study (GWAS). In stage II, human leukocyte antigen (HLA) in chromosome 6 (chr6) (P = 6.73E-08), microRNA (MIR) MIR548F3 in chr7 (P = 4.25E-07), myosin light chain 2 (MYL2) in chr12 (P = 4.39E-07), and glycoprotein precursor (GPC)6 in chr13 (P = 5.43E-07), as suggested by the GWAS, were assessed by single nucleotide polymorphism (SNP) association analysis of whole NAFLD against non-NAFLD in 9,726 members of the general population. A minor allele of the secondary lead SNP in chr6, rs2076529, was significantly associated (odds ratio [OR], 1.19; 95% confidence interval [CI], 1.11-1.28; P = 2.10E-06) and the lead SNP in chr7 was weakly associated (OR 1.15; 95% CI, 1.04-1.27; P = 6.19E-03) with increased NAFLD risk. Imputation-based typing of HLA showed a significant difference in the distribution of HLA-B, HLA-DR-beta chain 1 (DRB1), and HLA-DQ-beta chain 1 (DQB1) alleles in lean NAFLD GWAS. Next-generation sequence-based typing of HLA in 5,649 members of the general population replicated the significant difference of HLA-B allele distribution and the significant increase of the HLA-B*54:01 allele in whole NAFLD. Fecal metagenomic analysis of 3,420 members of the general population showed significant dissimilarity in beta-diversity analysis of rs2076529 and HLA-B*54:01 allele carriers from noncarriers. Veillonellaceae was increased but Verrucomicrobia was decreased in rs2076529 minor allele and HLA-B*54:01 allele carriers as in NAFLD. Conclusion: HLA was identified as a novel locus associated with NAFLD susceptibility, which might be affected by the alteration of gut microbiota.
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Affiliation(s)
- Ken Yoshida
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan
| | - Kazuha Yokota
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan
| | - Yukinobu Kutsuwada
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan.,Forensic Science Laboratory Tochigi Prefecture Police Headquarters Utsunomiya Japan
| | - Kazuhiro Nakayama
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan.,Laboratory of Evolutionary Anthropology Department of Integrated Biosciences Graduate School of Frontier Sciences University of Tokyo Kashiwa Japan
| | - Kazuhisa Watanabe
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan
| | - Ayumi Matsumoto
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan
| | | | - Seik-Soon Khor
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Yosuke Kawai
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization Tohoku University Sendai Japan.,Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto Japan
| | - Sadahiko Iwamoto
- Division of Human Genetics Center for Molecular Medicine Jichi Medical University Shimotsuke Japan
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7
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Amiri Roudbar M, Mohammadabadi MR, Ayatollahi Mehrgardi A, Abdollahi-Arpanahi R, Momen M, Morota G, Brito Lopes F, Gianola D, Rosa GJM. Integration of single nucleotide variants and whole-genome DNA methylation profiles for classification of rheumatoid arthritis cases from controls. Heredity (Edinb) 2020; 124:658-674. [PMID: 32127659 DOI: 10.1038/s41437-020-0301-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 02/17/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
This study evaluated the use of multiomics data for classification accuracy of rheumatoid arthritis (RA). Three approaches were used and compared in terms of prediction accuracy: (1) whole-genome prediction (WGP) using SNP marker information only, (2) whole-methylome prediction (WMP) using methylation profiles only, and (3) whole-genome/methylome prediction (WGMP) with combining both omics layers. The number of SNP and of methylation sites varied in each scenario, with either 1, 10, or 50% of these preselected based on four approaches: randomly, evenly spaced, lowest p value (genome-wide association or epigenome-wide association study), and estimated effect size using a Bayesian ridge regression (BRR) model. To remove effects of high levels of pairwise linkage disequilibrium (LD), SNPs were also preselected with an LD-pruning method. Five Bayesian regression models were studied for classification, including BRR, Bayes-A, Bayes-B, Bayes-C, and the Bayesian LASSO. Adjusting methylation profiles for cellular heterogeneity within whole blood samples had a detrimental effect on the classification ability of the models. Overall, WGMP using Bayes-B model has the best performance. In particular, selecting SNPs based on LD-pruning with 1% of the methylation sites selected based on BRR included in the model, and fitting the most significant SNP as a fixed effect was the best method for predicting disease risk with a classification accuracy of 0.975. Our results showed that multiomics data can be used to effectively predict the risk of RA and identify cases in early stages to prevent or alter disease progression via appropriate interventions.
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Affiliation(s)
- Mahmoud Amiri Roudbar
- Department of Animal Science, Safiabad-Dezful Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Dezful, Iran.
| | - Mohammad Reza Mohammadabadi
- Department of Animal Science, College of Agriculture, Shahid Bahonar University of Kerman, 76169-133, Kerman, Iran
| | - Ahmad Ayatollahi Mehrgardi
- Department of Animal Science, College of Agriculture, Shahid Bahonar University of Kerman, 76169-133, Kerman, Iran
| | - Rostam Abdollahi-Arpanahi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, 465, Pakdasht, Tehran, Iran
| | - Mehdi Momen
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Fernando Brito Lopes
- Department of Animal Sciences, Sao Paulo State University, Julio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, Jaboticabal, SP, 14884-900, Brazil
| | - Daniel Gianola
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Guilherme J M Rosa
- Department of Animal Sciences, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, 53792, USA
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8
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Lu KL, Wu MY, Wang CH, Wang CW, Hung SI, Chung WH, Chen CB. The Role of Immune Checkpoint Receptors in Regulating Immune Reactivity in Lupus. Cells 2019; 8:E1213. [PMID: 31597242 PMCID: PMC6829486 DOI: 10.3390/cells8101213] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 09/29/2019] [Accepted: 10/03/2019] [Indexed: 12/26/2022] Open
Abstract
Immune checkpoint receptors with co-stimulatory and co-inhibitory signals are important modulators for the immune system. However, unrestricted co-stimulation and/or inadequate co-inhibition may cause breakdown of self-tolerance, leading to autoimmunity. Systemic lupus erythematosus (SLE) is a complex multi-organ disease with skewed and dysregulated immune responses interacting with genetics and the environment. The close connections between co-signaling pathways and SLE have gradually been established in past research. Also, the recent success of immune checkpoint blockade in cancer therapy illustrates the importance of the co-inhibitory receptors in cancer immunotherapy. Moreover, immune checkpoint blockade could result in substantial immune-related adverse events that mimic autoimmune diseases, including lupus. Together, immune checkpoint regulators represent viable immunotherapeutic targets for the treatment of both autoimmunity and cancer. Therefore, it appears reasonable to treat SLE by restoring the out-of-order co-signaling axis or by manipulating collateral pathways to control the pathogenic immune responses. Here, we review the current state of knowledge regarding the relationships between SLE and the co-signaling pathways of T cells, B cells, dendritic cells, and neutrophils, and highlight their potential clinical implications. Current clinical trials targeting the specific co-signaling axes involved in SLE help to advance such knowledge, but further in-depth exploration is still warranted.
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Affiliation(s)
- Kun-Lin Lu
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
| | - Ming-Ying Wu
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
| | - Chi-Hui Wang
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
| | - Chuang-Wei Wang
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou 333, Taiwan
| | - Shuen-Iu Hung
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou 333, Taiwan
| | - Wen-Hung Chung
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung 204, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen 361000, China
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
| | - Chun-Bing Chen
- Chang Gung Memorial Hospital, Linkou 333, Taiwan; (K.-L.L.); (M.-Y.W.); , (C.-W.W.); (S.-I.H.)
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
- Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Taipei 105, Taiwan
- Cancer Vaccine and Immune Cell Therapy Core Laboratory, Chang Gung Immunology Consortium, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung 204, Taiwan
- Immune-Oncology Center of Excellence, Chang Gung Memorial Hospital, Linkou 333, Taiwan
- Department of Dermatology, Xiamen Chang Gung Hospital, Xiamen 361000, China
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan 333, Taiwan
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9
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Systematic analysis of genes and diseases using PheWAS-Associated networks. Comput Biol Med 2019; 109:311-321. [DOI: 10.1016/j.compbiomed.2019.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/28/2019] [Accepted: 04/28/2019] [Indexed: 02/08/2023]
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10
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Tian X, Lin Y, Cui C, Su M, Lai L. BTNL2-Ig Protein Attenuates Type 1 Diabetes in Non-Obese Diabetic (NOD) Mice. Adv Healthc Mater 2019; 8:e1800987. [PMID: 30884196 DOI: 10.1002/adhm.201800987] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Indexed: 12/23/2022]
Abstract
Type 1 diabetes (T1D) is a T cell-mediated autoimmune disease in which insulin-producing β-cells are destroyed. Although butyrophilin-like 2 (BTNL2) has been shown to be a negative T cell regulator in vitro, its ability to inhibit T cell responses in vivo has not been determined. In this study, the effect of a recombinant BTNL2-IgG2a Fc (rBTNL2-Ig) fusion protein on T1D development in vivo is determined. It is shown here that in vivo administration of rBTNL2-Ig ameliorates T1D in non-obese diabetic (NOD) mice. This is associated with the ability of rBTNL2-Ig to inhibit the proliferation, activation, and inflammatory cytokine production from autoreactive T cells in vivo. In addition, rBTNL2-Ig treatment increases the generation of regulatory T cells. The results suggest that targeting the BTNL2 pathway has the potential to be used in the prevention and treatment of patients with T1D.
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Affiliation(s)
- Xiaohong Tian
- Department of Allied Health SciencesUniversity of Connecticut Storrs CT 06269 USA
- Department of Tissue engineeringSchool of Fundamental ScienceChina Medical University Shenyang Liaoning 110122 China
| | - Yujun Lin
- Department of Allied Health SciencesUniversity of Connecticut Storrs CT 06269 USA
| | - Cheng Cui
- Department of Allied Health SciencesUniversity of Connecticut Storrs CT 06269 USA
| | - Min Su
- Department of Allied Health SciencesUniversity of Connecticut Storrs CT 06269 USA
| | - Laijun Lai
- Department of Allied Health SciencesUniversity of Connecticut Storrs CT 06269 USA
- University of Connecticut Stem Cell InstituteUniversity of Connecticut Storrs CT 06269 USA
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11
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Hippich M, Beyerlein A, Hagopian WA, Krischer JP, Vehik K, Knoop J, Winker C, Toppari J, Lernmark Å, Rewers MJ, Steck AK, She JX, Akolkar B, Robertson CC, Onengut-Gumuscu S, Rich SS, Bonifacio E, Ziegler AG. Genetic Contribution to the Divergence in Type 1 Diabetes Risk Between Children From the General Population and Children From Affected Families. Diabetes 2019; 68:847-857. [PMID: 30655385 PMCID: PMC6425872 DOI: 10.2337/db18-0882] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/04/2019] [Indexed: 12/20/2022]
Abstract
The risk for autoimmunity and subsequently type 1 diabetes is 10-fold higher in children with a first-degree family history of type 1 diabetes (FDR children) than in children in the general population (GP children). We analyzed children with high-risk HLA genotypes (n = 4,573) in the longitudinal TEDDY birth cohort to determine how much of the divergent risk is attributable to genetic enrichment in affected families. Enrichment for susceptible genotypes of multiple type 1 diabetes-associated genes and a novel risk gene, BTNL2, was identified in FDR children compared with GP children. After correction for genetic enrichment, the risks in the FDR and GP children converged but were not identical for multiple islet autoantibodies (hazard ratio [HR] 2.26 [95% CI 1.6-3.02]) and for diabetes (HR 2.92 [95% CI 2.05-4.16]). Convergence varied depending upon the degree of genetic susceptibility. Risks were similar in the highest genetic susceptibility group for multiple islet autoantibodies (14.3% vs .12.7%) and diabetes (4.8% vs. 4.1%) and were up to 5.8-fold divergent for children in the lowest genetic susceptibility group, decreasing incrementally in GP children but not in FDR children. These findings suggest that additional factors enriched within affected families preferentially increase the risk of autoimmunity and type 1 diabetes in lower genetic susceptibility strata.
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Affiliation(s)
- Markus Hippich
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Andreas Beyerlein
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Jan Knoop
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Christiane Winker
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, and Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | | | | | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Ezio Bonifacio
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- DFG Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
- Forschergruppe Diabetes e.V., Helmholtz Zentrum München (German Research Center for Environmental Health), Munich-Neuherberg, Germany
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12
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Saad MN, Mabrouk MS, Eldeib AM, Shaker OG. Comparative study for haplotype block partitioning methods - Evidence from chromosome 6 of the North American Rheumatoid Arthritis Consortium (NARAC) dataset. PLoS One 2019; 13:e0209603. [PMID: 30596705 PMCID: PMC6312333 DOI: 10.1371/journal.pone.0209603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Haplotype-based methods compete with “one-SNP-at-a-time” approaches on being preferred for association studies. Chromosome 6 contains most of the known genetic biomarkers for rheumatoid arthritis (RA) disease. Therefore, chromosome 6 serves as a benchmark for the haplotype methods testing. The aim of this study is to test the North American Rheumatoid Arthritis Consortium (NARAC) dataset to find out if haplotype block methods or single-locus approaches alone can sufficiently provide the significant single nucleotide polymorphisms (SNPs) associated with RA. In addition, could we be satisfied with only one method of the haplotype block methods for partitioning chromosome 6 of the NARAC dataset? In the NARAC dataset, chromosome 6 comprises 35,574 SNPs for 2,062 individuals (868 cases, 1,194 controls). Individual SNP approach and three haplotype block methods were applied to the NARAC dataset to identify the RA biomarkers. We employed three haplotype partitioning methods which are confidence interval test (CIT), four gamete test (FGT), and solid spine of linkage disequilibrium (SSLD). P-values after stringent Bonferroni correction for multiple testing were measured to assess the strength of association between the genetic variants and RA susceptibility. Moreover, the block size (in base pairs (bp) and number of SNPs included), number of blocks, percentage of uncovered SNPs by the block method, percentage of significant blocks from the total number of blocks, number of significant haplotypes and SNPs were used to compare among the three haplotype block methods. Individual SNP, CIT, FGT, and SSLD methods detected 432, 1,086, 1,099, and 1,322 associated SNPs, respectively. Each method identified significant SNPs that were not detected by any other method (Individual SNP: 12, FGT: 37, CIT: 55, and SSLD: 189 SNPs). 916 SNPs were discovered by all the three haplotype block methods. 367 SNPs were discovered by the haplotype block methods and the individual SNP approach. The P-values of these 367 SNPs were lower than those of the SNPs uniquely detected by only one method. The 367 SNPs detected by all the methods represent promising candidates for RA susceptibility. They should be further investigated for the European population. A hybrid technique including the four methods should be applied to detect the significant SNPs associated with RA for chromosome 6 of the NARAC dataset. Moreover, SSLD method may be preferred for its favored benefits in case of selecting only one method.
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Affiliation(s)
- Mohamed N. Saad
- Biomedical Engineering Department, Faculty of Engineering, Minia University, Minia, Egypt
- * E-mail: ,
| | - Mai S. Mabrouk
- Biomedical Engineering Department, Faculty of Engineering, Misr University for Science and Technology (MUST), 6th of October City, Egypt
| | - Ayman M. Eldeib
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Giza, Egypt
| | - Olfat G. Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
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13
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Cui C, Tian X, Lin Y, Su M, Chen Q, Wang SY, Lai L. In vivo administration of recombinant BTNL2-Fc fusion protein ameliorates graft-versus-host disease in mice. Cell Immunol 2018; 335:22-29. [PMID: 30389093 DOI: 10.1016/j.cellimm.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/02/2018] [Accepted: 10/24/2018] [Indexed: 10/28/2022]
Abstract
Although hematopoietic stem cell transplantation (HSCT) has been widely used in the treatment of many diseases, graft-versus-host disease (GVHD) remains a major complication after allogeneic HSCT. Butyrophilin-like 2 (BTNL2) protein has been reported to have the ability to inhibit T cell proliferation in vitro; its ability to inhibit T cell responses in vivo has not been determined. We show here that in vivo administration of recombinant BTNL2-IgG2a Fc (rBTNL2-Ig) fusion protein ameliorates GVHD in mice. This is related to the ability of rBTNL2-Ig to inhibit T cell proliferation, activation and Th1/Th17 cytokine production in vivo. Furthermore, rBTNL2-Ig treatment increases the generation of regulatory T cells. Our results suggest that rBTNL2-Ig has the potential to be used in the prevention and treatment of patients with GVHD.
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Affiliation(s)
- Cheng Cui
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States; Department of Physiology, College of Basic Medical Science, China Medical University, Shenyang, Liaoning, China
| | - Xiaohong Tian
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States
| | - Yujun Lin
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States
| | - Min Su
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States
| | - Qingquan Chen
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States
| | - Shao-Yuan Wang
- Fujian Institute of Hematology, Hematology Department of Fujian Medical University Union Hospital, China
| | - Laijun Lai
- Department of Allied Health Sciences, University of Connecticut, Storrs, CT, United States; University of Connecticut Stem Cell Institute, University of Connecticut, Storrs, CT, United States.
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14
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Moon CM, Kim SW, Ahn JB, Ma HW, Che X, Kim TI, Kim WH, Cheon JH. Deep Resequencing of Ulcerative Colitis-Associated Genes Identifies Novel Variants in Candidate Genes in the Korean Population. Inflamm Bowel Dis 2018; 24:1706-1717. [PMID: 29733354 DOI: 10.1093/ibd/izy122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 01/08/2023]
Abstract
BACKGROUND Genome-wide association studies and meta-analyses have revealed the genetic background of ulcerative colitis (UC) by identifying common variants. However, these variants do not fully explain the disease variance in UC. To identify novel variants, we performed deep resequencing of UC-associated genes in Korean UC patients and subsequently investigated the functional roles of identified susceptibility genes. METHODS We performed targeted deep resequencing of 108 genes in 24 Korean UC patients and then performed association analysis with data from 126 healthy controls. We validated these variants using 2-stage replication studies including 793 UC patients and 783 controls. We performed in silico and pathway analyses and functional analyses. RESULTS The combined analysis including 2 replication studies identified 6 novel susceptibility loci and reconfirmed 10 previously reported loci. Among the novel single nucleotide variants (SNVs), rs10035653 in C5orf55 (P = 2.08 × 10-3; OR = 1.50), rs41417449 in BTNL2 (P = 1.27 × 10-2; OR = 1.32), rs3117099 in HCG23 (P = 9.98 × 10-6; OR = 1.40), rs7192 in HLA-DRA (P = 6.95 × 10-9; OR = 1.57), and rs3744246 in ORMDL3 (P = 2.21 × 10-2; OR = 1.21) were identified as causal variants, whereas rs713669 in IL17REL (P = 2.69 × 10-2; OR = 0.84) as a protective variant for UC. When correcting multiple testing, 3 novel SNVs (rs41417449 in BTNL2, rs3744246 in ORMDL3, and rs713669 in IL17REL) and 4 previously reported SNVs did not reach a statistical significance. Functional study suggested that SNVs of BTNL2 and C5orf55 exacerbated the inflammatory response both in vitro and in vivo. CONCLUSIONS This study identified 3 novel susceptibility loci and validated 6 previously reported SNVs for UC through deep resequencing in Koreans and revealed the functional roles of BTNL2 and C5orf55.
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Affiliation(s)
- Chang Mo Moon
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seung Won Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Bum Ahn
- Department of Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyun Woo Ma
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Xiumei Che
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Won Ho Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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15
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Prediction of Disordered Regions and Their Roles in the Anti-Pathogenic and Immunomodulatory Functions of Butyrophilins. Molecules 2018; 23:molecules23020328. [PMID: 29401697 PMCID: PMC6017450 DOI: 10.3390/molecules23020328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 12/13/2022] Open
Abstract
Butyrophilins (BTNs) are a group of the moonlighting proteins, some members of which are secreted in milk. They constitute a large family of structurally similar type 1 transmembrane proteins from the immunoglobulin superfamily. Although the founding member of this family is related to lactation, participating in the secretion, formation and stabilization of milk fat globules, it may also have a cell surface receptor function. Generally, the BTN family members are known to modulate co-stimulatory responses, T cell selection, differentiation, and cell fate determination. Polymorphism of these genes was shown to be associated with the pathology of several human diseases. Despite their biological significance, structural information on human butyrophilins is rather limited. Based on their remarkable multifunctionality, butyrophilins seem to belong to the category of moonlighting proteins, which are known to contain intrinsically disordered protein regions (IDPRs). However, the disorder status of human BTNs was not systematically investigated as of yet. The goal of this study is to fill this gap and to evaluate peculiarities of intrinsic disorder predisposition of the members of human BTN family, and to find if they have IDPRs that can be attributed to the multifunctionality of these important proteins.
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16
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Butyrophilins: an important new element of resistance. Cent Eur J Immunol 2017; 42:399-403. [PMID: 29472819 PMCID: PMC5820976 DOI: 10.5114/ceji.2017.72806] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/13/2017] [Indexed: 11/18/2022] Open
Abstract
Butyrophilins belonging to the immunoglobulin superfamily are new immune system regulators because they are present on lymphocytes, dendritic cells, monocytes, macrophages, neutrophils and eosinophils, and they exert a stimulatory and (or) inhibitory effect on them. The role of butyrophilins is associated and results from their similarity to the regulatory B7 protein family involved in the modulation of immune phenomena. Butyrophilins are glycoproteins built of two extracellular immunoglobulin domains, stabilized with disulfide bonds: constant IgC, and variable IgV and a transmembrane region. Most of these proteins contain a conserved domain encoded by a single exon – B30.2, also referred to as PRYSPRY. In humans, the family of butyrophilins includes 7 butyrophilin proteins, 5 butyrophilin-like proteins and the SKINT-like factor. Butyrophilins have been also demonstrated to play a role in various infections, e.g. tuberculosis or diseases that include sarcoidosis, systemic lupus erythematosus, rheumatoid arthritis, genetic metabolic diseases, ulcerative colitis, cancer and kidney disease.
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Tong X, Ma Y, Niu X, Yan Z, Liu S, Peng B, Peng S, Fan H. The BTNL2 G16071A gene polymorphism increases granulomatous disease susceptibility: A meta-analysis including FPRP test of 8710 participants. Medicine (Baltimore) 2016; 95:e4325. [PMID: 27472712 PMCID: PMC5265849 DOI: 10.1097/md.0000000000004325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE The butyrophilin-like 2 (BTNL2) G16071A gene polymorphism has been implicated in the susceptibility to granulomatous diseases, but the results were inconclusive. The objective of the current study was to precisely explore the relationship between BTNL2 G16071A gene polymorphism and granulomatous disease susceptibility by the meta-analysis including false-positive report probability (FPRP) test. METHODS A systematic literature search in the PubMed, Embase, and Wanfang databases, China National Knowledge Internet, and commercial Internet search engines was conducted to identify studies published up to April 1, 2016. The odds ratio (OR) with 95% confidence interval (CI) was used to assess the effect size. Statistical analysis was conducted using the STATA 12.0 software and FPRP test sheet. RESULTS In total, all 4324 cases and 4386 controls from 14 eligible studies were included in the current meta-analysis. By the overall meta-analysis, we found a significant association between BTNL2 G16071A gene polymorphism and granulomatous disease susceptibility (A vs G: OR = 1.25, 95% CI = 1.07-1.45, P = 0.005). The meta-regression analyses showed that a large proportion of the between-study heterogeneity was significantly attributed to the ethnicity (A vs G, P = 0.013) and the types of granulomatous diseases (A vs G, P = 0.002). By the subgroup meta-analysis, the BTNL2 G16071A gene polymorphism was associated with granulomatous disease susceptibility in Caucasians (A vs G: OR = 1.37, 95% CI = 1.18-1.58, P < 0.001). Moreover, a significant relationship between the BTNL2 G16071A gene polymorphism and sarcoidosis susceptibility (A vs G: OR = 1.52, 95% CI = 1.39-1.66, P < 0.001) was found. However, to avoid the "false-positive report," we further investigated the significant associations observed in the present meta-analysis by the FPRP test. Interestingly, the results of FPRP test indicated that the BTNL2 G16071A gene polymorphism was truly associated with sarcoidosis susceptibility (A vs G, FPRP < 0.001). Additionally, the FPRP test confirmed that the BTNL2 G16071A gene polymorphism was associated only with granulomatous disease susceptibility among Caucasians (A vs G, FPRP < 0.001) at the level of a prior probability, which was 0.001. CONCLUSION The meta-analysis indicated that BTNL2 G16071A gene polymorphism may as a likelihood factor contributed to granulomatous disease susceptibility, especially increasing the sarcoidosis susceptibility. In addition, the polymorphism may be greatly associated with likelihood of granulomatous diseases among Caucasians.
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Affiliation(s)
- Xiang Tong
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Yao Ma
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Xundong Niu
- Department of Endocrinology, The Second Affiliated Hospital of Ningxia Medical University, Yinchuan, Ningxia
| | - Zhipeng Yan
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Sitong Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Bo Peng
- Department of Internal Medicine, Leshan Traditional Chinese Medicine Hospital, Leshan, Sichuan, China
| | - Shifeng Peng
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Hong Fan
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
- Correspondence: Hong Fan, Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan 610041, China (e-mail: fanhongfanscu@.sina.cn, )
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18
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Affiliation(s)
- David A. Rhodes
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom; ,
| | - Walter Reith
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, CH-1211 Geneva 4, Switzerland;
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom; ,
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Bagley SC, Sirota M, Chen R, Butte AJ, Altman RB. Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants. PLoS Comput Biol 2016; 12:e1004885. [PMID: 27115429 PMCID: PMC4846031 DOI: 10.1371/journal.pcbi.1004885] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/29/2016] [Indexed: 12/24/2022] Open
Abstract
Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism, which sometimes can be explained by shared genetics. In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease. Records of pairs of diseases were combined from two different electronic medical systems (Columbia, Stanford), and compared to a large database of published disease-associated genetic variants (VARIMED); data on 35 disorders were available across all three sources, which include medical records for over 1.2 million patients and variants from over 17,000 publications. Based on the sources in which they appeared, disease pairs were categorized as having predominant clinical, genetic, or both kinds of manifestations. Confounding effects of age on disease incidence were controlled for by only comparing diseases when they fall in the same cluster of similarly shaped incidence patterns. We find that disease pairs that are overrepresented in both electronic medical record systems and in VARIMED come from two main disease classes, autoimmune and neuropsychiatric. We furthermore identify specific genes that are shared within these disease groups.
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Affiliation(s)
- Steven C. Bagley
- Department of Genetics, Stanford University, Stanford, California, United States of America
- * E-mail:
| | - Marina Sirota
- UCSF Institute for Computational Health Sciences, San Francisco, California, United States of America
| | - Richard Chen
- Personalis, Inc., Menlo Park, California, United States of America
| | - Atul J. Butte
- UCSF Institute for Computational Health Sciences, San Francisco, California, United States of America
| | - Russ B. Altman
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
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20
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Shen C, Gao J, Sheng Y, Dou J, Zhou F, Zheng X, Ko R, Tang X, Zhu C, Yin X, Sun L, Cui Y, Zhang X. Genetic Susceptibility to Vitiligo: GWAS Approaches for Identifying Vitiligo Susceptibility Genes and Loci. Front Genet 2016; 7:3. [PMID: 26870082 PMCID: PMC4740779 DOI: 10.3389/fgene.2016.00003] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/11/2016] [Indexed: 01/15/2023] Open
Abstract
Vitiligo is an autoimmune disease with a strong genetic component, characterized by areas of depigmented skin resulting from loss of epidermal melanocytes. Genetic factors are known to play key roles in vitiligo through discoveries in association studies and family studies. Previously, vitiligo susceptibility genes were mainly revealed through linkage analysis and candidate gene studies. Recently, our understanding of the genetic basis of vitiligo has been rapidly advancing through genome-wide association study (GWAS). More than 40 robust susceptible loci have been identified and confirmed to be associated with vitiligo by using GWAS. Most of these associated genes participate in important pathways involved in the pathogenesis of vitiligo. Many susceptible loci with unknown functions in the pathogenesis of vitiligo have also been identified, indicating that additional molecular mechanisms may contribute to the risk of developing vitiligo. In this review, we summarize the key loci that are of genome-wide significance, which have been shown to influence vitiligo risk. These genetic loci may help build the foundation for genetic diagnosis and personalize treatment for patients with vitiligo in the future. However, substantial additional studies, including gene-targeted and functional studies, are required to confirm the causality of the genetic variants and their biological relevance in the development of vitiligo.
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Affiliation(s)
- Changbing Shen
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Jing Gao
- Department of Dermatology, The Second Affiliated Hospital, Anhui Medical University Hefei, China
| | - Yujun Sheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Jinfa Dou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Fusheng Zhou
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Xiaodong Zheng
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Randy Ko
- Department of Biochemistry, University of New Mexico Albuquerque, NM, USA
| | - Xianfa Tang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Caihong Zhu
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Xianyong Yin
- Department of Genetics and Renaissance Computing Institute, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Liangdan Sun
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical University Hefei, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital Beijing, China
| | - Xuejun Zhang
- Institute and Department of Dermatology, The First Affiliated Hospital, Anhui Medical UniversityHefei, China; Department of Dermatology, The Second Affiliated Hospital, Anhui Medical UniversityHefei, China
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Guo Y, Wang AY. Novel Immune Check-Point Regulators in Tolerance Maintenance. Front Immunol 2015; 6:421. [PMID: 26347744 PMCID: PMC4539525 DOI: 10.3389/fimmu.2015.00421] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/02/2015] [Indexed: 01/24/2023] Open
Abstract
The great success of anti-cytotoxic lymphocyte antigen 4 (CTLA4) and anti-programed cell death protein 1 (PD1) in cancer treatment has encouraged more effort in harnessing the immune response through immunomodulatory molecules in various diseases. The immunoglobulin (Ig) super family comprises the majority of immunomodulatory molecules. Discovery of novel Ig super family members has brought novel insights into the function of different immune cells in tolerance maintenance. In this review, we discuss the function of newly identified B7 family molecules, B7-H4 and V-domain Ig Suppressor of T cell Activation (VISTA), and the butyrophilin/butyrophilin-like family members. We discuss the current stages of immunomodulatory molecules in clinical trials of organ transplantation. The potential of engaging the novel Ig superfamily members in tolerance maintenance is also discussed. We conclude with the challenges remaining to manipulate these molecules in the immune response.
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Affiliation(s)
- Yanxia Guo
- Merck Research Laboratories , Palo Alto, CA , USA
| | - Adele Y Wang
- Merck Research Laboratories , Palo Alto, CA , USA
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22
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Zheng W, Rao S. Knowledge-based analysis of genetic associations of rheumatoid arthritis to inform studies searching for pleiotropic genes: a literature review and network analysis. Arthritis Res Ther 2015; 17:202. [PMID: 26253105 PMCID: PMC4529690 DOI: 10.1186/s13075-015-0715-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 07/13/2015] [Indexed: 12/29/2022] Open
Abstract
Introduction Pleiotropy describes the genetic effect of a single gene on multiple phenotypic traits. Gene variants directly affect the normal processes of a series of physiological and biochemical reactions, and therefore cause a variety of diseases traits to be changed accordingly. Moreover, a shared genetic susceptibility mechanism may exist between different diseases. Therefore, shared genes, with pleiotropic effects, are important to understand the sharing pathogenesis and hence the mechanisms underlying comorbidity. Methods In this study, we proposed combining genome-wide association studies (GWAS) and public knowledge databases to search for potential pleiotropic genes associated with rheumatoid arthritis (RA) and eight other related diseases. Here, a GWAS-based network analysis is used to recognize risk genes significantly associated with RA. These RA risk genes are re-extracted as potential pleiotropic genes if they have been proved to be susceptible genes for at least one of eight other diseases in the OMIM or PubMed databases. Results In total, we extracted 116 potential functional pleiotropic genes for RA and eight other diseases, including five hub pleiotropic genes, BTNL2, HLA-DRA, NOTCH4, TNXB, and C6orf10, where BTNL2, NOTCH4, and C6orf10 are novel pleiotropic genes identified by our analysis. Conclusions This study demonstrates that pleiotropy is a common property of genes associated with disease traits. Our results ascertained the shared genetic risk profiles that predisposed individuals to RA and other diseases, which could have implications for identification of molecular targets for drug development, and classification of diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13075-015-0715-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weiying Zheng
- College of Biomedical Engineering, Capital Medical University, 10 Xitoutiao Youanmen Fengtai, Beijing, 100069, People's Republic of China.
| | - Shaoqi Rao
- College of Biomedical Engineering, Capital Medical University, 10 Xitoutiao Youanmen Fengtai, Beijing, 100069, People's Republic of China. .,Institute of Medical Systems Biology and School of Public Health, Guangdong Medical College, 1 Xin Cheng Avenue, Songshan Lake, Dongguan, 523808, Guangdong, People's Republic of China.
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Subramaniam KS, Spaulding E, Ivan E, Mutimura E, Kim RS, Liu X, Dong C, Feintuch CM, Zhang X, Anastos K, Lauvau G, Daily JP. The T-Cell Inhibitory Molecule Butyrophilin-Like 2 Is Up-regulated in Mild Plasmodium falciparum Infection and Is Protective During Experimental Cerebral Malaria. J Infect Dis 2015; 212:1322-31. [PMID: 25883389 DOI: 10.1093/infdis/jiv217] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 04/01/2015] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum infection can result in severe disease that is associated with elevated inflammation and vital organ dysfunction; however, malaria-endemic residents gain protection from lethal outcomes and manifest only mild symptoms during infection. To characterize host responses associated with this more effective antimalarial response, we characterized whole-blood transcriptional profiles in Rwandan adults during a mild malaria episode and compared them with findings from a convalescence sample. We observed transcriptional up-regulation in many pathways, including type I interferon, interferon γ, complement activation, and nitric oxide during malaria infection, which provide benchmarks of mild disease physiology. Transcripts encoding negative regulators of T-cell activation, such as programmed death ligand 1 (PD-L1), programmed death 1 ligand 2 (PD-L2), and the butyrophilin family member butyrophilin-like 2 (BTNL2) were also increased. To support an important functional role for BTNL2 during malaria infection, we studied chimeric mice reconstituted with BTNL2(-/-) or wild-type hematopoietic cells that were inoculated with Plasmodium berghei ANKA, a murine model of cerebral malaria. We found that BTNL2(-/-) chimeric mice had a significant decrease in survival compared with wild-type counterparts. Collectively these data characterize the immune responses associated with mild malaria and uncover a novel role for BTNL2 in the host response to malaria.
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Affiliation(s)
| | | | - Emil Ivan
- Department of Biomedical Laboratory Sciences, College of Medicine and Health Sciences, University of Rwanda
| | | | | | - Xikui Liu
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston
| | - Chen Dong
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston
| | | | | | - Kathryn Anastos
- Medicine, Albert Einstein College of Medicine, Bronx, New York
| | | | - Johanna P Daily
- Departments of Microbiology and Immunology Medicine, Albert Einstein College of Medicine, Bronx, New York
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25
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Genetics of canine anal furunculosis in the German shepherd dog. Immunogenetics 2014; 66:311-24. [DOI: 10.1007/s00251-014-0766-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 02/25/2014] [Indexed: 12/25/2022]
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26
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Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell 2013; 152:743-54. [PMID: 23415224 DOI: 10.1016/j.cell.2013.01.015] [Citation(s) in RCA: 519] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 07/28/2012] [Accepted: 01/07/2013] [Indexed: 02/06/2023]
Abstract
Long noncoding RNAs (lncRNAs) are increasingly appreciated as regulators of cell-specific gene expression. Here, an enhancer-like lncRNA termed NeST (nettoie Salmonella pas Theiler's [cleanup Salmonella not Theiler's]) is shown to be causal for all phenotypes conferred by murine viral susceptibility locus Tmevp3. This locus was defined by crosses between SJL/J and B10.S mice and contains several candidate genes, including NeST. The SJL/J-derived locus confers higher lncRNA expression, increased interferon-γ (IFN-γ) abundance in activated CD8(+) T cells, increased Theiler's virus persistence, and decreased Salmonella enterica pathogenesis. Transgenic expression of NeST lncRNA alone was sufficient to confer all phenotypes of the SJL/J locus. NeST RNA was found to bind WDR5, a component of the histone H3 lysine 4 methyltransferase complex, and to alter histone 3 methylation at the IFN-γ locus. Thus, this lncRNA regulates epigenetic marking of IFN-γ-encoding chromatin, expression of IFN-γ, and susceptibility to a viral and a bacterial pathogen.
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Affiliation(s)
- J Antonio Gomez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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27
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Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2. J Hum Genet 2013; 58:210-5. [DOI: 10.1038/jhg.2013.2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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28
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Spagnolo P, Luppi F, Cerri S, Richeldi L. Genetic testing in diffuse parenchymal lung disease. Orphanet J Rare Dis 2012; 7:79. [PMID: 23075428 PMCID: PMC3489730 DOI: 10.1186/1750-1172-7-79] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 10/14/2012] [Indexed: 02/06/2023] Open
Abstract
Diffuse parenchymal lung diseases (DPLD) represent a diverse group of disorders affecting the distal lung parenchyma, specifically the tissue and spaces surrounding the alveoli, which may be filled with inflammatory cells, proliferating fibroblasts or established fibrosis, often leading to architectural distortion and impaired gas exchange. While the underlying pathogenetic mechanisms are known or inferred for some DPLD (such as sarcoidosis, silicosis, drug reactions and collagen vascular diseases), the pathogenesis of the majority of these entities - particularly those characterized by progressive fibrosis - is poorly understood. Several lines of evidence indicate that the development of pulmonary fibrosis is genetically determined. They include: 1. familial clustering; 2. the occurrence of pulmonary fibrosis in the context of rare inherited disorders; 3. substantial variability in the development of pulmonary fibrosis amongst individuals exposed to organic or inorganic dusts; 4. difference in susceptibility to fibrogenic stimuli amongst inbred strains of mice. This review focuses on idiopathic pulmonary fibrosis (IPF) and sarcoidosis, the two most common DPLD and the two entities for which there is stronger evidence of a genetic predisposition, although how aberrant genes interact with each other and with environmental factors, such as smoking in IPF and infectious agents in sarcoidosis, in determining disease susceptibility and clinical phenotypes is largely unknown. Finally, we discuss practical issues and implications for both patients and physicians of recent advances in the genetics of sarcoidosis and IPF.
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Affiliation(s)
- Paolo Spagnolo
- Department of Oncology, Center for Rare Lung Disease, Hematology, and Respiratory Diseases, University of Modena and Reggio Emilia, Via del Pozzo 71, Modena, 41124, Italy.
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Leveraging models of cell regulation and GWAS data in integrative network-based association studies. Nat Genet 2012; 44:841-7. [PMID: 22836096 DOI: 10.1038/ng.2355] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kota SK, Meher LK, Jammula S, Kota SK, Modi KD. Clinical profile of coexisting conditions in type 1 diabetes mellitus patients. Diabetes Metab Syndr 2012; 6:70-76. [PMID: 23153973 DOI: 10.1016/j.dsx.2012.08.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
AIMS Type 1 diabetes mellitus (T1DM) is associated with various genetic and autoimmune diseases implicated in its etiopathogenesis. We hereby profile the clinical association of such diseases among patients from our center. METHODS Consecutive patients of T1DM presenting to department of Endocrinology from May 1997 to December 2011 were retrospectively analyzed in context of associated clinical profile. RESULTS Among 260 patients diagnosed as T1DM, 21 (8%) had hypothyroidism, 4 (1.5%) had hyperthyroidism and 2 (0.7%) had primary adrenal insufficiency. Eighteen patients (7%) had celiac disease, 9 (3.5%) had Turner's syndrome, 5 patients (1.9%) had Klinefelter's syndrome, whereas Down's syndrome and Noonan's syndrome was present in 2 and 1 patients (0.7%) respectively. One patient had Wolframs' syndrome and 1 patients had myasthenia gravis. Systemic lupus erythematosus and rheumatoid arthritis were present in 3 and 1 patients respectively. Total of 5 patients with cerebral palsy, 4 cases with deaf mutism, 4 cases with acute psychosis and 16 patients with depression were noted. Mean age of study patients was 20.8±9.8 years (range, 3-23 years). CONCLUSION Various conditions including genetic (Down, Turner, Noonan, and Klinefelter's), autoimmune (thyroid and adrenal disorders, myasthenia gravis, SLE, rheumatoid arthritis) and central nervous system diseases were the associated diseases encountered in our patients. Routine screening is required for early diagnosis and treatment of associated co morbidities.
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Affiliation(s)
- Sunil K Kota
- Department of Endocrinology, Medwin hospital, Nampally, Hyderabad, Andhra pradesh, India.
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Abeler-Dörner L, Swamy M, Williams G, Hayday AC, Bas A. Butyrophilins: an emerging family of immune regulators. Trends Immunol 2011; 33:34-41. [PMID: 22030238 DOI: 10.1016/j.it.2011.09.007] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/04/2011] [Accepted: 09/19/2011] [Indexed: 11/17/2022]
Abstract
Butyrophilins (Btns) and butyrophilin-like (Btnl) molecules are emerging as novel regulators of immune responses in mice and humans. Several clues point to their probable importance: many of the genes are located within the MHC; they are structurally related to B7-co-stimulatory molecules; they are functionally implicated in T cell inhibition and in the modulation of epithelial cell-T cell interactions; and they are genetically associated with inflammatory diseases. Nonetheless, initial immersion into the current literature can uncover confusion over even basic information such as gene names and expression patterns, and seemingly conflicting data regarding the biological activities of different family members. This review addresses each of these issues, concluding with the attractive potential of Btn and Btnl molecules to act as specific attenuators of tissue-associated inflammatory responses.
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Affiliation(s)
- Lucie Abeler-Dörner
- Peter Gorer Department of Immunobiology, King's College School of Medicine, Guy's Hospital, London SE1 9RT, UK
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Milman N, Svendsen CB, Nielsen FC, van Overeem Hansen T. The BTNL2 A allele variant is frequent in Danish patients with sarcoidosis. CLINICAL RESPIRATORY JOURNAL 2011; 5:105-11. [PMID: 21410903 DOI: 10.1111/j.1752-699x.2010.00206.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND The butyrophilin-like 2 (BTNL2) gene is located on chromosome 6p21.3 close to the HLA-class II genes. An association has been reported between sarcoidosis and a single nucleotide polymorphism in BTNL2, rs2076530, also termed the A allele. OBJECTIVES To evaluate whether patients with sarcoidosis carry the A allele more frequently than healthy subjects. METHODS The series comprised 87 ethnic Danes with sarcoidosis and 113 healthy control subjects. Analysis of rs2076530 was performed by Taqman assay, polymerase chain reaction and sequencing of genomic DNA. RESULTS Sarcoidosis patients had a higher frequency of the A allele than controls (73.9% vs 55.8%) (P < 0.025). The frequency of GG, GA and AA genotype was 5.7%, 40.2% and 54.0% in patients vs 16.0%, 56.6% and 27.4% in controls (P < 0.001). The AA genotype was associated with increased risk of sarcoidosis in both a dominant [odds ratio (OR) 3.1; 95% confidence interval (CI) 1.1-8.7; P < 0.03] and a recessive model (OR 3.1; 95% CI 1.72-5.61; P < 0.001). Population attributable fraction for disease was 50% in a dominant model and 25% in a recessive model. CONCLUSIONS The BTNL2 A allele variant occurs with a high frequency in Danish patients with sarcoidosis and the AA genotype is associated with a ∼threefold higher risk of sarcoidosis than the GG genotype. Our results should encourage future studies on the interrelationship between the BTNL2 protein and granuloma formation in sarcoidosis.
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Affiliation(s)
- Nils Milman
- Department of Rheumatology, Rigshospitalet, Copenhagen University Hospital, Denmark.
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Abstract
In the past decade, the availability and abundance of individual-level molecular data, such as gene expression, proteomics and sequence data, has enabled the use of integrative computational approaches to pose and answer novel questions about disease. In this article, we discuss several examples of applications of bioinformatics techniques to study autoimmune and rheumatic disorders. We focus our discussion on how integrative techniques can be applied to analyze gene expression and genetic variation data across different diseases, and discuss the implications of such analyses. We also outline current challenges and future directions of these approaches. We show that integrative computational methods are essential for translational research and provide a powerful opportunity to improve human health by refining the current knowledge about diagnostics, therapeutics and mechanisms of disease pathogenesis.
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Jin Y, Birlea SA, Fain PR, Gowan K, Riccardi SL, Holland PJ, Bennett DC, Herbstman DM, Wallace MR, McCormack WT, Kemp EH, Gawkrodger DJ, Weetman AP, Picardo M, Leone G, Taïeb A, Jouary T, Ezzedine K, van Geel N, Lambert J, Overbeck A, Spritz RA. Genome-wide analysis identifies a quantitative trait locus in the MHC class II region associated with generalized vitiligo age of onset. J Invest Dermatol 2011; 131:1308-12. [PMID: 21326295 DOI: 10.1038/jid.2011.12] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Generalized vitiligo is a common autoimmune disease in which acquired patchy depigmentation of skin, hair, and mucous membranes results from loss of melanocytes from involved areas. Previous genetic analyses have focused on vitiligo susceptibility, and have identified a number of genes involved in disease risk. Age of onset of generalized vitiligo also involves a substantial genetic component, but has not previously been studied systematically. In this study, we report a genome-wide association study of vitiligo age of onset in 1,339 generalized vitiligo patients, with replication in an independent cohort of 677 cases. We identified a quantitative trait locus for vitiligo age of onset in the major histocompatibility complex (MHC) class II region, located near c6orf10-BTNL2 (rs7758128; P=8.14 × 10(-11)), a region that is also associated with generalized vitiligo susceptibility. In contrast, there was no association of vitiligo age of onset with any other MHC or non-MHC loci that are associated with vitiligo susceptibility. These findings highlight the differing roles played by genes involved in vitiligo susceptibility versus vitiligo age of onset, and illustrate that genome-wide analyses can be used to identify genes involved in quantitative aspects of disease natural history, as well as disease susceptibility per se.
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Affiliation(s)
- Ying Jin
- Human Medical Genetics Program, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA
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Wijnen PA, Voorter CE, Nelemans PJ, Verschakelen JA, Bekers O, Drent M. Butyrophilin-like 2 in pulmonary sarcoidosis: a factor for susceptibility and progression? Hum Immunol 2011; 72:342-7. [PMID: 21256912 DOI: 10.1016/j.humimm.2011.01.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 12/18/2010] [Accepted: 01/13/2011] [Indexed: 12/19/2022]
Abstract
The aims of this study were to assess the association of BTNL2G16071A with the course of pulmonary sarcoidosis and to verify the association with disease predisposition. In addition, the linkage between BTNL2G16071A and certain human leukocyte antigen (HLA)-DRB1/DQB1 types was investigated. In a retrospective case-control study BTNL2G16071A, HLA-DQB1, and HLA-DRB1 were typed in 632 sarcoidosis patients. These patients were classified into 304 patients with persistent sarcoidosis and 328 patients with nonpersistent sarcoidosis. The BTNL2 16071A variant allele was present significantly more often in patients with persistent disease (92.4%; 281/304) compared with patients demonstrating a nonpersistent course (86.6%; 284/328; odds ratio (OR) = 1.89 with 95% confidence interval (95% CI) 1.11-3.22). Furthermore, BTNL2 16071A variant allele carriers have an increased risk (OR = 1.85, 95% CI 1.19-2.88) of developing sarcoidosis. Moreover, the strong linkage between variant allele and HLA-DRB1*15 presence (OR = 8.43, 95% CI 3.02-23.5) was confirmed. The presence of a BTNL2G16071A variant allele almost doubles the risk of progressing to persistent pulmonary sarcoidosis in addition to increasing the risk of developing sarcoidosis. Presumably, these increased risks are caused by the strong linkage between BTNL2G16071A and DRB1*15. The choice between determining BTNL2G16071A SNP or the HLA-DRB1 type depends on the ability and/or availability to perform either test.
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Affiliation(s)
- Petal A Wijnen
- Department of Clinical Chemistry, Maastricht University Medical Centre, Maastricht, The Netherlands
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Yoshida T, Kato K, Oguri M, Horibe H, Kawamiya T, Yokoi K, Fujimaki T, Watanabe S, Satoh K, Aoyagi Y, Tanaka M, Yoshida H, Shinkai S, Nozawa Y, Yamada Y. Association of a polymorphism of BTN2A1 with chronic kidney disease in individuals with or without hypertension or diabetes mellitus. Exp Ther Med 2011; 2:325-331. [PMID: 22977505 DOI: 10.3892/etm.2011.191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 01/04/2011] [Indexed: 11/06/2022] Open
Abstract
Hypertension and diabetes mellitus are important risk factors for chronic kidney disease (CKD). We previously showed that the C→T polymorphism (rs6929846) of BTN2A1 was significantly associated with myocardial infarction. The purpose of the present study was to examine an association of rs6929846 of BTN2A1 with CKD in individuals with or without hypertension or diabetes mellitus, thereby contributing to the personalized prevention of CKD in such individuals separately. The study population comprised 7,542 unrelated individuals, including 2,289 subjects with CKD [estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m(2)] and 5,253 controls (eGFR ≥60 ml/min/1.73 m(2)) with or without hypertension or diabetes mellitus. The Chi-square test, a multivariable logistic regression analysis with adjustment for covariates, as well as a stepwise forward selection procedure revealed that the C→T polymorphism (rs6929846) of BTN2A1 was significantly associated with CKD in normotensive individuals, in diabetic individuals and in individuals with hypertension and diabetes mellitus, or without either condition, with the T allele representing a risk factor for CKD. Stratification of subjects based on hypertension or diabetes mellitus may thus be important in order to achieve personalized prevention of CKD with the use of genetic information.
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Affiliation(s)
- Tetsuro Yoshida
- Department of Cardiovascular Medicine, Onga Nakama Medical Association Onga Hospital, Onga
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Yamada Y, Nishida T, Ichihara S, Sawabe M, Fuku N, Nishigaki Y, Aoyagi Y, Tanaka M, Fujiwara Y, Yoshida H, Shinkai S, Satoh K, Kato K, Fujimaki T, Yokoi K, Oguri M, Yoshida T, Watanabe S, Nozawa Y, Hasegawa A, Kojima T, Han BG, Ahn Y, Lee M, Shin DJ, Lee JH, Jang Y. Association of a polymorphism of BTN2A1 with myocardial infarction in East Asian populations. Atherosclerosis 2010; 215:145-52. [PMID: 21211798 DOI: 10.1016/j.atherosclerosis.2010.12.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 10/13/2010] [Accepted: 12/04/2010] [Indexed: 11/18/2022]
Abstract
OBJECTIVE We have performed a genome-wide association study (GWAS) to identify genetic variants that confer susceptibility to myocardial infarction (MI) in Japanese and Korean populations. METHODS A total of 17,447 Japanese or Korean individuals from four independent subject panels was examined. Japanese subject panels A, B, and C comprised 134 individuals with MI and 137 controls, 1431 individuals with MI and 3161 controls, and 643 individuals with MI and 1347 controls, respectively, whereas the Korean population comprised 1880 individuals with MI and 8714 controls. A GWAS for MI was performed in Japanese subject panel A with the use of the Affymetrix GeneChip Human Mapping 500K Array Set. RESULTS Seventy single nucleotide polymorphisms (SNPs) significantly (P<1.0×10(-7)) associated with MI by the GWAS were examined further in Japanese subject panel B, revealing two SNPs (rs6929846 of BTN2A1, rs2569512 of ILF3) to be significantly (P<0.0007) associated with MI. The rs6929846 SNP of BTN2A1, but not rs2569512 of ILF3, was also significantly associated with MI in Japanese subject panel C. However, the association of neither rs6929846 nor rs2569512 with MI was replicated in the Korean population. CONCLUSION BTN2A1 may be a susceptibility gene for MI in Japanese individuals.
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Affiliation(s)
- Yoshiji Yamada
- Life Science Research Center, Mie University, Tsu, Japan.
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38
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Abstract
The intestine is subjected to a barrage of insults from food, bacterial flora, and pathogens. Despite this constant antigenic challenge, the mucosal tissues lining the intestinal tract remain largely under control. The mechanisms regulating the homeostatic balance in the gut have been investigated for many years by many groups, but the precise nature of the regulatory control remains elusive. In this review, we provide an overview of pathways proposed to be involved in dampening the inflammatory response and maintaining the homeostatic balance in the intestine, and how these pathways may be disrupted in ulcerative colitis and Crohn's disease.
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Aporntewan C, Ballard DH, Lee JY, Lee JS, Wu Z, Zhao H. Gene hunting of the Genetic Analysis Workshop 16 rheumatoid arthritis data using rough set theory. BMC Proc 2009; 3 Suppl 7:S126. [PMID: 20017992 PMCID: PMC2795899 DOI: 10.1186/1753-6561-3-s7-s126] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We propose to use the rough set theory to identify genes affecting rheumatoid arthritis risk from the data collected by the North American Rheumatoid Arthritis Consortium. For each gene, we employ generalized dynamic reducts in the rough set theory to select a subset of single-nucleotide polymorphisms (SNPs) to represent the genetic information from this gene. We then group the study subjects into different clusters based on their genotype similarity at the selected markers. Statistical association between disease status and cluster membership is then studied to identify genes associated with rheumatoid arthritis. Based on our proposed approach, we are able to identify a number of statistically significant genes associated with rheumatoid arthritis. Aside from genes on chromosome 6, our identified genes include known disease-associated genes such as PTPN22 and TRAF1. In addition, our list contains other biologically plausible genes, such as ADAM15 and AGPAT2. Our findings suggest that ADAM15 and AGPAT2 may contribute to a genetic predisposition through abnormal angiogenesis and adipose tissue.
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Affiliation(s)
- Chatchawit Aporntewan
- Department of Psychiatry, Yale University, 300 George Street, Suite 503, New Haven, Connecticut 06511, USA.
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Wang M, Chen X, Zhang M, Zhu W, Cho K, Zhang H. Detecting significant single-nucleotide polymorphisms in a rheumatoid arthritis study using random forests. BMC Proc 2009; 3 Suppl 7:S69. [PMID: 20018063 PMCID: PMC2795970 DOI: 10.1186/1753-6561-3-s7-s69] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Random forest is an efficient approach for investigating not only the effects of individual markers on a trait but also the effect of the interactions among the markers in genetic association studies. This approach is especially appealing for the analysis of genome-wide data, such as those obtained from gene expression/single-nucleotide polymorphism (SNP) array experiments in which the number of candidate genes/SNPs is vast. We applied this approach to the Genetic Analysis Workshop 16 Problem 1 data to identify SNPs that contribute to rheumatoid arthritis. The random forest computed a raw importance score for each SNP marker, where higher importance score suggests higher level of association between the marker and the trait. The significance level of the association was determined empirically by repeatedly reapplying the random forest on randomly generated data under the null hypothesis that no association exists between the markers and the trait. Using random forest, we were able to identify 228 significant SNPs (at the genome-wide significant level of 0.05) across the whole genome, over two-thirds of which are located on chromosome 6, especially clustered in the region of 6p21 containing the human leukocyte antigen (HLA) genes, such as gene HLA-DRB1 and HLA-DRA. Further analysis of this region indicates a strong association to the rheumatoid arthritis status.
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Affiliation(s)
- Minghui Wang
- Department of Epidemiology and Public Health, 60 College Street, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
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41
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Taylor KE, Criswell LA. Conditional analysis of the major histocompatibility complex in rheumatoid arthritis. BMC Proc 2009; 3 Suppl 7:S36. [PMID: 20018027 PMCID: PMC2795934 DOI: 10.1186/1753-6561-3-s7-s36] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
We performed a whole-genome association study of rheumatoid arthritis susceptibility using Illumina 550k single-nucleotide polymorphism (SNP) genotypes of 868 cases and 1194 controls from the North American Rheumatoid Arthritis Consortium (NARAC). Structured association analysis with adjustment for potential population stratification yielded 200 SNPs with p < 1 x 10-8 for association with RA, all of which were on chromosome 6 in a 2.7-Mb region of the major histocompatibility complex (MHC). Given the extensive linkage equilibrium in the region and known risk of HLA-DRB1 alleles, we then applied conditional analyses to ascertain independent signals for RA susceptibility among these 200 candidate SNPs. Conditional analyses incorporating risk categories of the HLA-DRB1 "shared epitope" revealed three SNPs having independent associations with RA (conditional p < 0.001). This supports the presence of significant effects on RA susceptibility in the MHC in addition to the shared epitope.
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Affiliation(s)
- Kimberly E Taylor
- The Rosalind Russell Medical Research Center for Arthritis, University of California San Francisco, 374 Parnassus Ave, San Francisco, California 94143 USA.
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42
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Jiang R, Dong J, Dai Y. Genome-wide association study of rheumatoid arthritis by a score test based on wavelet transformation. BMC Proc 2009; 3 Suppl 7:S8. [PMID: 20018075 PMCID: PMC2795982 DOI: 10.1186/1753-6561-3-s7-s8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background We have conducted a genome-wide association study on the Genetic Analysis Workshop (GAW) 16 rheumatoid arthritis data using a multilocus score test based on wavelet transform proposed recently by the authors. The wavelet-based test automatically adjusts for the amount of noise suppressed from the data. The power of the test is also increased by using the genetic information contained in the spatial ordering of single-nucleotide polymorphisms on a chromosome. Results After adjusting for the effect of population stratification, the test identified some previously discovered rheumatoid arthritis susceptibility loci (HLA-DRB1 and rs3761847) as well as some loci (rs2076530 and rs3130340) known to have association with sarcoidosis and bone mineral density. It was previously reported that patients with rheumatoid arthritis have elevated prevalence of sarcoidosis and have reduced bone mass. Conclusion This new test provides a useful tool in genome-wide association studies.
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Affiliation(s)
- Renfang Jiang
- Department of Mathematical Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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43
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Zhang M, Lin Y, Wang L, Pungpapong V, Fleet JC, Zhang D. Case-control genome-wide association study of rheumatoid arthritis from Genetic Analysis Workshop 16 using penalized orthogonal-components regression-linear discriminant analysis. BMC Proc 2009; 3 Suppl 7:S17. [PMID: 20018006 PMCID: PMC2795913 DOI: 10.1186/1753-6561-3-s7-s17] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Currently, genome-wide association studies (GWAS) are conducted by collecting a massive number of SNPs (i.e., large p) for a relatively small number of individuals (i.e., small n) and associations are made between clinical phenotypes and genetic variation one single-nucleotide polymorphism (SNP) at a time. Univariate association approaches like this ignore the linkage disequilibrium between SNPs in regions of low recombination. This results in a low reliability of candidate gene identification. Here we propose to improve the case-control GWAS approach by implementing linear discriminant analysis (LDA) through a penalized orthogonal-components regression (POCRE), a newly developed variable selection method for large p small n data. The proposed POCRE-LDA method was applied to the Genetic Analysis Workshop 16 case-control data for rheumatoid arthritis (RA). In addition to the two regions on chromosomes 6 and 9 previously associated with RA by GWAS, we identified SNPs on chromosomes 10 and 18 as potential candidates for further investigation.
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Affiliation(s)
- Min Zhang
- Department of Statistics, Purdue University, 150 North University Street, West Lafayette, IN 47907, USA.
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Sirota M, Schaub MA, Batzoglou S, Robinson WH, Butte AJ. Autoimmune disease classification by inverse association with SNP alleles. PLoS Genet 2009; 5:e1000792. [PMID: 20041220 PMCID: PMC2791168 DOI: 10.1371/journal.pgen.1000792] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 11/25/2009] [Indexed: 11/24/2022] Open
Abstract
With multiple genome-wide association studies (GWAS) performed across autoimmune diseases, there is a great opportunity to study the homogeneity of genetic architectures across autoimmune disease. Previous approaches have been limited in the scope of their analysis and have failed to properly incorporate the direction of allele-specific disease associations for SNPs. In this work, we refine the notion of a genetic variation profile for a given disease to capture strength of association with multiple SNPs in an allele-specific fashion. We apply this method to compare genetic variation profiles of six autoimmune diseases: multiple sclerosis (MS), ankylosing spondylitis (AS), autoimmune thyroid disease (ATD), rheumatoid arthritis (RA), Crohn's disease (CD), and type 1 diabetes (T1D), as well as five non-autoimmune diseases. We quantify pair-wise relationships between these diseases and find two broad clusters of autoimmune disease where SNPs that make an individual susceptible to one class of autoimmune disease also protect from diseases in the other autoimmune class. We find that RA and AS form one such class, and MS and ATD another. We identify specific SNPs and genes with opposite risk profiles for these two classes. We furthermore explore individual SNPs that play an important role in defining similarities and differences between disease pairs. We present a novel, systematic, cross-platform approach to identify allele-specific relationships between disease pairs based on genetic variation as well as the individual SNPs which drive the relationships. While recognizing similarities between diseases might lead to identifying novel treatment options, detecting differences between diseases previously thought to be similar may point to key novel disease-specific genes and pathways.
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Affiliation(s)
- Marina Sirota
- Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children’s Hospital, Palo Alto, California, United States of America
| | - Marc A. Schaub
- Computer Science Department, Stanford University, Stanford, California, United States of America
| | - Serafim Batzoglou
- Computer Science Department, Stanford University, Stanford, California, United States of America
| | - William H. Robinson
- Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, California, United States of America
- Geriatric Research Education and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Atul J. Butte
- Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
- Lucile Packard Children’s Hospital, Palo Alto, California, United States of America
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45
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Nurieva RI, Liu X, Dong C. Yin-Yang of costimulation: crucial controls of immune tolerance and function. Immunol Rev 2009; 229:88-100. [PMID: 19426216 DOI: 10.1111/j.1600-065x.2009.00769.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
SUMMARY In addition to signals from the T-cell receptor complex, it has been recognized for many years that a 'second' signal, most notably from CD28, is also important in T-cell activation. In the recent years, many new members of CD28 family as well as the molecules that share structural homology to CD28 ligands CD80 and CD86 have been discovered. Interestingly, some of these proteins function to dampen T-cell activation and regulate the induction of T-cell tolerance. Therefore, positive and negative costimulation are the two sides of the coin to fine tune T-cell receptor signaling to determine the outcome of T-cell receptor engagement-tolerance versus function.
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Affiliation(s)
- Roza I Nurieva
- Department of Immunology, MD Anderson Cancer Center, Houston, TX, USA
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46
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Konno S, Takahashi D, Hizawa N, Hattori T, Takahashi A, Isada A, Maeda Y, Huang SK, Nishimura M. Genetic impact of a butyrophilin-like 2 (BTNL2) gene variation on specific IgE responsiveness to Dermatophagoides farinae (Der f) in Japanese. Allergol Int 2009; 58:29-35. [PMID: 19050377 DOI: 10.2332/allergolint.08-oa-0005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Accepted: 06/30/2008] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Dermatophagoides farinae (Der f) is one of the most frequently implicated allergens in several allergic diseases. Several genome-wide screens have identified a linkage between chromosome 6p21 and mite-specific IgE responsiveness. Butyrophilin-like 2 (BTNL2) is a member of the immunoglobulin superfamily and, on the basis of its homology to B7-1, has been implicated as a costimulatory molecule involved in T-cell activation. BTNL2 resides in the HLA region on chromosome 6p21, and significant associations between BTNL2 gene polymorphisms and several inflammatory diseases have been reported. OBJECTIVE The aim of this study was to examine whether BTNL2 gene polymorphisms are associated with specific IgE responses to Der f. METHODS Three single nucleotide polymorphisms (SNPs), including 2 coding SNPs and 1 intron SNP, were studied. One of the coding SNPs was the rs2076530 A > G, which has a functional consequence. A total of 863 unrelated Japanese subjects (447 positive and 416 negative for IgE to Der f) were recruited for a case-control study. RESULTS Controlling for gender, age, smoking, and the presence of asthma, multiple logistic regression analyses showed that homozygosity of the rs2076530 A allele, which has been reported to be a risk allele for sarcoidosis, was associated with a risk of sensitization towards Der f (Odds ratio; 1.55, p = 0.0060). CONCLUSIONS Although an association which may be due to the linkage disequilibrium with other genes in 6p21 needs to be ruled out, the present findings suggest that the BTNL2 gene might be one of the candidate genes that is responsible for the pathogenesis of Der f-specific IgE responsiveness.
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Affiliation(s)
- Satoshi Konno
- First Department of Medicine, Hokkaido University School of Medicine, Hokkaido, Japan.
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47
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Eike MC, Humphreys K, Becker T, Olsson M, Lie BA. Three microsatellites from the T1DGC MHC data set show highly significant association with type 1 diabetes, independent of the HLA-DRB1, -DQA1 and -DQB1 genes. Diabetes Obes Metab 2009; 11 Suppl 1:17-24. [PMID: 19143811 PMCID: PMC2760257 DOI: 10.1111/j.1463-1326.2008.00999.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIM The aim of this study was to test the microsatellites in the Type 1 Diabetes Genetics Consortium major histocompatibility complex (MHC) data set for association with type 1 diabetes (T1D) independent of the HLA-DRB1, -DQA1 and -DQB1 genes. METHODS The data set was edited to contain only one affected child per family, and broad ethnic subgroups were defined. Genotypes for HLA-DRB1, -DQA1 and -DQB1 were replaced by a haplotype code spanning all three loci, with phase inferred based on common haplotypes. The final data set contained 8190 samples in 2301 families, 59 microsatellites and the DRB1-DQA1-DQB1 haplotype code. Statistical analyses consisted of conditional logistic regression and haplotype estimations and linkage disequilibrium calculations. RESULTS The data set was screened using a main effects test approach adjusted for DRB1-DQA1-DQB1, and significant results tested for validity. After these procedures, four markers remained significant at the Bonferroni-corrected threshold: D6S2773 (p = 0.00014), DG6S185 (p = 0.00015), DG6S398 (p = 0.00043) and D6S2998 (p = 0.00015). These results were supported by allelic tests conditioned on DRB1-DQA1-DQB1 haplotypes, except for DG6S185, which may contain artefacts. CONCLUSIONS We have identified three microsatellites that mark additional risk factors for T1D at highly significant levels in the MHC. Further analyses are needed to establish the relationship with other possible genetic determinants in this region.
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Affiliation(s)
- M C Eike
- Institute of Immunology, Rikshospitalet University Hospital, Oslo, Norway.
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Vang T, Miletic AV, Arimura Y, Tautz L, Rickert RC, Mustelin T. Protein tyrosine phosphatases in autoimmunity. Annu Rev Immunol 2008; 26:29-55. [PMID: 18303998 DOI: 10.1146/annurev.immunol.26.021607.090418] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are important regulators of many cellular functions and a growing number of PTPs have been implicated in human disease conditions, such as developmental defects, neoplastic disorders, and immunodeficiency. Here, we review the involvement of PTPs in human autoimmunity. The leading examples include the allelic variant of the lymphoid tyrosine phosphatase (PTPN22), which is associated with multiple autoimmune diseases, and mutations that affect the exon-intron splicing of CD45 (PTPRC). We also find it likely that additional PTPs are involved in susceptibility to autoimmune and inflammatory diseases. Finally, we discuss the possibility that PTPs regulating the immune system may serve as therapeutic targets.
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Affiliation(s)
- Torkel Vang
- Burnham Institute for Medical Research, La Jolla, California 92037, USA.
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49
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Spagnolo P, Sato H, Grutters JC, Renzoni EA, Marshall SE, Ruven HJT, Wells AU, Tzouvelekis A, van Moorsel CHM, van den Bosch JMM, du Bois RM, Welsh KI. Analysis of BTNL2 genetic polymorphisms in British and Dutch patients with sarcoidosis. ACTA ACUST UNITED AC 2007; 70:219-27. [PMID: 17661910 DOI: 10.1111/j.1399-0039.2007.00879.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Sarcoidosis is a heterogeneous disorder, both phenotypically and genetically. Two independent studies have recently shown that a functional polymorphism within butyrophilin-like 2 (BTNL2) gene predisposes to sarcoidosis independently of the human leukocyte antigen (HLA)-DRB1 alleles. However, in both studies, data analysis was not stratified by Löfgren's syndrome, a clinically and genetically distinct sarcoidosis subset. BTNL2, potentially encoding an immune coreceptor, is adjacent and in linkage disequilibrium (LD) with HLA-DRB1. We investigated six BTNL2 variants, including the functional rs2076530 (G > A), as well as HLA-DRB1 alleles, by sequence-specific primers-polymerase chain reaction, in 288 patients and 446 controls from two European countries. In the patient group as a whole, the HLA-DRB1*14 [odds ratio (OR) = 3.1, P(c) = 0.0003], DRB1*12 (OR = 2.5, P(c) = 0.003), and BTNL2 rs2076530 A allele (OR = 1.49, P(c) = 0.002) were all associated with disease susceptibility. However, after exclusion of patients presenting with Löfgren's syndrome and after adjusting for HLA-DRB1 alleles, the association between BTNL2 rs2076530 A and disease disappeared (P = 0.23). By contrast, both HLA-DRB1*14 and DRB1*12 remained strongly significant (OR = 3.60, P < 0.0001 and OR = 3.03, P = 0.003, respectively). BTNL2 haplotype 4, tagged by the rs2076530 G allele, also remained associated with non-Löfgren sarcoidosis after adjusting for HLA-DRB1 alleles (OR 0.37, P = 0.016). In summary, HLA-DRB1*14, DRB1*12, and BTNL2 haplotype 4--but not rs2076530 A--are associated with non-Löfgren sarcoidosis. However, the tight LD across the HLA complex makes it difficult to identify the precise location of the susceptibility locus/i. Larger sample sets from different ethnic groups, finer mapping, and more robust LD analyses across the HLA region are needed.
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Affiliation(s)
- P Spagnolo
- Clinical Genomic Group, National Heart and Lung Institute, Department of Occupational and Environmental Medicine, Imperial College, 1B Manresa Road, London, UK.
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Sato H, Spagnolo P, Silveira L, Welsh KI, du Bois RM, Newman LS, Maier LA. BTNL2 allele associations with chronic beryllium disease in HLA-DPB1*Glu69-negative individuals. ACTA ACUST UNITED AC 2007; 70:480-6. [PMID: 17927685 DOI: 10.1111/j.1399-0039.2007.00944.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Butyrophilin-like 2 (BTNL2) polymorphisms have been associated with sarcoidosis. We hypothesized that BTNL2 variants might confer a human leukocyte antigen (HLA)-independent risk for chronic beryllium disease (CBD), a granulomatous lung disease with similar clinical, radiological, and pathological features to sarcoidosis. Genomic DNA was obtained from CBD (n= 88), beryllium sensitized (BeS, n= 86), and beryllium exposed nondiseased control subjects (Be-exp, n= 173). Six BTNL2 polymorphisms, HLA-DPB1, DRB1, and DQB1 alleles were determined by sequence-specific primer-PCR. All BTNL2 polymorphisms were in Hardy-Weinberg equilibrium. No significant differences were found between BTNL2 polymorphisms or haplotypes and CBD, BeS, or Be-exp. In HLA-DPB1*Glu69-negative subjects (n= 10 CBD, n= 13 BeS, n= 102 Be-exp), DRB1*13 and BTNL2 rs3117099TT homozygosity were increased in CBD (70% and 40%, respectively) vs Be-exp (16%, P= 0.001 and 2.9%, P= 0.001, respectively). The BTNL2 rs3117099T-HLA-DRB1*13 combination was significantly increased in CBD (50%) compared with Be-exp (6.9%, P= 0.001). In conclusion, both DRB1*13 and rs3117099TT homozygosity are associated with CBD in *Glu69-negative subjects, while DPB1*Glu69 is associated with CBD and BeS compared with Be-exp. As a result of the small sample size and strong linkage disequilibrium between DRB1*13-DQB1*0603/4/9 and the BTNL2 rs3117099T allele, it is difficult to assess the primary association in DPB1*Glu69-negative CBD cases.
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Affiliation(s)
- H Sato
- Department of Medicine, National Jewish Medical and Research Center, Denver, CO 80206, USA
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