1
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Renaudineau Y, Charras A, Natoli V, Fusaro M, Smith EMD, Beresford MW, Hedrich CM. Type I interferon associated epistasis may contribute to early disease-onset and high disease activity in juvenile-onset lupus. Clin Immunol 2024; 262:110194. [PMID: 38508295 DOI: 10.1016/j.clim.2024.110194] [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: 12/04/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
Pathologic type I interferon (T1IFN) expression is a key feature in systemic lupus erythematosus (SLE) that associates with disease activity. When compared to adult-onset disease, juvenile-onset (j)SLE is characterized by increased disease activity and damage, which likely relates to increased genetic burden. To identify T1IFN-associated gene polymorphisms (TLR7, IRAK1, miR-3142/miR-146a, IRF5, IRF7, IFIH1, IRF8, TYK2, STAT4), identify long-range linkage disequilibrium and gene:gene interrelations, 319 jSLE patients were genotyped using panel sequencing. Coupling phenotypic quantitative trait loci (QTL) analysis identified 10 jSLE QTL that associated with young age at onset (<12 years; IRAK1 [rs1059702], TLR7 [rs3853839], IFIH1 [rs11891191, rs1990760, rs3747517], STAT4 [rs3021866], TYK2 [rs280501], IRF8 [rs1568391, rs6638]), global disease activity (SLEDAI-2 K >10; IFIH1 [rs1990760], STAT4 [rs3021866], IRF8 [rs903202, rs1568391, rs6638]), and mucocutaneous involvement (TLR7 [rs3853839], IFIH1 [rs11891191, rs1990760]). This study suggests T1IFN-associated polymorphisms and gene:gene interrelations in jSLE. Genotyping of jSLE patients may allow for individualized treatment and care.
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Affiliation(s)
- Yves Renaudineau
- Immunology Department Laboratory, Referral Medical Biology Laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France; INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France
| | - Amandine Charras
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, UK
| | - Valentina Natoli
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, UK; Università degli Studi di Genova, Dipartimento di Neuroscienze, riabilitazione, oftalmologia, genetica e scienze materno-infantili, DINOGMI, Genoa, Italy
| | - Mathieu Fusaro
- Immunology Department Laboratory, Referral Medical Biology Laboratory, Institut Fédératif de Biologie, Toulouse University Hospital Center, France; INFINITy, Toulouse Institute for Infectious and Inflammatory Diseases, INSERM U1291, CNRS U5051, University Toulouse III, Toulouse, France
| | - Eve M D Smith
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, UK; Department of Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Michael W Beresford
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, UK; Department of Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - Christian M Hedrich
- Department of Women's & Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, UK; Department of Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK.
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2
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Zhang Y, Hou G, Shen N. Non-coding DNA variants for risk in lupus. Best Pract Res Clin Rheumatol 2024:101937. [PMID: 38429183 DOI: 10.1016/j.berh.2024.101937] [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: 01/17/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 03/03/2024]
Abstract
Systemic Lupus Erythematosus (SLE) is a multifactorial autoimmune disease that arises from a dynamic interplay between genetics and environmental triggers. The advent of sophisticated genomics technology has catalyzed a shift in our understanding of disease etiology, spotlighting the pivotal role of non-coding DNA variants in SLE pathogenesis. In this review, we present a comprehensive examination of the non-coding variants associated with SLE, shedding light on their role in influencing disease risk and progression. We discuss the latest methodological advancements that have been instrumental in the identification and functional characterization of these genomic elements, with a special focus on the transformative power of CRISPR-based gene-editing technologies. Additionally, the review probes into the therapeutic opportunities that arise from modulating non-coding regions associated with SLE. Through an exploration of the complex network of non-coding DNA, this review aspires to decode the genetic puzzle of SLE and set the stage for groundbreaking gene-based therapeutic interventions and the advancement of precision medicine strategies tailored to SLE management.
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Affiliation(s)
- Yutong Zhang
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Guojun Hou
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, 200001, China.
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3
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Goldmann K, Spiliopoulou A, Iakovliev A, Plant D, Nair N, Cubuk C, McKeigue P, Barnes MR, Barton A, Pitzalis C, Lewis MJ. Expression quantitative trait loci analysis in rheumatoid arthritis identifies tissue specific variants associated with severity and outcome. Ann Rheum Dis 2024; 83:288-299. [PMID: 37979960 PMCID: PMC10894812 DOI: 10.1136/ard-2023-224540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/20/2023] [Indexed: 11/20/2023]
Abstract
OBJECTIVE Genome-wide association studies have successfully identified more than 100 loci associated with susceptibility to rheumatoid arthritis (RA). However, our understanding of the functional effects of genetic variants in causing RA and their effects on disease severity and response to treatment remains limited. METHODS In this study, we conducted expression quantitative trait locus (eQTL) analysis to dissect the link between genetic variants and gene expression comparing the disease tissue against blood using RNA-Sequencing of synovial biopsies (n=85) and blood samples (n=51) from treatment-naïve patients with RA from the Pathobiology of Early Arthritis Cohort. RESULTS This identified 898 eQTL genes in synovium and genes loci in blood, with 232 genes in common to both synovium and blood, although notably many eQTL were tissue specific. Examining the HLA region, we uncovered a specific eQTL at HLA-DPB2 with the critical triad of single-nucleotide polymorphisms (SNPs) rs3128921 driving synovial HLA-DPB2 expression, and both rs3128921 and HLA-DPB2 gene expression correlating with clinical severity and increasing probability of the lympho-myeloid pathotype. CONCLUSIONS This analysis highlights the need to explore functional consequences of genetic associations in disease tissue. HLA-DPB2 SNP rs3128921 could potentially be used to stratify patients to more aggressive treatment immediately at diagnosis.
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Affiliation(s)
- Katriona Goldmann
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Athina Spiliopoulou
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Andrii Iakovliev
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester Centre for Musculoskeletal Research, Manchester, UK
| | - Nisha Nair
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester Centre for Musculoskeletal Research, Manchester, UK
| | - Cankut Cubuk
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Paul McKeigue
- Centre for Population Health Sciences, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Michael R Barnes
- Centre for Translational Bioinformatics, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, University of Manchester Centre for Musculoskeletal Research, Manchester, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Myles J Lewis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London, London, UK
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4
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Garrett-Sinha LA. An update on the roles of transcription factor Ets1 in autoimmune diseases. WIREs Mech Dis 2023; 15:e1627. [PMID: 37565573 PMCID: PMC10842644 DOI: 10.1002/wsbm.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Transcription factors are crucial to regulate gene expression in immune cells and in other cell types. In lymphocytes, there are a large number of different transcription factors that are known to contribute to cell differentiation and the balance between quiescence and activation. One such transcription factor is E26 oncogene homolog 1 (Ets1). Ets1 expression is high in quiescent B and T lymphocytes and its levels are decreased upon activation. The human ETS1 gene has been identified as a susceptibility locus for many autoimmune and inflammatory diseases. In accord with this, gene knockout of Ets1 in mice leads to development of a lupus-like autoimmune disease, with enhanced activation and differentiation of both B cells and T cells. Prior reviews have summarized functional roles for Ets1 based on studies of Ets1 knockout mice. In recent years, numerous additional studies have been published that further validate ETS1 as a susceptibility locus for human diseases where immune dysregulation plays a causative role. In this update, new information that further links Ets1 to human autoimmune diseases is organized and collated to serve as a resource. This update also describes recent studies that seek to understand molecularly how Ets1 regulates immune cell activation, either using human cells and tissues or mouse models. This resource is expected to be useful to investigators seeking to understand how Ets1 may regulate the human immune response, particularly in terms of its roles in autoimmunity and inflammation. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
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5
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Li M, Liu Q, Wang W, Jiang L. HLA-DRB1*14:54 Is Associated with Pulmonary Alveolar Proteinosis: A Retrospective Real-World Audit. Biomedicines 2023; 11:2909. [PMID: 38001910 PMCID: PMC10669482 DOI: 10.3390/biomedicines11112909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/14/2023] [Accepted: 10/23/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Pulmonary alveolar proteinosis (PAP) is a rare pulmonary disease characterized by abnormal accumulation of pulmonary surfactant lipids in alveoli or terminal bronchioles, leading to increased infection risk and progressive respiratory failure. Approximately more than 90% of all cases are autoimmune PAP (aPAP). Since one of the predisposing factors has been identified as genes located within the major-histocompatibility-complex region, an investigation of human leukocyte antigen (HLA) alleles associated with the risk of aPAP is warranted. METHODS We retrospectively studied 60 patients pathologically diagnosed with PAP from 2019 to 2022. Patients were divided into the aPAP group or secondary PAP (sPAP) group according to their clinical information. Qualified DNA was extracted from the paraffin-embedded tissue of 28 patients, and the PCR-sequence-based typing method was used for HLA-DRB1 genotyping. RESULTS A similar HLA-DRB1 allele profile (including the HLA-DRB1*08:03) between the aPAP group and sPAP group was revealed, except that HLA-DRB1*14:54, which has never been reported in aPAP patients, was only detected in the aPAP group rather than the sPAP group (19.4% vs. 0.0%, p = 0.030). Under inhaled granulocyte-macrophage colony-stimulating factor therapy, more clinical remission was observed in HLA-DRB1*14:54 carriers rather than in HLA-DRB1*08:03 carriers (80.0% vs. 57.1%). CONCLUSIONS Our real-world study revealed for the first time that a population with HLA-DRB1*14:54 was subject to aPAP, and HLA-DRB1*14:54 might imply a response in aPAP patients to inhaled granulocyte-macrophage colony-stimulating factor in aPAP patients.
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Affiliation(s)
| | | | | | - Lili Jiang
- Department of Pathology, West China Hospital, Sichuan University, Chengdu 610041, China; (M.L.); (Q.L.); (W.W.)
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6
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Vinuesa CG, Shen N, Ware T. Genetics of SLE: mechanistic insights from monogenic disease and disease-associated variants. Nat Rev Nephrol 2023; 19:558-572. [PMID: 37438615 DOI: 10.1038/s41581-023-00732-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 07/14/2023]
Abstract
The past few years have provided important insights into the genetic architecture of systemic autoimmunity through aggregation of findings from genome-wide association studies (GWAS) and whole-exome or whole-genome sequencing studies. In the prototypic systemic autoimmune disease systemic lupus erythematosus (SLE), monogenic disease accounts for a small fraction of cases but has been instrumental in the elucidation of disease mechanisms. Defects in the clearance or digestion of extracellular or intracellular DNA or RNA lead to increased sensing of nucleic acids, which can break B cell tolerance and induce the production of type I interferons leading to tissue damage. Current data suggest that multiple GWAS SLE risk alleles act in concert with rare functional variants to promote SLE development. Moreover, introduction of orthologous variant alleles into mice has revealed that pathogenic X-linked dominant and recessive SLE can be caused by novel variants in TLR7 and SAT1, respectively. Such bespoke models of disease help to unravel pathogenic pathways and can be used to test targeted therapies. Cell type-specific expression data revealed that most GWAS SLE risk genes are highly expressed in age-associated B cells (ABCs), which supports the view that ABCs produce lupus autoantibodies and contribute to end-organ damage by persisting in inflamed tissues, including the kidneys. ABCs have thus emerged as key targets of promising precision therapeutics.
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Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- China Australia Centre for Personalized Immunology (CACPI), Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- Center for Autoimmune Genomics and Aetiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Paediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Thuvaraka Ware
- The Francis Crick Institute, London, UK
- University College London, London, UK
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7
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Singh P, Zhou L, Shah DA, Cejas RB, Crossman DK, Jouni M, Magdy T, Wang X, Sharafeldin N, Hageman L, McKenna DE, Horvath S, Armenian SH, Balis FM, Hawkins DS, Keller FG, Hudson MM, Neglia JP, Ritchey AK, Ginsberg JP, Landier W, Burridge PW, Bhatia S. Identification of novel hypermethylated or hypomethylated CpG sites and genes associated with anthracycline-induced cardiomyopathy. Sci Rep 2023; 13:12683. [PMID: 37542143 PMCID: PMC10403495 DOI: 10.1038/s41598-023-39357-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/24/2023] [Indexed: 08/06/2023] Open
Abstract
Anthracycline-induced cardiomyopathy is a leading cause of late morbidity in childhood cancer survivors. Aberrant DNA methylation plays a role in de novo cardiovascular disease. Epigenetic processes could play a role in anthracycline-induced cardiomyopathy but remain unstudied. We sought to examine if genome-wide differential methylation at 'CpG' sites in peripheral blood DNA is associated with anthracycline-induced cardiomyopathy. This report used participants from a matched case-control study; 52 non-Hispanic White, anthracycline-exposed childhood cancer survivors with cardiomyopathy were matched 1:1 with 52 survivors with no cardiomyopathy. Paired ChAMP (Chip Analysis Methylation Pipeline) with integrated reference-based deconvolution of adult peripheral blood DNA methylation was used to analyze data from Illumina HumanMethylation EPIC BeadChip arrays. An epigenome-wide association study (EWAS) was performed, and the model was adjusted for GrimAge, sex, interaction terms of age at enrollment, chest radiation, age at diagnosis squared, and cardiovascular risk factors (CVRFs: diabetes, hypertension, dyslipidemia). Prioritized genes were functionally validated by gene knockout in human induced pluripotent stem cell cardiomyocytes (hiPSC-CMs) using CRISPR/Cas9 technology. DNA-methylation EPIC array analyses identified 32 differentially methylated probes (DMP: 15 hyper-methylated and 17 hypo-methylated probes) that overlap with 23 genes and 9 intergenic regions. Three hundred and fifty-four differential methylated regions (DMRs) were also identified. Several of these genes are associated with cardiac dysfunction. Knockout of genes EXO6CB, FCHSD2, NIPAL2, and SYNPO2 in hiPSC-CMs increased sensitivity to doxorubicin. In addition, EWAS analysis identified hypo-methylation of probe 'cg15939386' in gene RORA to be significantly associated with anthracycline-induced cardiomyopathy. In this genome-wide DNA methylation profile study, we observed significant differences in DNA methylation at the CpG level between anthracycline-exposed childhood cancer survivors with and without cardiomyopathy, implicating differential DNA methylation of certain genes could play a role in pathogenesis of anthracycline-induced cardiomyopathy.
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Affiliation(s)
- Purnima Singh
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Liting Zhou
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Disheet A Shah
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Romina B Cejas
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - David K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mariam Jouni
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Tarek Magdy
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
- Department of Pathology and Translational Pathobiology and Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center-Shreveport, Shreveport, LA, USA
| | - Xuexia Wang
- Department of Biostatistics, Florida International University, Miami, FL, USA
| | - Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lindsey Hageman
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Donald E McKenna
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Saro H Armenian
- Department of Population Sciences, City of Hope, Duarte, CA, USA
| | - Frank M Balis
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Frank G Keller
- Children's Healthcare of Atlanta, Emory University, Atlanta, GA, USA
| | | | | | - A Kim Ritchey
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | - Wendy Landier
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University, Chicago, IL, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL, USA.
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8
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Owen KA, Bell KA, Price A, Bachali P, Ainsworth H, Marion MC, Howard TD, Langefeld CD, Shen N, Yazdany J, Dall'era M, Grammer AC, Lipsky PE. Molecular pathways identified from single nucleotide polymorphisms demonstrate mechanistic differences in systemic lupus erythematosus patients of Asian and European ancestry. Sci Rep 2023; 13:5339. [PMID: 37005464 PMCID: PMC10067935 DOI: 10.1038/s41598-023-32569-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/29/2023] [Indexed: 04/04/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a multi-organ autoimmune disorder with a prominent genetic component. Individuals of Asian-Ancestry (AsA) disproportionately experience more severe SLE compared to individuals of European-Ancestry (EA), including increased renal involvement and tissue damage. However, the mechanisms underlying elevated severity in the AsA population remain unclear. Here, we utilized available gene expression data and genotype data based on all non-HLA SNP associations in EA and AsA SLE patients detected using the Immunochip genotyping array. We identified 2778 ancestry-specific and 327 trans-ancestry SLE-risk polymorphisms. Genetic associations were examined using connectivity mapping and gene signatures based on predicted biological pathways and were used to interrogate gene expression datasets. SLE-associated pathways in AsA patients included elevated oxidative stress, altered metabolism and mitochondrial dysfunction, whereas SLE-associated pathways in EA patients included a robust interferon response (type I and II) related to enhanced cytosolic nucleic acid sensing and signaling. An independent dataset derived from summary genome-wide association data in an AsA cohort was interrogated and identified similar molecular pathways. Finally, gene expression data from AsA SLE patients corroborated the molecular pathways predicted by SNP associations. Identifying ancestry-related molecular pathways predicted by genetic SLE risk may help to disentangle the population differences in clinical severity that impact AsA and EA individuals with SLE.
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Affiliation(s)
- Katherine A Owen
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA.
| | - Kristy A Bell
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Andrew Price
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Prathyusha Bachali
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Hannah Ainsworth
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Miranda C Marion
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Timothy D Howard
- Department of Biochemistry, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinoos Yazdany
- University of California San Francisco, San Francisco, CA, 94117, USA
| | - Maria Dall'era
- University of California San Francisco, San Francisco, CA, 94117, USA
| | - Amrie C Grammer
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
| | - Peter E Lipsky
- AMPEL BioSolutions LLC and the RILITE Research Institute, Charlottesville, VA, 22902, USA
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9
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The role of lysosomes in metabolic and autoimmune diseases. Nat Rev Nephrol 2023; 19:366-383. [PMID: 36894628 DOI: 10.1038/s41581-023-00692-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 03/11/2023]
Abstract
Lysosomes are catabolic organelles that contribute to the degradation of intracellular constituents through autophagy and of extracellular components through endocytosis, phagocytosis and macropinocytosis. They also have roles in secretory mechanisms, the generation of extracellular vesicles and certain cell death pathways. These functions make lysosomes central organelles in cell homeostasis, metabolic regulation and responses to environment changes including nutrient stresses, endoplasmic reticulum stress and defects in proteostasis. Lysosomes also have important roles in inflammation, antigen presentation and the maintenance of long-lived immune cells. Their functions are tightly regulated by transcriptional modulation via TFEB and TFE3, as well as by major signalling pathways that lead to activation of mTORC1 and mTORC2, lysosome motility and fusion with other compartments. Lysosome dysfunction and alterations in autophagy processes have been identified in a wide variety of diseases, including autoimmune, metabolic and kidney diseases. Deregulation of autophagy can contribute to inflammation, and lysosomal defects in immune cells and/or kidney cells have been reported in inflammatory and autoimmune pathologies with kidney involvement. Defects in lysosomal activity have also been identified in several pathologies with disturbances in proteostasis, including autoimmune and metabolic diseases such as Parkinson disease, diabetes mellitus and lysosomal storage diseases. Targeting lysosomes is therefore a potential therapeutic strategy to regulate inflammation and metabolism in a variety of pathologies.
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10
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Kain J, Owen KA, Marion MC, Langefeld CD, Grammer AC, Lipsky PE. Mendelian randomization and pathway analysis demonstrate shared genetic associations between lupus and coronary artery disease. Cell Rep Med 2022; 3:100805. [PMID: 36334592 PMCID: PMC9729823 DOI: 10.1016/j.xcrm.2022.100805] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 07/08/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Coronary artery disease (CAD) is a leading cause of death in patients with systemic lupus erythematosus (SLE). Despite clinical evidence supporting an association between SLE and CAD, pleiotropy-adjusted genetic association studies are limited and focus on only a few common risk loci. Here, we identify a net positive causal estimate of SLE-associated non-HLA SNPs on CAD by traditional Mendelian randomization (MR) approaches. Pathway analysis using SNP-to-gene mapping followed by unsupervised clustering based on protein-protein interactions (PPIs) identifies biological networks composed of positive and negative causal sets of genes. In addition, we confirm the casual effects of specific SNP-to-gene modules on CAD using only SNP mapping to each PPI-defined functional gene set as instrumental variables. This PPI-based MR approach elucidates various molecular pathways with causal implications between SLE and CAD and identifies biological pathways likely causative of both pathologies, revealing known and novel therapeutic interventions for managing CAD in SLE.
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Affiliation(s)
- Jessica Kain
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
| | - Katherine A Owen
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA.
| | - Miranda C Marion
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, and Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Amrie C Grammer
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
| | - Peter E Lipsky
- AMPEL BioSolutions, LLC, Charlottesville, VA, USA; The RILITE Research Institute, Charlottesville, VA, USA
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11
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Abstract
Macroautophagy/autophagy, a fundamental cell process for nutrient recycling and defense against pathogens (termed xenophagy), is crucial to human health. ATG16L2 (autophagy related 16 like 2) is an autophagic protein and a paralog of ATG16L1. Both proteins are implicated in similar diseases such as cancer and other chronic diseases; however, most autophagy studies to date have primarily focused on the function of ATG16L1, with ATG16L2 remaining uncharacterized and understudied. Overexpression of ATG16L2 has been reported in various cancers including colorectal, gastric, and prostate carcinomas, whereas altered methylation of ATG16L2 has been associated with lung cancer formation and poorer response to therapy in leukemia. In addition, ATG16L2 polymorphisms have been implicated in a range of other diseases including inflammatory bowel diseases and neurodegenerative disorders. Despite this likely role in human health, the function of this enigmatic protein in autophagy remains unknown. Here, we review current studies on ATG16L2 and collate evidence that suggests that this protein is a potential modulator of autophagy as well as the implications this has on pathogenesis.Abbreviations: ATG5: autophagy related 5; ATG12: autophagy related 12; ATG16L1: autophagy related 16 like 1; ATG16L2: autophagy related 16 like 2; CD: Crohn disease; IBD: inflammatory bowel diseases; IRGM: immunity related GTPase M; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PE: phosphatidylethanolamine; RB1CC1: RB1 inducible coiled-coil 1; SLE: systemic lupus erythematosus; WIPI2B: WD repeat domain, phosphoinositide interacting 2B.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia,CONTACT Laurence Don Wai Luu School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Nadeem O. Kaakoush
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia,Natalia Castaño-Rodríguez School of Biotechnology and Biomolecular Sciences, Faculty of Science, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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12
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Salavaty A, Shehni SA, Ramialison M, Currie PD. Systematic molecular profiling of acute leukemia cancer stem cells allows identification of druggable targets. Heliyon 2022; 8:e11093. [PMID: 36281397 PMCID: PMC9586918 DOI: 10.1016/j.heliyon.2022.e11093] [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: 08/23/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia (AML) is one of the most prevalent and acute blood cancers with a poor prognosis and low overall survival rate, especially in the elderly. Although several new AML markers and drug targets have been recently identified, the rate of long-term cancer eradication has not improved significantly due to the presence and drug resistance of AML cancer stem cells (CSCs). Here we develop a novel computational pipeline to analyze the transcriptomic profiles of AML cancer (stem) cells and identify novel candidate AML CSC markers and drug targets. In our novel pipeline we apply a top-down meta-analysis strategy to integrate The Cancer Genome Atlas data with CSC datasets to infer cell stemness features. As a result, a set of genes termed the "AML key CSC genes" along with all the available drugs/compounds that could target them were identified. Overall, our novel computational pipeline could retrieve known cancer drugs (Carfilzomib) and predicted novel drugs such as Zonisamide, Amitriptyline, and their targets amongst the top ranked drugs and drug targets for targeting AML. Additionally, the pipeline applied in this study could be used for the identification of CSC-specific markers, drivers and their respective targeting drugs in other cancer types.
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Affiliation(s)
- Adrian Salavaty
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
| | - Sara Alaei Shehni
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- Systems Biology Institute Australia, Monash University, Clayton, VIC 3800, Australia
- Novo Nordisk Foundation Center for Stem Cell Medicine, Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, VIC, 3052, Australia
- Department of Pediatrics, The Royal Children's Hospital, University of Melbourne Parkville, VIC, 3052, Australia
| | - Peter D. Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
- EMBL Australia, Monash University, Clayton, VIC 3800, Australia
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13
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Starskaia I, Laajala E, Grönroos T, Härkönen T, Junttila S, Kattelus R, Kallionpää H, Laiho A, Suni V, Tillmann V, Lund R, Elo LL, Lähdesmäki H, Knip M, Kalim UU, Lahesmaa R. Early DNA methylation changes in children developing beta cell autoimmunity at a young age. Diabetologia 2022; 65:844-860. [PMID: 35142878 PMCID: PMC8960578 DOI: 10.1007/s00125-022-05657-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022]
Abstract
AIMS/HYPOTHESIS Type 1 diabetes is a chronic autoimmune disease of complex aetiology, including a potential role for epigenetic regulation. Previous epigenomic studies focused mainly on clinically diagnosed individuals. The aim of the study was to assess early DNA methylation changes associated with type 1 diabetes already before the diagnosis or even before the appearance of autoantibodies. METHODS Reduced representation bisulphite sequencing (RRBS) was applied to study DNA methylation in purified CD4+ T cell, CD8+ T cell and CD4-CD8- cell fractions of 226 peripheral blood mononuclear cell samples longitudinally collected from seven type 1 diabetes-specific autoantibody-positive individuals and control individuals matched for age, sex, HLA risk and place of birth. We also explored correlations between DNA methylation and gene expression using RNA sequencing data from the same samples. Technical validation of RRBS results was performed using pyrosequencing. RESULTS We identified 79, 56 and 45 differentially methylated regions in CD4+ T cells, CD8+ T cells and CD4-CD8- cell fractions, respectively, between type 1 diabetes-specific autoantibody-positive individuals and control participants. The analysis of pre-seroconversion samples identified DNA methylation signatures at the very early stage of disease, including differential methylation at the promoter of IRF5 in CD4+ T cells. Further, we validated RRBS results using pyrosequencing at the following CpG sites: chr19:18118304 in the promoter of ARRDC2; chr21:47307815 in the intron of PCBP3; and chr14:81128398 in the intergenic region near TRAF3 in CD4+ T cells. CONCLUSIONS/INTERPRETATION These preliminary results provide novel insights into cell type-specific differential epigenetic regulation of genes, which may contribute to type 1 diabetes pathogenesis at the very early stage of disease development. Should these findings be validated, they may serve as a potential signature useful for disease prediction and management.
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Affiliation(s)
- Inna Starskaia
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
| | - Essi Laajala
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Toni Grönroos
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Taina Härkönen
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sini Junttila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Roosa Kattelus
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Henna Kallionpää
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
| | - Veronika Suni
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Vallo Tillmann
- Children's Clinic of Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Riikka Lund
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Mikael Knip
- Pediatric Research Center, Children's Hospital, University of Helsinki, and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Ubaid Ullah Kalim
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
| | - Riitta Lahesmaa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
- Institute of Biomedicine, University of Turku, Turku, Finland.
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14
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Wang D, Yuan T, Liu J, Wen Z, Shen Y, Tang J, Wang Z, Wu X. ATG16L2 inhibits NLRP3 inflammasome activation through promoting ATG5‐12‐16L1 complex assembly and autophagy. Eur J Immunol 2022; 52:1321-1334. [PMID: 35426127 DOI: 10.1002/eji.202149764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/24/2022] [Accepted: 04/13/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Dongyang Wang
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Tianli Yuan
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Jiamin Liu
- Hongqiao International Institute of Medicine Shanghai Tongren Hospital/Faculty of Basic Medicine Shanghai Institute of Immunology Department of Immunology and Microbiology Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Zhoujin Wen
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Yuguang Shen
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Jian Tang
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Zheng Wang
- Department of Gastrointestinal Surgery Renji Hospital Affiliated Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
| | - Xuefeng Wu
- Hongqiao International Institute of Medicine Shanghai Tongren Hospital/Faculty of Basic Medicine Shanghai Institute of Immunology Department of Immunology and Microbiology Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education Shanghai Jiao Tong University School of Medicine Shanghai 200025 China
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15
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Marion MC, Ramos PS, Bachali P, Labonte AC, Zimmerman KD, Ainsworth HC, Heuer SE, Robl RD, Catalina MD, Kelly JA, Howard TD, Lipsky PE, Grammer AC, Langefeld CD. Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting. Genes (Basel) 2021; 12:genes12121898. [PMID: 34946847 PMCID: PMC8701117 DOI: 10.3390/genes12121898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.
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Affiliation(s)
- Miranda C. Marion
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Paula S. Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Prathyusha Bachali
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Adam C. Labonte
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Hannah C. Ainsworth
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Sarah E. Heuer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
- The Jackson Laboratory, Tufts Graduate School of Biomedical Sciences, Bar Harbor, ME 04609, USA
| | - Robert D. Robl
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Michelle D. Catalina
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Amrie C. Grammer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
- Correspondence:
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16
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Wang YF, Wei W, Tangtanatakul P, Zheng L, Lei Y, Lin Z, Qian C, Qin X, Hou F, Zhang X, Shao L, Satproedprai N, Mahasirimongkol S, Pisitkun P, Song Q, Lau YL, Zhang Y, Hirankarn N, Yang W. Multi-ancestral GWAS identifies shared and Asian-specific loci for SLE and links type III interferon signaling and lysosomal function to the disease. Arthritis Rheumatol 2021; 74:840-848. [PMID: 34783190 DOI: 10.1002/art.42021] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/21/2021] [Accepted: 11/09/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with differences in prevalence and severity among ancestral groups. This study aims to identify novel genetic components either shared or distinct between Asian and European populations. METHODS Both trans-ancestral and ancestry-specific meta-analyses of genome-wide association studies (GWAS) for SLE were performed, involving 30,604 participants of European, Chinese or Thai origin. Using public epigenomic data and expression quantitative trait loci, fine-mapping analyses were conducted to identify putative causal variants and genes for the newly identified loci. Performance of polygenic risk scores (PRS) for the Thai cohort was evaluated comparing different training data. RESULTS We identified ten novel SLE susceptibility loci, four of which were found by Asian-specific meta-analyses. A 1bp deletion upstream of IFNLR1 was found associated with SLE, with the risk allele correlated with increased expression of IFNLR1. This gene encodes interferon lambda receptor 1, pointing to the role of type III interferon signaling in SLE. An intronic variant in SLC29A3 was found associated with SLE only in Asians. The putative risk variant may modulate SLC29A3 expression in a monocyte-specific manner. SLC29A3 encodes a lysosomal nucleoside transporter, and subsequent analyses suggest reduced lysosomal function and phagocytosis might be the mechanism underlying this association. In addition, trans-ancestral meta-analysis was proved to be valuable in risk prediction for individuals without ancestry-matched data. CONCLUSION Multi-ancestral GWAS identified both shared and Asian-specific loci for SLE, and functional annotation pointed to the involvement of increased type III interferon signaling and reduced lysosomal function in SLE.
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Affiliation(s)
- Yong-Fei Wang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,Shenzhen Futian hospital for rheumatic diseases, Shenzhen, China
| | - Wei Wei
- Medical Research Center, Affiliated Hospital of Jining Medical University, Shandong, China.,Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Pattarin Tangtanatakul
- Department of Transfusion Sciences and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Lichuan Zheng
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yao Lei
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhiming Lin
- Department of Rheumatology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Chengmin Qian
- School of Biomedical Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Qin
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Fei Hou
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Shandong, China
| | - Xinyu Zhang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China.,Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Li Shao
- Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Nusara Satproedprai
- Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | | | - Prapaporn Pisitkun
- Division of Allergy, Immunology, and Rheumatology, Department of Medicine, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Qin Song
- Department of Rheumatology and Lupus Research Institute, The Affiliated Hospital of Jining Medical University, Shandong, China
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
| | - Yan Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Nattiya Hirankarn
- Centre of Excellent in Immunology and Immune-Mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong, China
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17
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Ha E, Bae SC, Kim K. Recent advances in understanding the genetic basis of systemic lupus erythematosus. Semin Immunopathol 2021; 44:29-46. [PMID: 34731289 DOI: 10.1007/s00281-021-00900-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/14/2021] [Indexed: 12/22/2022]
Abstract
Systemic lupus erythematosus (SLE) is a polygenic chronic autoimmune disease leading to multiple organ damage. A large heritability of up to 66% is estimated in SLE, with roughly 180 reported susceptibility loci that have been identified mostly by genome-wide association studies (GWASs) and account for approximately 30% of genetic heritability. A vast majority of risk variants reside in non-coding regions, which makes it quite challenging to interpret their functional implications in the SLE-affected immune system, suggesting the importance of understanding cell type-specific epigenetic regulation around SLE GWAS variants. The latest genetic studies have been highly fruitful as several dozens of SLE loci were newly discovered in the last few years and many loci have come to be understood in systemic approaches integrating GWAS signals with other biological resources. In this review, we summarize SLE-associated genetic variants in both the major histocompatibility complex (MHC) and non-MHC loci, examining polygenetic risk scores for SLE and their associations with clinical features. Finally, variant-driven pathogenetic functions underlying genetic associations are described, coupled with discussion about challenges and future directions in genetic studies on SLE.
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Affiliation(s)
- Eunji Ha
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea.,Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea. .,Hanyang University Institute for Rheumatology Research, Seoul, Republic of Korea.
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea. .,Department of Biomedical and Pharmaceutical Sciences, Kyung Hee University, Seoul, Republic of Korea.
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18
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Tayel SI, Muharram NM, Fotoh DS, Elbarbary HS, Abd-Elhafiz HI, El-Masry EA, Taha AE, Soliman SE. Prognostic Impact of Genetic Variants of MECP2 and TIRAP on Clinical Outcomes of Systemic Lupus Erythematosus with and without Nephritis. Biomolecules 2021; 11:1378. [PMID: 34572591 PMCID: PMC8466489 DOI: 10.3390/biom11091378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/11/2021] [Accepted: 09/12/2021] [Indexed: 12/16/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune illness with a growing prevalence in many populations. Few studies have examined genetic predisposition to SLE, so we aimed to examine the clinical impact of the genetic polymorphisms MECP2 rs2734647and TIRAP rs8177374 on the outcomes and therapeutic precision of SLE with and without nephritis. This study included 110 SLE patients-divided into 63 with lupus nephritis (LN), and 47 without nephritis-and 100 controls. Laboratory measurements including CRP, ESR, ACR, CBC, anti-ds-DNA, vitamin A, C3, and C4 were carried out, along with genotyping of MECP2 rs2734647and TIRAP rs8177374 by real-time PCR and sequencing. Treg %, vitamin A, C3, and C4 were lower, whereas Th17 % was higher, in patients vs. controls (p < 0.001). The T allele of MECP2 rs2734647 was higher in LN than in non-nephritis and control subjects. Moreover, the T allele of TIRAP rs8177374 was higher in LN than in non-nephritis and control subjects. The MECP2 and TIRAP genes could play a role in predisposition to SLE, and can also predict disease progress to nephritis, helping to personalize medicine.
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Affiliation(s)
- Safaa I. Tayel
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, College of Medicine, Al Baha University, Al Baha 65779, Saudi Arabia
| | - Nashwa M. Muharram
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, College of Medicine, Al Baha University, Al Baha 65779, Saudi Arabia
| | - Dina S. Fotoh
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
| | - Hany S. Elbarbary
- Renal Unit, Department of Internal Medicine, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
- Renal Unit, Department of Internal Medicine, College of Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
| | - Huda I. Abd-Elhafiz
- Clinical Pharmacology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt;
| | - Eman A. El-Masry
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia; (E.A.E.-M.); (A.E.T.)
- Medical Microbiology and Immunology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt
| | - Ahmed E. Taha
- Microbiology and Immunology Unit, Department of Pathology, College of Medicine, Jouf University, Sakaka 72388, Saudi Arabia; (E.A.E.-M.); (A.E.T.)
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Shimaa E. Soliman
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Shebin el Kom 32511, Egypt; (N.M.M.); (S.E.S.)
- Medical Biochemistry Unit, Department of Pathology, College of Medicine, Qassim University, Buraydah 51452, Saudi Arabia
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19
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McCaffrey TA, Toma I, Yang Z, Katz R, Reiner J, Mazhari R, Shah P, Tackett M, Jones D, Jepson T, Falk Z, Wargodsky R, Shtakalo D, Antonets D, Ertle J, Kim JH, Lai Y, Arslan Z, Aledort E, Alfaraidy M, Laurent GS. RNA sequencing of blood in coronary artery disease: involvement of regulatory T cell imbalance. BMC Med Genomics 2021; 14:216. [PMID: 34479557 PMCID: PMC8414682 DOI: 10.1186/s12920-021-01062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 08/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Cardiovascular disease had a global prevalence of 523 million cases and 18.6 million deaths in 2019. The current standard for diagnosing coronary artery disease (CAD) is coronary angiography. Surprisingly, despite well-established clinical indications, up to 40% of the one million invasive cardiac catheterizations return a result of ‘no blockage’. The present studies employed RNA sequencing of whole blood to identify an RNA signature in patients with angiographically confirmed CAD.
Methods Whole blood RNA was depleted of ribosomal RNA (rRNA) and analyzed by single-molecule sequencing of RNA (RNAseq) to identify transcripts associated with CAD (TRACs) in a discovery group of 96 patients presenting for elective coronary catheterization. The resulting transcript counts were compared between groups to identify differentially expressed genes (DEGs).
Results Surprisingly, 98% of DEGs/TRACs were down-regulated ~ 1.7-fold in patients with mild to severe CAD (> 20% stenosis). The TRACs were independent of comorbid risk factors for CAD, such as sex, hypertension, and smoking. Bioinformatic analysis identified an enrichment in transcripts such as FoxP1, ICOSLG, IKZF4/Eos, SMYD3, TRIM28, and TCF3/E2A that are likely markers of regulatory T cells (Treg), consistent with known reductions in Tregs in CAD. A validation cohort of 80 patients confirmed the overall pattern (92% down-regulation) and supported many of the Treg-related changes. TRACs were enriched for transcripts associated with stress granules, which sequester RNAs, and ciliary and synaptic transcripts, possibly consistent with changes in the immune synapse of developing T cells.
Conclusions These studies identify a novel mRNA signature of a Treg-like defect in CAD patients and provides a blueprint for a diagnostic test for CAD. The pattern of changes is consistent with stress-related changes in the maturation of T and Treg cells, possibly due to changes in the immune synapse. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-01062-2.
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Affiliation(s)
- Timothy A McCaffrey
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA. .,The St. Laurent Institute, Vancouver, WA, USA. .,Department of Microbiology, Immunology, and Tropical Medicine, The George Washington University, Washington, DC, 20037, USA. .,True Bearing Diagnostics, Washington, DC, 20037, USA.
| | - Ian Toma
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA.,Department of Clinical Research and Leadership, The George Washington University, Washington, DC, 20037, USA.,True Bearing Diagnostics, Washington, DC, 20037, USA
| | - Zhaoquing Yang
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Richard Katz
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Jonathan Reiner
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Ramesh Mazhari
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Palak Shah
- Inova Heart and Vascular Institute, Fairfax, VA, USA
| | | | | | - Tisha Jepson
- SeqLL, Inc., Woburn, MA, USA.,The St. Laurent Institute, Vancouver, WA, USA.,True Bearing Diagnostics, Washington, DC, 20037, USA
| | - Zachary Falk
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Richard Wargodsky
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Dmitry Shtakalo
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjeva Ave, Novosibirsk, Russia, 630090
| | - Denis Antonets
- A.P. Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjeva Ave, Novosibirsk, Russia, 630090
| | - Justin Ertle
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Ju H Kim
- Division of Cardiology, Department of Medicine, The George Washington University , Washington, DC, 20037, USA
| | - Yinglei Lai
- Department of Statistics, Biostatistics Center, The George Washington University, Washington, DC, 20037, USA
| | - Zeynep Arslan
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Emily Aledort
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
| | - Maha Alfaraidy
- Division of Genomic Medicine, Department of Medicine, The George Washington Medical Center, The George Washington University, 2300 I Street NW, Ross Hall 443A, Washington, DC, 20037, USA
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20
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Li Y, Wang A, Long F, Gao F, Gao S, Wei S, Liu A, Li X, Sun W, Li J, Liu Q. Lack of WDFY4 Aggravates Ovalbumin-Induced Asthma via Enhanced Th2 Cell Differentiation. Int Arch Allergy Immunol 2021; 182:1089-1096. [PMID: 34425575 PMCID: PMC8619739 DOI: 10.1159/000516970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Asthma is a chronic inflammatory airway disease, and Th2 cells play an important role in asthma. WDFY4 (WDFY family member 4) is a susceptibility gene in several autoimmune diseases. OBJECTIVE In this study, the roles of WDFY4 in Th2 cell differentiation and Th2-dependent asthma were investigated. METHODS Naïve CD4+ T cells were isolated from wild-type and WDFY4-deficient mice and induced to differentiate in vitro. Subsequently, a mouse model of asthma was established by sensitization with ovalbumin. RESULTS Study results showed that WDFY4 deficiency could promote the differentiation of Th2 cells and the production of Th2 cytokines. WDFY4-deficient asthmatic mice showed higher levels of Th2 cytokines in the lungs and bronchoalveolar lavage fluid than wild-type mice. Moreover, infiltration of inflammatory cells, hyperplasia of goblet cells, production of mucus, and deposition of collagen were enhanced in WDFY4-deficient asthmatic mice. CONCLUSIONS Our study demonstrates the pivotal role of WDFY4 in the pathogenesis of asthma and in Th2 cell differentiation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Medical Genetics, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
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21
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Nam SW, Lee KS, Yang JW, Ko Y, Eisenhut M, Lee KH, Shin JI, Kronbichler A. Understanding the genetics of systemic lupus erythematosus using Bayesian statistics and gene network analysis. Clin Exp Pediatr 2021; 64:208-222. [PMID: 32683804 PMCID: PMC8103040 DOI: 10.3345/cep.2020.00633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023] Open
Abstract
The publication of genetic epidemiology meta-analyses has increased rapidly, but it has been suggested that many of the statistically significant results are false positive. In addition, most such meta-analyses have been redundant, duplicate, and erroneous, leading to research waste. In addition, since most claimed candidate gene associations were false-positives, correctly interpreting the published results is important. In this review, we emphasize the importance of interpreting the results of genetic epidemiology meta-analyses using Bayesian statistics and gene network analysis, which could be applied in other diseases.
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Affiliation(s)
- Seoung Wan Nam
- Department of Rheumatology, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Kwang Seob Lee
- Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Yongin, Korea
| | - Michael Eisenhut
- Department of Pediatrics, Luton & Dunstable University Hospital NHS Foundation Trust, Luton, UK
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea.,Division of Pediatric Nephrology, Severance Children's Hospital, Seoul, Korea.,Institute of Kidney Disease Research, Yonsei University College of Medicine, Seoul, Korea
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
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22
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Sakaue S, Yamaguchi E, Inoue Y, Takahashi M, Hirata J, Suzuki K, Ito S, Arai T, Hirose M, Tanino Y, Nikaido T, Ichiwata T, Ohkouchi S, Hirano T, Takada T, Miyawaki S, Dofuku S, Maeda Y, Nii T, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Sonehara K, Tazawa R, Morimoto K, Takaki M, Konno S, Suzuki M, Tomii K, Nakagawa A, Handa T, Tanizawa K, Ishii H, Ishida M, Kato T, Takeda N, Yokomura K, Matsui T, Watanabe M, Inoue H, Imaizumi K, Goto Y, Kida H, Fujisawa T, Suda T, Yamada T, Satake Y, Ibata H, Hizawa N, Mochizuki H, Kumanogoh A, Matsuda F, Nakata K, Hirota T, Tamari M, Okada Y. Genetic determinants of risk in autoimmune pulmonary alveolar proteinosis. Nat Commun 2021; 12:1032. [PMID: 33589587 PMCID: PMC7884840 DOI: 10.1038/s41467-021-21011-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
Pulmonary alveolar proteinosis (PAP) is a devastating lung disease caused by abnormal surfactant homeostasis, with a prevalence of 6-7 cases per million population worldwide. While mutations causing hereditary PAP have been reported, the genetic basis contributing to autoimmune PAP (aPAP) has not been thoroughly investigated. Here, we conducted a genome-wide association study of aPAP in 198 patients and 395 control participants of Japanese ancestry. The common genetic variant, rs138024423 at 6p21, in the major-histocompatibility-complex (MHC) region was significantly associated with disease risk (Odds ratio [OR] = 5.2; P = 2.4 × 10-12). HLA fine-mapping revealed that the common HLA class II allele, HLA-DRB1*08:03, strongly drove this signal (OR = 4.8; P = 4.8 × 10-12), followed by an additional independent risk allele at HLA-DPβ1 amino acid position 8 (OR = 0.28; P = 3.4 × 10-7). HLA-DRB1*08:03 was also associated with an increased level of anti-GM-CSF antibody, a key driver of the disease (β = 0.32; P = 0.035). Our study demonstrated a heritable component of aPAP, suggesting an underlying genetic predisposition toward an abnormal antibody production.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
- Center for Data Sciences, Harvard Medical School, Boston, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Etsuro Yamaguchi
- Division of Respiratory Medicine and Allergology, Department of Internal Medicine, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Pharmaceutical Discovery Research Laboratories, TEIJIN PHARMA LIMITED, Hino, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Ito
- Division of Respiratory Medicine and Allergology, Department of Internal Medicine, School of Medicine, Aichi Medical University, Aichi, Japan
| | - Toru Arai
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Masaki Hirose
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Yoshinori Tanino
- Department of Pulmonary Medicine, Fukushima Medical University, Fukushima, Japan
| | - Takefumi Nikaido
- Department of Pulmonary Medicine, Fukushima Medical University, Fukushima, Japan
| | - Toshio Ichiwata
- Department Respiratory Medicine, Tokyo Medical University, Tokyo, Japan
| | - Shinya Ohkouchi
- Occupational Health, Graduate School of Medicine, Tohoku University, Miyagi, Japan
| | - Taizou Hirano
- Respiratory Medicine, School of Medicine, Tohoku University, Miyagi, Japan
| | - Toshinori Takada
- Uonuma Institute of Community Medicine, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Shogo Dofuku
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryushi Tazawa
- Student Support and Health Administration Organization, Tokyo Medical and Dental University, Tokyo, Japan
| | - Konosuke Morimoto
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Masahiro Takaki
- Department of Infectious Diseases, Nagasaki University Hospital, Nagasaki University, Nagasaki, Japan
| | - Satoshi Konno
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masaru Suzuki
- Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Keisuke Tomii
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Atsushi Nakagawa
- Department of Respiratory Medicine, Kobe City Medical Center General Hospital, Kobe, Japan
| | - Tomohiro Handa
- Department of Advanced Medicine for Respiratory Failure, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kiminobu Tanizawa
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruyuki Ishii
- Department of Respiratory Medicine, Kyorin University, Mitaka, Japan
| | - Manabu Ishida
- Department of Respiratory Medicine, Kyorin University, Mitaka, Japan
| | - Toshiyuki Kato
- Department of Respiratory Medicine and Allergology, Kariya Toyota General Hospital, Kariya, Japan
| | - Naoya Takeda
- Department of Respiratory Medicine and Allergology, Kariya Toyota General Hospital, Kariya, Japan
| | - Koshi Yokomura
- Department of Respiratory Medicine, Respiratory Disease Center, Seirei Mikatahara General Hospital, Hamamatsu, Japan
| | - Takashi Matsui
- Department of Respiratory Medicine, Respiratory Disease Center, Seirei Mikatahara General Hospital, Hamamatsu, Japan
| | - Masaki Watanabe
- Department of Pulmonary Medicine, Graduate School of Medical & Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Graduate School of Medical & Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Kazuyoshi Imaizumi
- Department of Respiratory Medicine, Fujita Health University School of Medicine, Aichi, Japan
| | - Yasuhiro Goto
- Department of Respiratory Medicine, Fujita Health University School of Medicine, Aichi, Japan
| | - Hiroshi Kida
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine, National Hospital Organization Osaka Toneyama Medical Center, Toyonaka, Japan
| | - Tomoyuki Fujisawa
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takashi Yamada
- Department of Respiratory Medicine, Shizuoka City Shizuoka Hospital, Shizuoka, Japan
| | - Yasuomi Satake
- Department of Respiratory Medicine, Shizuoka City Shizuoka Hospital, Shizuoka, Japan
| | - Hidenori Ibata
- Department of Respiratory Medicine, National Hospital Organization Mie Chuo Medical Center, Tsu, Japan
| | - Nobuyuki Hizawa
- Department of Pulmonary Medicine, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Immunopathology, World Premier International 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
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koh Nakata
- Division of Advanced Medical Development, Niigata University Medical and Dental Hospital, Niigata, Japan
| | - Tomomitsu Hirota
- Division of Molecular Genetics, the Jikei University School of Medicine, Research Center for Medical Science, Tokyo, Japan
| | - Mayumi Tamari
- Division of Molecular Genetics, the Jikei University School of Medicine, Research Center for Medical Science, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory of Statistical Immunology, World Premier International Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
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23
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Vyse TJ, Cunninghame Graham DS. Trans-Ancestral Fine-Mapping and Epigenetic Annotation as Tools to Delineate Functionally Relevant Risk Alleles at IKZF1 and IKZF3 in Systemic Lupus Erythematosus. Int J Mol Sci 2020; 21:ijms21218383. [PMID: 33182226 PMCID: PMC7664943 DOI: 10.3390/ijms21218383] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/09/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022] Open
Abstract
Background: Prioritizing tag-SNPs carried on extended risk haplotypes at susceptibility loci for common disease is a challenge. Methods: We utilized trans-ancestral exclusion mapping to reduce risk haplotypes at IKZF1 and IKZF3 identified in multiple ancestries from SLE GWAS and ImmunoChip datasets. We characterized functional annotation data across each risk haplotype from publicly available datasets including ENCODE, RoadMap Consortium, PC Hi-C data from 3D genome browser, NESDR NTR conditional eQTL database, GeneCards Genehancers and TF (transcription factor) binding sites from Haploregv4. Results: We refined the 60 kb associated haplotype upstream of IKZF1 to just 12 tag-SNPs tagging a 47.7 kb core risk haplotype. There was preferential enrichment of DNAse I hypersensitivity and H3K27ac modification across the 3′ end of the risk haplotype, with four tag-SNPs sharing allele-specific TF binding sites with promoter variants, which are eQTLs for IKZF1 in whole blood. At IKZF3, we refined a core risk haplotype of 101 kb (27 tag-SNPs) from an initial extended haplotype of 194 kb (282 tag-SNPs), which had widespread DNAse I hypersensitivity, H3K27ac modification and multiple allele-specific TF binding sites. Dimerization of Fox family TFs bound at the 3′ and promoter of IKZF3 may stabilize chromatin looping across the locus. Conclusions: We combined trans-ancestral exclusion mapping and epigenetic annotation to identify variants at both IKZF1 and IKZF3 with the highest likelihood of biological relevance. The approach will be of strong interest to other complex trait geneticists seeking to attribute biological relevance to risk alleles on extended risk haplotypes in their disease of interest.
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24
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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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25
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Roberts AD, Davenport TM, Dickey AM, Ahn R, Sochacki KA, Taraska JW. Structurally distinct endocytic pathways for B cell receptors in B lymphocytes. Mol Biol Cell 2020; 31:2826-2840. [PMID: 33085561 PMCID: PMC7851864 DOI: 10.1091/mbc.e20-08-0532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
B lymphocytes play a critical role in adaptive immunity. On antigen binding, B cell receptors (BCR) cluster on the plasma membrane and are internalized by endocytosis. In this process, B cells capture diverse antigens in various contexts and concentrations. However, it is unclear whether the mechanism of BCR endocytosis changes in response to these factors. Here, we studied the mechanism of soluble antigen-induced BCR clustering and internalization in a cultured human B cell line using correlative superresolution fluorescence and platinum replica electron microscopy. First, by visualizing nanoscale BCR clusters, we provide direct evidence that BCR cluster size increases with F(ab’)2 concentration. Next, we show that the physical mechanism of internalization switches in response to BCR cluster size. At low concentrations of antigen, B cells internalize small BCR clusters by classical clathrin-mediated endocytosis. At high antigen concentrations, when cluster size increases beyond the size of a single clathrin-coated pit, B cells retrieve receptor clusters using large invaginations of the plasma membrane capped with clathrin. At these sites, we observed early and sustained recruitment of actin and an actin polymerizing protein FCHSD2. We further show that actin recruitment is required for the efficient generation of these novel endocytic carriers and for their capture into the cytosol. We propose that in B cells, the mechanism of endocytosis switches to accommodate large receptor clusters formed when cells encounter high concentrations of soluble antigen. This mechanism is regulated by the organization and dynamics of the cortical actin cytoskeleton.
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Affiliation(s)
- Aleah D Roberts
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Thaddeus M Davenport
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Andrea M Dickey
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Regina Ahn
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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26
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In Vivo Remodeling of Altered Autophagy-Lysosomal Pathway by a Phosphopeptide in Lupus. Cells 2020; 9:cells9102328. [PMID: 33092174 PMCID: PMC7589999 DOI: 10.3390/cells9102328] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 09/30/2020] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
The phosphopeptide P140/Lupuzor, which improves the course of lupus disease in mice and patients, targets chaperone-mediated autophagy (CMA), a selective form of autophagy that is abnormally upregulated in lupus-prone MRL/lpr mice. Administered intravenously to diseased mice, P140 reduces the expression level of two major protein players of CMA, LAMP2A and HSPA8, and inhibits CMA in vitro in a cell line that stably expresses a CMA reporter. Here, we aimed to demonstrate that P140 also affects CMA in vivo and to unravel the precise cellular mechanism of how P140 interacts with the CMA process. MRL/lpr mice and CBA/J mice used as control received P140 or control peptides intravenously. Lysosome-enriched fractions of spleen or liver were prepared to examine lysosomal function. Highly purified lysosomes were further isolated and left to incubate with the CMA substrate to study at which cellular step P140 interacts with the CMA process. The data show that P140 effectively regulates CMA in vivo in MRL/lpr mice at the step of substrate lysosomal uptake and restores some alterations of defective lysosomes. For the first time, it is demonstrated that by occluding the intralysosome uptake of CMA substrates, a therapeutic molecule can attenuate excessive CMA activity in a pathological pro-inflammatory context and protect against hyperinflammation. This recovery effect of P140 on hyperactivated CMA is not only important for lupus therapy but potentially also for treating other (auto)inflammatory diseases, including neurologic and metabolic disorders, where CMA modulation would be highly beneficial.
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27
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Analysis of clinical and laboratory characteristics and pathology of lupus nephritis-based on 710 renal biopsies in China. Clin Rheumatol 2020; 39:3353-3363. [PMID: 32435895 DOI: 10.1007/s10067-020-05115-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 04/04/2020] [Accepted: 04/16/2020] [Indexed: 10/24/2022]
Abstract
OBJECTIVES This study aimed to analyse the clinical and laboratory characteristics of different pathologic classifications of lupus nephritis (LN) patients in terms of age at systemic lupus erythematosus (SLE) diagnosis and nephritis onset. METHOD Clinical, laboratory, and pathological data of 710 LN patients diagnosed by renal biopsy at our institution between 2000 and 2018 were retrospectively analysed. Patients were divided into the different pathological classification groups; childhood-, adult- and elderly-onset SLE groups and early- and late-onset LN groups. RESULTS Class IV occurred most frequently and had the lowest complement C3 level. There was an obvious increase in active index in class IV and class V + IV. Patients with class VI showed some clinical characteristics similar to end-stage renal disease. Patients with proliferative nephritis were younger at SLE diagnosis and had higher blood pressure, higher frequency of proteinuria and urinary erythrocyte and lower haemoglobin and complement C3. Pathologic classification between childhood-, adult- and elderly-onset SLE patients or between early- and late-onset LN patients was not significantly different. Elderly-onset SLE patients had the highest chronic index (CI), IgA, IgG and Sjögren's syndrome A antibodies and Sjögren's syndrome B antibodies rates, whereas late-onset LN patients showed significantly higher CI, haemoglobin, complement C3 and C4 but lower uric acid, IgM and IgG. CONCLUSIONS LN patients present with different clinical and laboratory characteristics according to pathological classification, age at SLE diagnosis and nephritis onset. These results might be valuable for estimating the pathology and guiding treatment and prognosis. Key Points • Patients with proliferative nephritis have more severe immune disorders, worse renal function and stronger inflammatory state. • The elderly-onset SLE patients showed a poorer condition. • The late-onset LN patients might have a more stable status.
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28
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Wen L, Liu L, Shen X, Li H, Zhu Z, Huang H, Cai M, Qian D, Shen S, Qiu Y, Cui Y, Sheng Y. The association of the UHRF1BP1 gene with systemic lupus erythematosus was replicated in a Han Chinese population from mainland China. Ann Hum Genet 2020; 84:221-228. [PMID: 31691269 DOI: 10.1111/ahg.12362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 08/15/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) in the UHRF gene have been shown to be associated with systemic lupus erythematosus (SLE) in European and Hong Kong Chinese, but statistically significant evidence for association has not been found in a mainland Han Chinese population. Therefore, we selected SNP rs13205210 located in UHRF1BP1 as a candidate association from our previously published genome-wide association study (GWAS) data of SLE (1,047 cases and 1,205 controls from a mainland Han Chinese population) to explore the association between the UHRF1BP1 gene and SLE. We conducted a large-scale replication study in an additional independent sample of 3,509 cases and 8,246 controls from a mainland Han Chinese population. Real-time PCR was used to determine gene expression differences in peripheral blood mononuclear cells (PBMCs) from cases and controls. As a result, we replicated the association between the UHRF1BP1 gene and SLE (rs13205210, missense, Pmeta = 2.26E-17, odds ratio = 1.41) by a meta-analysis of our previous GWAS and this replication study involving a total of 4,556 cases and 9,451 controls. The UHRF1BP1 mRNA expression level in PBMCs was significantly decreased in patients with SLE compared with that in healthy controls. SNP rs13205210 exhibited an expression quantitative trait loci effect on the UHRF1BP1 gene in PBMCs from patients. In conclusion, this study not only suggests that the UHRF1BP1 gene was associated with SLE in a mainland Han Chinese population, but also implied that it might be a common genetic factor contributing to SLE susceptibility in multiple populations.
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Affiliation(s)
- Leilei Wen
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Lu Liu
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Xue Shen
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Hui Li
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Zhengwei Zhu
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - He Huang
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Minglong Cai
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Danfeng Qian
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Songke Shen
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
| | - Ying Qiu
- Department of Dermatology, Jining No. 1 People's Hospital, Shandong, China
| | - Yong Cui
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Department of Dermatology, China-Japan Friendship Hospital, Chaoyang District, Beijing, China
| | - Yujun Sheng
- Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
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29
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McCartney DL, Zhang F, Hillary RF, Zhang Q, Stevenson AJ, Walker RM, Bermingham ML, Boutin T, Morris SW, Campbell A, Murray AD, Whalley HC, Porteous DJ, Hayward C, Evans KL, Chandra T, Deary IJ, McIntosh AM, Yang J, Visscher PM, McRae AF, Marioni RE. An epigenome-wide association study of sex-specific chronological ageing. Genome Med 2019; 12:1. [PMID: 31892350 PMCID: PMC6938636 DOI: 10.1186/s13073-019-0693-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/15/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Advanced age is associated with cognitive and physical decline and is a major risk factor for a multitude of disorders. There is also a gap in life expectancy between males and females. DNA methylation differences have been shown to be associated with both age and sex. Here, we investigate age-by-sex differences in blood-based DNA methylation in an unrelated cohort of 2586 individuals between the ages of 18 and 87 years, with replication in a further 4450 individuals between the ages of 18 and 93 years. METHODS Linear regression models were applied, with stringent genome-wide significance thresholds (p < 3.6 × 10-8) used in both the discovery and replication data. A second, highly conservative mixed linear model method that better controls the false-positive rate was also applied, using the same genome-wide significance thresholds. RESULTS Using the linear regression method, 52 autosomal and 597 X-linked CpG sites, mapping to 251 unique genes, replicated with concordant effect size directions in the age-by-sex interaction analysis. The site with the greatest difference mapped to GAGE10, an X-linked gene. Here, DNA methylation levels remained stable across the male adult age range (DNA methylation by age r = 0.02) but decreased across female adult age range (DNA methylation by age r = - 0.61). One site (cg23722529) with a significant age-by-sex interaction also had a quantitative trait locus (rs17321482) that is a genome-wide significant variant for prostate cancer. The mixed linear model method identified 11 CpG sites associated with the age-by-sex interaction. CONCLUSION The majority of differences in age-associated DNA methylation trajectories between sexes are present on the X chromosome. Several of these differences occur within genes that have been implicated in sexually dimorphic traits.
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Affiliation(s)
- Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Futao Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Mairead L Bermingham
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Thibaud Boutin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Stewart W Morris
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, Scotland, UK
| | - Heather C Whalley
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, Scotland, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Tamir Chandra
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
- Department of Psychology, University of Edinburgh, Edinburgh, Scotland, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK
- Division of Psychiatry, Royal Edinburgh Hospital, University of Edinburgh, Edinburgh, Scotland, UK
| | - Jian Yang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Institute for Advanced Research, Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, Scotland, UK.
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30
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Abstract
Lysosomes are membrane-bound organelles with roles in processes involved in degrading and recycling cellular waste, cellular signalling and energy metabolism. Defects in genes encoding lysosomal proteins cause lysosomal storage disorders, in which enzyme replacement therapy has proved successful. Growing evidence also implicates roles for lysosomal dysfunction in more common diseases including inflammatory and autoimmune disorders, neurodegenerative diseases, cancer and metabolic disorders. With a focus on lysosomal dysfunction in autoimmune disorders and neurodegenerative diseases - including lupus, rheumatoid arthritis, multiple sclerosis, Alzheimer disease and Parkinson disease - this Review critically analyses progress and opportunities for therapeutically targeting lysosomal proteins and processes, particularly with small molecules and peptide drugs.
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Affiliation(s)
- Srinivasa Reddy Bonam
- CNRS-University of Strasbourg, Biotechnology and Cell Signalling, Illkirch, France
- Laboratory of Excellence Medalis, Team Neuroimmunology and Peptide Therapy, Institut de Science et d'Ingénierie Supramoléculaire (ISIS), Strasbourg, France
| | - Fengjuan Wang
- CNRS-University of Strasbourg, Biotechnology and Cell Signalling, Illkirch, France
- Laboratory of Excellence Medalis, Team Neuroimmunology and Peptide Therapy, Institut de Science et d'Ingénierie Supramoléculaire (ISIS), Strasbourg, France
| | - Sylviane Muller
- CNRS-University of Strasbourg, Biotechnology and Cell Signalling, Illkirch, France.
- Laboratory of Excellence Medalis, Team Neuroimmunology and Peptide Therapy, Institut de Science et d'Ingénierie Supramoléculaire (ISIS), Strasbourg, France.
- University of Strasbourg Institute for Advanced Study, Strasbourg, France.
- Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg University, Strasbourg, France.
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Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ. Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 203:1820-1829. [PMID: 31451676 PMCID: PMC6761021 DOI: 10.4049/jimmunol.1800419] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/30/2019] [Indexed: 12/19/2022]
Abstract
The clear role of autophagy in human inflammatory diseases such as Crohn disease was first identified by genome-wide association studies and subsequently dissected in multiple mechanistic studies. ATG16L1 has been particularly well studied in knockout and hypomorph settings as well as models recapitulating the Crohn disease-associated T300A polymorphism. Interestingly, ATG16L1 has a single homolog, ATG16L2, which is independently implicated in diseases, including Crohn disease and systemic lupus erythematosus. However, the contribution of ATG16L2 to canonical autophagy pathways and other cellular functions is poorly understood. To better understand its role, we generated and analyzed the first, to our knowledge, ATG16L2 knockout mouse. Our results show that ATG16L1 and ATG16L2 contribute very distinctly to autophagy and cellular ontogeny in myeloid, lymphoid, and epithelial lineages. Dysregulation of any of these lineages could contribute to complex diseases like Crohn disease and systemic lupus erythematosus, highlighting the value of examining cell-specific effects. We also identify a novel genetic interaction between ATG16L2 and epithelial ATG16L1. These findings are discussed in the context of how these genes may contribute distinctly to human disease.
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Affiliation(s)
- Bernard Khor
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and.,Pathology Service, Massachusetts General Hospital, Boston, MA 02114
| | - Kara L Conway
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Abdifatah S Omar
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Moshe Biton
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Adam L Haber
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Noga Rogel
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Leigh A Baxt
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Jakob Begun
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Petric Kuballa
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - John D Gagnon
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Kara G Lassen
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Aviv Regev
- The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114; .,Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114.,The Broad Institute of Massachusetts Institute of Technology and Harvard, 7 Cambridge Center, Cambridge, MA 02142; and
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32
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Kwon YC, Chun S, Kim K, Mak A. Update on the Genetics of Systemic Lupus Erythematosus: Genome-Wide Association Studies and Beyond. Cells 2019; 8:cells8101180. [PMID: 31575058 PMCID: PMC6829439 DOI: 10.3390/cells8101180] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 12/11/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of complex etiology that primarily affects women of childbearing age. The development of SLE is attributed to the breach of immunological tolerance and the interaction between SLE-susceptibility genes and various environmental factors, resulting in the production of pathogenic autoantibodies. Working in concert with the innate and adaptive arms of the immune system, lupus-related autoantibodies mediate immune-complex deposition in various tissues and organs, leading to acute and chronic inflammation and consequent end-organ damage. Over the past two decades or so, the impact of genetic susceptibility on the development of SLE has been well demonstrated in a number of large-scale genetic association studies which have uncovered a large fraction of genetic heritability of SLE by recognizing about a hundred SLE-susceptibility loci. Integration of genetic variant data with various omics data such as transcriptomic and epigenomic data potentially provides a unique opportunity to further understand the roles of SLE risk variants in regulating the molecular phenotypes by various disease-relevant cell types and in shaping the immune systems with high inter-individual variances in disease susceptibility. In this review, the catalogue of SLE susceptibility loci will be updated, and biological signatures implicated by the SLE-risk variants will be critically discussed. It is optimistically hoped that identification of SLE risk variants will enable the prognostic and therapeutic biomarker armamentarium of SLE to be strengthened, a major leap towards precision medicine in the management of the condition.
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Affiliation(s)
- Young-Chang Kwon
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, 222–1 Wangsimni-ro, Seongdong-gu, Seoul 04763, Korea;
| | - Sehwan Chun
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
| | - Anselm Mak
- Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore 119228, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (K.K.); (A.M.); Tel.: +82-29610604 (K.K.); +65-82338216 (A.M.)
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33
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Zhang R, Pan B, Li Y, Li X. SNP rs4937333 in the miRNA-5003-Binding Site of the ETS1 3'-UTR Decreases ETS1 Expression. Front Genet 2019; 10:581. [PMID: 31275358 PMCID: PMC6593064 DOI: 10.3389/fgene.2019.00581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/04/2019] [Indexed: 12/13/2022] Open
Abstract
Mutations in and reduced expression of the ETS1 gene may be associated with systemic lupus erythematosus (SLE). Here, we report a replication study to investigate associations of eight ETS1 single-nucleotide polymorphisms in the 3′-untranslated region (3′-UTR) with SLE and their regulation of ETS1 expression in a study population. We found that the rs4937333 T allele was associated with a significantly increased risk of SLE (odds ratio: 1.800, 95% confidence interval: 1.02–3.157, P = 0.040) and with dramatically reduced levels of ETS1 in B cells from SLE subjects. Functionally, the rs4937333 T allele alters the binding affinity between miR-5003 and its ETS1 3′-UTR target, thus enhancing suppression of ETS1 expression. Furthermore, immunoglobulin M-secreting plasmacytes were significantly reduced among B cells with the rs4937333 C allele versus the T allele according to FACS and ELISA. Additionally, miR-5003 expression was higher in B cells than in T cells from SLE patients, and a negative correlation between miR-5003 and ETS1 was found, especially in B cells with the T allele. These findings suggest that the rs4937333 T allele is a risk factor for susceptibility to SLE in the studied population. The rs4937333 T allele may enhance the binding of miR-5003 to ETS1, which probably promotes the involvement of ETS1 in the differentiation of B cells into plasmacytes.
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Affiliation(s)
- Ruixian Zhang
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China.,Yunnan Center for Disease Control and Prevention, Kunming, China
| | - Bangpin Pan
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yi Li
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolan Li
- Department of Dermatology, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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34
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Molineros JE, Looger LL, Kim K, Okada Y, Terao C, Sun C, Zhou XJ, Raj P, Kochi Y, Suzuki A, Akizuki S, Nakabo S, Bang SY, Lee HS, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Zuo X, Yamamoto K, Li QZ, Shen N, Porter LL, Harley JB, Chua KH, Zhang H, Wakeland EK, Tsao BP, Bae SC, Nath SK. Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians. PLoS Genet 2019; 15:e1008092. [PMID: 31022184 PMCID: PMC6504188 DOI: 10.1371/journal.pgen.1008092] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/07/2019] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology. The Human leukocyte antigen (HLA) region is a key genetic factor conferring risk of systemic lupus erythematosus (SLE). In spite of multiple SLE association signals identified in the HLA region, only amino-acid residues within HLA-DRB1 have been specifically described previously. In this study, we performed an imputation-based analysis on individuals with East Asian ancestry, and characterized SLE risk within the HLA region for all involved independent genes (HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-A, and HLA-B). Furthermore, we identified a characteristic SLE risk residue signature as well as a pattern of specific nRNP and Ro/La autoantibody residues located in the peptide-binding grooves, suggesting their key involvement in autoantibody production.
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Affiliation(s)
- Julio E. Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Chikashi Terao
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuichiro Nakabo
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Mo Kang
- School of Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University Hospital, Suwon, Korea
| | - Won Tae Chung
- Dong-A University Hospital, Department of Internal Medicine, Busan, Korea
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Seung-Cheol Shim
- Daejeon Rheumatoid & Degenerative Arthritis Center, Chungnam National University Hospital, Daejeon, Korea
| | - Shin-Seok Lee
- Department of Rheumatology, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nan Shen
- Department of Rheumatology and Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lauren L. Porter
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Betty P. Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- * E-mail: (SCB); (SKN)
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail: (SCB); (SKN)
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Caberlotto L, Nguyen TP, Lauria M, Priami C, Rimondini R, Maioli S, Cedazo-Minguez A, Sita G, Morroni F, Corsi M, Carboni L. Cross-disease analysis of Alzheimer's disease and type-2 Diabetes highlights the role of autophagy in the pathophysiology of two highly comorbid diseases. Sci Rep 2019; 9:3965. [PMID: 30850634 PMCID: PMC6408545 DOI: 10.1038/s41598-019-39828-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/29/2019] [Indexed: 12/24/2022] Open
Abstract
Evidence is accumulating that the main chronic diseases of aging Alzheimer's disease (AD) and type-2 diabetes mellitus (T2DM) share common pathophysiological mechanisms. This study aimed at applying systems biology approaches to increase the knowledge of the shared molecular pathways underpinnings of AD and T2DM. We analysed transcriptomic data of post-mortem AD and T2DM human brains to obtain disease signatures of AD and T2DM and combined them with protein-protein interaction information to construct two disease-specific networks. The overlapping AD/T2DM network proteins were then used to extract the most representative Gene Ontology biological process terms. The expression of genes identified as relevant was studied in two AD models, 3xTg-AD and ApoE3/ApoE4 targeted replacement mice. The present transcriptomic data analysis revealed a principal role for autophagy in the molecular basis of both AD and T2DM. Our experimental validation in mouse AD models confirmed the role of autophagy-related genes. Among modulated genes, Cyclin-Dependent Kinase Inhibitor 1B, Autophagy Related 16-Like 2, and insulin were highlighted. In conclusion, the present investigation revealed autophagy as the central dys-regulated pathway in highly co-morbid diseases such as AD and T2DM allowing the identification of specific genes potentially involved in disease pathophysiology which could become novel targets for therapeutic intervention.
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Affiliation(s)
- Laura Caberlotto
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Rovereto, Italy.
- Aptuit an Evotec company Drug Design and Discovery, Verona, Italy.
| | - T-Phuong Nguyen
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Rovereto, Italy
- Life Sciences Research Unit, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Megeno S.A.6A, avenue des Hauts-FourneauxL-4362 Esch-sur-Alzette, Esch-sur-Alzette, Luxembourg
| | - Mario Lauria
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Rovereto, Italy
- Department of Mathematics, University of Trento, Povo, Trento, Italy
| | - Corrado Priami
- The Microsoft Research, University of Trento Centre for Computational Systems Biology (COSBI), Rovereto, Italy
| | - Roberto Rimondini
- Department of Medical and Surgical Science, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Silvia Maioli
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Angel Cedazo-Minguez
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, Stockholm, Sweden
| | - Giulia Sita
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Fabiana Morroni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Mauro Corsi
- Aptuit, an Evotec company, Drug Design and Discovery, Verona, Italy
| | - Lucia Carboni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Bologna, Italy
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36
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Martínez-Bueno M, Alarcón-Riquelme ME. Exploring Impact of Rare Variation in Systemic Lupus Erythematosus by a Genome Wide Imputation Approach. Front Immunol 2019; 10:258. [PMID: 30863397 PMCID: PMC6399402 DOI: 10.3389/fimmu.2019.00258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/29/2019] [Indexed: 01/31/2023] Open
Abstract
The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. Genome-wide association studies are therefore, underpowered to detect rare variation. We have used a combined approach of genome-wide-based imputation with a highly stringent sequence kernel association (SKAT) test and a case-control burden test. We identified 98 candidate genes containing rare variation that in aggregate show association with SLE many of which have recognized immunological function, but also function and expression related to relevant tissues such as the joints, skin, blood or central nervous system. In addition we also find that there is a significant enrichment of genes annotated for disease-causing mutations in the OMIM database, suggesting that in complex diseases such as SLE, such mutations may be involved in subtle or combined phenotypes or could accelerate specific organ abnormalities found in the disease. We here provide an important resource of candidate genes for SLE.
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Affiliation(s)
- Manuel Martínez-Bueno
- Department of Medical Genomics, GENYO, Center for Genomics and Oncological Research Pfizer, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- Unit of Chronic Inflammation, Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
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37
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Belbasis L, Dosis V, Evangelou E. Elucidating the environmental risk factors for rheumatic diseases: An umbrella review of meta-analyses. Int J Rheum Dis 2018; 21:1514-1524. [PMID: 30146746 DOI: 10.1111/1756-185x.13356] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022]
Abstract
AIMS Although rheumatic diseases constitute a leading cause of disability, the environmental risk factors for these diseases are not clarified. In the present study, we aim to systematically appraise the epidemiological credibility of the environmental risk factors for rheumatic diseases. METHODS We systematically searched PubMed to capture meta-analyses of observational studies on environmental risk factors for the most prevalent rheumatic diseases. For each association, we estimated the summary effect size estimate, the 95% confidence and prediction intervals, and the I2 metric. We further examined the presence of small-study effects and excess significance bias. RESULTS Overall, we identified 30 eligible papers describing 42 associations. Thirty-three associations were statistically significant at P < 0.05, whereas 13 of them were statistically significant at P < 1 × 10-6 . Thirty-two associations had large or very large between-study heterogeneity. In 12 associations, evidence of small-study effects and/or excess significance bias was found. Six risk factors (nine associations) presented convincing or highly suggestive evidence of association: smoking and pack-years of smoking for rheumatoid arthritis; BMI (per 5 kg/m2 increase) for gout and hip osteoarthritis; alcohol consumption for gout; BMI (overweight vs lean, obese vs lean), knee injury and participation in heavy work for knee osteoarthritis. CONCLUSION Our umbrella review indicated that a narrow range of risk factors has been examined for rheumatic diseases. Current evidence strongly supports that smoking, obesity, alcohol consumption, knee injury, and work activities are associated with risk for at least one rheumatic disease.
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Affiliation(s)
- Lazaros Belbasis
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Vasilios Dosis
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, Greece.,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
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38
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Joo YB, Lim J, Tsao BP, Nath SK, Kim K, Bae SC. Genetic variants in systemic lupus erythematosus susceptibility loci, XKR6 and GLT1D1 are associated with childhood-onset SLE in a Korean cohort. Sci Rep 2018; 8:9962. [PMID: 29967481 PMCID: PMC6028392 DOI: 10.1038/s41598-018-28128-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/15/2018] [Indexed: 12/21/2022] Open
Abstract
Impact of genetic variants on the age of systemic lupus erythematosus (SLE) onset was not fully understood. We investigated a cumulative effect of SLE-risk variants on the age of SLE onset and scanned genome-wide SNPs to search for new risk loci of childhood-onset SLE (cSLE). We analyzed 781 Korean single-center SLE subjects who previously genotyped by both Immunochip and genome-wide SNP arrays. Individual genetic risk scores (GRS) from well-validated SLE susceptibility loci were calculated and tested for their association with cSLE (<16 years at onset). Single-variant association tests were performed using a multivariable logistic regression adjusting for population stratification. GRS from SLE susceptibility loci was significantly higher in cSLE than aSLE (p = 1.23 × 10−3). Two SNPs, rs7460469 in XKR6 (p = 1.26 × 10−8, OR = 5.58) and rs7300146 in GLT1D1 p = 1.49 × 10−8, OR = 2.85), showed the most significant associations with cSLE. The model consisting of GRS of SLE and two newly identified loci showed an area under curve (AUC) of 0.71 in a receiver operating characteristics (ROC) curve for prediction of cSLE. In conclusion, cSLE is associated with a high cumulative SLE-risk effect and two novel SNPs rs7460469 and rs7300146, providing the first predictive model for cSLE in Koreans.
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Affiliation(s)
- Young Bin Joo
- Department of Rheumatology, St. Vincent's Hospital, The Catholic University of Korea, Suwon, Republic of Korea
| | - Jiwoo Lim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Betty P Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea.
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39
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Patel ZH, Lu X, Miller D, Forney CR, Lee J, Lynch A, Schroeder C, Parks L, Magnusen AF, Chen X, Pujato M, Maddox A, Zoller EE, Namjou B, Brunner HI, Henrickson M, Huggins JL, Williams AH, Ziegler JT, Comeau ME, Marion MC, Glenn SB, Adler A, Shen N, Nath SK, Stevens AM, Freedman BI, Pons-Estel BA, Tsao BP, Jacob CO, Kamen DL, Brown EE, Gilkeson GS, Alarcón GS, Martin J, Reveille JD, Anaya JM, James JA, Sivils KL, Criswell LA, Vilá LM, Petri M, Scofield RH, Kimberly RP, Edberg JC, Ramsey-Goldman R, Bang SY, Lee HS, Bae SC, Boackle SA, Cunninghame Graham D, Vyse TJ, Merrill JT, Niewold TB, Ainsworth HC, Silverman ED, Weisman MH, Wallace DJ, Raj P, Guthridge JM, Gaffney PM, Kelly JA, Alarcón-Riquelme ME, Langefeld CD, Wakeland EK, Kaufman KM, Weirauch MT, Harley JB, Kottyan LC. A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Hum Mol Genet 2018; 27:2392-2404. [PMID: 29912393 PMCID: PMC6005081 DOI: 10.1093/hmg/ddy140] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 03/21/2018] [Accepted: 04/13/2018] [Indexed: 01/01/2023] Open
Abstract
Systemic lupus erythematosus (SLE or lupus) (OMIM: 152700) is a chronic autoimmune disease with debilitating inflammation that affects multiple organ systems. The STAT1-STAT4 locus is one of the first and most highly replicated genetic loci associated with lupus risk. We performed a fine-mapping study to identify plausible causal variants within the STAT1-STAT4 locus associated with increased lupus disease risk. Using complementary frequentist and Bayesian approaches in trans-ancestral Discovery and Replication cohorts, we found one variant whose association with lupus risk is supported across ancestries in both the Discovery and Replication cohorts: rs11889341. In B cell lines from patients with lupus and healthy controls, the lupus risk allele of rs11889341 was associated with increased STAT1 expression. We demonstrated that the transcription factor HMGA1, a member of the HMG transcription factor family with an AT-hook DNA-binding domain, has enriched binding to the risk allele compared with the non-risk allele of rs11889341. We identified a genotype-dependent repressive element in the DNA within the intron of STAT4 surrounding rs11889341. Consistent with expression quantitative trait locus (eQTL) analysis, the lupus risk allele of rs11889341 decreased the activity of this putative repressor. Altogether, we present a plausible molecular mechanism for increased lupus risk at the STAT1-STAT4 locus in which the risk allele of rs11889341, the most probable causal variant, leads to elevated STAT1 expression in B cells due to decreased repressor activity mediated by increased binding of HMGA1.
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Affiliation(s)
- Zubin H Patel
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical Scientist Training Program, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaoming Lu
- Immunology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Daniel Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Carmy R Forney
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Joshua Lee
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Arthur Lynch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Connor Schroeder
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lois Parks
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Albert F Magnusen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Mario Pujato
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Avery Maddox
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erin E Zoller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Hermine I Brunner
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael Henrickson
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jennifer L Huggins
- Division of Rheumatology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Adrienne H Williams
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Julie T Ziegler
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Mary E Comeau
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Miranda C Marion
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Stuart B Glenn
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Adam Adler
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Nan Shen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, P.R. China
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Anne M Stevens
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Barry I Freedman
- Section on Nephrology, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | | | - Betty P Tsao
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Chaim O Jacob
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Diane L Kamen
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Elizabeth E Brown
- Division of Molecular and Cellular Pathology, Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gary S Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Graciela S Alarcón
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada 18001-18016, Spain
| | - John D Reveille
- Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), Universidad del Rosario, Bogota 111711, Colombia
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Kathy L Sivils
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Lindsey A Criswell
- Department of Medicine, Rosalind Russell/Ephraim P Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, CA 94143-0500, USA
| | - Luis M Vilá
- Division of Rheumatology, Department of Medicine, University of Puerto Rico Medical Sciences Campus, San Juan, PR 00936, USA
| | - Michelle Petri
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - R Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- United States Department of Veterans Affairs Medical Center, Oklahoma City, OK 73104, USA
| | - Robert P Kimberly
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jeffrey C Edberg
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Rosalind Ramsey-Goldman
- Division of Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul 04763, Korea
| | - Susan A Boackle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Deborah Cunninghame Graham
- Divisions of Genetics/Molecular Medicine and Immunology, King’s College London, Guy’s Hospital, London SE1 9RT, UK
| | - Timothy J Vyse
- Divisions of Genetics/Molecular Medicine and Immunology, King’s College London, Guy’s Hospital, London SE1 9RT, UK
| | - Joan T Merrill
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
| | - Timothy B Niewold
- Division of Rheumatology, Department of Pathology, New York University, New York, NY 10016, USA
| | - Hannah C Ainsworth
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Earl D Silverman
- Division of Rheumatology, The Hospital for Sick Children, Hospital for Sick Research Institute, University of Toronto, Toronto, ON M5G 1X8, Canada
| | - Michael H Weisman
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Daniel J Wallace
- Division of Rheumatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, United States of America
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Marta E Alarcón-Riquelme
- Unit of Chronic Inflammatory Diseases, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 17167, Sweden
- Center for Genomics and Oncological Research, Pfizer-University of Granada-Junta de Andalucia, Parque Tecnológica de la Salud, Granada 18016, Spain
| | - Carl D Langefeld
- Center for Public Health Genomics and the Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- United States Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- United States Department of Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
| | - Leah C Kottyan
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45220, USA
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IRF5 is elevated in childhood-onset SLE and regulated by histone acetyltransferase and histone deacetylase inhibitors. Oncotarget 2018; 8:47184-47194. [PMID: 28525378 PMCID: PMC5564555 DOI: 10.18632/oncotarget.17586] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 04/17/2017] [Indexed: 11/25/2022] Open
Abstract
Interferon regulatory factor 5 (IRF5) plays a critical role in the induction of type I interferon, proinflammatory cytokines and chemokines, and participates in the pathogenesis of autoimmune diseases such as systemic lupus erythematosus (SLE). However, the relationship between IRF5 and childhood-onset SLE remains elusive. In the present study, we demonstrated that levels of mRNA expression of IRF5, IFN-α, and Sp1 were significantly increased in childhood-onset SLE, as seen on quantitative real-time PCR, and the expression of Sp1 and IFN-α was positively correlated with IRF5. In addition to being used as antitumor drugs, a number of histone deacetylase inhibitors (HDACi) display potent anti-inflammatory properties; however, their effects on IRF5 expression remain unclear. In this study, we identified that HDACi trichostatin A (TSA) and histone acetyltransferase (HAT)-p300 downregulated IRF5 promoter activity, mRNA expression, and protein level, whereas the HAT-p300/CBP-associated factor had no effect. Moreover, TSA inhibited the production of TNF-α and IL-6 in differentiated THP-1cells. Furthermore, chromatin immunoprecipitation assays revealed that TSA inhibited DNA binding of Sp1, RNA polymerase II, HDAC3, and p300 to the core promoter region of IRF5. Our results suggest that HDACi may have therapeutic potential in patients with autoimmune diseases such as SLE through repression of IRF5 expression.
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Wen J, Liu H, Wang L, Wang X, Gu N, Liu Z, Xu T, Gomez DR, Komaki R, Liao Z, Wei Q. Potentially Functional Variants of ATG16L2 Predict Radiation Pneumonitis and Outcomes in Patients with Non-Small Cell Lung Cancer after Definitive Radiotherapy. J Thorac Oncol 2018; 13:660-675. [PMID: 29454863 DOI: 10.1016/j.jtho.2018.01.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/13/2017] [Accepted: 01/26/2018] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Autophagy not only plays an important role in the progression of cancer but is also involved in tissue inflammatory response. However, few published studies have investigated associations between functional genetic variants of autophagy-related genes and radiation pneumonitis (RP) as well as clinical outcomes in patients with NSCLC after definitive radiotherapy. METHODS We genotyped nine potentially functional single-nucleotide polymorphisms (SNPs) in four autophagy-related genes (autophagy related 2B gene [ATG2B], autophagy related 10 gene [ATG10], autophagy related 12 gene [ATG12], and autophagy related 16 like 2 gene [ATG16L2]) in 393 North American patients with NSCLC treated by definitive radiotherapy and assessed their associations with RP, local recurrence-free survival (LRFS), progression-free survival (PFS), and overall survival (OS) in multivariable Cox proportional hazard regression analyses. RESULTS We found that patients with the ATG16L2 rs10898880 CC variant genotype had a better LRFS, PFS, and OS (adjusted hazard ratio = 0.59, 0.64, and 0.64; 95% confidence interval: 0.45-0.79, 0.48-0.84, and 0.48-0.86; p = 0.0004, 0.002, and 0.003, respectively), but a greater risk for development of severe RP (adjusted hazard ratio = 1.80, 95% confidence interval: 1.04-3.12, p = 0.037) than did patients with AA/AC genotypes. Further functional analyses suggested that the ATG16L2 rs10898880 C variant allele modulated expression of the ATG16L2 gene. CONCLUSION This is the first report that one potentially functional SNP rs10898880 in ATG16L2 may be a predictor of RP, LRFS, PFS, and OS in patients with NSCLC after definitive radiotherapy. Additional larger, prospective studies are needed to confirm these findings.
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Affiliation(s)
- Juyi Wen
- Department of Radiation Oncology, Navy General Hospital, Beijing, People's Republic of China; Department of Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Lili Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Xiaomeng Wang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Ning Gu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Ting Xu
- Department of Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Daniel R Gomez
- Department of Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Ritsuko Komaki
- Department of Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Zhongxing Liao
- Department of Radiation Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina; Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina.
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Abstract
PURPOSE OF REVIEW Our understanding on genetic basis of SLE has been advanced through genome-wide association studies. We review recent progress in lupus genetics with a focus on SLE-associated loci that have been functionally characterized, and discuss the potential for clinical translation of genetics data. RECENT FINDINGS Over 100 loci have been confirmed to show robust association with SLE and many share with other immune-mediated diseases. Although causative variants captured at these established loci are limited, they guide biological studies of gene targets for functional characterization which highlight the importance of aberrant recognition of self-nucleic acid, type I interferon overproduction, and defective immune cell signaling underlying the pathogenesis of SLE. Increasing examples illustrate a predictive value of genetic findings in susceptibility/prognosis prediction, clinical classification, and pharmacological implication. Genetic findings provide a foundation for better understanding of disease pathogenic mechanisms and opportunities for target selection in lupus drug development.
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Abstract
PURPOSE OF REVIEW To describe the recent studies on the genetics of systemic lupus erythematosus (SLE) and Sjögren's syndrome. RECENT FINDINGS We overview the most recent findings on the genetic susceptibility of the diseases and provide information on their genetic similarities and differences. SUMMARY SLE and Sjögren's syndrome are two closely related systemic autoimmune diseases that share multiple clinical and molecular aspects, including a significant number of susceptibility genes. Several genome-wide association studies were recently published in different populations that provide a better picture of their molecular mechanisms. It is becoming clear that their genetic architecture is quite well established, but more information is required on expression quantitative trait loci, epigenetic genome-wide analyses, gene × gene interactions and the role of rare variants.
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44
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Wen LL, Zhu ZW, Yang C, Liu L, Zuo XB, Morris DL, Dou JF, Ye L, Cheng YY, Guo HM, Huang HQ, Lin Y, Zhu CH, Tang LL, Chen MY, Zhou Y, Ding YT, Liang B, Zhou FS, Gao JP, Tang XF, Zheng XD, Wang WJ, Yin XY, Tang HY, Sun LD, Yang S, Zhang XJ, Sheng YJ, Cui Y. Multiple variants in 5q31.1 are associated with systemic lupus erythematosus susceptibility and subphenotypes in the Han Chinese population. Br J Dermatol 2017; 177:801-808. [PMID: 28144936 DOI: 10.1111/bjd.15362] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND A previous study provided evidence for a genetic association between PPP2CA on 5q31.1 and systemic lupus erythematosus (SLE) across multi-ancestral cohorts, but failed to find significant evidence for an association in the Han Chinese population. OBJECTIVES To explore the association between this locus and SLE using data from our previously published genome-wide association study (GWAS). METHODS Single-nucleotide polymorphisms (SNPs) rs7726414 and rs244689 (near TCF7 and PPP2CA in 5q31.1) were selected as candidate independent associations from a large-scale study in a Han Chinese population consisting of 1047 cases and 1205 controls. Subsequently, 3509 cases and 8246 controls were genotyped in two further replication studies. We then investigated the SNPs' associations with SLE subphenotypes and gene expression in peripheral blood mononuclear cells. RESULTS Highly significant associations with SLE in the Han Chinese population were detected for SNPs rs7726414 and rs244689 by combining the genotype data from our previous GWAS and two independent replication cohorts. Further conditional analyses indicated that these two SNPs contribute to disease susceptibility independently. A significant association with SLE, age at diagnosis < 20 years, was found for rs7726414 (P = 0·001). The expression levels of TCF7 and PPP2CA messenger RNA in patients with SLE were significantly decreased compared with those in healthy controls. CONCLUSIONS This study found evidence for multiple associations with SLE in 5q31.1 at genome-wide levels of significance for the first time in a Han Chinese population, in a combined genotype dataset. These findings suggest that variants in the 5q31.1 locus not only provide novel insights into the genetic architecture of SLE, but also contribute to the complex subphenotypes of SLE.
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Affiliation(s)
- L L Wen
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Z W Zhu
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - C Yang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - L Liu
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - X B Zuo
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - D L Morris
- Division of Genetics and Molecular Medicine, King's College London, U.K
| | - J F Dou
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - L Ye
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y Y Cheng
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - H M Guo
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - H Q Huang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y Lin
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China.,Department of Dermatology, the Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, 230032, China
| | - C H Zhu
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - L L Tang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - M Y Chen
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y Zhou
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y T Ding
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - B Liang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - F S Zhou
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - J P Gao
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - X F Tang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - X D Zheng
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - W J Wang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - X Y Yin
- Department of Genetics, and Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, U.S.A
| | - H Y Tang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - L D Sun
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - S Yang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - X J Zhang
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y J Sheng
- Institute of Dermatology and Department of Dermatology, the First Affiliated Hospital, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, 230032, China.,Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, China, Hefei, Anhui, 230032, China
| | - Y Cui
- Department of Dermatology, China-Japan Friendship Hospital, East Street Cherry Park, Chaoyang District, Beijing, 100029, China
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Molineros JE, Yang W, Zhou XJ, Sun C, Okada Y, Zhang H, Heng Chua K, Lau YL, Kochi Y, Suzuki A, Yamamoto K, Ma J, Bang SY, Lee HS, Kim K, Bae SC, Zhang H, Shen N, Looger LL, Nath SK. Confirmation of five novel susceptibility loci for systemic lupus erythematosus (SLE) and integrated network analysis of 82 SLE susceptibility loci. Hum Mol Genet 2017; 26:1205-1216. [PMID: 28108556 DOI: 10.1093/hmg/ddx026] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/13/2017] [Indexed: 01/13/2023] Open
Abstract
We recently identified ten novel SLE susceptibility loci in Asians and uncovered several additional suggestive loci requiring further validation. This study aimed to replicate five of these suggestive loci in a Han Chinese cohort from Hong Kong, followed by meta-analysis (11,656 cases and 23,968 controls) on previously reported Asian and European populations, and to perform bioinformatic analyses on all 82 reported SLE loci to identify shared regulatory signatures. We performed a battery of analyses for these five loci, as well as joint analyses on all 82 SLE loci. All five loci passed genome-wide significance: MYNN (rs10936599, Pmeta = 1.92 × 10-13, OR = 1.14), ATG16L2 (rs11235604, Pmeta = 8.87 × 10 -12, OR = 0.78), CCL22 (rs223881, Pmeta = 5.87 × 10-16, OR = 0.87), ANKS1A (rs2762340, Pmeta = 4.93 × 10-15, OR = 0.87) and RNASEH2C (rs1308020, Pmeta = 2.96 × 10-19, OR = 0.84) and co-located with annotated gene regulatory elements. The novel loci share genetic signatures with other reported SLE loci, including effects on gene expression, transcription factor binding, and epigenetic characteristics. Most (56%) of the correlated (r2 > 0.8) SNPs from the 82 SLE loci were implicated in differential expression (9.81 × 10-198 < P < 5 × 10-3) of cis-genes. Transcription factor binding sites for p53, MEF2A and E2F1 were significantly (P < 0.05) over-represented in SLE loci, consistent with apoptosis playing a critical role in SLE. Enrichment analysis revealed common pathways, gene ontology, protein domains, and cell type-specific expression. In summary, we provide evidence of five novel SLE susceptibility loci. Integrated bioinformatics using all 82 loci revealed that SLE susceptibility loci share many gene regulatory features, suggestive of conserved mechanisms of SLE etiopathogenesis.
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Affiliation(s)
- Julio E Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Huoru Zhang
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Yu-Lung Lau
- Department of Paediatrics and Adolescent Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jianyang Ma
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul 02447, Korea
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - Nan Shen
- Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, and Shanghai Jiaotong University School of Medicine, Shanghai 200025, People's Republic of China
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
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Kwon KS, Cho HY, Chung YJ. Recapitulation of Candidate Systemic Lupus Erythematosus-Associated Variants in Koreans. Genomics Inform 2016; 14:85-89. [PMID: 27729837 PMCID: PMC5056901 DOI: 10.5808/gi.2016.14.3.85] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 08/26/2016] [Accepted: 08/28/2016] [Indexed: 11/29/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association. For this, we selected five SNPs (rs1801274 in FCGR2A and rs2286672 in PLD2, rs887369 in CXorf21, rs9782955 in LYST, and rs3794060 in NADSYN1). Through the replication study with 656 cases and 622 controls, rs1801274 in FCGR2A was found to be significantly associated with SLE in Koreans (odds ratio, 1.26, 95% confidence interval, 1.06 to 1.50; p = 0.01 in allelic model). This association was also significant in two other models (dominant and recessive). The other four SNPs did not show a significant association. Our data support that FCGR polymorphisms play important roles in the susceptibility to SLE in diverse populations, including Koreans.
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Affiliation(s)
- Ki-Sung Kwon
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye-Young Cho
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yeun-Jun Chung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea.; Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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Alarcón-Riquelme ME, Ziegler JT, Molineros J, Howard TD, Moreno-Estrada A, Sánchez-Rodríguez E, Ainsworth HC, Ortiz-Tello P, Comeau ME, Rasmussen A, Kelly JA, Adler A, Acevedo-Vázquez EM, Cucho-Venegas JM, García-De la Torre I, Cardiel MH, Miranda P, Catoggio LJ, Maradiaga-Ceceña M, Gaffney PM, Vyse TJ, Criswell LA, Tsao BP, Sivils KL, Bae SC, James JA, Kimberly RP, Kaufman KM, Harley JB, Esquivel-Valerio JA, Moctezuma JF, García MA, Berbotto GA, Babini AM, Scherbarth H, Toloza S, Baca V, Nath SK, Aguilar Salinas C, Orozco L, Tusié-Luna T, Zidovetzki R, Pons-Estel BA, Langefeld CD, Jacob CO. Genome-Wide Association Study in an Amerindian Ancestry Population Reveals Novel Systemic Lupus Erythematosus Risk Loci and the Role of European Admixture. Arthritis Rheumatol 2016; 68:932-43. [PMID: 26606652 DOI: 10.1002/art.39504] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 11/03/2015] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Systemic lupus erythematosus (SLE) is a chronic autoimmune disease with a strong genetic component. We undertook the present work to perform the first genome-wide association study on individuals from the Americas who are enriched for Native American heritage. METHODS We analyzed 3,710 individuals from the US and 4 countries of Latin America who were diagnosed as having SLE, and healthy controls. Samples were genotyped with HumanOmni1 BeadChip. Data on out-of-study controls genotyped with HumanOmni2.5 were also included. Statistical analyses were performed using SNPtest and SNPGWA. Data were adjusted for genomic control and false discovery rate. Imputation was performed using Impute2 and, for classic HLA alleles, HiBag. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. RESULTS The IRF5-TNPO3 region showed the strongest association and largest OR for SLE (rs10488631: genomic control-adjusted P [Pgcadj ] = 2.61 × 10(-29), OR 2.12 [95% CI 1.88-2.39]), followed by HLA class II on the DQA2-DQB1 loci (rs9275572: Pgcadj = 1.11 × 10(-16), OR 1.62 [95% CI 1.46-1.80] and rs9271366: Pgcadj = 6.46 × 10(-12), OR 2.06 [95% CI 1.71-2.50]). Other known SLE loci found to be associated in this population were ITGAM, STAT4, TNIP1, NCF2, and IRAK1. We identified a novel locus on 10q24.33 (rs4917385: Pgcadj = 1.39 × 10(-8)) with an expression quantitative trait locus (eQTL) effect (Peqtl = 8.0 × 10(-37) at USMG5/miR1307), and several new suggestive loci. SLE risk loci previously identified in Europeans and Asians were corroborated. Local ancestry estimation showed that the HLA allele risk contribution is of European ancestral origin. Imputation of HLA alleles suggested that autochthonous Native American haplotypes provide protection against development of SLE. CONCLUSION Our results demonstrate that studying admixed populations provides new insights in the delineation of the genetic architecture that underlies autoimmune and complex diseases.
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Affiliation(s)
| | - Julie T Ziegler
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | | | - Andrés Moreno-Estrada
- Stanford University School of Medicine, Stanford, California, and Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | | | | | - Patricia Ortiz-Tello
- Stanford University School of Medicine, Stanford, California, and Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Mexico
| | - Mary E Comeau
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | | | - Adam Adler
- Oklahoma Medical Research Foundation, Oklahoma City
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sang-Cheol Bae
- Hanyang University Hospital for Rheumatic Diseases, Seoul, Republic of Korea
| | - Judith A James
- Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City
| | | | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Jorge A Esquivel-Valerio
- Hospital Universitario Dr. José Eleuterio González Universidad Autonoma de Nuevo León, Monterrey, Mexico
| | | | - Mercedes A García
- Hospital Interzonal General de Agudos General San Martin, La Plata, Argentina
| | | | | | - Hugo Scherbarth
- Hospital Interzonal General de Agudos Oscar E. Alende, Mar del Plata, Argentina
| | - Sergio Toloza
- Hospital Interzonal San Juan Bautista, San Fernando del Valle de Catamarca, Argentina
| | - Vicente Baca
- Hospital de Peditaria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Carlos Aguilar Salinas
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Lorena Orozco
- Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Teresa Tusié-Luna
- Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán and Instituto de Investigaciones Biomédicas de la Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | | | | | - Chaim O Jacob
- University of Southern California School of Medicine, Los Angeles
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Garrett-Sinha LA, Kearly A, Satterthwaite AB. The Role of the Transcription Factor Ets1 in Lupus and Other Autoimmune Diseases. Crit Rev Immunol 2016; 36:485-510. [PMID: 28845756 DOI: 10.1615/critrevimmunol.2017020284] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by excess B- and T-cell activation, the development of autoantibodies against self-antigens including nuclear antigens, and immune complex deposition in target organs, which triggers an inflammatory response and tissue damage. The genetic and environmental factors that contribute to the development of SLE have been studied extensively in both humans and mouse models of the disease. One of the important genetic contributions to SLE development is an alteration in the expression of the transcription factor Ets1, which regulates the functional differentiation of lymphocytes. Here, we review the genetic, biochemical, and immunological studies that have linked low levels of Ets1 to aberrant lymphocyte differentiation and to the pathogenesis of SLE.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203
| | - Alyssa Kearly
- Department of Biochemistry, State University of New York at Buffalo, Buffalo, NY 14203
| | - Anne B Satterthwaite
- Department of Internal Medicine, Rheumatic Diseases Division; Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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