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Fang F, Sun Y. Prediction of systemic lupus erythematosus-related genes based on graph attention network and deep neural network. Comput Biol Med 2024; 175:108371. [PMID: 38691916 DOI: 10.1016/j.compbiomed.2024.108371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/13/2024] [Accepted: 03/24/2024] [Indexed: 05/03/2024]
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder intricately linked to genetic factors, with numerous approaches having identified genes linked to its development, diagnosis and prognosis. Despite genome-wide association analysis and gene knockout experiments confirming some genes associated with SLE, there are still numerous potential genes yet to be discovered. The search for relevant genes through biological experiments entails significant financial and human resources. With the advancement of computational technologies like deep learning, we aim to identify SLE-related genes through deep learning methods, thereby narrowing down the scope for biological experimentation. This study introduces SLEDL, a deep learning-based approach that leverages DNN and graph neural networks to effectively identify SLE-related genes by capturing relevant features in the gene interaction network. The above steps transform the identification of SLE related genes into a binary classification problem, ultimately solved through a fully connected layer. The results demonstrate the superiority of SLEDL, achieving higher AUC (0.7274) and AUPR (0.7599), further validated through case studies.
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Affiliation(s)
- Fang Fang
- Department of Rheumatology and Immunology, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yizhou Sun
- Department of Ophthalmology, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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Qian J, Chen Y, Yang X, Wang Q, Zhao J, Deng X, Ding Y, Li S, Liu Y, Tian Z, Shen J, Liao Q, Wang Y, Zuo X, Zhang X, Li M, Cui Y, Yu X, Zeng X. Association Study Identified HLA-DQA1 as a Novel Genetic Risk of Systemic Lupus Erythematosus-Associated Pulmonary Arterial Hypertension. Arthritis Rheumatol 2023; 75:2207-2215. [PMID: 37382296 DOI: 10.1002/art.42641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/19/2023] [Accepted: 06/27/2023] [Indexed: 06/30/2023]
Abstract
OBJECTIVE Pulmonary arterial hypertension (PAH) is a severe complication of systemic lupus erythematosus (SLE). However, the genetic signatures of SLE-associated PAH have not been well studied. We aimed to identify genetic variants implicated in SLE-associated PAH susceptibility within the major histocompatibility complex (MHC) region and assess the contribution to clinical outcomes. METHODS A total of 172 patients with SLE-associated PAH confirmed by right heart catheterization, 1,303 patients with SLE without PAH, and 9,906 healthy controls were included. Deep sequencing of the MHC region was performed to identify alleles, single-nucleotide polymorphisms, and amino acids. We compared patients with SLE-associated PAH with patients with SLE without PAH and healthy controls. Clinical association study was conducted to explore the contribution to phenotypes. RESULTS A total of 19,881 genetic variants were identified within the MHC region. HLA-DQA1*03:02 was identified as a novel genetic variant associated with SLE-associated PAH in the discovery cohort (P = 5.68 × 10-12 ) and authenticated in an independent replication cohort (P = 1.30 × 10-9 ). The strongest associated amino acid position was mapped to HLA-DQα1 in the region affecting MHC/peptide-CD4+ T cell receptor affinity and antigen binding. Clinical association study demonstrated that patients with SLE-associated PAH with HLA-DQA1*03:02 had significantly lower rates of target role achievement (P = 0.005) and survival (P = 0.04). CONCLUSION This study, based on the largest cohort of SLE-associated PAH, is the first to investigate how MHC region genetic variants contribute to SLE-associated PAH susceptibility. HLA-DQA1*03:02 is a novel genetic risk factor and a prognostic factor in SLE-associated PAH. Patients with SLE with this allele require regular monitoring and careful follow-up for early diagnosis and interventions for potential PAH.
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Affiliation(s)
- Junyan Qian
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | | | - Xinzhuang Yang
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Xiaoyue Deng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yufang Ding
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Shengjie Li
- Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yongtai Liu
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Zhuang Tian
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | | | | | - Yanhong Wang
- Department of Epidemiology and Bio-Statistics, Institute of Basic Medical Sciences, China Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xianbo Zuo
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xuejun Zhang
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
| | - Yong Cui
- Department of Dermatology, China-Japan Friendship Hospital, Beijing, China
| | - Xueqing Yu
- Division of Nephrology, Guangdong Provincial People's Hospital and Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, National Clinical Research Center for Dermatologic and Immunologic Diseases, Ministry of Science and Technology, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education and State Key Laboratory of Complex Severe and Rare Diseases, Ministry of Science and Technology, Beijing, China
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Gatto M, Depascale R, Stefanski AL, Schrezenmeier E, Dörner T. Translational implications of newly characterized pathogenic pathways in systemic lupus erythematosus. Best Pract Res Clin Rheumatol 2023; 37:101864. [PMID: 37625930 DOI: 10.1016/j.berh.2023.101864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023]
Abstract
Improved characterization of relevant pathogenic pathways in systemic lupus erythematosus (SLE) has been further delineated over the last decades. This led to the development of targeted treatments including belimumab and anifrolumab, which recently became available in clinics. Therapeutic targets in SLE encompass interferon (IFN) signaling, B-T costimulation including immune checkpoints, and increasing modalities of B lineage targeting, such as chimeric antigen receptor (CAR) T cells directed against CD19 or sequential anti-B cell targeting. Patient profiling based on characterization of underlying molecular abnormalities, often performed through comprehensive omics analyses, has recently been shown to better predict patients' treatment responses and also holds promise to unravel key molecular mechanisms driving SLE. SLE carries two key signatures, namely the IFN and B lineage/plasma cell signatures. Recent advances in SLE treatments clearly indicate that targeting innate and adaptive immunity is successful in such a complex autoimmune disease. Although those signatures may interact at the molecular level and provide the basis for the first selective treatments in SLE, it remains to be clarified whether these distinct treatments show different treatment responses among certain patient subsets. In fact, notwithstanding the remarkable amount of novel clues for innovative SLE treatment, harmonization of big data within tailored treatment strategies will be instrumental to better understand and treat this challenging autoimmune disorder. This review will provide an overview of recent improvements in SLE pathogenesis, related insights by analyses of big data and machine learning as well as technical improvements in conducting clinical trials with the ultimate goal that translational research results in improved patient outcomes.
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Affiliation(s)
- Mariele Gatto
- Unit of Rheumatology, Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Roberto Depascale
- Unit of Rheumatology, Department of Medicine, University of Padova, Padova, Italy
| | - Ana Luisa Stefanski
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany
| | - Eva Schrezenmeier
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany; Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Dörner
- Deutsches Rheumaforschungszentrum Berlin, a Leibniz Institute, Berlin, Germany; Department of Rheumatology and Clinical Immunology - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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Abstract
Systemic lupus erythematosus (SLE) is a severe multisystem autoimmune disease that can cause injury in almost every body system. While considered a classic example of autoimmunity, it is still relatively poorly understood. Treatment with immunosuppressive agents is challenging, as many agents are relatively non-specific, and the underlying disease is characterized by unpredictable flares and remissions. This State of The Art Review provides a comprehensive current summary of systemic lupus erythematosus based on recent literature. In basic and translational science, this summary includes the current state of genetics, epigenetics, differences by ancestry, and updates about the molecular and immunological pathogenesis of systemic lupus erythematosus. In clinical science, the summary includes updates in diagnosis and classification, clinical features and subphenotypes, and current guidelines and strategies for treatment. The paper also provides a comprehensive review of the large number of recent clinical trials in systemic lupus erythematosus. Current knowns and unknowns are presented, and potential directions for the future are suggested. Improved knowledge of immunological pathogenesis and the molecular differences that exist between patients should help to personalize treatment, minimize side effects, and achieve better outcomes in this difficult disease.
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Affiliation(s)
- Eric F Morand
- School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
- Department of Rheumatology, Monash Health, Melbourne, VIC, Australia
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Crow MK. Pathogenesis of systemic lupus erythematosus: risks, mechanisms and therapeutic targets. Ann Rheum Dis 2023; 82:999-1014. [PMID: 36792346 DOI: 10.1136/ard-2022-223741] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Research elucidating the pathogenesis of systemic lupus erythematosus (SLE) has defined two critical families of mediators, type I interferon (IFN-I) and autoantibodies targeting nucleic acids and nucleic acid-binding proteins, as fundamental contributors to the disease. On the fertile background of significant genetic risk, a triggering stimulus, perhaps microbial, induces IFN-I, autoantibody production or most likely both. When innate and adaptive immune system cells are engaged and collaborate in the autoimmune response, clinical SLE can develop. This review describes recent data from genetic analyses of patients with SLE, along with current studies of innate and adaptive immune function that contribute to sustained IFN-I pathway activation, immune activation and autoantibody production, generation of inflammatory mediators and tissue damage. The goal of these studies is to understand disease mechanisms, identify therapeutic targets and stimulate development of therapeutics that can achieve improved outcomes for patients.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York, USA
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Velastegui E, Vera E, Vanden Berghe W, Muñoz MS, Orellana-Manzano A. "HLA-C: evolution, epigenetics, and pathological implications in the major histocompatibility complex". Front Genet 2023; 14:1206034. [PMID: 37465164 PMCID: PMC10350511 DOI: 10.3389/fgene.2023.1206034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/20/2023] [Indexed: 07/20/2023] Open
Abstract
HLA-C, a gene located within the major histocompatibility complex, has emerged as a prominent target in biomedical research due to its involvement in various diseases, including cancer and autoimmune disorders; even though its recent addition to the MHC, the interaction between HLA-C and KIR is crucial for immune responses, particularly in viral infections. This review provides an overview of the structure, origin, function, and pathological implications of HLA-C in the major histocompatibility complex. In the last decade, we systematically reviewed original publications from Pubmed, ScienceDirect, Scopus, and Google Scholar. Our findings reveal that genetic variations in HLA-C can determine susceptibility or resistance to certain diseases. However, the first four exons of HLA-C are particularly susceptible to epigenetic modifications, which can lead to gene silencing and alterations in immune function. These alterations can manifest in diseases such as alopecia areata and psoriasis and can also impact susceptibility to cancer and the effectiveness of cancer treatments. By comprehending the intricate interplay between genetic and epigenetic factors that regulate HLA-C expression, researchers may develop novel strategies for preventing and treating diseases associated with HLA-C dysregulation.
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Affiliation(s)
- Erick Velastegui
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Edwin Vera
- Escuela Politécnica Nacional, Departamento de Ciencias de los Alimentos y Biotecnología, Facultad de Ingeniería Química y Agroindustria, Quito, Ecuador
| | - Wim Vanden Berghe
- Epigenetic Signaling Lab, Faculty Biomedical Sciences, PPES, University of Antwerp, Antwerp, Belgium
| | - Mindy S. Muñoz
- Facultad de Medicina Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Andrea Orellana-Manzano
- Escuela Superior Politécnica del Litoral, Laboratorio para investigaciones biomédicas, Facultad de Ciencias de la Vida (FCV), Guayaquil, Ecuador
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8
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Guga S, Wang Y, Graham DC, Vyse TJ. A review of genetic risk in systemic lupus erythematosus. Expert Rev Clin Immunol 2023; 19:1247-1258. [PMID: 37496418 DOI: 10.1080/1744666x.2023.2240959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 05/10/2023] [Indexed: 07/28/2023]
Abstract
INTRODUCTION Systemic Lupus Erythematosus (SLE) is a complex multisystem autoimmune disease with a wide range of signs and symptoms in affected individuals. The utilization of genome-wide association study (GWAS) technology has led to an explosion in the number of genetic risk factors mapped for autoimmune diseases, including SLE. AREAS COVERED In this review, we summarize the more recent genetic risk loci mapped in SLE, which bring the total number of loci mapped to approximately 200. We review prioritization analyses of the associated variants and experimental validation of the putative causal variants. This includes the implementation of new bioinformatic techniques to align genomic and functional data and the use of transcriptomics with single-cell RNA-sequencing, CRISPR genome editing, and Massive Parallel Reporter Assays to analyze non-coding regulatory genetics. EXPERT OPINION Despite progress in identifying more genetic risk loci and variant-gene pairs for SLE, understanding its pathogenesis and applying findings clinically remains challenging. The polygenic risk score (PRS) has been used as an application of SLE genetics, but with limited performance in non-EUR populations. In the next few years, advancements in proteomics, post-translational modification estimation, and whole-genome sequencing will enhance disease understanding.
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Affiliation(s)
- Suri Guga
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Yuxuan Wang
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK
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Li X, Wang Q. Platelet-Derived Microparticles and Autoimmune Diseases. Int J Mol Sci 2023; 24:10275. [PMID: 37373420 DOI: 10.3390/ijms241210275] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Extracellular microparticles provide a means of cell-to-cell communication and can promote information exchanges between adjacent or distant cells. Platelets are cell fragments that are derived from megakaryocytes. Their main functions are to stop bleeding, regulate inflammation, and maintain the integrity of blood vessels. When platelets are activated, they can perform related tasks by secreting platelet-derived microparticles that contain lipids, proteins, nucleic acids, and even organelles. There are differences in the circulating platelet levels in many autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, antiphospholipid antibody syndrome, and Sjogren's syndrome. In this paper, the latest findings in the research field of platelet-derived microparticles are reviewed, including the potential pathogenesis of platelet-derived microparticles in various types of immune diseases, their potential as related markers, and for monitoring the progress and prognosis of disease treatment are expounded.
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Affiliation(s)
- Xiaoshuai Li
- Department of Blood Transfusion, Shengjing Hospital of China Medical University, Shenyang 110801, China
| | - Qiushi Wang
- Department of Blood Transfusion, Shengjing Hospital of China Medical University, Shenyang 110801, China
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Kawasaki A, Kusumawati PA, Kawamura Y, Kondo Y, Kusaoi M, Amano H, Kusanagi Y, Itoh K, Fujimoto T, Tamura N, Hashimoto H, Matsumoto I, Sumida T, Tsuchiya N. Genetic dissection of HLA-DRB1*15:01 and XL9 region variants in Japanese patients with systemic lupus erythematosus: primary role for HLA-DRB1*15:01. RMD Open 2023; 9:rmdopen-2023-003214. [PMID: 37258043 DOI: 10.1136/rmdopen-2023-003214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
OBJECTIVE Major histocompatibility complex strongly contributes to susceptibility to systemic lupus erythematosus (SLE). In the European populations, HLA-DRB1*03:01 and DRB1*15:01 are susceptibility alleles, but C4 locus was reported to account for the association of DRB1*03:01. With respect to DRB1*15:01, strong linkage disequilibrium with a variant rs2105898T in the XL9 region, located between DRB1 and DQA1 and regulates HLA-class II expression levels, was reported; however, the causative allele remains to be determined. Leveraging the genetic background of the Japanese population, where DRB1*15:01 and DRB1*15:02 are commonly present and only DRB1*15:01 is associated with SLE, this study aimed to distinguish the genetic contribution of DRB1*15:01 and XL9 variants. METHODS Among the XL9 variants, two (rs2105898 and rs9271593) previously associated variants in the European populations and two (rs9271375 and rs9271378) which showed a trend towards association in a Japanese Genome-Wide Association Study were selected. Associations of the XL9 variants and HLA-DRB1 were examined in 442 Japanese SLE patients and 779 controls. Genotyping of the XL9 variants was performed by TaqMan SNP Genotyping Assay and direct sequencing. HLA-DRB1 alleles were determined by PCR-reverse sequence-specific oligonucleotide probes. RESULTS Among the XL9 variants, associations of rs2105898T and rs9271593C were replicated in the Japanese population. However, these associations became no longer significant when conditioned on DRB1*15:01. In contrast, the association of DRB1*15:01 remained significant after conditioning on the XL9 variants. CONCLUSION In the Japanese population, HLA-DRB1*15:01 was found to be primarily associated with SLE, and to account for the apparent association of XL9 region.
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Affiliation(s)
- Aya Kawasaki
- Molecular and Genetic Epidemiology Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- College of Medical Sciences, University of Tsukuba, Tsukuba, Japan
| | - Premita Ari Kusumawati
- Molecular and Genetic Epidemiology Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuka Kawamura
- Molecular and Genetic Epidemiology Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- College of Medical Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yuya Kondo
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Makio Kusaoi
- Department of Internal Medicine and Rheumatology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Hirofumi Amano
- Department of Internal Medicine and Rheumatology, Faculty of Medicine, Juntendo University, Tokyo, Japan
- Department of Internal Medicine and Rheumatology, Juntendo University Nerima Hospital, Tokyo, Japan
| | - Yasuyoshi Kusanagi
- Division of Hematology and Rheumatology, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Kenji Itoh
- Division of Hematology and Rheumatology, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Japan
| | - Takashi Fujimoto
- Department of General Medicine, Nara Medical University, Kashihara, Japan
| | - Naoto Tamura
- Department of Internal Medicine and Rheumatology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | | | - Isao Matsumoto
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takayuki Sumida
- Department of Rheumatology, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naoyuki Tsuchiya
- Molecular and Genetic Epidemiology Laboratory, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Master's Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Japan
- College of Medical Sciences, University of Tsukuba, Tsukuba, Japan
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Khandelwal P, Govindarajan S, Bagga A. Management and outcomes in children with lupus nephritis in the developing countries. Pediatr Nephrol 2023; 38:987-1000. [PMID: 36255555 DOI: 10.1007/s00467-022-05769-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/14/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Lupus nephritis (LN) has variable prevalence, severity, and outcomes across the world. OBJECTIVES This review compares the outcomes of childhood LN in low- and middle-income countries (LMICs) and high-income countries (HICs) and aims to summarize long-term outcomes of pediatric LN from LMICs. DATA SOURCES A systematic literature search, conducted in PubMed, EMBASE, and Cochrane database in the last 30-years from January 1992, published in the English language, identified 113 studies including 52 from lower (n = 1336) and upper MICs (n = 3014). STUDY ELIGIBILITY CRITERIA Cohort studies or randomized controlled trials, of patients ≤ 18 years of age (or where such data can be separately extracted), with > 10 patients with clinically or histologically diagnosed LN and outcomes reported beyond 12 months were included. PARTICIPANTS AND INTERVENTIONS Patients ≤ 18 years of age with clinically or histologically diagnosed LN; effect of an intervention was not measured. STUDY APPRAISAL AND SYNTHESIS METHODS Two authors independently extracted data. We separately analyzed studies from developed countries (high income countries; HIC) and developing countries (LMICs). Middle-income countries were further classified as lower and upper MICs. Meta-analyses of data were performed by calculating a pooled estimate utilizing the random-effects model. Test for heterogeneity was applied using I2 statistics. Publication bias was assessed using funnel plots. RESULTS Kidney remission was similar across MICs and HICs with 1-year pooled complete remission rates of 59% (95% CI 51-67%); one third of patients had kidney flares. The pooled 5-year survival free of stage 5 chronic kidney disease (CKD5) was lower in MICs, especially in lower MICs compared to HICs (83% vs. 93%; P = 0.002). The pooled 5-year patient survival was significantly lower in MICs than HICs (85% vs. 94%; P < 0.001). In patients with class IV LN, the 5-and 10-year respective risk of CKD5 was 14% and 30% in MICs; corresponding risks in HICs were 8% and 17%. Long-term data from developing countries was limited. Sepsis (48.8%), kidney failure (14%), lupus activity (18.1%), and intracranial hemorrhage/infarct (5.4%) were chief causes of death; mortality due to complications of kidney failure was more common in lower MICs (25.6%) than HICs (6.4%). LIMITATIONS The review is limited by heterogenous approach to diagnosis and management that has changed over the period spanning the review. World Bank classification based on income might not correlate with the standards of medical care. The overall quality of evidence is low since included studies were chiefly retrospective and single center. CONCLUSIONS AND IMPLICATIONS OF KEY FINDINGS Challenges in LMICs include limited access to pediatric nephrology care, dialysis, increased risk of infection-induced mortality, lack of frequent monitoring, and non-compliance due to cost of therapy. Attention to these issues might update the existing data and improve patient follow-up and outcomes. SYSTEMATIC REVIEW REGISTRATION NUMBER PROSPERO 2022 number: CRD42022359002, available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022359002.
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Affiliation(s)
- Priyanka Khandelwal
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Srinivasavaradan Govindarajan
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India
| | - Arvind Bagga
- Division of Nephrology, Department of Pediatrics, ICMR Center for Advanced Research in Nephrology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India.
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12
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Novel polymorphism of IFI44L associated with the susceptibility and clinical characteristics of systemic lupus erythematosus in a Chinese population. Int Immunopharmacol 2023; 117:109979. [PMID: 36893516 DOI: 10.1016/j.intimp.2023.109979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/08/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND Interferon-inducible 44 like (IFI44L) is a newly discovered gene which has been reported to associate with the susceptibility of some infectious diseases, but there is no data on IFI44L SNP polymorphism associated with Systemic lupus erythematosus (SLE). In this study, we aimed to evaluate the association of IFI44L rs273259 polymorphism with the susceptibility and clinical characteristics of SLE in a Chinese population. METHODS 576 SLE patients and 600 controls were recruited in this case-control study. Blood DNA was extracted and IFI44L rs273259 polymorphism was detected by TaqMan SNP Genotyping Assay Kit. The expression levels of IFI44L in Peripheral blood mononuclear cells were detected by RT-qPCR. The DNA methylation levels of IFI44L promoter were detected by bisulfite pyrosequencing. RESULTS The genotype and allele frequencies of IFI44L rs273259 in SLE patients have a significantly difference compared to healthy controls (P < 0.001). The genotype AG (vs. AA: OR = 2.849; P < 0.001) and the allele G (vs. A: OR = 1.454; P < 0.001) were associated with increased susceptibility of SLE. IFI44L rs273259 polymorphism was associated with clinical characteristics of SLE including malar rash (P < 0.001), discoid rash (P < 0.001), lupus nephritis (P < 0.001) and anti-Smith antibodies (P < 0.001). The expression levels of IFI44L were most significantly increased in genotype AG than genotype AA and GG (P < 0.01). The DNA methylation levels of IFI44L promoter were most significantly decreased in genotype AG than genotype AA and GG (P < 0.01). CONCLUSIONS Our results indicate novel polymorphism of IFI44L rs273259 was associated with the susceptibility and clinical characteristics of SLE in the Chinese population.
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13
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Acosta-Colman I, Cabrera-Villalba S, Ayala-Lugo A, Jolly V, Vazquez M, Morel Z, Langjahr P, Duarte M, Zarate R, Acosta ME, Avila-Pedretti G, Julià A, Martinez MT, Marsal S. Association of class II HLA alleles with susceptibility to develop immune-mediated diseases in Paraguayan patients. Int J Immunogenet 2023; 50:12-18. [PMID: 36543746 DOI: 10.1111/iji.12609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/06/2022] [Accepted: 11/14/2022] [Indexed: 12/24/2022]
Abstract
Genetic and nongenetic factors are involved in the pathogenesis of immune-mediated inflammatory diseases (IMIDs). The best-known genetic factor for susceptibility to IMIDs is the human leukocyte antigen (HLA). The aim of the present study was to evaluate the association of HLA class II genes with the risk of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and systemic sclerosis (SSc) in the Paraguayan population. We included 254 patients with IMIDs (101 SLE, 103 RA, and 50 SSc) and 50 healthy controls. The haplotypes of five genes corresponding to HLA class II genes and their relationship to the IMIDs studied were determined. Note that 84.6% were women, with a mean age of 43.4 ± 14 years. Among the associated HLA alleles, we found the previously identified risk factors in other populations like HLA-DRB1*03:01 and HLA-DRB1*14:02 for RA, as well as new ones not previously identified, such as DPA1*02:01 for SLE and, DB1*02:01 for RA and SSc. In the genetic association analysis, already known associations have been replicated, and unpublished associations have been identified in Paraguayan patients with IMIDs. This is the first genetic association study in Paraguayan patients with IMIDs.
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Affiliation(s)
- Isabel Acosta-Colman
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Sonia Cabrera-Villalba
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Ana Ayala-Lugo
- Instituto de Investigación en Ciencias de la Salud, Laboratorio de Genética Molecular, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Valerie Jolly
- Instituto de Investigación en Ciencias de la Salud, Laboratorio de Genética Molecular, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Marcos Vazquez
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Zoilo Morel
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Patricia Langjahr
- Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Margarita Duarte
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | | | - Maria Eugenia Acosta
- Instituto de Investigación en Ciencias de la Salud, Laboratorio de Genética Molecular, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Gabriela Avila-Pedretti
- Departamento de Reumatología, Facultad de Ciencias Médicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Antonio Julià
- Group de Recerca en Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
| | | | - Sara Marsal
- Group de Recerca en Reumatologia, Institut de Recerca Vall d'Hebron, Barcelona, Spain
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14
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Berndt SI, Vijai J, Benavente Y, Camp NJ, Nieters A, Wang Z, Smedby KE, Kleinstern G, Hjalgrim H, Besson C, Skibola CF, Morton LM, Brooks-Wilson AR, Teras LR, Breeze C, Arias J, Adami HO, Albanes D, Anderson KC, Ansell SM, Bassig B, Becker N, Bhatti P, Birmann BM, Boffetta P, Bracci PM, Brennan P, Brown EE, Burdett L, Cannon-Albright LA, Chang ET, Chiu BCH, Chung CC, Clavel J, Cocco P, Colditz G, Conde L, Conti DV, Cox DG, Curtin K, Casabonne D, De Vivo I, Diepstra A, Diver WR, Dogan A, Edlund CK, Foretova L, Fraumeni JF, Gabbas A, Ghesquières H, Giles GG, Glaser S, Glenn M, Glimelius B, Gu J, Habermann TM, Haiman CA, Haioun C, Hofmann JN, Holford TR, Holly EA, Hutchinson A, Izhar A, Jackson RD, Jarrett RF, Kaaks R, Kane E, Kolonel LN, Kong Y, Kraft P, Kricker A, Lake A, Lan Q, Lawrence C, Li D, Liebow M, Link BK, Magnani C, Maynadie M, McKay J, Melbye M, Miligi L, Milne RL, Molina TJ, Monnereau A, Montalvan R, North KE, Novak AJ, Onel K, Purdue MP, Rand KA, Riboli E, Riby J, Roman E, Salles G, Sborov DW, Severson RK, Shanafelt TD, Smith MT, Smith A, Song KW, Song L, Southey MC, Spinelli JJ, Staines A, Stephens D, Sutherland HJ, Tkachuk K, Thompson CA, Tilly H, Tinker LF, Travis RC, Turner J, Vachon CM, Vajdic CM, Van Den Berg A, Van Den Berg DJ, Vermeulen RCH, Vineis P, Wang SS, Weiderpass E, Weiner GJ, Weinstein S, Doo NW, Ye Y, Yeager M, Yu K, Zeleniuch-Jacquotte A, Zhang Y, Zheng T, Ziv E, Sampson J, Chatterjee N, Offit K, Cozen W, Wu X, Cerhan JR, Chanock SJ, Slager SL, Rothman N. Distinct germline genetic susceptibility profiles identified for common non-Hodgkin lymphoma subtypes. Leukemia 2022; 36:2835-2844. [PMID: 36273105 PMCID: PMC10337695 DOI: 10.1038/s41375-022-01711-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/22/2022] [Accepted: 09/15/2022] [Indexed: 11/08/2022]
Abstract
Lymphoma risk is elevated for relatives with common non-Hodgkin lymphoma (NHL) subtypes, suggesting shared genetic susceptibility across subtypes. To evaluate the extent of mutual heritability among NHL subtypes and discover novel loci shared among subtypes, we analyzed data from eight genome-wide association studies within the InterLymph Consortium, including 10,629 cases and 9505 controls. We utilized Association analysis based on SubSETs (ASSET) to discover loci for subsets of NHL subtypes and evaluated shared heritability across the genome using Genome-wide Complex Trait Analysis (GCTA) and polygenic risk scores. We discovered 17 genome-wide significant loci (P < 5 × 10-8) for subsets of NHL subtypes, including a novel locus at 10q23.33 (HHEX) (P = 3.27 × 10-9). Most subset associations were driven primarily by only one subtype. Genome-wide genetic correlations between pairs of subtypes varied broadly from 0.20 to 0.86, suggesting substantial heterogeneity in the extent of shared heritability among subtypes. Polygenic risk score analyses of established loci for different lymphoid malignancies identified strong associations with some NHL subtypes (P < 5 × 10-8), but weak or null associations with others. Although our analyses suggest partially shared heritability and biological pathways, they reveal substantial heterogeneity among NHL subtypes with each having its own distinct germline genetic architecture.
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Affiliation(s)
- Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA.
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yolanda Benavente
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Nicola J Camp
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Alexandra Nieters
- Institute for Immunodeficiency, University Medical Center Freiburg, Freiburg, Germany
| | - Zhaoming Wang
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, USA
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Karin E Smedby
- Department of Medicine, Solna, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Haematology, Rigshospitalet, Copenhagen, Denmark
- Danish Cancer Society Research Center, Danish Cancer Society, Copenhagen, Denmark
| | - Caroline Besson
- Centre Hospitalier de Versailles, Le Chesnay, France
- Université Paris-Saclay, UVSQ, Inserm, Équipe "Exposome et Hérédité", CESP, Villejuif, France
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Angela R Brooks-Wilson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, BC, Canada
| | - Lauren R Teras
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Charles Breeze
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Joshua Arias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Institute of Health and Society, Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Stephen M Ansell
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nikolaus Becker
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Parveen Bhatti
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Paolo Boffetta
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, New York, 11794, NY, USA
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, 41026, Italy
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Lisa A Cannon-Albright
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
- George E. Wahlen Department of Veterans Affairs Medical Center, Salt Lake City, UT, USA
| | - Ellen T Chang
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Center for Health Sciences, Exponent, Inc., Menlo Park, CA, USA
| | - Brian C H Chiu
- Department of Public Health Sciences University of Chicago, Chicago, IL, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Jacqueline Clavel
- CRESS, UMR1153, INSERM, Villejuif, France
- Université de Paris-Cité, Villejuif, France
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Science, Health Services Research & Primary Care, University of Manchester, Manchester, United Kingdom
| | - Graham Colditz
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - David V Conti
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Cox
- INSERM U1052, Cancer Research Center of Lyon, Centre Léon Bérard, Lyon, France
| | - Karen Curtin
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Delphine Casabonne
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER de Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - W Ryan Diver
- Department of Population Science, American Cancer Society, Atlanta, GA, USA
| | - Ahmet Dogan
- Departments of Laboratory Medicine and Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher K Edlund
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Attilio Gabbas
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Monserrato, Cagliari, Italy
| | - Hervé Ghesquières
- Department of Hematology, Hospices Civils de Lyon, Lyon Sud Hospital, Pierre Benite, France
- CIRI, Centre International de Recherche en Infectiologie, Team Lymphoma Immuno-Biology, Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, Lyon, France
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Sally Glaser
- Cancer Prevention Institute of California, Fremont, CA, USA
- Stanford Cancer Institute, Stanford, CA, USA
| | - Martha Glenn
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jian Gu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | | | - Christopher A Haiman
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Corinne Haioun
- Lymphoid Malignancies Unit, Henri Mondor Hospital and University Paris Est, Créteil, France
| | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Theodore R Holford
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Aalin Izhar
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, The Ohio State University, Columbus, OH, USA
| | - Ruth F Jarrett
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rudolph Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | - Laurence N Kolonel
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Yinfei Kong
- Information Systems and Decision Sciences, California State University, Fullerton, Fullerton, CA, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, NSW, Australia
| | - Annette Lake
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | | | - Dalin Li
- F. Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Mark Liebow
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Corrado Magnani
- CPO-Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Marc Maynadie
- INSERM U1231, EA 4184, Registre des Hémopathies Malignes de Côte d'Or, University of Burgundy and Dijon University Hospital, Dijon, France
| | - James McKay
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Mads Melbye
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Jebsen Center for Genetic epidemiology, NTNU, Trondheim, Norway
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Genetics, Stanford University Medical School, Stanford, CA, USA
| | - Lucia Miligi
- Environmental and Occupational Epidemiology Unit, Cancer Prevention and Research Institute (ISPO), Florence, Italy
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
| | - Thierry J Molina
- Department of Pathology, APHP, Necker and Robert Debré, Université Paris Cité, Institut Imagine, INSERM U1163, Paris, France
| | - Alain Monnereau
- CRESS, UMR1153, INSERM, Villejuif, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, Bordeaux, Cedex, France
| | | | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne J Novak
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Kenan Onel
- Donald and Barbara Zucker School of Medicine, Hofstra/Northwell, Hempstead, New York, NY, USA
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Kristin A Rand
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Jacques Riby
- Department of Epidemiology, School of Public Health and Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Gilles Salles
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas W Sborov
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, MI, USA
| | - Tait D Shanafelt
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Martyn T Smith
- Division of Environmental Health Sciences, University of California Berkeley School of Public Health, Berkeley, CA, USA
| | - Alexandra Smith
- Department of Health Sciences, University of York, York, United Kingdom
| | - Kevin W Song
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Lei Song
- Center for Cancer Research, National Cancer Institute, Frederick, MA, USA
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VC, Australia
- Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, VC, 3010, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Anthony Staines
- School of Nursing, Psychotherapy and Community Health, Dublin City University, Dublin, Ireland
| | - Deborah Stephens
- Department of Internal Medicine and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Heather J Sutherland
- Leukemia/Bone Marrow Transplantation Program, BC Cancer Agency, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kaitlyn Tkachuk
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Hervé Tilly
- Centre Henri Becquerel, Université de Rouen, Rouen, France
| | - Lesley F Tinker
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Jenny Turner
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, NSW, Australia
| | - Celine M Vachon
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Claire M Vajdic
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anke Van Den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, USC Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Roel C H Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, United Kingdom
- Human Genetics Foundation, Turin, Italy
| | - Sophia S Wang
- Division of Health Analytics, City of Hope Beckman Research Institute, Duarte, CA, USA
| | | | - George J Weiner
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Stephanie Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nicole Wong Doo
- Concord Clinical School, University of Sydney, Concord, NSW, Australia
| | - Yuanqing Ye
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MA, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, NY, USA
| | - Yawei Zhang
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Tongzhang Zheng
- Department of Epidemiology, Brown University, Providence, RI, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Institute of Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MA, USA
| | - Kenneth Offit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wendy Cozen
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, USA
| | - Xifeng Wu
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, USA
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Md, USA
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15
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Ortíz-Fernández L, Martín J, Alarcón-Riquelme ME. A Summary on the Genetics of Systemic Lupus Erythematosus, Rheumatoid Arthritis, Systemic Sclerosis, and Sjögren's Syndrome. Clin Rev Allergy Immunol 2022; 64:392-411. [PMID: 35749015 DOI: 10.1007/s12016-022-08951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, and Sjögren's syndrome are four major autoimmune rheumatic diseases characterized by the presence of autoantibodies, caused by a dysregulation of the immune system that leads to a wide variety of clinical manifestations. These conditions present complex etiologies strongly influenced by multiple environmental and genetic factors. The human leukocyte antigen (HLA) region was the first locus identified to be associated and still represents the strongest susceptibility factor for each of these conditions, particularly the HLA class II genes, including DQA1, DQB1, and DRB1, but class I genes have also been associated. Over the last two decades, the genetic component of these disorders has been extensively investigated and hundreds of non-HLA risk genetic variants have been uncovered. Furthermore, it is widely accepted that autoimmune rheumatic diseases share molecular disease pathways, such as the interferon (IFN) type I pathways, which are reflected in a common genetic background. Some examples of well-known pleiotropic loci for autoimmune rheumatic diseases are the HLA region, DNASEL13, TNIP1, and IRF5, among others. The identification of the causal molecular mechanisms behind the genetic associations is still a challenge. However, recent advances have been achieved through mouse models and functional studies of the loci. Here, we provide an updated overview of the genetic architecture underlying these four autoimmune rheumatic diseases, with a special focus on the HLA region.
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Affiliation(s)
- Lourdes Ortíz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av de la Ilustración 114, Parque Tecnológico de La Salud, 18016, Granada, Spain. .,Institute for Environmental Medicine, Karolinska Institutet, 171 77, Solna, Sweden.
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16
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Selvaraja M, Too CL, Tan LK, Koay BT, Abdullah M, Shah AM, Arip M, Amin-Nordin S. Human leucocyte antigens profiling in Malay female patients with systemic lupus erythematosus: are we the same or different? Lupus Sci Med 2022; 9:9/1/e000554. [PMID: 35105721 PMCID: PMC8808435 DOI: 10.1136/lupus-2021-000554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 01/08/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE SLE is a heterogeneous autoimmune disease, in terms of clinical presentation, incidence and severity across diverse ethnic populations. We investigated the human leucocyte antigens (HLA) profile (ie, HLA-A, HLA-B and HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1) in Malaysian Malay female patients with SLE and determined the generalisability of the published HLA risk factors across different ethnic populations globally including Malaysia. METHODS One hundred Malay female patients with SLE were recruited between January 2016 and October 2017 from a nephrology clinic. All patients were genotyped for HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DPA1 and HLA-DPB1 alleles using PCR sequence-specific oligonucleotides method on Luminex platform. A total of 951 HLA genotyped population-based Malay control subjects was used for association testing by means of OR with 95% CIs. RESULTS Our findings convincingly validated common associations between HLA-A*11 (OR=1.65, p=3.36×10-3, corrected P (Pc)=4.03×10-2) and DQB1*05:01 (OR=1.56, p=2.02×10-2, Pc=non-significant) and SLE susceptibility in the Malay population. In contrast, DQB1*03:01 (OR=0.51, p=4.06×10-4, Pc=6.50×10-3) were associated with decreased risk of SLE in Malay population. Additionally, we also detected novel associations of susceptibility HLA genes (ie, HLA-B*38:02, DPA1*02:02, DPB1*14:01) and protective HLA genes (ie, DPA1*01:03). When comparing the current data with data from previously published studies from Caucasian, African and Asian populations, DRB1*15 alleles, DQB1*03:01 and DQA1*01:02 were corroborated as universal susceptibility and protective genes. CONCLUSIONS This study reveals multiple HLA alleles associated with susceptibility and protection against risk of developing SLE in Malay female population with renal disorders. In addition, the published data from different ethnic populations together with our study further support the notion that the genetic effects from association with DRB1*15:01/02, DQB1*03:01 and DQA1*01:02 alleles are generalised to multiple ethnic populations of Caucasian, African and Asian descents.
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Affiliation(s)
- Malarvili Selvaraja
- Faculty of Pharmaceutical Sciences, No 1, Jalan Gading, UCSI Heights, Taman Connaught, UCSI University, Cheras, Kuala Lumpur, Malaysia.,Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Chun Lai Too
- Immunogenetic Unit, Allergy and Immunology Research Centre, Ministry of Health Malaysia, National Institutes of Health Complex, Institute for Medical Research, Shah Alam, Selangor, Malaysia .,Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lay Kim Tan
- Immunogenetic Unit, Allergy and Immunology Research Centre, Ministry of Health Malaysia, National Institutes of Health Complex, Institute for Medical Research, Shah Alam, Selangor, Malaysia
| | - Bee Tee Koay
- Transplantation Immunology Unit, Allergy and Immunology Research Centre, Ministry of Health Malaysia, National Institutes of Health Complex, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - Maha Abdullah
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Anim Md Shah
- Department of Medicine, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Masita Arip
- Allergy and Immunology Research Centre, Ministry of Health. National Institutes of Health Complex, Institute for Medical Research, Shah Alam, Selangor, Malaysia
| | - Syafinaz Amin-Nordin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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17
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Soetjipto, Rochmah N, Faizi M, Hisbiyah Y, Endaryanto A. HLA-DQA1 and HLA-DQB1 Gene Polymorphism in Indonesian Children with Type I Diabetes Mellitus. Appl Clin Genet 2022; 15:11-17. [PMID: 35046698 PMCID: PMC8763574 DOI: 10.2147/tacg.s348115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/18/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND More than 40 genes influence the progression of type 1 diabetes mellitus (T1DM), including human leukocyte antigen (HLA) alleles. Different HLA genotype patterns result in diverse rates of T1DM development. HLA class II DR, DQ, and DP vary among different populations and ethnicities. Data on HLA polymorphism in T1DM in Indonesia are lacking. Therefore, this study was designed to evaluate the gene polymorphism of HLA-DQA1 and HLA-DQB1 in Indonesian children with T1DM. PATIENTS AND METHODS In this study, 31 patients with T1DM and 31 controls were enrolled from April 2020 to April 2021. This study was conducted at Dr. Soetomo Hospital, Indonesia. We evaluated the gene polymorphism of HLA-DQA1 and HLA-DQB1 using polymerase chain reaction-restriction fragment length polymorphism. The primers used were as follows: for HLA-DQA1, DQAS34: 5'-GGTGTAAACTTGTACCAG-3' (forward) and DQAA261: 5'-ATTGGTAGCAGCGGTAGA-3' (reverse); for HLA-DQB1, DQBS43: 5'-TGCTACT- TCACCAA(C/T)GGG-3' (forward) and DQBA249: 5'-GTAGTTGTGTCTGCA (C/T)AC-3' (reverse). RESULTS The most common HLA-DQA1 subtype in the T1DM group was 0101/0102 accounting for 67.6%, and 01/03 and 02/03 were found in the T1DM group only. Meanwhile, the most common HLA-DQB1 subtype in the T1DM group was 0301, accounting for 54.8%. Most subjects in this study were Javanese. CONCLUSION HLA-DQA1 0101/0102 and HLA-DQB1 0301 were commonly found in Indonesian children with T1DM.
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Affiliation(s)
- Soetjipto
- Department of Medical Biochemistry, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Nur Rochmah
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
- Faculty of Medicine, Department of Child Health, Dr. Soetomo General Hospital, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Muhammad Faizi
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
- Faculty of Medicine, Department of Child Health, Dr. Soetomo General Hospital, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Yuni Hisbiyah
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
- Faculty of Medicine, Department of Child Health, Dr. Soetomo General Hospital, Universitas Airlangga, Surabaya, East Java, Indonesia
| | - Anang Endaryanto
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Airlangga, Surabaya, East Java, Indonesia
- Faculty of Medicine, Department of Child Health, Dr. Soetomo General Hospital, Universitas Airlangga, Surabaya, East Java, Indonesia
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18
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Zhang R, Cao L, Chen W, Ge H, Hu X, Li Z, Wang Y, Fan W, Yong L, Yu Y, Mao Y, Zhen Q, Liu H, Zhang F, Sun L. Fine-Mapping of the Major Histocompatibility Complex Region Linked to Leprosy in Northern China. Front Genet 2022; 12:768259. [PMID: 34976012 PMCID: PMC8716717 DOI: 10.3389/fgene.2021.768259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/29/2021] [Indexed: 01/31/2023] Open
Abstract
Background: Leprosy is a chronic infectious skin and neurological disease, and genetic background is considered to be one of the major factors of risk. The major histocompatibility complex (MHC) region not only affects susceptibility to leprosy but also its development and outcome. Given the complex traits of the MHC region, variants and the potential mechanism by which HLA influences leprosy development need to be further explored. Methods: We extracted previous genome-wide association study data from the Northern Han Chinese population to perform HLA fine-mapping. Using the 1,000 Genome Project Phase 3 dataset as the reference panel, single-nucleotide polymorphisms (SNP), insertion and deletion (INDEL) and copy number variant (CNV) imputation were carried out. HLA classical alleles and amino acids in the MHC region were imputed using the HAN-MHC database. Further stepwise regression analysis was conducted to analyze independent signals of variants related to leprosy. Results: We identified four independent variants: esv3608598, rs7754498, rs3130781 and rs144388449. Among them, esv3608598 is a CNV and the first HLA CNV associated with leprosy risk. SNP annotation using RegulomeDB, HaploReg, and rVarBase showed that three SNPs are likely to affect the pathogenesis of leprosy. Conclusion: In summary, this is the first study to assess the association between HLA CNV and leprosy susceptibility in a Northern Han Chinese population. By fine mapping of the MHC region in this population, our findings provide evidence for the contribution of HLA to leprosy susceptibility.
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Affiliation(s)
- Ruixue Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Lu Cao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Huiyao Ge
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xia Hu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Zhuo Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yirui Wang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Wencheng Fan
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liang Yong
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yafen Yu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yiwen Mao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qi Zhen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Hong Liu
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Furen Zhang
- Shandong Provincial Hospital for Skin Diseases and Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China.,Institute of Dermatology, Anhui Medical University, Hefei, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China.,Anhui Provincial Institute of Translational Medicine, Hefei, China.,Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
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19
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Naito T, Okada Y. HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases. Semin Immunopathol 2022; 44:15-28. [PMID: 34786601 PMCID: PMC8837514 DOI: 10.1007/s00281-021-00901-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.
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Affiliation(s)
- Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan.
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
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20
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Degenhardt F, Mayr G, Wendorff M, Boucher G, Ellinghaus E, Ellinghaus D, ElAbd H, Rosati E, Hübenthal M, Juzenas S, Abedian S, Vahedi H, Thelma BK, Yang SK, Ye BD, Cheon JH, Datta LW, Daryani NE, Ellul P, Esaki M, Fuyuno Y, McGovern DPB, Haritunians T, Hong M, Juyal G, Jung ES, Kubo M, Kugathasan S, Lenz TL, Leslie S, Malekzadeh R, Midha V, Motyer A, Ng SC, Okou DT, Raychaudhuri S, Schembri J, Schreiber S, Song K, Sood A, Takahashi A, Torres EA, Umeno J, Alizadeh BZ, Weersma RK, Wong SH, Yamazaki K, Karlsen TH, Rioux JD, Brant SR, Franke A. Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations. Hum Mol Genet 2021; 30:356-369. [PMID: 33555323 PMCID: PMC8098114 DOI: 10.1093/hmg/ddab017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/27/2020] [Accepted: 12/23/2020] [Indexed: 12/24/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabriele Mayr
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Gabrielle Boucher
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, 0372 Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway
| | - Hesham ElAbd
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Dermatology, Venerology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Simonas Juzenas
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Homayon Vahedi
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, Delhi 110021, India
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Lisa Wu Datta
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Naser Ebrahim Daryani
- Department of Gastroenterology, Emam Hospital, Tehran University of Medical Sciences, Tehran 1419733141, Iran
| | - Pierre Ellul
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuta Fuyuno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Myhunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 351-0198, Japan
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.,Pediatric Institute, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Stephen Leslie
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran 1411713135, Iran
| | - Vandana Midha
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Allan Motyer
- Schools of Mathematics and Statistics and BioSciences and Melbourne Integrative Genomics, University of Melbourne, Victoria 3010, Australia
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - David T Okou
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA.,Centre for Genetics and Genomics Versus Arthritis, Division of Musculosceletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK
| | - John Schembri
- Department of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany.,Department of Medicine, Christian-Albrechts-University, 24105 Kiel, Germany
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, 136-701 Korea
| | - Ajit Sood
- Dayanand Medical College and Hospital, Ludhiana, Punjab 141001, India
| | - Atsushi Takahashi
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, Riken, Yokohama, 230-0045, Japan
| | - Esther A Torres
- Department of Medicine, University of Puerto Rico Center for IBD, University of Puerto Rico School of Medicine, Rio Piedras, San Juan, PR 00936-5067, USA
| | - Junji Umeno
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University Medical Center Groningen, 9713 Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700 AB Groningen, The Netherlands
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, Riken, Yokohama 351-0198, Japan
| | - Tom H Karlsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, 0372 Oslo, Norway.,Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, 0372 Oslo, Norway
| | - John D Rioux
- Research Center, Montréal Heart Institute, Université de Montréal and the Montréal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, John Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Medicine, Rutgers Robert Wood Johnson School of Medicine and Department of Genetics, Rutgers University Brunswick and Piscataway, NJ 08903-0019, USA
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, 24105 Kiel, Germany
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21
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Owen KA, Price A, Ainsworth H, Aidukaitis BN, Bachali P, Catalina MD, Dittman JM, Howard TD, Kingsmore KM, Labonte AC, Marion MC, Robl RD, Zimmerman KD, Langefeld CD, Grammer AC, Lipsky PE. Analysis of Trans-Ancestral SLE Risk Loci Identifies Unique Biologic Networks and Drug Targets in African and European Ancestries. Am J Hum Genet 2020; 107:864-881. [PMID: 33031749 PMCID: PMC7675009 DOI: 10.1016/j.ajhg.2020.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of African ancestry (AA) experience the disease more severely and with an increased co-morbidity burden compared to European ancestry (EA) populations. We hypothesize that the disparities in disease prevalence, activity, and response to standard medications between AA and EA populations is partially conferred by genomic influences on biological pathways. To address this, we applied a comprehensive approach to identify all genes predicted from SNP-associated risk loci detected with the Immunochip. By combining genes predicted via eQTL analysis, as well as those predicted from base-pair changes in intergenic enhancer sites, coding-region variants, and SNP-gene proximity, we were able to identify 1,731 potential ancestry-specific and trans-ancestry genetic drivers of SLE. Gene associations were linked to upstream and downstream regulators using connectivity mapping, and predicted biological pathways were mined for candidate drug targets. Examination of trans-ancestral pathways reflect the well-defined role for interferons in SLE and revealed pathways associated with tissue repair and remodeling. EA-dominant genetic drivers were more often associated with innate immune and myeloid cell function pathways, whereas AA-dominant pathways mirror clinical findings in AA subjects, suggesting disease progression is driven by aberrant B cell activity accompanied by ER stress and metabolic dysfunction. Finally, potential ancestry-specific and non-specific drug candidates were identified. The integration of all SLE SNP-predicted genes into functional pathways revealed critical molecular pathways representative of each population, underscoring the influence of ancestry on disease mechanism and also providing key insight for therapeutic selection.
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MESH Headings
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Black People
- Bortezomib/therapeutic use
- DNA, Intergenic/genetics
- DNA, Intergenic/immunology
- Enhancer Elements, Genetic
- Gene Expression
- Gene Ontology
- Gene Regulatory Networks
- Genetic Predisposition to Disease
- Genome, Human
- Genome-Wide Association Study
- Heterocyclic Compounds/therapeutic use
- Humans
- Interferons/genetics
- Interferons/immunology
- Isoquinolines/therapeutic use
- Lactams
- Lupus Erythematosus, Systemic/drug therapy
- Lupus Erythematosus, Systemic/ethnology
- Lupus Erythematosus, Systemic/genetics
- Lupus Erythematosus, Systemic/immunology
- Molecular Sequence Annotation
- Polymorphism, Single Nucleotide
- Protein Array Analysis
- Quantitative Trait Loci
- Quantitative Trait, Heritable
- White People
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Affiliation(s)
| | - Andrew Price
- AMPEL BioSolutions LLC, Charlottesville, VA 22902, USA
| | | | | | | | | | | | | | | | | | | | - Robert D Robl
- AMPEL BioSolutions LLC, Charlottesville, VA 22902, USA
| | - Kip D Zimmerman
- Wake Forest School of Medicine, Winston-Salem, NC 27109, USA
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22
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Abstract
Systemic lupus erythematosus (SLE) is a chronic multisystem autoimmune disease characterized by autoantibody production and diverse clinical manifestations. The many complex, overlapping, and closely associated factors that influence SLE susceptibility and outcomes include ethnic disparities, low adherence to medications, and poverty, and geography. Epigenetic mechanisms may provide the link between these environmental exposures and behaviors and the disproportionate burden of SLE seen in ethnic minorities. Attention to these modifiable social determinants of health would not only improve outcomes for vulnerable patients with SLE but likely reduce susceptibility to SLE as well through epigenetic changes.
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Affiliation(s)
- Christine A Peschken
- Rady Faculty of Health Sciences, University of Manitoba, RR149 Arthritis Centre, 800 Sherbrook Street, Winnipeg, Manitoba R3A1M4, Canada.
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23
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Cui J, Raychaudhuri S, Karlson EW, Speyer C, Malspeis S, Guan H, Sparks JA, Ni H, Liu X, Stevens E, Williams JN, Davenport EE, Knevel R, Costenbader KH. Interactions Between Genome-Wide Genetic Factors and Smoking Influencing Risk of Systemic Lupus Erythematosus. Arthritis Rheumatol 2020; 72:1863-1871. [PMID: 32969204 DOI: 10.1002/art.41414] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/12/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To identify interactions between genetic factors and current or recent smoking in relation to risk of developing systemic lupus erythematosus (SLE). METHODS For the study, 673 patients with SLE (diagnosed according to the American College of Rheumatology 1997 updated classification criteria) were matched by age, sex, and race (first 3 genetic principal components) to 3,272 control subjects without a history of connective tissue disease. Smoking status was classified as current smoking/having recently quit smoking within 4 years before diagnosis (or matched index date for controls) versus distant past/never smoking. In total, 86 single-nucleotide polymorphisms and 10 classic HLA alleles previously associated with SLE were included in a weighted genetic risk score (wGRS), with scores dichotomized as either low or high based on the median value in control subjects (low wGRS being defined as less than or equal to the control median; high wGRS being defined as greater than the control median). Conditional logistic regression models were used to estimate both the risk of SLE and risk of anti-double-stranded DNA autoantibody-positive (dsDNA+) SLE. Additive interactions were assessed using the attributable proportion (AP) due to interaction, and multiplicative interactions were assessed using a chi-square test (with 1 degree of freedom) for the wGRS and for individual risk alleles. Separate repeated analyses were carried out among subjects of European ancestry only. RESULTS The mean ± SD age of the SLE patients at the time of diagnosis was 36.4 ± 15.3 years. Among the 673 SLE patients included, 92.3% were female and 59.3% were dsDNA+. Ethnic distributions were as follows: 75.6% of European ancestry, 4.5% of Asian ancestry, 11.7% of African ancestry, and 8.2% classified as other ancestry. A high wGRS (odds ratio [OR] 2.0, P = 1.0 × 10-51 versus low wGRS) and a status of current/recent smoking (OR 1.5, P = 0.0003 versus distant past/never smoking) were strongly associated with SLE risk, with significant additive interaction (AP 0.33, P = 0.0012), and associations with the risk of anti-dsDNA+ SLE were even stronger. No significant multiplicative interactions with the total wGRS (P = 0.58) or with the HLA-only wGRS (P = 0.06) were found. Findings were similar in analyses restricted to only subjects of European ancestry. CONCLUSION The strong additive interaction between an updated SLE genetic risk score and current/recent smoking suggests that smoking may influence specific genes in the pathogenesis of SLE.
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Affiliation(s)
- Jing Cui
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Elizabeth W Karlson
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Cameron Speyer
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Susan Malspeis
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hongshu Guan
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Sparks
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Hongru Ni
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Xinyi Liu
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emma Stevens
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Jessica N Williams
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Emma E Davenport
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Rachel Knevel
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, and Leiden University Medical Center, Leiden, The Netherlands
| | - Karen H Costenbader
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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24
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Beik P, Ciesielska M, Kucza M, Kurczewska A, Kuźmińska J, Maćkowiak B, Niechciał E. Prevention of Type 1 Diabetes: Past Experiences and Future Opportunities. J Clin Med 2020; 9:E2805. [PMID: 32872668 PMCID: PMC7563637 DOI: 10.3390/jcm9092805] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 12/11/2022] Open
Abstract
Type 1 diabetes (T1D) results from autoimmune destruction of insulin-producing beta-cells in the pancreas, caused by the interplay of genetic and environmental factors. Despite the introduction of advanced technologies for diabetes management, most patients fail to achieve target glycemic control, and T1D still has a high burden of long-term end-organ complications. Over several decades, multiple clinical trials have attempted to find prevention for T1D in at-risk individuals or to stabilize, ultimately reverse, the disease in those with T1D. To date, T1D remains yet incurable condition; however, recently improved understanding of the natural history of the disease may lead to new strategies to preserve or improve beta-cell function in those at increased risk and T1D patients. This publication aims to provide an overview of past experiences and recent findings in the prevention of T1D.
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Affiliation(s)
| | | | | | | | | | | | - Elżbieta Niechciał
- Department of Pediatric Diabetes and Obesity, Poznan University of Medical Sciences, Szpitalna Street 27/33, 60-572 Poznan, Poland; (P.B.); (M.C.); (M.K.); (A.K.); (J.K.); (B.M.)
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25
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Catalina MD, Bachali P, Yeo AE, Geraci NS, Petri MA, Grammer AC, Lipsky PE. Patient ancestry significantly contributes to molecular heterogeneity of systemic lupus erythematosus. JCI Insight 2020; 5:140380. [PMID: 32759501 PMCID: PMC7455079 DOI: 10.1172/jci.insight.140380] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023] Open
Abstract
Gene expression signatures can stratify patients with heterogeneous diseases, such as systemic lupus erythematosus (SLE), yet understanding the contributions of ancestral background to this heterogeneity is not well understood. We hypothesized that ancestry would significantly influence gene expression signatures and measured 34 gene modules in 1566 SLE patients of African ancestry (AA), European ancestry (EA), or Native American ancestry (NAA). Healthy subject ancestry-specific gene expression provided the transcriptomic background upon which the SLE patient signatures were built. Although standard therapy affected every gene signature and significantly increased myeloid cell signatures, logistic regression analysis determined that ancestral background significantly changed 23 of 34 gene signatures. Additionally, the strongest association to gene expression changes was found with autoantibodies, and this also had etiology in ancestry: the AA predisposition to have both RNP and dsDNA autoantibodies compared with EA predisposition to have only anti-dsDNA. A machine learning approach was used to determine a gene signature characteristic to distinguish AA SLE and was most influenced by genes characteristic of the perturbed B cell axis in AA SLE patients. Transcriptional profiling of lupus patients and healthy controls reveals ancestry-related differences and transcriptional heterogeneity among lupus patients.
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Affiliation(s)
- Michelle D Catalina
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA.,EMD Serono Research & Development Institute, Billerica, Massachusetts, USA
| | - Prathyusha Bachali
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | | | - Nicholas S Geraci
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | - Michelle A Petri
- Division of Rheumatology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Amrie C Grammer
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
| | - Peter E Lipsky
- AMPEL BioSolutions LLC & RILITE Research Institute, Charlottesville, Virginia, USA
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26
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Kamitaki N, Sekar A, Handsaker RE, de Rivera H, Tooley K, Morris DL, Taylor KE, Whelan CW, Tombleson P, Loohuis LMO, Boehnke M, Kimberly RP, Kaufman KM, Harley JB, Langefeld CD, Seidman CE, Pato MT, Pato CN, Ophoff RA, Graham RR, Criswell LA, Vyse TJ, McCarroll SA. Complement genes contribute sex-biased vulnerability in diverse disorders. Nature 2020; 582:577-581. [PMID: 32499649 PMCID: PMC7319891 DOI: 10.1038/s41586-020-2277-x] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/28/2020] [Indexed: 12/18/2022]
Abstract
Many common illnesses differentially affect men and women for unknown reasons. The autoimmune diseases lupus and Sjögren’s syndrome affect nine times more women than men1, whereas schizophrenia affects men more frequently and severely2. All three illnesses have their strongest common genetic associations in the Major Histocompatibility Complex (MHC) locus, an association that in lupus and Sjögren’s syndrome has long been thought to arise from alleles of the human leukocyte antigen (HLA) genes at that locus3–6. Here we show that the complement component 4 (C4) genes, which are also in the MHC locus and were recently found to increase risk for schizophrenia7, generate 7-fold variation in risk for lupus (95% CI: 5.88–8.61; p < 10−117 in total) and 16-fold variation in risk for Sjögren’s syndrome (95% CI: 8.59–30.89; p < 10−23 in total) among individuals with common C4 genotypes, with C4A protecting more strongly than C4B in both illnesses. The same alleles that increase risk for schizophrenia greatly reduced risk for lupus and Sjögren’s syndrome. In all three illnesses, C4 alleles acted more strongly in men than in women: common combinations of C4A and C4B generated 14-fold variation in risk for lupus, 31-fold variation in risk for Sjögren’s syndrome, and 1.7-fold variation in schizophrenia risk among men (vs. 6-fold, 15-fold, and 1.26-fold among women respectively). At a protein level, both C4 and its effector C3 were present at greater levels in men than women in cerebrospinal fluid (p < 10−5 for both C4 and C3) and plasma8,9 among adults ages 20–50, corresponding to the ages of differential disease vulnerability. Sex differences in complement protein levels may help explain the larger effects of C4 alleles in men, women’s greater risk of SLE and Sjögren’s, and men’s greater vulnerability in schizophrenia. These results implicate the complement system as a source of sexual dimorphism in vulnerability to diverse illnesses.
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Affiliation(s)
- Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Aswin Sekar
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heather de Rivera
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine Tooley
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David L Morris
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Kimberly E Taylor
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, CA, USA
| | - Christopher W Whelan
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philip Tombleson
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Loes M Olde Loohuis
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Robert P Kimberly
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Department of Pediatrics, Cincinnati Children's Medical Center & University of Cincinnati and the US Department of Veterans Affairs Medical Center, Cincinnati, OH, USA
| | - Carl D Langefeld
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Cardiovascular Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Roel A Ophoff
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | | | - Lindsey A Criswell
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, CA, USA
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK.
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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Hu F, Liu X, Zhang L, Chen C, Gong X, Lin J, An D, Zhou D, Hong Z. Novel findings of HLA association with anti-LGI1 encephalitis: HLA-DRB1*03:01 and HLA-DQB1*02:01. J Neuroimmunol 2020; 344:577243. [PMID: 32417596 DOI: 10.1016/j.jneuroim.2020.577243] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/04/2020] [Accepted: 04/14/2020] [Indexed: 02/05/2023]
Abstract
This study was to investigate whether autoimmune encephalitis is associated with the human leukocyte antigen (HLA) genotypes in Chinese Han population. We compared and analyzed the HLA genotypes of 101 patients with autoimmune encephalitis (77 anti-NMDAR, 11 anti-LGI1 and 13 anti-GABABR antibody, respectively) to the 200 healthy control groups. Our results showed that the DRB1*03:01 or DQB1*02:01 allele and the extended DRB1*03:01 ~ DQB1*02:01 haplotype represented the strong susceptibility locus for anti-LGI1 encephalitis (OR = 18.84, 95% CI = 5.01-70.89, Pc = 0.004; OR = 18.84, 95% CI = 5.01-70.89, Pc = 0.004; OR = 18.84, 95% CI = 5.01-70.89, Pc = 0.001). Additionally, the DRB1*08:03 ~ DQB1*06:01 or B*08:01 ~ C*07:02 haplotype was likely to be associated with anti-LGI1 encephalitis (OR = 10.23, 95% CI = 2.87-36.42, Pc = 0.039; OR = 74.62, 95% CI = 6.97-799.06, Pc = 0.043). No statistically significant differences were found for HLA association between patients with anti-NMDAR or anti-GABABR encephalitis and healthy controls. These results indicated that HLA subtypes were only associated with anti-LGI1 encephalitis.
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Affiliation(s)
- Fayun Hu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Xu Liu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Le Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Chu Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Xue Gong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Jingfang Lin
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Dongmei An
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.
| | - Zhen Hong
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China.
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28
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Glanville KP, Coleman JRI, Hanscombe KB, Euesden J, Choi SW, Purves KL, Breen G, Air TM, Andlauer TFM, Baune BT, Binder EB, Blackwood DHR, Boomsma DI, Buttenschøn HN, Colodro-Conde L, Dannlowski U, Direk N, Dunn EC, Forstner AJ, de Geus EJC, Grabe HJ, Hamilton SP, Jones I, Jones LA, Knowles JA, Kutalik Z, Levinson DF, Lewis G, Lind PA, Lucae S, Magnusson PK, McGuffin P, McIntosh AM, Milaneschi Y, Mors O, Mostafavi S, Müller-Myhsok B, Pedersen NL, Penninx BWJH, Potash JB, Preisig M, Ripke S, Shi J, Shyn SI, Smoller JW, Streit F, Sullivan PF, Tiemeier H, Uher R, Van der Auwera S, Weissman MM, O'Reilly PF, Lewis CM. Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression. Biol Psychiatry 2020; 87:419-430. [PMID: 31570195 PMCID: PMC7001040 DOI: 10.1016/j.biopsych.2019.06.031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 06/26/2019] [Accepted: 06/27/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND The prevalence of depression is higher in individuals with autoimmune diseases, but the mechanisms underlying the observed comorbidities are unknown. Shared genetic etiology is a plausible explanation for the overlap, and in this study we tested whether genetic variation in the major histocompatibility complex (MHC), which is associated with risk for autoimmune diseases, is also associated with risk for depression. METHODS We fine-mapped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4 complement component 4 (C4) haplotypes in studies from the Psychiatric Genomics Consortium Major Depressive Disorder Working Group and the UK Biobank. The total sample size was 45,149 depression cases and 86,698 controls. We tested for association between depression status and imputed MHC variants, applying both a region-wide significance threshold (3.9 × 10-6) and a candidate threshold (1.6 × 10-4). RESULTS No HLA alleles or C4 haplotypes were associated with depression at the region-wide threshold. HLA-B*08:01 was associated with modest protection for depression at the candidate threshold for testing in HLA genes in the meta-analysis (odds ratio = 0.98, 95% confidence interval = 0.97-0.99). CONCLUSIONS We found no evidence that an increased risk for depression was conferred by HLA alleles, which play a major role in the genetic susceptibility to autoimmune diseases, or C4 haplotypes, which are strongly associated with schizophrenia. These results suggest that any HLA or C4 variants associated with depression either are rare or have very modest effect sizes.
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Affiliation(s)
- Kylie P Glanville
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom.
| | - Jonathan R I Coleman
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; National Institute for Health Research Biomedical Research Centre South London and Maudsley National Health Service Trust, King's College London, London, United Kingdom
| | - Ken B Hanscombe
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Jack Euesden
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Shing Wan Choi
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York
| | - Kirstin L Purves
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Gerome Breen
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; National Institute for Health Research Biomedical Research Centre South London and Maudsley National Health Service Trust, King's College London, London, United Kingdom
| | - Tracy M Air
- Discipline of Psychiatry, Adelaide Medical School, University of Adelaide, Adelaide, South Australia, Australia
| | - Till F M Andlauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Münster, Germany; Munich Cluster for Systems Neurology (SyNergy), Münster, Germany
| | - Bernhard T Baune
- Department of Psychiatry, Melbourne Medical School, University of Melbourne, Melbourne, Victoria, Australia; Florey Institute for Neuroscience and Mental Health, University of Melbourne, Melbourne, Victoria, Australia; Department of Psychiatry, University of Münster, Münster, Germany
| | - Elisabeth B Binder
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Emory University, Atlanta, Georgia; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Münster, Germany
| | | | - Dorret I Boomsma
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Henriette N Buttenschøn
- NIDO | Danmark, Regional Hospital West Jutland, Herning, Denmark; iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark
| | - Lucía Colodro-Conde
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Udo Dannlowski
- Department of Psychiatry, University of Münster, Münster, Germany
| | - Nese Direk
- Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Psychiatry, Dokuz Eylul University School Of Medicine, Izmir, Turkey
| | - Erin C Dunn
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts
| | - Andreas J Forstner
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany; Centre for Human Genetics, University of Marburg, Marburg, Germany; Department of Psychiatry, University of Basel, Basel, Switzerland; Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Eco J C de Geus
- Department of Biological Psychology and EMGO+ Institute for Health and Care Research, Vrije Universiteit Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands; Amsterdam Public Health Institute, Vrije Universiteit Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Steven P Hamilton
- Department of Psychiatry, Kaiser Permanente Northern California, San Francisco, California
| | - Ian Jones
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, United Kingdom
| | - Lisa A Jones
- Department of Psychological Medicine, University of Worcester, Worcester, United Kingdom
| | - James A Knowles
- Psychiatry and the Behavioral Sciences, University of Southern California, Los Angeles, California
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Douglas F Levinson
- Psychiatry and Behavioral Sciences, Stanford University, Stanford, California
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, United Kingdom
| | - Penelope A Lind
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter McGuffin
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, United Kingdom; Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Universiteit Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Denmark; Psychosis Research Unit, Aarhus University Hospital, Risskov, Aarhus, Denmark
| | - Sara Mostafavi
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada; Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bertram Müller-Myhsok
- University of Liverpool, Liverpool, United Kingdom; Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Münster, Germany; Munich Cluster for Systems Neurology (SyNergy), Münster, Germany
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Universiteit Medical Center, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Martin Preisig
- Department of Psychiatry, University Hospital of Lausanne, Prilly, Switzerland
| | - Stephan Ripke
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Department of Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts; Department of Psychiatry and Psychotherapy, Universitätsmedizin Berlin Campus Charité Mitte, Berlin, Germany
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Stanley I Shyn
- Behavioral Health Services, Kaiser Permanente Washington, Seattle, Washington
| | - Jordan W Smoller
- Department of Psychiatry, Massachusetts General Hospital, Boston, Massachusetts; Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts; Stanley Center for Psychiatric Research, Broad Institute, Cambridge, Massachusetts
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Henning Tiemeier
- Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Child and Adolescent Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands; Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Rudolf Uher
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Myrna M Weissman
- Division of Epidemiology, New York State Psychiatric Institute, New York, New York; Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, New York
| | - Paul F O'Reilly
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, New York
| | - Cathryn M Lewis
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
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Li L, Tian W, Zhang J. A laboratory practice that uses the polymerase chain reaction-sequence specific priming technique to rapidly screen for HLA-DR2 allotype from germline DNA in immunology course for undergraduate medical students. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:175-180. [PMID: 31794631 DOI: 10.1002/bmb.21322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/20/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023]
Abstract
In this article, we describe an in-house polymerase chain reaction-sequence specific priming (PCR-SSP) assay designed for undergraduate medical students as part of the experimental pathogen biology and immunology (EPBI) course. It screens human leukocyte antigen (HLA)-DR2 allotype from genomic DNA samples using a rapid and single-tube PCR technique, yielding definitive typing result without conventional post-amplification step like probing or Sanger sequencing. This laboratory exercise offers the undergraduate medical students an opportunity to learn about current molecular biology techniques in HLA genotyping with limited effort and cost, in addition to a better understanding of concepts presented in the classroom lectures. Upon completing this experiment module, the students show statistically significant improvement in several key indexes, such as the knowledge about the mainstream HLA DNA typing techniques, awareness of the relevance of this knowledge for their future scientific research, immunogenetics-related basic laboratory skills they acquire, and interest and desire for mastering this assay (all p < .05). This easy to implement set of experiments is composed of a two-session lab module occupying eight teaching hours, and has been run successfully in our laboratory.
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Affiliation(s)
- LiXin Li
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Wei Tian
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, China
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, China
| | - Jie Zhang
- Laboratory of Cellular and Molecular Biology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, China
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Human Leukocyte Antigen (HLA) and Islet Autoantibodies Are Tools to Characterize Type 1 Diabetes in Arab Countries: Emphasis on Kuwait. DISEASE MARKERS 2019; 2019:9786078. [PMID: 31827651 PMCID: PMC6886320 DOI: 10.1155/2019/9786078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/15/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
The incidence rate of type 1 diabetes in Kuwait had been increasing exponentially and has doubled in children ≤ 14 years old within almost two decades. Therefore, there is a dire need for a careful systematic familial cohort study. Several immunogenetic factors affect the pathogenesis of the disease. The human leukocyte antigen (HLA) accounts for the major genetic susceptibility to the disease. The triggering agents initiate disease onset by type 1 destruction of pancreatic β-cells. Both HLA and anti-islet antibodies can be used to characterize, predict susceptibility to the disease, innovate, or delay the β-cell destruction. Evidence from prospective longitudinal studies suggested that the underlying disease process represents a continuum that begins before the symptoms are clinically evident. Autoimmunity of the functional pancreatic β-cells results in symptomatic type 1 diabetes and lifelong insulin dependence. The autoantibodies against glutamic acid decarboxylase (GADA), insulinoma antigen-2 (IA-2A), insulin (IAA), and zinc transporter-8 (ZnT-8A) comprise the most reliable biomarkers for type 1 diabetes in both children and adults. Although Kuwait is the second among the top 10 countries with a high incidence rate of type 1 diabetes, there have been no proper diagnostic and prediction tools as per the World Health Organization. The Kuwaiti Type 1 Diabetes Study (KADS) was initiated to understand the disease pathogenesis as well as the HLA and anti-islet autoantibody profile of type 1 diabetes in Kuwait. Understanding the disease sequela in a homogenous gene pool and highly consanguineous population of Kuwaitis could help solve the challenges and pathogenesis, as well as hasten the prevention, of type 1 diabetes.
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Siegel RJ, Bridges SL, Ahmed S. HLA-C: An Accomplice in Rheumatic Diseases. ACR Open Rheumatol 2019; 1:571-579. [PMID: 31777841 PMCID: PMC6858028 DOI: 10.1002/acr2.11065] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 07/08/2019] [Indexed: 01/14/2023] Open
Abstract
Human leukocyte antigen c (HLA-C) is a polymorphic membrane protein encoded by the HLA-C gene in the class I major histocompatibility complex. HLA-C plays an essential role in protection against cancer and viruses but has also been implicated in allograft rejection, preeclampsia, and autoimmune disease. This review summarizes reports and proposed mechanisms for the accessory role of HLA-C in rheumatic diseases. Historically, contributions of HLA-C to rheumatic diseases were eclipsed by the stronger association with HLA-DRB1 alleles containing the "shared epitope" with rheumatoid arthritis. Larger genetic association studies and more powerful analytical approaches have revealed independent associations of HLA-C with rheumatic disease-associated phenotypes, including development of anticitrullinated peptide antibodies. HLA-C functions by presenting antigens to T cells and by binding activatory and inhibitory receptors on natural killer (NK) cells, but the exact mechanisms by which the HLA-C locus contributes to autoimmunity are largely undefined. Studies have suggested that HLA-C and NK cell receptor polymorphisms may predict responsiveness to pharmacotherapy. Understanding the mechanisms of the role of HLA-C in rheumatic disease could uncover therapeutic targets or guide precision pharmacologic treatments.
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Affiliation(s)
- Ruby J. Siegel
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
| | - S. Louis Bridges
- Division of Clinical Immunology and RheumatologyUniversity of Alabama at BirminghamBirminghamAlabama
| | - Salahuddin Ahmed
- Department of Pharmaceutical SciencesWashington State University College of Pharmacy and Pharmaceutical SciencesSpokaneWashington
- Division of RheumatologyUniversity of Washington School of MedicineSeattleWashington
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33
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Clancy RM, Marion MC, Ainsworth HC, Blaser MJ, Chang M, Howard TD, Izmirly PM, Lacher C, Masson M, Robins K, Buyon JP, Langefeld CD. Salivary dysbiosis and the clinical spectrum in anti-Ro positive mothers of children with neonatal lupus. J Autoimmun 2019; 107:102354. [PMID: 31677965 DOI: 10.1016/j.jaut.2019.102354] [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: 09/05/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
Mothers giving birth to children with manifestations of neonatal lupus (NL) represent a unique population at risk for the development of clinically evident pathologic autoimmunity since many are asymptomatic and only become aware of anti-SSA/Ro positivity (anti-Ro+) based on heart block in their fetus. Accordingly, we hypothesized that the microbiome in saliva is associated with the development of autoreactivity and in some cases the progression in health status from benign to overt clinical disease including Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE). The study comprised a clinical spectrum of anti-Ro+ mothers, all of whom gave birth to a child with NL: 9 were asymptomatic or had an undifferentiated autoimmune disease (Asym/UAS) and 16 fulfilled criteria for SS and/or SLE. Microbial diversity was reduced across all levels from kingdom to species for the anti-Ro+ mothers vs healthy controls; however, there were no significant differences between Asym/UAS and SS/SLE mothers. Relative abundance of Proteobacteria and more specifically class Betaproteobacteria decreased with clinical severity (healthy controls < Asym/UAS < SS/SLE). These ordered differences were maintained through the taxonomic hierarchy to three genera (Lautropia, Comamonas, and Neisseria) and species within these genera (L. mirabilis, N. flavescens and N. oralis). Biometric analysis comparing von Willebrand Factor domains present in human Ro60 with L. mirabilis proteins support the hypothesis of molecular mimicry. These data position the microbiome in the development of anti-Ro reactivity and subsequent clinical spectrum of disease.
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Affiliation(s)
- R M Clancy
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA.
| | - M C Marion
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - H C Ainsworth
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - M J Blaser
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - M Chang
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA
| | - T D Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - P M Izmirly
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA
| | - C Lacher
- Rutgers University, Center for Advanced Biotechnology and Medicine, Piscataway, NJ, USA
| | - M Masson
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA
| | - K Robins
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA
| | - J P Buyon
- NYU Langone Health, Department of Medicine, Division of Rheumatology, New York, NY, USA
| | - C D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
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