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Chen CC, Howie J, Ebrahimi M, Teymouri K, Woo JJ, Tiwari AK, Zai CC, Kennedy JL. Analysis of the complement component C4 gene with schizophrenia subphenotypes. Schizophr Res 2024; 271:309-318. [PMID: 39084106 DOI: 10.1016/j.schres.2024.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND The complement component C4 gene has been identified as a strong marker for schizophrenia (SCZ) risk. The C4 gene has a complex genetic structure consisting of variable structural elements (C4A, C4B, C4L, and C4S) and compound structural forms (C4AL, C4BL, C4AS and C4BS). In addition, the variations in C4 structural forms may have a direct or indirect effect on the brain expression level of C4A and C4B proteins. Previous studies have associated C4AL with higher brain C4A expression and sex-dimorphism of C4 between males and females was observed. STUDY DESIGN A total of 613 patients with DSM-IV SCZ or schizoaffective disorder (SCZ-AFF) were recruited to investigate the relationship between C4 gene variants and clinical characteristics of SCZ (age of onset, symptom severity, and global assessment of functioning (GAF)). This study also explored the effect of sex on the association of C4 with SCZ. 434 patients were included in the final analyses after genetic quality control. RESULTS We observed associations between C4 and clinical characteristics of SCZ (age of onset, symptom severity, GAF) and found significant differences when males and females were examined separately. CONCLUSION Overall, our preliminary findings encourage future investigations of C4 in SCZ-related phenotypes, including antipsychotic response and side effects. The study sample was of moderate size; therefore, further studies in larger samples are needed to extend and validate these results.
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Affiliation(s)
- Cheng C Chen
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Joshua Howie
- Department of Psychiatry, University of Saskatchewan, Saskatoon, Canada
| | - Mahbod Ebrahimi
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Kowsar Teymouri
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Julia J Woo
- Department of Psychiatry and Behavioural Neurosciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Arun K Tiwari
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Clement C Zai
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada; Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - James L Kennedy
- Tanenbaum Centre for Pharmacogenetics, Molecular Brain Science, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.
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2
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Mariaselvam CM, Seth G, Kavadichanda C, Boukouaci W, Wu CL, Costes B, Thabah MM, Krishnamoorthy R, Leboyer M, Negi VS, Tamouza R. Low C4A copy numbers and higher HERV gene insertion contributes to increased risk of SLE, with absence of association with disease phenotype and disease activity. Immunol Res 2024:10.1007/s12026-024-09475-8. [PMID: 38594415 DOI: 10.1007/s12026-024-09475-8] [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: 01/18/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024]
Abstract
Low copy numbers (CNs) of C4 genes are associated with systemic autoimmune disorders and affects autoantibody diversity and disease subgroups. The primary objective of this study was to characterize diversity of complement (C4) and C4-Human Endogenous Retrovirus (HERV) gene copy numbers in SLE. We also sought to assess the association of C4 and C4-HERV CNs with serum complement levels, autoantibodies, disease phenotypes and activity. Finally, we checked the association of C4 and HERV CNs with specific HLA alleles. Genomic DNA from 70 SLE and 90 healthy controls of south Indian Tamil origin were included. Demographic, clinical and serological data was collected in a predetermined proforma. CNs of C4A and C4B genes and the frequency of insertion of 6.4kb HERV within C4 gene (C4AL, C4BL) was determined using droplet digital polymerase chain reaction (ddPCR). A four digit high resolution HLA genotyping was done using next generation sequencing. In our cohort, the total C4 gene copies ranged from 2 to 6. Compared to controls, presence of two or less copies of C4A gene was associated with SLE risk (p = 0.005; OR = 2.79; 95% CI = 1.29-6.22). Higher frequency of HERV insertion in C4A than in C4B increases such risk (p = 0.000; OR = 12.67; 95% CI = 2.80-115.3). AL-AL-AL-BS genotype was significantly higher in controls than SLE (9%vs1%, p = 0.04; OR = 0.15, 95% CI = 0.00-0.16). Distribution of HLA alleles was not different in SLE compared to controls as well as in SLE subjects with ≤ 2 copies and > 2 copies of C4A, but HLA allele distribution was diverse in subjects with C4B ≤ 2 copies and > 2 copies. Finally, there was no correlation between the C4 and the C4-HERV diversity and complement levels, autoantibodies, disease phenotypes and activity. In conclusion, our data show that, low C4A copy number and higher insertion of HERV-K in C4A increases the risk for SLE. C4 and C4-HERV CNs did not correlate with serum complements, autoantibodies, disease phenotypes and activity in SLE. Further validation in a larger homogenous SLE cohort is needed.
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Affiliation(s)
- Christina Mary Mariaselvam
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India.
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France.
| | - Gaurav Seth
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Chengappa Kavadichanda
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Wahid Boukouaci
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Ching-Lien Wu
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Bruno Costes
- IMRB, INSERM U955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Molly Mary Thabah
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Rajagopal Krishnamoorthy
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Marion Leboyer
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Vir Singh Negi
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Ryad Tamouza
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
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3
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Onengut-Gumuscu S, Webb-Robertson BJM, Sarkar S, Manichaikul A, Hu X, Frazer-Abel A, Holers VM, Rewers MJ, Rich SS. Genetic variants in the complement system and their potential link in the aetiology of type 1 diabetes. Diabetes Metab Res Rev 2024; 40:e3716. [PMID: 37649398 DOI: 10.1002/dmrr.3716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/30/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
Type 1 diabetes is an autoimmune disease in which one's own immune system destroys insulin-secreting beta cells in the pancreas. This process results in life-long dependence on exogenous insulin for survival. Both genetic and environmental factors play a role in disease initiation, progression, and ultimate clinical diagnosis of type 1 diabetes. This review will provide background on the natural history of type 1 diabetes and the role of genetic factors involved in the complement system, as several recent studies have identified changes in levels of these proteins as the disease evolves from pre-clinical through to clinically apparent disease.
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Affiliation(s)
- Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Bobbie-Jo M Webb-Robertson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
- Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Xiaowei Hu
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Ashley Frazer-Abel
- Exsera BioLabs, Division of Rheumatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - V Michael Holers
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
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4
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Kalinowski A, Tian L, Pattni R, Ollila H, Khan M, Manko C, Silverman M, Ma M, Columbo L, Farhadian B, Swedo S, Murphy T, Johnson M, Fernell E, Gillberg C, Thienemann M, Mellins ED, Levinson DF, Urban AE, Frankovich J. Evaluation of C4 Gene Copy Number in Pediatric Acute Neuropsychiatric Syndrome. Dev Neurosci 2023; 45:315-324. [PMID: 37379808 DOI: 10.1159/000531707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/16/2023] [Indexed: 06/30/2023] Open
Abstract
Pediatric acute-onset neuropsychiatric syndrome (PANS) is an abrupt-onset neuropsychiatric disorder. PANS patients have an increased prevalence of comorbid autoimmune illness, most commonly arthritis. In addition, an estimated one-third of PANS patients present with low serum C4 protein, suggesting decreased production or increased consumption of C4 protein. To test the possibility that copy number (CN) variation contributes to risk of PANS illness, we compared mean total C4A and total C4B CN in ethnically matched subjects from PANS DNA samples and controls (192 cases and 182 controls). Longitudinal data from the Stanford PANS cohort (n = 121) were used to assess whether the time to juvenile idiopathic arthritis (JIA) or autoimmune disease (AI) onset was a function of total C4A or C4B CN. Lastly, we performed several hypothesis-generating analyses to explore the correlation between individual C4 gene variants, sex, specific genotypes, and age of PANS onset. Although the mean total C4A or C4B CN did not differ in PANS compared to controls, PANS patients with low C4B CN were at increased risk for subsequent JIA diagnosis (hazard ratio = 2.7, p value = 0.004). We also observed a possible increase in risk for AI in PANS patients and a possible correlation between lower C4B and PANS age of onset. An association between rheumatoid arthritis and low C4B CN has been reported previously. However, patients with PANS develop different types of JIA: enthesitis-related arthritis, spondyloarthritis, and psoriatic arthritis. This suggests that C4B plays a role that spans these arthritis types.
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Affiliation(s)
- Agnieszka Kalinowski
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
- Sierra Pacific Mental Illness Research Education and Clinical Center (MIRECC), VA Palo Alto Health Care System, Palo Alto, California, USA
| | - Lu Tian
- Stanford University Department of Biomedical Data Science, Stanford, California, USA
| | - Reenal Pattni
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
- Stanford University Department of Genetics, Stanford, California, USA
| | - Hanna Ollila
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Boston, Massachusetts, USA
| | - Maroof Khan
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Cindy Manko
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Melissa Silverman
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Meiqian Ma
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Laurie Columbo
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Bahare Farhadian
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Susan Swedo
- National Institutes of Health, Pediatrics and Developmental Neuroscience Branch, Bethesda, Maryland, USA
| | - Tanya Murphy
- Department of Pediatrics and Department of Psychiatry and Neurosciences, University of South Florida, Tampa, Florida, USA
- John Hopkins Medicine, Baltimore, Maryland, USA
| | - Mats Johnson
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | - Elisabeth Fernell
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Margo Thienemann
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Elizabeth D Mellins
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
| | - Douglas F Levinson
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
| | - Alexander E Urban
- Stanford University Department of Psychiatry and Behavioral Sciences, Stanford, California, USA
- Stanford University Department of Genetics, Stanford, California, USA
| | - Jennifer Frankovich
- Immune Behavioral Health Clinic, Stanford University Department of Pediatrics, Stanford, California, USA
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5
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Coss SL, Zhou D, Chua GT, Aziz RA, Hoffman RP, Wu YL, Ardoin SP, Atkinson JP, Yu CY. The complement system and human autoimmune diseases. J Autoimmun 2023; 137:102979. [PMID: 36535812 PMCID: PMC10276174 DOI: 10.1016/j.jaut.2022.102979] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Genetic deficiencies of early components of the classical complement activation pathway (especially C1q, r, s, and C4) are the strongest monogenic causal factors for the prototypic autoimmune disease systemic lupus erythematosus (SLE), but their prevalence is extremely rare. In contrast, isotype genetic deficiency of C4A and acquired deficiency of C1q by autoantibodies are frequent among patients with SLE. Here we review the genetic basis of complement deficiencies in autoimmune disease, discuss the complex genetic diversity seen in complement C4 and its association with autoimmune disease, provide guidance as to when clinicians should suspect and test for complement deficiencies, and outline the current understanding of the mechanisms relating complement deficiencies to autoimmunity. We focus primarily on SLE, as the role of complement in SLE is well-established, but will also discuss other informative diseases such as inflammatory arthritis and myositis.
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Affiliation(s)
- Samantha L Coss
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
| | - Danlei Zhou
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Gilbert T Chua
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rabheh Abdul Aziz
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Allergy, Immunology and Rheumatology, University of Buffalo, NY, USA
| | - Robert P Hoffman
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Yee Ling Wu
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Stacy P Ardoin
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - John P Atkinson
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Chack-Yung Yu
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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6
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Hernandez LM, Kim M, Zhang P, Bethlehem RAI, Hoftman G, Loughnan R, Smith D, Bookheimer SY, Fan CC, Bearden CE, Thompson WK, Gandal MJ. Multi-ancestry phenome-wide association of complement component 4 variation with psychiatric and brain phenotypes in youth. Genome Biol 2023; 24:42. [PMID: 36882872 PMCID: PMC9990244 DOI: 10.1186/s13059-023-02878-0] [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: 04/20/2022] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Increased expression of the complement component 4A (C4A) gene is associated with a greater lifetime risk of schizophrenia. In the brain, C4A is involved in synaptic pruning; yet, it remains unclear the extent to which upregulation of C4A alters brain development or is associated with the risk for psychotic symptoms in childhood. Here, we perform a multi-ancestry phenome-wide association study in 7789 children aged 9-12 years to examine the relationship between genetically regulated expression (GREx) of C4A, childhood brain structure, cognition, and psychiatric symptoms. RESULTS While C4A GREx is not related to childhood psychotic experiences, cognition, or global measures of brain structure, it is associated with a localized reduction in regional surface area (SA) of the entorhinal cortex. Furthermore, we show that reduced entorhinal cortex SA at 9-10 years predicts a greater number and severity of psychosis-like events at 1-year and 2-year follow-up time points. We also demonstrate that the effects of C4A on the entorhinal cortex are independent of genome-wide polygenic risk for schizophrenia. CONCLUSIONS Our results suggest neurodevelopmental effects of C4A on childhood medial temporal lobe structure, which may serve as a biomarker for schizophrenia risk prior to symptom onset.
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Affiliation(s)
- Leanna M. Hernandez
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Minsoo Kim
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Pan Zhang
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Richard A. I. Bethlehem
- University of Cambridge, Department of Psychiatry, Cambridge Biomedical Campus, Cambridge, CB2 0SZ UK
| | - Gil Hoftman
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Robert Loughnan
- Population Neuroscience and Genetics Lab, University of California, San Diego, San Diego, CA 92093 USA
| | - Diana Smith
- Population Neuroscience and Genetics Lab, University of California, San Diego, San Diego, CA 92093 USA
| | - Susan Y. Bookheimer
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Chun Chieh Fan
- Population Neuroscience and Genetics Lab, University of California, San Diego, San Diego, CA 92093 USA
| | - Carrie E. Bearden
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Wesley K. Thompson
- Population Neuroscience and Genetics Lab, University of California, San Diego, San Diego, CA 92093 USA
| | - Michael J. Gandal
- Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095 USA
- Department of Psychiatry, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
- Lifespan Brain Institute at Penn Med and the Children’s Hospital of Philadelphia, Philadelphia, PA USA
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA USA
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7
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Zhou D, King EH, Rothwell S, Krystufkova O, Notarnicola A, Coss S, Abdul-Aziz R, Miller KE, Dang A, Yu GR, Drew J, Lundström E, Pachman LM, Mamyrova G, Curiel RV, De Paepe B, De Bleecker JL, Payton A, Ollier W, O'Hanlon TP, Targoff IN, Flegel WA, Sivaraman V, Oberle E, Akoghlanian S, Driest K, Spencer CH, Wu YL, Nagaraja HN, Ardoin SP, Chinoy H, Rider LG, Miller FW, Lundberg IE, Padyukov L, Vencovský J, Lamb JA, Yu CY. Low copy numbers of complement C4 and C4A deficiency are risk factors for myositis, its subgroups and autoantibodies. Ann Rheum Dis 2023; 82:235-245. [PMID: 36171069 PMCID: PMC9887400 DOI: 10.1136/ard-2022-222935] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/02/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Idiopathic inflammatory myopathies (IIM) are a group of autoimmune diseases characterised by myositis-related autoantibodies plus infiltration of leucocytes into muscles and/or the skin, leading to the destruction of blood vessels and muscle fibres, chronic weakness and fatigue. While complement-mediated destruction of capillary endothelia is implicated in paediatric and adult dermatomyositis, the complex diversity of complement C4 in IIM pathology was unknown. METHODS We elucidated the gene copy number (GCN) variations of total C4, C4A and C4B, long and short genes in 1644 Caucasian patients with IIM, plus 3526 matched healthy controls using real-time PCR or Southern blot analyses. Plasma complement levels were determined by single radial immunodiffusion. RESULTS The large study populations helped establish the distribution patterns of various C4 GCN groups. Low GCNs of C4T (C4T=2+3) and C4A deficiency (C4A=0+1) were strongly correlated with increased risk of IIM with OR equalled to 2.58 (2.28-2.91), p=5.0×10-53 for C4T, and 2.82 (2.48-3.21), p=7.0×10-57 for C4A deficiency. Contingency and regression analyses showed that among patients with C4A deficiency, the presence of HLA-DR3 became insignificant as a risk factor in IIM except for inclusion body myositis (IBM), by which 98.2% had HLA-DR3 with an OR of 11.02 (1.44-84.4). Intragroup analyses of patients with IIM for C4 protein levels and IIM-related autoantibodies showed that those with anti-Jo-1 or with anti-PM/Scl had significantly lower C4 plasma concentrations than those without these autoantibodies. CONCLUSIONS C4A deficiency is relevant in dermatomyositis, HLA-DRB1*03 is important in IBM and both C4A deficiency and HLA-DRB1*03 contribute interactively to risk of polymyositis.
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Affiliation(s)
- Danlei Zhou
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA,Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Emily H King
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA,Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Simon Rothwell
- National Institute for Health Research Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, The University of Manchester, Manchester, UK,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Olga Krystufkova
- Institute of Rheumatology and Department of Rheumatology, Charles University, Prague, Czech Republic
| | - Antonella Notarnicola
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, University Hospital Karolinska, Stockholm, Sweden
| | - Samantha Coss
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA,Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Rabheh Abdul-Aziz
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA,Division of Allergy/Immunology and Rheumatology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | - Katherine E Miller
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA,Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Amanda Dang
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - G Richard Yu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Joanne Drew
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Emeli Lundström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, University Hospital Karolinska, Stockholm, Sweden
| | - Lauren M Pachman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Gulnara Mamyrova
- Division of Rheumatology, Department of Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rodolfo V Curiel
- Division of Rheumatology, Department of Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Boel De Paepe
- Department of Neurology, Ghent University Hospital, Ghent, Belgium
| | | | - Antony Payton
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - William Ollier
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - Terrance P O'Hanlon
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Bethesda, MD, USA
| | - Ira N Targoff
- Veteran’s Affairs Medical Center, University of Oklahoma Health Sciences Center, and Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Vidya Sivaraman
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Edward Oberle
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Shoghik Akoghlanian
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kyla Driest
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | | | - Yee Ling Wu
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Haikady N Nagaraja
- Division of Biostatistics, The Ohio State University, Columbus, Ohio, USA
| | - Stacy P Ardoin
- Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Hector Chinoy
- National Institute for Health Research Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, The University of Manchester, Manchester, UK,Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Bethesda, MD, USA
| | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health, Bethesda, MD, USA
| | - Ingrid E Lundberg
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, University Hospital Karolinska, Stockholm, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, University Hospital Karolinska, Stockholm, Sweden
| | - Jiří Vencovský
- Institute of Rheumatology and Department of Rheumatology, Charles University, Prague, Czech Republic
| | - Janine A Lamb
- Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Chack-Yung Yu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, Ohio, USA,Division of Rheumatology, Nationwide Children’s Hospital and Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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8
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Lundtoft C, Pucholt P, Martin M, Bianchi M, Lundström E, Eloranta ML, Sandling JK, Sjöwall C, Jönsen A, Gunnarsson I, Rantapää-Dahlqvist S, Bengtsson AA, Leonard D, Baecklund E, Jonsson R, Hammenfors D, Forsblad-d'Elia H, Eriksson P, Mandl T, Magnusson Bucher S, Norheim KB, Auglaend Johnsen SJ, Omdal R, Kvarnström M, Wahren-Herlenius M, Notarnicola A, Andersson H, Molberg Ø, Diederichsen LP, Almlöf J, Syvänen AC, Kozyrev SV, Lindblad-Toh K, Nilsson B, Blom AM, Lundberg IE, Nordmark G, Diaz-Gallo LM, Svenungsson E, Rönnblom L. Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases. Arthritis Rheumatol 2022; 74:1440-1450. [PMID: 35315244 PMCID: PMC9543510 DOI: 10.1002/art.42122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/20/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE Copy number variation of the C4 complement components, C4A and C4B, has been associated with systemic inflammatory autoimmune diseases. This study was undertaken to investigate whether C4 copy number variation is connected to the autoimmune repertoire in systemic lupus erythematosus (SLE), primary Sjögren's syndrome (SS), or myositis. METHODS Using targeted DNA sequencing, we determined the copy number and genetic variants of C4 in 2,290 well-characterized Scandinavian patients with SLE, primary SS, or myositis and 1,251 healthy controls. RESULTS A prominent relationship was observed between C4A copy number and the presence of SSA/SSB autoantibodies, which was shared between the 3 diseases. The strongest association was detected in patients with autoantibodies against both SSA and SSB and 0 C4A copies when compared to healthy controls (odds ratio [OR] 18.0 [95% confidence interval (95% CI) 10.2-33.3]), whereas a weaker association was seen in patients without SSA/SSB autoantibodies (OR 3.1 [95% CI 1.7-5.5]). The copy number of C4 correlated positively with C4 plasma levels. Further, a common loss-of-function variant in C4A leading to reduced plasma C4 was more prevalent in SLE patients with a low copy number of C4A. Functionally, we showed that absence of C4A reduced the individuals' capacity to deposit C4b on immune complexes. CONCLUSION We show that a low C4A copy number is more strongly associated with the autoantibody repertoire than with the clinically defined disease entities. These findings may have implications for understanding the etiopathogenetic mechanisms of systemic inflammatory autoimmune diseases and for patient stratification when taking the genetic profile into account.
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Affiliation(s)
| | | | | | - Matteo Bianchi
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | - Emeli Lundström
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | - Andreas Jönsen
- Lund University and Skåne University Hospital, Lund, Sweden
| | - Iva Gunnarsson
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | | | | | | | | | | | | | | - Roald Omdal
- Stavanger University Hospital, Stavanger, Norway
| | - Marika Kvarnström
- Karolinska Institutet, Karolinska University Hospital, and Stockholm Health Services, Region Stockholm, Stockholm, Sweden
| | - Marie Wahren-Herlenius
- Karolinska Institutet and Karolinska University Hospital Stockholm, Sweden, and University of Bergen, Bergen, Norway
| | | | | | | | - Louise Pyndt Diederichsen
- Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark, and Odense University Hospital, Odense, Denmark
| | - Jonas Almlöf
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | | | - Sergey V Kozyrev
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory and Uppsala University, Uppsala, Sweden, and Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | - Ingrid E Lundberg
- Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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9
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Zhou D, Rudnicki M, Chua GT, Lawrance SK, Zhou B, Drew JL, Barbar-Smiley F, Armstrong TK, Hilt ME, Birmingham DJ, Passler W, Auletta JJ, Bowden SA, Hoffman RP, Wu YL, Jarjour WN, Mok CC, Ardoin SP, Lau YL, Yu CY. Human Complement C4B Allotypes and Deficiencies in Selected Cases With Autoimmune Diseases. Front Immunol 2021; 12:739430. [PMID: 34764957 PMCID: PMC8577214 DOI: 10.3389/fimmu.2021.739430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Human complement C4 is one of the most diverse but heritable effectors for humoral immunity. To help understand the roles of C4 in the defense and pathogenesis of autoimmune and inflammatory diseases, we determined the bases of polymorphisms including the frequent genetic deficiency of C4A and/or C4B isotypes. We demonstrated the diversities of C4A and C4B proteins and their gene copy number variations (CNVs) in healthy subjects and patients with autoimmune disease, such as type 1 diabetes, systemic lupus erythematosus (SLE) and encephalitis. We identified subjects with (a) the fastest migrating C4B allotype, B7, or (b) a deficiency of C4B protein caused by genetic mutation in addition to gene copy-number variation. Those variants and mutants were characterized, sequenced and specific techniques for detection developed. Novel findings were made in four case series. First, the amino acid sequence determinant for C4B7 was likely the R729Q variation at the anaphylatoxin-like region. Second, in healthy White subject MS630, a C-nucleotide deletion at codon-755 led to frameshift mutations in his single C4B gene, which was a private mutation. Third, in European family E94 with multiplex lupus-related mortality and low serum C4 levels, the culprit was a recurrent haplotype with HLA-A30, B18 and DR7 that segregated with two defective C4B genes and identical mutations at the donor splice site of intron-28. Fourth, in East-Asian subject E133P with anti-NMDA receptor encephalitis, the C4B gene had a mutation that changed tryptophan-660 to a stop-codon (W660x), which was present in a haplotype with HLA-DRB1*04:06 and B*15:27. The W660x mutation is recurrent among East-Asians with a frequency of 1.5% but not detectable among patients with SLE. A meticulous annotation of C4 sequences revealed clusters of variations proximal to sites for protein processing, activation and inactivation, and binding of interacting molecules.
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Affiliation(s)
- Danlei Zhou
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Michael Rudnicki
- Department of Internal Medicine IV - Nephrology and Hypertension, Medical University Innsbruck, Innsbruck, Austria
| | - Gilbert T Chua
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong, SAR China
| | - Simon K Lawrance
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Biology & Earth Science, Otterbein University, Westerville, OH, United States
| | - Bi Zhou
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Joanne L Drew
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Fatima Barbar-Smiley
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
| | - Taylor K Armstrong
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, United States
| | - Miranda E Hilt
- Department of Biology & Earth Science, Otterbein University, Westerville, OH, United States
| | - Daniel J Birmingham
- Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Werner Passler
- Division of Nephrology and Dialysis, City Hospital, Bolzano, Italy
| | - Jeffrey J Auletta
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Hematology/Oncology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Sasigarn A Bowden
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Endocrinology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Robert P Hoffman
- Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Division of Endocrinology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Yee Ling Wu
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, United States
| | - Wael N Jarjour
- Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Chi Chiu Mok
- Department of Medicine, Tuen Mun Hospital, Hong Kong, Hong Kong, SAR China
| | - Stacy P Ardoin
- Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States.,Department of Internal Medicine, The Ohio State University, Columbus, OH, United States
| | - Yu Lung Lau
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong, SAR China
| | - Chack Yung Yu
- Center for Microbial Pathogenesis, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University, Columbus, OH, United States
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10
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Khan A, Shang N, Petukhova L, Zhang J, Shen Y, Hebbring SJ, Moncrieffe H, Kottyan LC, Namjou-Khales B, Knevel R, Raychaudhuri S, Karlson EW, Harley JB, Stanaway IB, Crosslin D, Denny JC, Elkind MS, Gharavi AG, Hripcsak G, Weng C, Kiryluk K. Medical Records-Based Genetic Studies of the Complement System. J Am Soc Nephrol 2021; 32:2031-2047. [PMID: 33941608 PMCID: PMC8455263 DOI: 10.1681/asn.2020091371] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/09/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Genetic variants in complement genes have been associated with a wide range of human disease states, but well-powered genetic association studies of complement activation have not been performed in large multiethnic cohorts. METHODS We performed medical records-based genome-wide and phenome-wide association studies for plasma C3 and C4 levels among participants of the Electronic Medical Records and Genomics (eMERGE) network. RESULTS In a GWAS for C3 levels in 3949 individuals, we detected two genome-wide significant loci: chr.1q31.3 (CFH locus; rs3753396-A; β=0.20; 95% CI, 0.14 to 0.25; P=1.52x10-11) and chr.19p13.3 (C3 locus; rs11569470-G; β=0.19; 95% CI, 0.13 to 0.24; P=1.29x10-8). These two loci explained approximately 2% of variance in C3 levels. GWAS for C4 levels involved 3998 individuals and revealed a genome-wide significant locus at chr.6p21.32 (C4 locus; rs3135353-C; β=0.40; 95% CI, 0.34 to 0.45; P=4.58x10-35). This locus explained approximately 13% of variance in C4 levels. The multiallelic copy number variant analysis defined two structural genomic C4 variants with large effect on blood C4 levels: C4-BS (β=-0.36; 95% CI, -0.42 to -0.30; P=2.98x10-22) and C4-AL-BS (β=0.25; 95% CI, 0.21 to 0.29; P=8.11x10-23). Overall, C4 levels were strongly correlated with copy numbers of C4A and C4B genes. In comprehensive phenome-wide association studies involving 102,138 eMERGE participants, we cataloged a full spectrum of autoimmune, cardiometabolic, and kidney diseases genetically related to systemic complement activation. CONCLUSIONS We discovered genetic determinants of plasma C3 and C4 levels using eMERGE genomic data linked to electronic medical records. Genetic variants regulating C3 and C4 levels have large effects and multiple clinical correlations across the spectrum of complement-related diseases in humans.
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Affiliation(s)
- Atlas Khan
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Ning Shang
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Lynn Petukhova
- Department of Dermatology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jun Zhang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Yufeng Shen
- Department of Systems Biology, Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, New York
| | - Scott J. Hebbring
- Center for Human Genetics, Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | - Halima Moncrieffe
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Leah C. Kottyan
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Bahram Namjou-Khales
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Elizabeth W. Karlson
- Division of Rheumatology, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - John B. Harley
- Department of Pediatrics, Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Ian B. Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - David Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee
| | - Mitchell S.V. Elkind
- Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Ali G. Gharavi
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - George Hripcsak
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Chunhua Weng
- Department of Biomedical Informatics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
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11
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Wang H, Liu M. Complement C4, Infections, and Autoimmune Diseases. Front Immunol 2021; 12:694928. [PMID: 34335607 PMCID: PMC8317844 DOI: 10.3389/fimmu.2021.694928] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Complement C4, a key molecule in the complement system that is one of chief constituents of innate immunity for immediate recognition and elimination of invading microbes, plays an essential role for the functions of both classical (CP) and lectin (LP) complement pathways. Complement C4 is the most polymorphic protein in complement system. A plethora of research data demonstrated that individuals with C4 deficiency are prone to microbial infections and autoimmune disorders. In this review, we will discuss the diversity of complement C4 proteins and its genetic structures. In addition, the current development of the regulation of complement C4 activation and its activation derivatives will be reviewed. Moreover, the review will provide the updates on the molecule interactions of complement C4 under the circumstances of bacterial and viral infections, as well as autoimmune diseases. Lastly, more evidence will be presented to support the paradigm that links microbial infections and autoimmune disorders under the condition of the deficiency of complement C4. We provide such an updated overview that would shed light on current research of complement C4. The newly identified targets of molecular interaction will not only lead to novel hypotheses on the study of complement C4 but also assist to propose new strategies for targeting microbial infections, as well as autoimmune disorders.
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Affiliation(s)
- Hongbin Wang
- Master Program of Pharmaceutical Sciences College of Graduate Studies, California Northstate University, Elk Grove, CA, United States.,Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, California Northstate University, Elk Grove, CA, United States.,Department of Basic Science College of Medicine, California Northstate University, Elk Grove, CA, United States
| | - Mengyao Liu
- Master Program of Pharmaceutical Sciences College of Graduate Studies, California Northstate University, Elk Grove, CA, United States
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12
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Al Naqbi H, Mawart A, Alshamsi J, Al Safar H, Tay GK. Major histocompatibility complex (MHC) associations with diseases in ethnic groups of the Arabian Peninsula. Immunogenetics 2021; 73:131-152. [PMID: 33528690 PMCID: PMC7946680 DOI: 10.1007/s00251-021-01204-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Abstract
Since the discovery of human leukocyte antigens (HLAs), the function of major histocompatibility complex (MHC) gene families in a wide range of diseases have been the subject of research for decades. In particular, the associations of autoimmune disorders to allelic variants and candidate genes encoding the MHC are well documented. However, despite decades of research, the knowledge of MHC associations with human disease susceptibility have been predominantly studied in European origin, with limited understanding in different populations and ethnic groups. This is particularly evident in countries and ethnic populations of the Arabian Peninsula. Human MHC haplotypes, and its association with diseases, of the variable ethnic groups of this region are poorly studied. This review compiled published manuscripts that have reported a list of autoimmune diseases (insulin-dependent diabetes mellitus, systemic lupus erythematosus, myasthenia gravis, rheumatoid arthritis, psoriasis vulgaris, and multiple sclerosis) associated with MHC class I and class II in the populations of the Arabian Peninsula, specifically Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, the United Arab Emirates, and Yemen. Data available was compared with other three ethnic groups, namely Caucasians, Asians, and Africans. The limited data available in the public domain on the association between MHC gene and autoimmune diseases highlight the challenges in the Middle Eastern region.
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Affiliation(s)
- Halima Al Naqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aurélie Mawart
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Jawaher Alshamsi
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Habiba Al Safar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Division of Psychiatry, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, WA, Australia.
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.
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13
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Dilthey AT. State-of-the-art genome inference in the human MHC. Int J Biochem Cell Biol 2021; 131:105882. [PMID: 33189874 DOI: 10.1016/j.biocel.2020.105882] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022]
Abstract
The Major Histocompatibility Complex (MHC) on the short arm of chromosome 6 is associated with more diseases than any other region of the genome; it encodes the antigen-presenting Human Leukocyte Antigen (HLA) proteins and is one of the key immunogenetic regions of the genome. Accurate genome inference and interpretation of MHC association signals have traditionally been hampered by the region's uniquely complex features, such as high levels of polymorphism; inter-gene sequence homologies; structural variation; and long-range haplotype structures. Recent algorithmic and technological advances have, however, significantly increased the accessibility of genetic variation in the MHC; these developments include (i) accurate SNP-based HLA type imputation; (ii) genome graph approaches for variation-aware genome inference from next-generation sequencing data; (iii) long-read-based diploid de novo assembly of the MHC; (iv) cost-effective targeted MHC sequencing methods. Applied to hundreds of thousands of samples over the last years, these technologies have already enabled significant biological discoveries, for example in the field of autoimmune disease genetics. Remaining challenges concern the development of integrated methods that leverage haplotype-resolved de novo assembly of the MHC for the development of improved MHC genotyping methods for short reads and the construction of improved reference panels for SNP-based imputation. Improved genome inference in the MHC can crucially contribute to an improved genetic and functional understanding of many immune-related phenotypes and diseases.
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Affiliation(s)
- Alexander T Dilthey
- Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany; Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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14
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Yandım C, Karakülah G. Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer. Cancer Genet 2019; 239:36-45. [PMID: 31536958 DOI: 10.1016/j.cancergen.2019.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/03/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022]
Abstract
Limited studies on breast cancer indicated pathogenic changes in the expressions of some repeat elements. A global analysis was much needed within this context to distinguish the most significant repeats from more than a thousand repeat motifs. Utilising a previously presented RNA-seq dataset, we studied expression changes of all repeats in ER+/HER2- human breast tumour samples obtained from 22 patients in comparison to matched normal tissues. Fifty six (56) repeat subtypes including satellites and transposons were found to be differentially expressed and most of them were novel for breast cancer. HERVKC4-int and HERV1_LTRc, whose expressions correlated well with that of the estrogen receptor gene ESR1, were upregulated at the highest level. REP522 and D20S16 satellites were also significantly upregulated along with insignificant increases in the expressions of other satellites including HSATI and BSR/beta. Interestingly, expressions of REP522 and D20S16 correlated with many key breast cancer pathway (e.g. BRCA1, BRCA2, AKT1, MTOR, KRAS) and survival genes; possibly highlighting their importance in the carcinogenesis of breast. Additional differentially expressed elements such as L1P and various MER transposons also exhibited a similar pattern. Finally, our repeat enrichment analysis on the promoters of differentially expressed genes revealed further links between additional repeats and nearby genes.
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Affiliation(s)
- Cihangir Yandım
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, İzmir, Turkey; İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, 35340, İnciraltı, İzmir, Turkey
| | - Gökhan Karakülah
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, 35340, İnciraltı, İzmir, Turkey; İzmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, 35340, İnciraltı, İzmir, Turkey.
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15
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Grandi N, Pisano MP, Tramontano E. The emerging field of human endogenous retroviruses: understanding their physiological role and contribution to diseases. Future Virol 2019. [DOI: 10.2217/fvl-2019-0061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Nicole Grandi
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
| | - Maria Paola Pisano
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
| | - Enzo Tramontano
- Department of Life & Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, SS554, 09042 Monserrato (Cagliari), Italy
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Savelli SL, Roubey RAS, Kitzmiller KJ, Zhou D, Nagaraja HN, Mulvihill E, Barbar-Smiley F, Ardoin SP, Wu YL, Yu CY. Opposite Profiles of Complement in Antiphospholipid Syndrome (APS) and Systemic Lupus Erythematosus (SLE) Among Patients With Antiphospholipid Antibodies (aPL). Front Immunol 2019; 10:885. [PMID: 31134052 PMCID: PMC6514053 DOI: 10.3389/fimmu.2019.00885] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 04/05/2019] [Indexed: 12/18/2022] Open
Abstract
APS is the association of antiphospholipid antibodies (aPL) with thromboses and/or recurrent pregnancy loss (RPL). Among patients with SLE, one-third have aPL and 10–15% have a manifestation of secondary APS. Animal studies suggested that complement activation plays an important role in the pathogenesis of thrombosis and pregnancy loss in APS. We performed a cross-sectional study on complement proteins and genes in 525 patients with aPL. Among them, 237 experienced thromboses and 293 had SLE; 111 had both SLE and thromboses, and 106 had neither SLE nor thrombosis. Complement protein levels were determined by radial immunodiffusion for C4, C3 and factor H; and by functional ELISA for mannan binding lectin (MBL). Total C4, C4A and C4B gene copy numbers (GCN) were measured by TaqMan-based realtime PCR. Two to six copies of C4 genes are frequently present in a diploid genome, and each copy may code for an acidic C4A or a basic C4B protein. We observed significantly (a) higher protein levels of total C4, C4A, C4B, C3, and anticardiolipin (ACLA) IgG, (b) increased frequencies of lupus anticoagulant and males, and (c) decreased levels of complement factor H, MBL and ACLA-IgM among patients with thrombosis than those without thrombosis (N = 288). We also observed significantly lower GCNs of total C4 and C4A among aPL-positive patients with both SLE and thrombosis than others. By contrast, aPL-positive subjects with SLE had significantly reduced protein levels of C3, total C4, C4A, C4B and ACLA-IgG, and higher frequency of females than those without SLE. Patients with thrombosis but without SLE (N = 126), and patients with SLE but without thrombosis (N = 182) had the greatest differences in mean protein levels of C3 (p = 2.6 × 10−6), C4 (p = 2.2 × 10−9) and ACLA-IgG (p = 1.2 × 10−5). RPL occurred in 23.7% of female patients and thrombotic SLE patients had the highest frequency of RPL (41.0%; p = 3.8 × 10−10). Compared with non-RPL females, RPL had significantly higher frequency of thrombosis and elevated C4 protein levels. Female patients with homozygous C4A deficiency all experienced RPL (p = 0.0001) but the opposite was true for patients with homozygous C4B deficiency (p = 0.017). These results provide new insights and biomarkers for diagnosis and management of APS and SLE.
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Affiliation(s)
- Stephanie L Savelli
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Division of Hematology/Oncology, Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Robert A S Roubey
- Division of Rheumatology, Allergy and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kathryn J Kitzmiller
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Danlei Zhou
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Haikady N Nagaraja
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH, United States
| | - Evan Mulvihill
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Fatima Barbar-Smiley
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Stacy P Ardoin
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Yee Ling Wu
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, United States
| | - Chack-Yung Yu
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH, United States.,Division of Rheumatology, Nationwide Children's Hospital, Columbus, OH, United States
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Grandi N, Tramontano E. Human Endogenous Retroviruses Are Ancient Acquired Elements Still Shaping Innate Immune Responses. Front Immunol 2018; 9:2039. [PMID: 30250470 PMCID: PMC6139349 DOI: 10.3389/fimmu.2018.02039] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/20/2018] [Indexed: 12/25/2022] Open
Abstract
About 8% of our genome is composed of sequences with viral origin, namely human Endogenous Retroviruses (HERVs). HERVs are relics of ancient infections that affected the primates' germ line along the last 100 million of years, and became stable elements at the interface between self and foreign DNA. Intriguingly, HERV co-evolution with the host led to the domestication of activities previously devoted to the retrovirus life cycle, providing novel cellular functions. For example, selected HERV envelope proteins have been coopted for pregnancy-related purposes, and proviral Long Terminal Repeats participate in the transcriptional regulation of various cellular genes. Given the HERV persistence in the host genome and its basal expression in most healthy tissues, it is reasonable that human defenses should prevent HERV-mediated immune activation. Despite this, HERVs and their products (including RNA, cytosolic DNA, and proteins) are still able to modulate and be influenced by the host immune system, fascinatingly suggesting a central role in the evolution and functioning of the human innate immunity. Indeed, HERV sequences had been major contributors in shaping and expanding the interferon network, dispersing inducible genes that have been occasionally domesticated in various mammalian lineages. Also the HERV integration within or near to genes encoding for critical immune factors has been shown to influence their activity, or to be responsible for their polymorphic variation in the human population, such as in the case of an HERV-K(HML10) provirus in the major histocompatibility complex region. In addition, HERV expressed products have been shown to modulate innate immunity effectors, being therefore often related on the one side to inflammatory and autoimmune disorders, while on the other side to the control of excessive immune activation through their immunosuppressive properties. Finally, HERVs have been proposed to establish a protective effect against exogenous infections. The present review summarizes the involvement of HERVs and their products in innate immune responses, describing how their intricate interplay with the first line of human defenses can actively contribute either to the host protection or to his damage, implying a subtle balance between the persistence of HERV expression and the maintenance of a basal immune alert.
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Affiliation(s)
- Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Cagliari, Italy
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18
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Wallace AD, Wendt GA, Barcellos LF, de Smith AJ, Walsh KM, Metayer C, Costello JF, Wiemels JL, Francis SS. To ERV Is Human: A Phenotype-Wide Scan Linking Polymorphic Human Endogenous Retrovirus-K Insertions to Complex Phenotypes. Front Genet 2018; 9:298. [PMID: 30154825 PMCID: PMC6102640 DOI: 10.3389/fgene.2018.00298] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Approximately 8% of the human genome is comprised of endogenous retroviral insertions (ERVs) originating from historic retroviral integration into germ cells. The function of ERVs as regulators of gene expression is well established. Less well studied are insertional polymorphisms of ERVs and their contribution to the heritability of complex phenotypes. The most recent integration of ERV, HERV-K, is expressed in a range of complex human conditions from cancer to neurologic diseases. Using an in-house computational pipeline and whole-genome sequencing data from the diverse 1,000 Genomes Phase 3 population (n = 2,504), we identified 46 polymorphic HERV-K insertions that are tagged by adjacent single nucleotide polymorphisms (SNPs). To test the potential role of polymorphic HERV-K in the heritability of complex diseases, existing databases were queried for enrichment of established relationships between the HERV-K insertion-associated SNPs (hiSNPs), and tissue specific gene expression and disease phenotypes. Overall, hiSNPs for the 46 polymorphic HERV-K sites were statistically enriched (p < 1.0E-16) for eQTLs across 44 human tissues. Fifteen of the 46 HERV-K insertions had hiSNPs annotated in the EMBL-EBI GWAS Catalog and cumulatively associated with >100 phenotypes. Experimental factor ontology enrichment analysis suggests that polymorphic HERV-K specifically contribute to neurologic and immunologic disease phenotypes, including traits related to intra cranial volume (FDR 2.00E-09), Parkinson's disease (FDR 1.80E-09), and autoimmune diseases (FDR 1.80E-09). These results provide strong candidates for context-specific study of polymorphic HERV-K insertions in disease-related traits, serving as a roadmap for future studies of the heritability of complex disease.
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Affiliation(s)
- Amelia D Wallace
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - George A Wendt
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States
| | - Lisa F Barcellos
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Kyle M Walsh
- Department of Neurosurgery, Duke University, Durham, NC, United States
| | - Catherine Metayer
- Division of Epidemiology, School of Public Health, University of California, Berkeley, Berkeley, CA, United States
| | - Joseph F Costello
- Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.,Department of Neurosurgery, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Stephen S Francis
- Division of Epidemiology, School of Community Health Sciences, University of Nevada, Reno, NV, United States.,Department of Epidemiology and Biostatistics, Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
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Margery-Muir AA, Bundell C, Wetherall JD, Whidborne R, Martinez P, Groth DM. Insights on the relationship between complement component C4 serum concentrations and C4 gene copy numbers in a Western Australian systemic lupus erythematosus cohort. Lupus 2018; 27:1687-1696. [PMID: 30041577 DOI: 10.1177/0961203318787039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The relationship between serum concentration of complement C4 ([C4]) and C4 gene copy number (GCN) was investigated in 56 systemic lupus erythematosus (SLE) patients and 33 age and sex-matched controls in a Western Australian population. C4A and C4B gene copy numbers (C4A & B GCN) together with the presence or absence of the ≈6.4-kb human endogenous retroviral element type K (hereafter HERV-K) in intron 9 were estimated by two TaqMan™ real-time PCR (RT-PCR) assays that measured total C4 and HERV-K GCNs, respectively. There was good correlation between the two methods; however, the HERV-K GCN method showed a positive bias (≈6%) relative to the C4A & B total GCN. Despite individual variation, excellent correlation between total C4 GCN and mean [C4] per GCN was observed for both the SLE and control cohorts ( R2 = 88% and R2 = 99%, respectively). It was noted that serum [C4] was significantly lower in the SLE patients than the controls ( p = 0.006) despite there being no difference between C4A and C4B GCN in both cohorts. The data therefore confirm previous reports that the C4A genes are preferentially associated with the presence of the HERV-K insertion relative to C4B genes and does not support the hypothesis that low [C4] in SLE is explained by low C4A GCNs. There was no evidence also that the presence of the HERV-K insertion in C4 genes influenced [C4]. This study supports the view that low [C4] in SLE patients is due to consumption rather than deficient synthesis related to lower C4A & B GCN.
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Affiliation(s)
- A A Margery-Muir
- 1 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - C Bundell
- 2 PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia
| | - J D Wetherall
- 1 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
| | - R Whidborne
- 3 PathWest Fiona Stanley Hospital (FSH) Network, Clinical Immunology Fiona Stanley Hospital, Murdoch, Australia
| | - P Martinez
- 3 PathWest Fiona Stanley Hospital (FSH) Network, Clinical Immunology Fiona Stanley Hospital, Murdoch, Australia.,4 School of Medicine, Division of Pathology and Laboratory Medicine, Faculty of Health and Medical Science, University of Western Australia, Crawley, Australia
| | - D M Groth
- 1 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, Australia
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Liesmaa I, Paakkanen R, Järvinen A, Valtonen V, Lokki ML. Clinical features of patients with homozygous complement C4A or C4B deficiency. PLoS One 2018; 13:e0199305. [PMID: 29928053 PMCID: PMC6013154 DOI: 10.1371/journal.pone.0199305] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 06/05/2018] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Homozygous deficiencies of complement C4A or C4B are detected in 1-10% of populations. In genome-wide association studies C4 deficiencies are missed because the genetic variation of C4 is complex. There are no studies where the clinical presentation of these patients is analyzed. This study was aimed to characterize the clinical features of patients with homozygous C4A or C4B deficiency. MATERIAL AND METHODS Thirty-two patients with no functional C4A, 87 patients with no C4B and 120 with normal amount of C4 genes were included. C4A and C4B numbers were assessed with genomic quantitative real-time PCR. Medical history was studied retrospectively from patients' files. RESULTS Novel associations between homozygous C4A deficiency and lymphoma, coeliac disease and sarcoidosis were detected. These conditions were present in 12.5%, (4/32 in patients vs. 0.8%, 1/120, in controls, OR = 17.00, 95%CI = 1.83-158.04, p = 0.007), 12.5% (4/32 in patients vs. 0%, 0/120 in controls, OR = 1.14, 95%CI = 1.00-1.30, p = 0.002) and 12.5%, respectively (4/32 in patients vs. 2.5%, 3/120 in controls, OR = 5.571, 95%CI = 1.79-2.32, p = 0.036). In addition, C4A and C4B deficiencies were both associated with adverse drug reactions leading to drug discontinuation (34.4%, 11/32 in C4A-deficient patients vs. 14.2%, 17/120 in controls, OR = 3.174, 95%CI = 1.30-7.74, p = 0.009 and 28.7%, 25/87 in C4B-deficient patients, OR = 2.44, 95%CI = 1.22-4.88, p = 0.010). CONCLUSION This reported cohort of homozygous deficiencies of C4A or C4B suggests that C4 deficiencies may have various unrecorded disease associations. C4 gene should be considered as a candidate gene in studying these selected disease associations.
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Affiliation(s)
- Inka Liesmaa
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- * E-mail:
| | - Riitta Paakkanen
- Transplantation Laboratory, Medicum, University of Helsinki, Helsinki, Finland
- Division of Cardiology, Department of Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Asko Järvinen
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Ville Valtonen
- Division of Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Medicum, University of Helsinki, Helsinki, Finland
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21
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Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
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Grandi N, Cadeddu M, Pisano MP, Esposito F, Blomberg J, Tramontano E. Identification of a novel HERV-K(HML10): comprehensive characterization and comparative analysis in non-human primates provide insights about HML10 proviruses structure and diffusion. Mob DNA 2017; 8:15. [PMID: 29118853 PMCID: PMC5667498 DOI: 10.1186/s13100-017-0099-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022] Open
Abstract
Background About half of the human genome is constituted of transposable elements, including human endogenous retroviruses (HERV). HERV sequences represent the 8% of our genetic material, deriving from exogenous infections occurred millions of years ago in the germ line cells and being inherited by the offspring in a Mendelian fashion. HERV-K elements (classified as HML1–10) are among the most studied HERV groups, especially due to their possible correlation with human diseases. In particular, the HML10 group was reported to be upregulated in persistent HIV-1 infected cells as well as in tumor cells and samples, and proposed to have a role in the control of host genes expression. An individual HERV-K(HML10) member within the major histocompatibility complex C4 gene has even been studied for its possible contribution to type 1 diabetes susceptibility. Following a first characterization of the HML10 group at the genomic level, performed with the innovative software RetroTector, we have characterized in detail the 8 previously identified HML10 sequences present in the human genome, and an additional HML10 partial provirus in chromosome 1p22.2 that is reported here for the first time. Results Using a combined approach based on RetroTector software and a traditional Genome Browser Blat search, we identified a novel HERV-K(HML10) sequence in addition to the eight previously reported in the human genome GRCh37/hg19 assembly. We fully characterized the nine HML10 sequences at the genomic level, including their classification in two types based on both structural and phylogenetic characteristics, a detailed analysis of each HML10 nucleotide sequence, the first description of the presence of an Env Rec domain in the type II HML10, the estimated time of integration of individual members and the comparative map of the HML10 proviruses in non-human primates. Conclusions We performed an unambiguous and exhaustive analysis of the nine HML10 sequences present in GRCh37/hg19 assembly, useful to increase the knowledge of the group’s contribution to the human genome and laying the foundation for a better understanding of the potential physiological effects and the tentative correlation of these sequences with human pathogenesis. Electronic supplementary material The online version of this article (10.1186/s13100-017-0099-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Maria Paola Pisano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Francesca Esposito
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
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Broecker F, Horton R, Heinrich J, Franz A, Schweiger MR, Lehrach H, Moelling K. The intron-enriched HERV-K(HML-10) family suppresses apoptosis, an indicator of malignant transformation. Mob DNA 2016; 7:25. [PMID: 27980690 PMCID: PMC5142424 DOI: 10.1186/s13100-016-0081-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/19/2016] [Indexed: 02/06/2023] Open
Abstract
Background Human endogenous retroviruses (HERVs) constitute 8% of the human genome and contribute substantially to the transcriptome. HERVs have been shown to generate RNAs that modulate host gene expression. However, experimental evidence for an impact of these regulatory transcripts on the cellular phenotype has been lacking. Results We characterized the previously little described HERV-K(HML-10) endogenous retrovirus family on a genome-wide scale. HML-10 invaded the ancestral genome of Old World monkeys about 35 Million years ago and is enriched within introns of human genes when compared to other HERV families. We show that long terminal repeats (LTRs) of HML-10 exhibit variable promoter activity in human cancer cell lines. One identified HML-10 LTR-primed RNA was in opposite orientation to the pro-apoptotic Death-associated protein 3 (DAP3). In HeLa cells, experimental inactivation of HML-10 LTR-primed transcripts induced DAP3 expression levels, which led to apoptosis. Conclusions Its enrichment within introns suggests that HML-10 may have been evolutionary co-opted for gene regulation more than other HERV families. We demonstrated such a regulatory activity for an HML-10 RNA that suppressed DAP3-mediated apoptosis in HeLa cells. Since HML-10 RNA appears to be upregulated in various tumor cell lines and primary tumor samples, it may contribute to evasion of apoptosis in malignant cells. However, the overall weak expression of HML-10 transcripts described here raises the question whether our result described for HeLa represent a rare event in cancer. A possible function in other cells or tissues requires further investigation. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0081-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Felix Broecker
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland ; Current affiliation: Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14424 Potsdam, Germany
| | - Roger Horton
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Jochen Heinrich
- Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
| | - Alexandra Franz
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: University of Zurich, Institute of Molecular Life Sciences, Winterthurerstr. 190, 8057 Zurich, Switzerland
| | - Michal-Ruth Schweiger
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Current affiliation: Functional Epigenomics, CCG, Cologne University Hospital, University of Cologne, Weyertal 115b, 50931 Cologne, Germany
| | - Hans Lehrach
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Dahlem Centre for Genome Research and Medical Systems Biology, Fabeckstr. 60-62, 14195 Berlin, Germany
| | - Karin Moelling
- Max Planck Institute for molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany ; Institute of Medical Microbiology, University of Zurich, Gloriastr. 32, 8006 Zurich, Switzerland
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24
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Grandi N, Cadeddu M, Blomberg J, Tramontano E. Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. Retrovirology 2016; 13:67. [PMID: 27613107 PMCID: PMC5016936 DOI: 10.1186/s12977-016-0301-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/23/2016] [Indexed: 12/21/2022] Open
Abstract
Background Human endogenous retroviruses (HERVs) are ancient sequences integrated in the germ line cells and vertically transmitted through the offspring constituting about 8 % of our genome. In time, HERVs accumulated mutations that compromised their coding capacity. A prominent exception is HERV-W locus 7q21.2, producing a functional Env protein (Syncytin-1) coopted for placental syncytiotrophoblast formation. While expression of HERV-W sequences has been investigated for their correlation to disease, an exhaustive description of the group composition and characteristics is still not available and current HERV-W group information derive from studies published a few years ago that, of course, used the rough assemblies of the human genome available at that time. This hampers the comparison and correlation with current human genome assemblies. Results In the present work we identified and described in detail the distribution and genetic composition of 213 HERV-W elements. The bioinformatics analysis led to the characterization of several previously unreported features and provided a phylogenetic classification of two main subgroups with different age and structural characteristics. New facts on HERV-W genomic context of insertion and co-localization with sequences putatively involved in disease development are also reported. Conclusions The present work is a detailed overview of the HERV-W contribution to the human genome and provides a robust genetic background useful to clarify HERV-W role in pathologies with poorly understood etiology, representing, to our knowledge, the most complete and exhaustive HERV-W dataset up to date. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0301-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicole Grandi
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Marta Cadeddu
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy
| | - Jonas Blomberg
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato SS554, 09042, Monserrato, Cagliari, Italy. .,Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy.
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Lintner KE, Wu YL, Yang Y, Spencer CH, Hauptmann G, Hebert LA, Atkinson JP, Yu CY. Early Components of the Complement Classical Activation Pathway in Human Systemic Autoimmune Diseases. Front Immunol 2016; 7:36. [PMID: 26913032 PMCID: PMC4753731 DOI: 10.3389/fimmu.2016.00036] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/24/2016] [Indexed: 01/06/2023] Open
Abstract
The complement system consists of effector proteins, regulators, and receptors that participate in host defense against pathogens. Activation of the complement system, via the classical pathway (CP), has long been recognized in immune complex-mediated tissue injury, most notably systemic lupus erythematosus (SLE). Paradoxically, a complete deficiency of an early component of the CP, as evidenced by homozygous genetic deficiencies reported in human, are strongly associated with the risk of developing SLE or a lupus-like disease. Similarly, isotype deficiency attributable to a gene copy-number (GCN) variation and/or the presence of autoantibodies directed against a CP component or a regulatory protein that result in an acquired deficiency are relatively common in SLE patients. Applying accurate assay methodologies with rigorous data validations, low GCNs of total C4, and heterozygous and homozygous deficiencies of C4A have been shown as medium to large effect size risk factors, while high copy numbers of total C4 or C4A as prevalent protective factors, of European and East-Asian SLE. Here, we summarize the current knowledge related to genetic deficiency and insufficiency, and acquired protein deficiencies for C1q, C1r, C1s, C4A/C4B, and C2 in disease pathogenesis and prognosis of SLE, and, briefly, for other systemic autoimmune diseases. As the complement system is increasingly found to be associated with autoimmune diseases and immune-mediated diseases, it has become an attractive therapeutic target. We highlight the recent developments and offer a balanced perspective concerning future investigations and therapeutic applications with a focus on early components of the CP in human systemic autoimmune diseases.
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Affiliation(s)
- Katherine E Lintner
- Center for Molecular and Human Genetics, Division of Pediatric Rheumatology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University , Columbus, OH , USA
| | - Yee Ling Wu
- Center for Molecular and Human Genetics, Division of Pediatric Rheumatology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University , Columbus, OH , USA
| | - Yan Yang
- Center for Molecular and Human Genetics, Division of Pediatric Rheumatology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University , Columbus, OH , USA
| | - Charles H Spencer
- Center for Molecular and Human Genetics, Division of Pediatric Rheumatology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University , Columbus, OH , USA
| | - Georges Hauptmann
- Laboratoire d'Immuno-Rhumatologie Moleculaire, INSERM UMR_S 1109, LabEx Transplantex, Faculté de Médecine, Université de Strasbourg , Strasbourg , France
| | - Lee A Hebert
- Division of Nephrology, College of Medicine, The Ohio State University , Columbus, OH , USA
| | - John P Atkinson
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine , St. Louis, MO , USA
| | - C Yung Yu
- Center for Molecular and Human Genetics, Division of Pediatric Rheumatology, Department of Pediatrics, Nationwide Children's Hospital, The Ohio State University , Columbus, OH , USA
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Sekar A, Bialas AR, de Rivera H, Davis A, Hammond TR, Kamitaki N, Tooley K, Presumey J, Baum M, Van Doren V, Genovese G, Rose SA, Handsaker RE, Daly MJ, Carroll MC, Stevens B, McCarroll SA. Schizophrenia risk from complex variation of complement component 4. Nature 2016; 530:177-83. [PMID: 26814963 PMCID: PMC4752392 DOI: 10.1038/nature16549] [Citation(s) in RCA: 1554] [Impact Index Per Article: 194.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 12/18/2015] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a heritable brain illness with unknown pathogenic mechanisms. Schizophrenia's strongest genetic association at a population level involves variation in the major histocompatibility complex (MHC) locus, but the genes and molecular mechanisms accounting for this have been challenging to identify. Here we show that this association arises in part from many structurally diverse alleles of the complement component 4 (C4) genes. We found that these alleles generated widely varying levels of C4A and C4B expression in the brain, with each common C4 allele associating with schizophrenia in proportion to its tendency to generate greater expression of C4A. Human C4 protein localized to neuronal synapses, dendrites, axons, and cell bodies. In mice, C4 mediated synapse elimination during postnatal development. These results implicate excessive complement activity in the development of schizophrenia and may help explain the reduced numbers of synapses in the brains of individuals with schizophrenia.
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Affiliation(s)
- Aswin Sekar
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Allison R Bialas
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Heather de Rivera
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Avery Davis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Timothy R Hammond
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Katherine Tooley
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jessy Presumey
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Matthew Baum
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- MD-PhD Program, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vanessa Van Doren
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Samuel A Rose
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Robert E Handsaker
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Michael C Carroll
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA
| | - Beth Stevens
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Department of Neurology, F.M. Kirby Neurobiology Center, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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Lintner KE, Patwardhan A, Rider LG, Abdul-Aziz R, Wu YL, Lundström E, Padyukov L, Zhou B, Alhomosh A, Newsom D, White P, Jones KB, O'Hanlon TP, Miller FW, Spencer CH, Yu CY. Gene copy-number variations (CNVs) of complement C4 and C4A deficiency in genetic risk and pathogenesis of juvenile dermatomyositis. Ann Rheum Dis 2015; 75:1599-606. [PMID: 26493816 DOI: 10.1136/annrheumdis-2015-207762] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/20/2015] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Complement-mediated vasculopathy of muscle and skin are clinical features of juvenile dermatomyositis (JDM). We assess gene copy-number variations (CNVs) for complement C4 and its isotypes, C4A and C4B, in genetic risks and pathogenesis of JDM. METHODS The study population included 105 patients with JDM and 500 healthy European Americans. Gene copy-numbers (GCNs) for total C4, C4A, C4B and HLA-DRB1 genotypes were determined by Southern blots and qPCRs. Processed activation product C4d bound to erythrocytes (E-C4d) was measured by flow cytometry. Global gene-expression microarrays were performed in 19 patients with JDM and seven controls using PAXgene-blood RNA. Differential expression levels for selected genes were validated by qPCR. RESULTS Significantly lower GCNs and differences in distribution of GCN groups for total C4 and C4A were observed in JDM versus controls. Lower GCN of C4A in JDM remained among HLA DR3-positive subjects (p=0.015). Homozygous or heterozygous C4A-deficiency was present in 40.0% of patients with JDM compared with 18.2% of controls (OR=3.00 (1.87 to 4.79), p=8.2×10(-6)). Patients with JDM had higher levels of E-C4d than controls (p=0.004). In JDM, C4A-deficient subjects had higher levels of E-C4d (p=0.0003) and higher frequency of elevated levels of multiple serum muscle enzymes at diagnosis (p=0.0025). Microarray profiling of blood RNA revealed upregulation of type I interferon-stimulated genes and lower abundance of transcripts for T-cell and chemokine function genes in JDM, but this was less prominent among C4A-deficient or DR3-positive patients. CONCLUSIONS Complement C4A deficiency appears to be an important factor for the genetic risk and pathogenesis of JDM, particularly in patients with a DR3-positive background.
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Affiliation(s)
- Katherine E Lintner
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Anjali Patwardhan
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Rabheh Abdul-Aziz
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Yee Ling Wu
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Emeli Lundström
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Bi Zhou
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Alaaedin Alhomosh
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - David Newsom
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Peter White
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Karla B Jones
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Terrance P O'Hanlon
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles H Spencer
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
| | - Chack Yung Yu
- Department of Pediatrics, The Research Institute at Nationwide Children's Hospital, The Ohio State University, Columbus, Ohio, USA
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28
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Chen L, Zhou W, Zhang L, Zhang F. Genome architecture and its roles in human copy number variation. Genomics Inform 2014; 12:136-44. [PMID: 25705150 PMCID: PMC4330246 DOI: 10.5808/gi.2014.12.4.136] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/12/2014] [Accepted: 11/12/2014] [Indexed: 02/06/2023] Open
Abstract
Besides single-nucleotide variants in the human genome, large-scale genomic variants, such as copy number variations (CNVs), are being increasingly discovered as a genetic source of human diversity and the pathogenic factors of diseases. Recent experimental findings have shed light on the links between different genome architectures and CNV mutagenesis. In this review, we summarize various genomic features and discuss their contributions to CNV formation. Genomic repeats, including both low-copy and high-copy repeats, play important roles in CNV instability, which was initially known as DNA recombination events. Furthermore, it has been found that human genomic repeats can also induce DNA replication errors and consequently result in CNV mutations. Some recent studies showed that DNA replication timing, which reflects the high-order information of genomic organization, is involved in human CNV mutations. Our review highlights that genome architecture, from DNA sequence to high-order genomic organization, is an important molecular factor in CNV mutagenesis and human genomic instability.
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Affiliation(s)
- Lu Chen
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Weichen Zhou
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ling Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Feng Zhang
- School of Life Sciences, Fudan University, Shanghai 200438, China. ; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China
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Margery-Muir AA, Wetherall JD, Castley ASL, Hew M, Whidborne RS, Mallon DFJ, Martinez P, Witt CS. Establishment of Gene Copy Number-Specific Normal Ranges for Serum C4 and Its Utility for Interpretation in Patients With Chronically Low Serum C4 Concentrations. Arthritis Rheumatol 2014; 66:2512-20. [DOI: 10.1002/art.38680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 04/17/2014] [Indexed: 12/18/2022]
Affiliation(s)
- Audrey A. Margery-Muir
- Curtin University School of Biomedical Sciences, Bentley Campus; Perth, Western Australia Australia
| | - John D. Wetherall
- Curtin University School of Biomedical Sciences, Bentley Campus; Perth, Western Australia Australia
| | | | - Meilyn Hew
- PathWest, Royal Perth Hospital, Perth, Western Australia and University Department of Medicine and Dentistry Fremantle Hospital; Fremantle, Western Australia Australia
| | | | | | - Patricia Martinez
- PathWest, Royal Perth Hospital, Perth, Western Australia and School of Pathology and Laboratory Medicine, University of Western Australia; Nedlands, Western Australia Australia
| | - Campbell S. Witt
- PathWest, Royal Perth Hospital, Perth, Western Australia and School of Pathology and Laboratory Medicine, University of Western Australia; Nedlands, Western Australia Australia
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30
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Flachsbart F, Caliebe A, Heinsen FA, Hemming-Karlsen T, Schreiber S, Franke A, Nebel A. Investigation of complement component C4 copy number variation in human longevity. PLoS One 2014; 9:e86188. [PMID: 24465950 PMCID: PMC3899116 DOI: 10.1371/journal.pone.0086188] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 12/06/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic factors have been estimated to account for about 25% of the variation in an adult's life span. The complement component C4 with the isotypes C4A and C4B is an effector protein of the immune system, and differences in the overall C4 copy number or gene size (long C4L; short C4S) may influence the strength of the immune response and disease susceptibilities. Previously, an association between C4B copy number and life span was reported for Hungarians and Icelanders, where the C4B*Q0 genotype, which is defined by C4B gene deficiency, showed a decrease in frequency with age. Additionally, one of the studies indicated that a low C4B copy number might be a genetic trait that is manifested only in the presence of the environmental risk factor "smoking". These observations prompted us to investigate the role of the C4 alleles in our large German longevity sample (∼ 700 cases; 94-110 years and ∼ 900 younger controls). No significant differences in the number of C4A, C4B and C4S were detected. Besides, the C4B*Q0 carrier state did not decrease with age, irrespective of smoking as an interacting variable. However, for C4L*Q0 a significantly different carrier frequency was observed in the cases compared with controls (cases: 5.08%; controls: 9.12%; p = 0.003). In a replication sample of 714 German cases (91-108 years) and 890 controls this result was not replicated (p = 0.14) although a similar trend of decreased C4L*Q0 carrier frequency in cases was visible (cases: 7.84%; controls: 10.00%).
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Affiliation(s)
- Friederike Flachsbart
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Amke Caliebe
- Institute of Medical Informatics and Statistics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Femke-Anouska Heinsen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom Hemming-Karlsen
- Norwegian PSC Research Center, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute for Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Division of Gastroenterology, Institute of Medicine, University of Bergen, Bergen, Norway
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- Department of General Medicine, University Hospital Schleswig-Holstein, Kiel, Germany
- Popgen Biobank, Christian-Albrechts-University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
- * E-mail:
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32
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Yu HL, Zhao ZK, Zhu F. The role of human endogenous retroviral long terminal repeat sequences in human cancer (Review). Int J Mol Med 2013; 32:755-62. [PMID: 23900638 DOI: 10.3892/ijmm.2013.1460] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/30/2013] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retrovirus (HERV) and solitary long terminal repeats (LTRs) constitute 8% of the human genome. Although most HERV genes are partially deleted and not intact, HERV LTRs comprise features including promoters, enhancers, selective splicer sites and polyadenylation sites in order to regulate the expression of neighboring genes. Owing to the genetic instability of LTRs, their wide distributions along human chromosomes are not only non-random, but are also correlated with gene density. Considerable evidence indicates that HERV LTRs regulate the expression of their adjacent viral and cellular genes in placental development and tumorigenesis. However, the regulatory mechanism of HERV LTRs on the expression of its neighboring cancer-associated genes in human cancers remains to be elucidated. Insertional mutagenesis, recombination and polymorphism are three principal factors of LTR that contribute to its genetic instability. Moreover, genetic instability, hypomethylation, transactivation and the antisense transcript of LTRs enhance the activity of LTRs and regulate the expression of their adjacent genes in human cancers. Therefore, in the present review, we examined the mechanism of HERV LTRs in tumorigenesis in combination with the structure and function of LTRs.
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Affiliation(s)
- Hong-Lian Yu
- Department of Medical Microbiology, School of Medicine, Wuhan University, Wuhan, Hubei 430071, PR China
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Bánlaki Z, Szabó JA, Szilágyi Á, Patócs A, Prohászka Z, Füst G, Doleschall M. Intraspecific evolution of human RCCX copy number variation traced by haplotypes of the CYP21A2 gene. Genome Biol Evol 2013; 5:98-112. [PMID: 23241443 PMCID: PMC3595039 DOI: 10.1093/gbe/evs121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The RCCX region is a complex, multiallelic, tandem copy number variation (CNV). Two complete genes, complement component 4 (C4) and steroid 21-hydroxylase (CYP21A2, formerly CYP21B), reside in its variable region. RCCX is prone to nonallelic homologous recombination (NAHR) such as unequal crossover, generating duplications and deletions of RCCX modules, and gene conversion. A series of allele-specific long-range polymerase chain reaction coupled to the whole-gene sequencing of CYP21A2 was developed for molecular haplotyping. By means of the developed techniques, 35 different kinds of CYP21A2 haplotype variant were experimentally determined from 112 unrelated European subjects. The number of the resolved CYP21A2 haplotype variants was increased to 61 by bioinformatic haplotype reconstruction. The CYP21A2 haplotype variants could be assigned to the haplotypic RCCX CNV structures (the copy number of RCCX modules) in most cases. The genealogy network constructed from the CYP21A2 haplotype variants delineated the origin of RCCX structures. The different RCCX structures were located in tight groups. The minority of groups with identical RCCX structure occurred once in the network, implying monophyletic origin, but the majority of groups occurred several times and in different locations, indicating polyphyletic origin. The monophyletic groups were often created by single unequal crossover, whereas recurrent unequal crossover events generated some of the polyphyletic groups. As a result of recurrent NAHR events, more CYP21A2 haplotype variants with different allele patterns belonged to the same RCCX structure. The intraspecific evolution of RCCX CNV described here has provided a reasonable expectation for that of complex, multiallelic, tandem CNVs in humans.
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Affiliation(s)
- Zsófia Bánlaki
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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Castley ASL, Martinez OP. Molecular analysis of complement component C4 gene copy number. Methods Mol Biol 2012; 882:159-71. [PMID: 22665233 DOI: 10.1007/978-1-61779-842-9_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Classical, alternative, or lectin pathways may activate the complement system cascade. The classical pathway includes the C4 protein and functions in the prevention of immune complex precipitation and in clearance of immune complexes.Two isotypes of C4-C4A and C4B-are coded by genes located at two loci within the major histocompatibility complex (MHC) on chromosome 6. While these isotypes share over 99% amino acid sequence homology, five nucleotide differences located in exon 26 are responsible for major structural and functional differences between the C4 isotypes.C4A and C4B are highly polymorphic with over 40 alleles, gene duplications, and "null alleles". C4 genes may be short (14.6 kb) or long (21 kb), due to the absence or presence of an endogenous retroviral sequence-HERV-K(C4)-in intron 9, respectively. The C4 gene copy number (GCN) can vary from 1-3 per haplotype or 2-6 per diploid genome. The variation in GCN leads to a range of C4 plasma protein concentrations among healthy subjects. In subjects with equal numbers of C4 genes, subjects with short genes have C4 plasma levels relatively higher than subjects with long genes.Variation of the C4 GCN, the gene size (long or short) and the C4 isotypes (C4A and C4B) may also lead to susceptibility to autoimmune disease. Therefore, in subjects with autoimmune disease, a low serum C4 level may be due to ongoing disease activity associated with complement activation and consumption or it may be due to genetic factors. Distinguishing between these will have clinical implications.Exact determination of GCN can be difficult, at least in part due to the high degree of homology between C4A and C4B and a variety of techniques has been described. This chapter describes a quantitative TaqMan real-time PCR (qPCR) copy number assay, based on our laboratory experience using this assay.
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Affiliation(s)
- Alison S L Castley
- Department of Clinical Immunology, PathWest Laboratory Medicine, Royal Perth Hospital, Perth, WA, Australia
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35
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Fernando MM, Boteva L, Morris DL, Zhou B, Wu YL, Lokki ML, Yu CY, Rioux JD, Hollox EJ, Vyse TJ. Assessment of complement C4 gene copy number using the paralog ratio test. Hum Mutat 2010; 31:866-74. [PMID: 20506482 PMCID: PMC3567757 DOI: 10.1002/humu.21259] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The complement C4 locus is in the class III region of the MHC, and exhibits copy number variation. Complement C4 null alleles have shown association with a number of diseases including systemic lupus erythematosus (SLE). However, most studies to date have used protein immunophenotyping and not direct interrogation of the genome to determine C4 null allele status. Moreover, a lack of accurate C4 gene copy number (GCN) estimation and tight linkage disequilibrium across the disease-associated MHC haplotypes has confounded attempts to establish whether or not these associations are causal. We have therefore developed a high throughput paralog ratio test (PRT) in association with two restriction enzyme digest variant ratio tests (REDVRs) to determine total C4 GCN, C4A GCN, and C4B GCN. In the densely genotyped CEU cohort we show that this method is accurate and reproducible when compared to gold standard Southern blot copy number estimation with a discrepancy rate of 9%. We find a broad range of C4 GCNs in the CEU and the 1958 British Birth Cohort populations under study. In addition, SNP-C4 CNV analyses show only moderate levels of correlation and therefore do not support the use of SNP genotypes as proxies for complement C4 GCN.
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Affiliation(s)
- Michelle M.A. Fernando
- Section of Rheumatology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Lora Boteva
- Section of Rheumatology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - David L. Morris
- Section of Rheumatology, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Bi Zhou
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
| | - Yee Ling Wu
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Chack Yung Yu
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
| | - John D. Rioux
- Montréal Heart Institute, Montréal, Quebec, Canada
- Université de Montréal, Montréal, Quebec, Canada
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Timothy J. Vyse
- Section of Rheumatology, Faculty of Medicine, Imperial College London, London, United Kingdom
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Coeli FB, Soardi FC, Bernardi RD, de Araújo M, Paulino LC, Lau IF, Petroli RJ, de Lemos-Marini SHV, Baptista MTM, Guerra-Júnior G, de-Mello MP. Novel deletion alleles carrying CYP21A1P/A2 chimeric genes in Brazilian patients with 21-hydroxylase deficiency. BMC MEDICAL GENETICS 2010; 11:104. [PMID: 20587039 PMCID: PMC3161346 DOI: 10.1186/1471-2350-11-104] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2009] [Accepted: 06/29/2010] [Indexed: 11/10/2022]
Abstract
BACKGROUND Congenital adrenal hyperplasia due to 21-hydroxylase deficiency is caused by deletions, large gene conversions or mutations in CYP21A2 gene. The human gene is located at 6p21.3 within a locus containing the genes for putative serine/threonine Kinase RP, complement C4, steroid 21-hydroxylase CYP21 tenascin TNX, normally, in a duplicated cluster known as RCCX module. The CYP21 extra copy is a pseudogene (CYP21A1P). In Brazil, 30-kb deletion forming monomodular alleles that carry chimeric CYP21A1P/A2 genes corresponds to ~9% of disease-causing alleles. Such alleles are considered to result from unequal crossovers within the bimodular C4/CYP21 locus. Depending on the localization of recombination breakpoint, different alleles can be generated conferring the locus high degree of allelic variability. The purpose of the study was to investigate the variability of deleted alleles in patients with 21-hydroxylase deficiency. METHODS We used different techniques to investigate the variability of 30-kb deletion alleles in patients with 21-hydroxylase deficiency. Alleles were first selected after Southern blotting. The composition of CYP21A1P/A2 chimeric genes was investigated by ASO-PCR and MLPA analyses followed by sequencing to refine the location of recombination breakpoints. Twenty patients carrying at least one allele with C4/CYP21 30-kb deletion were included in the study. RESULTS An allele carrying a CYP21A1P/A2 chimeric gene was found unusually associated to a C4B/C4A Taq I 6.4-kb fragment, generally associated to C4B and CYP21A1P deletions. A novel haplotype bearing both p.P34L and p.H62L, novel and rare mutations, respectively, was identified in exon 1, however p.P30L, the most frequent pseudogene-derived mutation in this exon, was absent. Four unrelated patients showed this haplotype. Absence of p.P34L in CYP21A1P of normal controls indicated that it is not derived from pseudogene. In addition, the combination of different approaches revealed nine haplotypes for deleted 21-hydroxylase deficiency alleles. CONCLUSIONS This study demonstrated high allelic variability for 30-kb deletion in patients with 21-hydroxylase deficiency indicating that a founder effect might be improbable for most monomodular alleles carrying CYP21A1P/A2 chimeric genes in Brazil.
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Affiliation(s)
- Fernanda B Coeli
- Laboratório de Genética Molecular Humana, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brasil
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Kallel-Sellami M, Laadhar L, Zerzeri Y, Makni S. Complement deficiency and systemic lupus erythematosus: consensus and dilemma. Expert Rev Clin Immunol 2010; 4:629-37. [PMID: 20476965 DOI: 10.1586/1744666x.4.5.629] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The involvement of the complement system in the pathogenesis of autoimmune diseases is a matter of debate. However, the link between complement abnormalities and systemic lupus erythematosus (SLE) is well established and widely described. Homozygous and/or heterozygous complement-component deficiencies of the classical pathway (C1q, C1r, C1s, C4A, C4B and C2) are causally associated with susceptibility to the development of SLE. Although the severity of the disease and the strength of the association are heterogeneous for deficiencies of these proteins, they commonly cause peculiar SLE syndromes with an early age of onset, a susceptibility to bacterial infections and negative anti-dsDNA antibodies. In this review, we highlight the available data on complement deficiency and SLE with a focus on deficiencies in classical complement pathway components. We also discuss the paradox of the link between complement deficiency and lupus. The complement system acts as a 'friend' through the clearance of immune complexes and apoptotic cells, which explains the close association between complement deficiency and lupus. It also acts as an 'enemy' by participating in the effector inflammatory phase of the autoimmune response. Understanding the importance of complement deficiencies should provide novel targets for therapeutic interventions in the modulation of the immune response.
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Balada E, Ordi-Ros J, Vilardell-Tarrés M. Molecular mechanisms mediated by human endogenous retroviruses (HERVs) in autoimmunity. Rev Med Virol 2009; 19:273-86. [DOI: 10.1002/rmv.622] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wu YL, Hauptmann G, Viguier M, Yu CY. Molecular basis of complete complement C4 deficiency in two North-African families with systemic lupus erythematosus. Genes Immun 2009; 10:433-45. [PMID: 19279649 PMCID: PMC2767122 DOI: 10.1038/gene.2009.10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/03/2009] [Accepted: 02/03/2009] [Indexed: 11/09/2022]
Abstract
Complete deficiency of complement C4 is among the strongest genetic risk factors for human systemic lupus erythematosus (SLE). C4 is a constituent of the RP-C4-CYP21-TNX (RCCX) module in the human leukocyte antigen (HLA) that exhibits inter-individual copy-number and gene-size variations. Here, we studied two North-African families with complete C4 deficiency and SLE. The first included a Moroccan male SLE patient (1P) and a sibling, who were both homozygous for HLA-A*02 B*17 DRB1*07. The second had an Algerian female SLE patient (2P) homozygous for HLA-A*01 B*17 DRB1*13. Early SLE disease onset, the presence of photosensitive rashes, anti-Ro/SSA, renal disease and high titers of antinuclear antibodies were the common features of complete C4 deficiency. Southern blot analyses showed that 1P had monomodular RCCX with a long C4A, whereas 2P had bimodular RCCX with one long C4A and one short C4B. Genomic DNA fragments for these mutant genes were amplified and sequenced. A C>T transition that created the R540X nonsense mutation in C4A was found in 1P. An identical 4-bp insertion that generated the Y1537X nonsense mutation was discovered in both C4A and C4B of 2P. The high concordance of SLE and C4 deficiency among patients with non-DR3 and non-DR2 haplotypes underscores the importance of C4 proteins in the protection against SLE.
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Affiliation(s)
- Yee Ling Wu
- Center for Molecular and Human Genetics, the Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
- Integrated Biomedical Science Graduate Program, The Ohio State University, Columbus, Ohio
| | - Georges Hauptmann
- Laboratoire d’Immunogenetique Moleculaire, Universite Louis Pasteur, Strasbourg, Cedex, France
| | - Manuelle Viguier
- Service de Dermatologie, Hôpital Saint-Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - C. Yung Yu
- Center for Molecular and Human Genetics, the Research Institute at Nationwide Children’s Hospital, Columbus, Ohio
- Integrated Biomedical Science Graduate Program, The Ohio State University, Columbus, Ohio
- Department of Pediatrics, The Ohio State University, 700 Children’s Drive, Columbus, Ohio 43205, USA
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, 700 Children’s Drive, Columbus, Ohio 43205, USA
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Saxena K, Kitzmiller KJ, Wu YL, Zhou B, Esack N, Hiremath L, Chung EK, Yang Y, Yu CY. Great genotypic and phenotypic diversities associated with copy-number variations of complement C4 and RP-C4-CYP21-TNX (RCCX) modules: a comparison of Asian-Indian and European American populations. Mol Immunol 2009; 46:1289-303. [PMID: 19135723 PMCID: PMC2716727 DOI: 10.1016/j.molimm.2008.11.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Accepted: 11/22/2008] [Indexed: 01/26/2023]
Abstract
Inter-individual gene copy-number variations (CNVs) probably afford human populations the flexibility to respond to a variety of environmental challenges, but also lead to differential disease predispositions. We investigated gene CNVs for complement component C4 and steroid 21-hydroxylase from the RP-C4-CYP21-TNX (RCCX) modules located in the major histocompatibility complex among healthy Asian-Indian Americans (AIA) and compared them to European Americans. A combination of definitive techniques that yielded cross-confirmatory results was used. The medium gene copy-numbers for C4 and its isotypes, acidic C4A and basic C4B, were 4, 2 and 2, respectively, but their frequencies were only 53-56%. The distribution patterns for total C4 and C4A are skewed towards the high copy-number side. For example, the frequency of AIA-subjects with three copies of C4A (30.7%) was 3.92-fold of those with a single copy (7.83%). The monomodular-short haplotype with a single C4B gene and the absence of C4A, which is in linkage-disequilibrium with HLA DRB1*0301 in Europeans and a strong risk factor for autoimmune diseases, has a frequency of 0.012 in AIA but 0.106 among healthy European Americans (p=6.6x10(-8)). The copy-number and the size of C4 genes strongly determine the plasma C4 protein concentrations. Parallel variations in copy-numbers of CYP21A (CYP21A1P) and TNXA with total C4 were also observed. Notably, 13.1% of AIA-subjects had three copies of the functional CYP21B, which were likely generated by recombinations between monomodular and bimodular RCCX haplotypes. The high copy-numbers of C4 and the high frequency of RCCX recombinants offer important insights to the prevalence of autoimmune and genetic diseases.
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Affiliation(s)
- Kapil Saxena
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
| | - Kathryn J. Kitzmiller
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Yee Ling Wu
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Bi Zhou
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
| | - Nazreen Esack
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
| | - Leena Hiremath
- Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Erwin K. Chung
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio
| | - Yan Yang
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio
| | - C. Yung Yu
- Center for Molecular and Human Genetics, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus Ohio 43205
- Department of Pediatrics, The Ohio State University, Columbus, Ohio
- Department of Molecular Virology, Immunology and Medical Genetics, The Ohio State University, Columbus, Ohio
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Wouters D, van Schouwenburg P, van der Horst A, de Boer M, Schooneman D, Kuijpers TW, Aarden LA, Hamann D. High-throughput analysis of the C4 polymorphism by a combination of MLPA and isotype-specific ELISA's. Mol Immunol 2009; 46:592-600. [DOI: 10.1016/j.molimm.2008.07.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Revised: 07/23/2008] [Accepted: 07/25/2008] [Indexed: 11/30/2022]
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Human endogenous retrovirus (HERV-K) reverse transcriptase as a breast cancer prognostic marker. Neoplasia 2008; 10:521-33. [PMID: 18516289 DOI: 10.1593/neo.07986] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Revised: 03/27/2008] [Accepted: 03/29/2008] [Indexed: 11/18/2022] Open
Abstract
A reverse transcriptase (RT) cDNA, designated HERV-K-T47D-RT, was isolated from a hormonally treated human breast cancer cell line. The protein product putative sequence is 97% identical to the human endogenous HERV-K retroviral sequences. Recombinant T47D-RT protein was used to generate polyclonal antibodies. The expression of HERV-K-T47D-RT protein increased in T47D cells after treatment with estrogen and progesterone. The RT-associated DNA polymerase activity was substantially increased after over-expressing a chimeric YFP-HERV-K-T47D-RT protein in cells. This RT-associated polymerase activity was significantly reduced by mutating the active site sequence YIDD to SIAA. Moreover, the endogenous RT activity observed in T47D cells was decreased by HERV-K-T47D-RT-specific siRNA, confirming the dependence of the endogenous enzymatic activity. To assess HERV-K-T47D-RT expression in human breast tumors, 110 paraffin sections of breast carcinoma biopsies were stained and subjected to confocal analysis. Twenty-six percent (28/110) of the tumor tissues and 18% (15/85) of the adjacent normal tissue, from the same patients, expressed the RT. HERV-K-T47D-RT expression significantly correlates with poor prognosis for disease-free patients and their overall survival. These results imply that HERV-K-T47D-RT might be expressed in early malignancy and might serve as a novel prognostic marker for breast cancer. Furthermore, these results provide evidence for the possible involvement of endogenous retrovirus in human breast carcinoma.
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Kulski JK, Shigenari A, Shiina T, Ota M, Hosomichi K, James I, Inoko H. Human endogenous retrovirus (HERVK9) structural polymorphism with haplotypic HLA-A allelic associations. Genetics 2008; 180:445-57. [PMID: 18757922 PMCID: PMC2535695 DOI: 10.1534/genetics.108.090340] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 07/09/2008] [Indexed: 11/18/2022] Open
Abstract
The frequency and HLA-A allelic associations of a HERVK9 DNA structural polymorphism located in close proximity to the highly polymorphic HLA-A gene within the major histocompatibility complex (MHC) genomic region were determined in Japanese, African Americans, and Australian Caucasians to better understand its human population evolutionary history. The HERVK9 insertion or deletion was detected as a 3' LTR or a solo LTR, respectively, by separate PCR assays. The average insertion frequency of the HERVK9.HG was significantly different (P < 1.083e(-6)) between the Japanese (0.59) and the African Americans (0.34) or Australian Caucasians (0.37). LD analysis predicted a highly significant (P < 1.0e(-5)) linkage between the HLA-A and HERVK9 alleles, probably as a result of hitchhiking (linkage). Evolutionary time estimates of the solo, 5' and 3' LTR nucleotide sequence divergences suggest that the HERVK9 was inserted 17.3 MYA with the first structural deletion occurring 15.1 MYA. The LTR/HLA-A haplotypes appear to have been formed mostly during the past 3.9 MY. The HERVK9 insertion and deletion, detected by a simple and economical PCR method, is an informative genetic and evolutionary marker for the study of HLA-A haplotype variations, human migration, the origins of contemporary populations, and the possibility of disease associations.
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Affiliation(s)
- Jerzy K Kulski
- Centre for Forensic Science, The University of Western Australia, Nedlands, Western Australia, Australia.
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44
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Chung EK, Wu YL, Yang Y, Zhou B, Yu CY. Human complement components C4A and C4B genetic diversities: complex genotypes and phenotypes. ACTA ACUST UNITED AC 2008; Chapter 13:Unit 13.8. [PMID: 18432942 DOI: 10.1002/0471142735.im1308s68] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit describes methods that can accurately determine the genotypes and phenotypes of human complement components C4A and C4B. Specifically, they allow investigators to determine how many C4 genes are present in a diploid genome of a human subject and to quantify how many of them encode C4A proteins and how many of them encode C4B proteins. In addition, methods to determine how many long and short C4 genes are present in a diploid genome of a subject are described together with experimental strategies to determine haplotypes and order or configuration of these genes in the MHC. Finally, methods to assess the degree of polymorphism in C4A and C4B proteins and whether low protein levels of plasma C4 may be caused by low C4 gene dosages and/or by mutant C4 genes.
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Affiliation(s)
- Erwin K Chung
- Columbus Children's Research Institute and The Ohio State University, Columbus, Ohio, USA
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45
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Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JGR, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S. Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics 2008; 60:1-18. [PMID: 18193213 PMCID: PMC2206249 DOI: 10.1007/s00251-007-0262-2] [Citation(s) in RCA: 235] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 10/29/2007] [Indexed: 02/05/2023]
Abstract
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
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Affiliation(s)
- Roger Horton
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard Gibson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Marcos Miretti
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Richard J. Allcock
- School of Surgery and Pathology, University of Western Australia, Nedlands, 6009 WA Australia
| | - Jeff Almeida
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Simon Forbes
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - James G. R. Gilbert
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Karen Halls
- The Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN UK
| | - Jennifer L. Harrow
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Elizabeth Hart
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Kevin Howe
- CRUK Cambridge Research Institute, Robinson Way, Cambridge, CB2 0RE UK
| | - David K. Jackson
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Anne N. Roberts
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - C. Andrew Stewart
- National Cancer Institute, P.O. Box B., 567/206, Frederick, MD 21702 USA
| | - James A. Traherne
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Steve Trevanion
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Laurens Wilming
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Pieter J. de Jong
- Children’s Hospital Oakland Research Institute, Oakland, CA 94609-1673 USA
| | - John F. Elliott
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 2QQ UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Cambridge, CB2 0XY UK
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, CB2 1QP UK
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA UK
- UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BD UK
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Moyes D, Griffiths DJ, Venables PJ. Insertional polymorphisms: a new lease of life for endogenous retroviruses in human disease. Trends Genet 2007; 23:326-33. [PMID: 17524519 DOI: 10.1016/j.tig.2007.05.004] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 04/16/2007] [Accepted: 05/11/2007] [Indexed: 10/23/2022]
Abstract
Human endogenous retroviruses (HERVs) result from ancestral infection by infectious viruses over millions of years of primate evolution. Some are transcriptionally active, express proteins and therefore have the potential to cause disease. Here we review the controversial attempts to link them with cancer and autoimmunity. The main difficulty is that most HERVs investigated to date are present at the same locus in 100% of the population. However, a new class of insertionally polymorphic HERV-K family members, present in a minority of individuals, has recently been described. We propose that insertionally polymorphic HERVs could be novel genetic risk factors and hence provide a new lease of life for research into HERVs and disease.
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Affiliation(s)
- David Moyes
- The Kennedy Institute of Rheumatology, Imperial College London, London, UK
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47
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Yang Y, Chung EK, Wu YL, Savelli SL, Nagaraja HN, Zhou B, Hebert M, Jones KN, Shu Y, Kitzmiller K, Blanchong CA, McBride KL, Higgins GC, Rennebohm RM, Rice RR, Hackshaw KV, Roubey RAS, Grossman JM, Tsao BP, Birmingham DJ, Rovin BH, Hebert LA, Yu CY. Gene copy-number variation and associated polymorphisms of complement component C4 in human systemic lupus erythematosus (SLE): low copy number is a risk factor for and high copy number is a protective factor against SLE susceptibility in European Americans. Am J Hum Genet 2007; 80:1037-54. [PMID: 17503323 PMCID: PMC1867093 DOI: 10.1086/518257] [Citation(s) in RCA: 348] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2006] [Accepted: 03/07/2007] [Indexed: 12/18/2022] Open
Abstract
Interindividual gene copy-number variation (CNV) of complement component C4 and its associated polymorphisms in gene size (long and short) and protein isotypes (C4A and C4B) probably lead to different susceptibilities to autoimmune disease. We investigated the C4 gene CNV in 1,241 European Americans, including patients with systemic lupus erythematosus (SLE), their first-degree relatives, and unrelated healthy subjects, by definitive genotyping and phenotyping techniques. The gene copy number (GCN) varied from 2 to 6 for total C4, from 0 to 5 for C4A, and from 0 to 4 for C4B. Four copies of total C4, two copies of C4A, and two copies of C4B were the most common GCN counts, but each constituted only between one-half and three-quarters of the study populations. Long C4 genes were strongly correlated with C4A (R=0.695; P<.0001). Short C4 genes were correlated with C4B (R=0.437; P<.0001). In comparison with healthy subjects, patients with SLE clearly had the GCN of total C4 and C4A shifting to the lower side. The risk of SLE disease susceptibility significantly increased among subjects with only two copies of total C4 (patients 9.3%; unrelated controls 1.5%; odds ratio [OR] = 6.514; P=.00002) but decreased in those with > or =5 copies of C4 (patients 5.79%; controls 12%; OR=0.466; P=.016). Both zero copies (OR=5.267; P=.001) and one copy (OR=1.613; P=.022) of C4A were risk factors for SLE, whereas > or =3 copies of C4A appeared to be protective (OR=0.574; P=.012). Family-based association tests suggested that a specific haplotype with a single short C4B in tight linkage disequilibrium with the -308A allele of TNFA was more likely to be transmitted to patients with SLE. This work demonstrates how gene CNV and its related polymorphisms are associated with the susceptibility to a human complex disease.
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Affiliation(s)
- Yan Yang
- Center for Molecular and Human Genetics, Columbus Children's Research Institute, Columbus, OH 43205, USA
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48
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Abstract
Complement is involved in the pathogenesis of systemic lupus erythematosus (SLE) in multiple ways and may act as both friend and foe. Inherited homozygous deficiency of one of the earliest components of the classical pathway is strongly associated with susceptibility to the development of SLE. However, complement is also implicated in the effector inflammatory phase of the autoimmune response that characterizes the disease. A further paradox in the links between complement and SLE is the observation that autoantibodies to some complement proteins, especially to C1q, develop as part of the autoantibody response. In this chapter, the role of the complement system in SLE is reviewed and hypotheses advanced to explain the complex relationships between complement and lupus.
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Affiliation(s)
- M J Lewis
- Division of Medicine, Faculty of Medicine, Rheumatology Section, Imperial College, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK
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49
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Szilagyi A, Blasko B, Szilassy D, Fust G, Sasvari-Szekely M, Ronai Z. Real-time PCR quantification of human complement C4A and C4B genes. BMC Genet 2006; 7:1. [PMID: 16403222 PMCID: PMC1360677 DOI: 10.1186/1471-2156-7-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Accepted: 01/10/2006] [Indexed: 11/23/2022] Open
Abstract
Background The fourth component of human complement (C4), an essential factor of the innate immunity, is represented as two isoforms (C4A and C4B) in the genome. Although these genes differ only in 5 nucleotides, the encoded C4A and C4B proteins are functionally different. Based on phenotypic determination, unbalanced production of C4A and C4B is associated with several diseases, such as systemic lupus erythematosus, type 1 diabetes, several autoimmune diseases, moreover with higher morbidity and mortality of myocardial infarction and increased susceptibility for bacterial infections. Despite of this major clinical relevance, only low throughput, time and labor intensive methods have been used so far for the quantification of C4A and C4B genes. Results A novel quantitative real-time PCR (qPCR) technique was developed for rapid and accurate quantification of the C4A and C4B genes applying a duplex, TaqMan based methodology. The reliable, single-step analysis provides the determination of the copy number of the C4A and C4B genes applying a wide range of DNA template concentration (0.3–300 ng genomic DNA). The developed qPCR was applied to determine C4A and C4B gene dosages in a healthy Hungarian population (N = 118). The obtained data were compared to the results of an earlier study of the same population. Moreover a set of 33 samples were analyzed by two independent methods. No significant difference was observed between the gene dosages determined by the employed techniques demonstrating the reliability of the novel qPCR methodology. A Microsoft Excel worksheet and a DOS executable are also provided for simple and automated evaluation of the measured data. Conclusion This report describes a novel real-time PCR method for single-step quantification of C4A and C4B genes. The developed technique could facilitate studies investigating disease association of different C4 isotypes.
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Affiliation(s)
- Agnes Szilagyi
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Bernadett Blasko
- 3rd Department of Medicine, Research Lab, Szentágothai János Knowledge Centre, Semmelweis University, Budapest, Hungary
| | | | - George Fust
- 3rd Department of Medicine, Research Lab, Szentágothai János Knowledge Centre, Semmelweis University, Budapest, Hungary
| | - Maria Sasvari-Szekely
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsolt Ronai
- Institute of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary
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Traherne JA, Horton R, Roberts AN, Miretti MM, Hurles ME, Stewart CA, Ashurst JL, Atrazhev AM, Coggill P, Palmer S, Almeida J, Sims S, Wilming LG, Rogers J, de Jong PJ, Carrington M, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S. Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet 2006; 2:e9. [PMID: 16440057 PMCID: PMC1331980 DOI: 10.1371/journal.pgen.0020009] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Accepted: 12/13/2005] [Indexed: 11/23/2022] Open
Abstract
The major histocompatibility complex (MHC) is recognised as one of the most important genetic regions in relation to common human disease. Advancement in identification of MHC genes that confer susceptibility to disease requires greater knowledge of sequence variation across the complex. Highly duplicated and polymorphic regions of the human genome such as the MHC are, however, somewhat refractory to some whole-genome analysis methods. To address this issue, we are employing a bacterial artificial chromosome (BAC) cloning strategy to sequence entire MHC haplotypes from consanguineous cell lines as part of the MHC Haplotype Project. Here we present 4.25 Mb of the human haplotype QBL (HLA-A26-B18-Cw5-DR3-DQ2) and compare it with the MHC reference haplotype and with a second haplotype, COX (HLA-A1-B8-Cw7-DR3-DQ2), that shares the same HLA-DRB1, -DQA1, and -DQB1 alleles. We have defined the complete gene, splice variant, and sequence variation contents of all three haplotypes, comprising over 259 annotated loci and over 20,000 single nucleotide polymorphisms (SNPs). Certain coding sequences vary significantly between different haplotypes, making them candidates for functional and disease-association studies. Analysis of the two DR3 haplotypes allowed delineation of the shared sequence between two HLA class II-related haplotypes differing in disease associations and the identification of at least one of the sites that mediated the original recombination event. The levels of variation across the MHC were similar to those seen for other HLA-disparate haplotypes, except for a 158-kb segment that contained the HLA-DRB1, -DQA1, and -DQB1 genes and showed very limited polymorphism compatible with identity-by-descent and relatively recent common ancestry (<3,400 generations). These results indicate that the differential disease associations of these two DR3 haplotypes are due to sequence variation outside this central 158-kb segment, and that shuffling of ancestral blocks via recombination is a potential mechanism whereby certain DR-DQ allelic combinations, which presumably have favoured immunological functions, can spread across haplotypes and populations.
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Affiliation(s)
- James A Traherne
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom
| | - Roger Horton
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anne N Roberts
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Marcos M Miretti
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - C. Andrew Stewart
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom
| | - Jennifer L Ashurst
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Alexey M Atrazhev
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, Canada
| | - Penny Coggill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophie Palmer
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jeff Almeida
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sarah Sims
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Laurens G Wilming
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Jane Rogers
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Pieter J. de Jong
- Children's Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Mary Carrington
- Basic Research Program, SAIC-Frederick, Inc., Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland, United States of America
| | - John F Elliott
- Alberta Diabetes Institute (ADI), Department of Medical Microbiology and Immunology, Division of Dermatology and Cutaneous Sciences, University of Alberta, Edmonton, Canada
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - John A Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - John Trowsdale
- Department of Pathology, Immunology Division, University of Cambridge, Cambridge, United Kingdom
| | - Stephan Beck
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
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