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Chen J, Landback P, Arsala D, Guzzetta A, Xia S, Atlas J, Sosa D, Zhang YE, Cheng J, Shen B, Long M. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.567139. [PMID: 38045239 PMCID: PMC10690195 DOI: 10.1101/2023.11.14.567139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are genetic novelties pivotal in mammalian evolution. Their phenotypic impacts and evolutionary pattern over time, however, remain elusive in humans due to the technical and ethical complexities in functional studies. By combining human gene age dating and Mendelian disease phenotyping, our research reveals a gradual increase in disease gene proportions with gene age. Logistic regression modeling indicates that this increase could be related to longer protein lengths and higher burdens of deleterious de novo germline variants (DNVs) for older genes. We also find a steady integration of new genes with biomedical phenotypes into the human genome over macroevolutionary timescales (~0.07% per million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Notably, young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit disease-related functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, musculoskeletal phenotypes, and color vision. We further reveal a logistic growth pattern of pleiotropy over evolutionary time, indicating a diminishing marginal growth of new functions for older genes due to intensifying selective constraints over time. We propose a "pleiotropy-barrier" model that delineates higher potentials of phenotypic innovation for young genes than for older genes, a process subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Patrick Landback
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Alexander Guzzetta
- Department of Pathology, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Jared Atlas
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
| | - Yong E. Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China University Hospital, Chengdu 610041, China
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, 1101 E 57th Street, Chicago, IL 60637
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Tusseau M, Khaldi-Plassart S, Cognard J, Viel S, Khoryati L, Benezech S, Mathieu AL, Rieux-Laucat F, Bader-Meunier B, Belot A. Mendelian Causes of Autoimmunity: the Lupus Phenotype. J Clin Immunol 2024; 44:99. [PMID: 38619739 DOI: 10.1007/s10875-024-01696-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/25/2024] [Indexed: 04/16/2024]
Abstract
Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that is characterized by its large heterogeneity in terms of clinical presentation and severity. The pathophysiology of SLE involves an aberrant autoimmune response against various tissues, an excess of apoptotic bodies, and an overproduction of type-I interferon. The genetic contribution to the disease is supported by studies of monozygotic twins, familial clustering, and genome-wide association studies (GWAS) that have identified numerous risk loci. In the early 70s, complement deficiencies led to the description of familial forms of SLE caused by a single gene defect. High-throughput sequencing has recently identified an increasing number of monogenic defects associated with lupus, shaping the concept of monogenic lupus and enhancing our insights into immune tolerance mechanisms. Monogenic lupus (moSLE) should be suspected in patients with either early-onset lupus or syndromic lupus, in male, or in familial cases of lupus. This review discusses the genetic basis of monogenic SLE and proposes its classification based on disrupted pathways. These pathways include defects in the clearance of apoptotic cells or immune complexes, interferonopathies, JAK-STATopathies, TLRopathies, and T and B cell dysregulations.
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Affiliation(s)
- Maud Tusseau
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
| | - Samira Khaldi-Plassart
- National Referee Centre for Rheumatic and AutoImmune and Systemic Diseases in Children, European Reference Network (ERN) for Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (RITA) Center, Hospices Civils de Lyon, Lyon, France
- Pediatric Nephrology, Rheumatology, Dermatology Unit, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France
| | - Jade Cognard
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
- Pediatric Nephrology, Rheumatology, Dermatology Unit, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France
| | - Sebastien Viel
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
| | - Liliane Khoryati
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
| | - Sarah Benezech
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
| | - Anne-Laure Mathieu
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France
| | - Fréderic Rieux-Laucat
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, France
| | - Brigitte Bader-Meunier
- National Referee Centre for Rheumatic and AutoImmune and Systemic Diseases in Children, European Reference Network (ERN) for Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (RITA) Center, Hospices Civils de Lyon, Lyon, France
- Laboratory of Immunogenetics of Pediatric Autoimmune Diseases, Imagine Institute, INSERM UMR 1163, Université Paris Cité, Paris, France
- Department for Immunology, Hematology and Pediatric Rheumatology, Necker Hospital, APHP, Institut IMAGINE, Paris, France
| | - Alexandre Belot
- Centre International de Recherche en Infectiologie, Inserm, U1111, University Claude Bernard, Lyon 1, Centre National de La Recherche Scientifique, UMR5308, ENS de Lyon, Lyon, France.
- National Referee Centre for Rheumatic and AutoImmune and Systemic Diseases in Children, European Reference Network (ERN) for Rare Immunodeficiency, Autoinflammatory and Autoimmune Diseases (RITA) Center, Hospices Civils de Lyon, Lyon, France.
- Pediatric Nephrology, Rheumatology, Dermatology Unit, Hôpital Femme Mère Enfant, Hospices Civils de Lyon, Lyon, France.
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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Rekvig OP. The greatest contribution to medical science is the transformation from studying symptoms to studying their causes-the unrelenting legacy of Robert Koch and Louis Pasteur-and a causality perspective to approach a definition of SLE. Front Immunol 2024; 15:1346619. [PMID: 38361929 PMCID: PMC10867267 DOI: 10.3389/fimmu.2024.1346619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
The basic initiative related to this study is derived from the fact that systemic lupus erythematosus (SLE) is a unique and fertile system science subject. We are, however, still far from understanding its nature. It may be fair to indicate that we are spending more time and resources on studying the complexity of classified SLE than studying the validity of classification criteria. This study represents a theoretical analysis of current instinctual SLE classification criteria based on "the causality principle." The discussion has its basis on the radical scientific traditions introduced by Robert Koch and Louis Pasteur. They announced significant changes in our thinking of disease etiology through the implementation of the modern version of "the causality principle." They influenced all aspects of today's medical concepts and research: the transformation of medical science from studies of symptoms to study their causes, relevant for monosymptomatic diseases as for syndromes. Their studies focused on bacteria as causes of infectious diseases and on how the immune system adapts to control and prevent contagious spreading. This is the most significant paradigm shift in the modern history of medicine and resulted in radical changes in our view of the immune system. They described acquired post-infection immunity and active immunization by antigen-specific vaccines. The paradigm "transformation" has a great theoretical impact also on current studies of autoimmune diseases like SLE: symptoms and their cause(s). In this study, the evolution of SLE classification and diagnostic criteria is discussed from "the causality principle" perspective, and if contemporary SLE classification criteria are as useful as believed today for SLE research. This skepticism is based on the fact that classification criteria are not selected based on cogent causal strategies. The SLE classification criteria do not harmonize with Koch's and Pasteur's causality principle paradigms and not with Witebsky's Koch-derived postulates for autoimmune and infectious diseases. It is not established whether the classification criteria can separate SLE as a "one disease entity" from "SLE-like non-SLE disorders"-the latter in terms of SLE imitations. This is discussed here in terms of weight, rank, and impact of the classification criteria: Do they all originate from "one basic causal etiology"? Probably not.
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Affiliation(s)
- Ole Petter Rekvig
- Section for Autoimmunity, Fürst Medical Laboratory, Oslo, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
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Rekvig OP. SLE classification criteria: Is "The causality principle" integrated and operative - and do the molecular and genetical network, on which criteria depend on, support the definition of SLE as "a one disease entity" - A theoretical discussion. Autoimmun Rev 2023; 22:103470. [PMID: 37884202 DOI: 10.1016/j.autrev.2023.103470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/23/2023] [Indexed: 10/28/2023]
Abstract
Molecular and cellular aspects of the autoimmune pathophysiology in SLE is linked to the "The causality principle". SLE Classification Criteria identify per definition disease measures (here: synonymous with classification criteria), but not diagnostic criteria within a classical framework. These two mostly theoretical criteria collections represent a salient conflict between phenomenology and the causality principle - between disease measures and molecular interactions that promote such measures, in other words their cause(s). Essentially, each criterion evolves from immunogenic and inflammatory signals - some are interconnected, some are not. Disparate signals instigated by disparate causes. These may promote clinically heterogenous SLE cohorts with respect to organ affection, autoimmunity, and disease course. There is today no concise measures or arguments that settle whether SLE cohorts evolve from one decisive etiological factor (homogenous cohorts), or if disparate patho-biological factors promote SLE (heterogenous cohorts). Current SLE cohorts are not ideal substrates to serve as study objects if the research aims are to describe etiology, and molecular interactions that cause - and link - primary and secondary pathophysiological events together - events that account for early and progressive SLE. We have to develop SLE criteria allowing us to identify definable categories of SLE in order to describe etiology, pathophysiology and diagnostic criteria of delimitated SLE versions. In this regard, the causality principle is central to define dominant etiologies of individual SLE categories, and subsequent and consequent down-stream diagnostic disease measures. In this sense, we may whether we like it or not identify different SLE categories like "genuine SLE" and "SLE-like non-SLE" syndromes. Many aspects of this problem are thoroughly discussed in this study.
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Affiliation(s)
- Ole Petter Rekvig
- Fürst Medical Laboratory, Oslo, Norway; Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway.
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Engavale M, Hernandez CJ, Infante A, LeRoith T, Radovan E, Evans L, Villarreal J, Reilly CM, Sutton RB, Keyel PA. Deficiency of macrophage-derived Dnase1L3 causes lupus-like phenotypes in mice. J Leukoc Biol 2023; 114:547-556. [PMID: 37804110 PMCID: PMC10843819 DOI: 10.1093/jleuko/qiad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/01/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease caused by environmental factors and loss of key proteins, including the endonuclease Dnase1L3. Dnase1L3 absence causes pediatric-onset lupus in humans, while reduced activity occurs in adult-onset SLE. The amount of Dnase1L3 that prevents lupus remains unknown. To genetically reduce Dnase1L3 levels, we developed a mouse model lacking Dnase1L3 in macrophages (conditional knockout [cKO]). Serum Dnase1L3 levels were reduced 67%, though Dnase1 activity remained constant. Homogeneous and peripheral antinuclear antibodies were detected in the sera by immunofluorescence, consistent with anti-double-stranded DNA (anti-dsDNA) antibodies. Total immunoglobulin M, total immunoglobulin G, and anti-dsDNA antibody levels increased in cKO mice with age. The cKO mice developed anti-Dnase1L3 antibodies. In contrast to global Dnase1L3-/- mice, anti-dsDNA antibodies were not elevated early in life. The cKO mice had minimal kidney pathology. Therefore, we conclude that an intermediate reduction in serum Dnase1L3 causes mild lupus phenotypes, and macrophage-derived DnaselL3 helps limit lupus.
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Affiliation(s)
- Minal Engavale
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Colton J. Hernandez
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Angelica Infante
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Tanya LeRoith
- Department of Cell Biology and Physiology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Elliott Radovan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Lauryn Evans
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Johanna Villarreal
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, United States
| | - Christopher M. Reilly
- Department of Cell Biology and Physiology, Virginia Tech, Blacksburg, VA 24061, United States
| | - R. Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, United States
| | - Peter A. Keyel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
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Chen J. Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection. RESEARCH SQUARE 2023:rs.3.rs-3632644. [PMID: 38045389 PMCID: PMC10690325 DOI: 10.21203/rs.3.rs-3632644/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
New genes (or young genes) are structural novelties pivotal in mammalian evolution. Their phenotypic impact on humans, however, remains elusive due to the technical and ethical complexities in functional studies. Through combining gene age dating with Mendelian disease phenotyping, our research reveals that new genes associated with disease phenotypes steadily integrate into the human genome at a rate of ~ 0.07% every million years over macroevolutionary timescales. Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures between young and old genes. Notably, young genes show significant enrichment in the male reproductive system, indicating strong sexual selection. Young genes also exhibit functions in tissues and systems potentially linked to human phenotypic innovations, such as increased brain size, bipedal locomotion, and color vision. Our findings further reveal increasing levels of pleiotropy over evolutionary time, which accompanies stronger selective constraints. We propose a "pleiotropy-barrier" model that delineates different potentials for phenotypic innovation between young and older genes subject to natural selection. Our study demonstrates that evolutionary new genes are critical in influencing human reproductive evolution and adaptive phenotypic innovations driven by sexual and natural selection, with low pleiotropy as a selective advantage.
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Alexeeva E, Shingarova M, Dvoryakovskaya T, Lomakina O, Fetisova A, Isaeva K, Chomakhidze A, Chibisova K, Krekhova E, Kozodaeva A, Savostyanov K, Pushkov A, Zhanin I, Demyanov D, Suspitsin E, Belozerov K, Kostik M. Safety and efficacy of canakinumab treatment for undifferentiated autoinflammatory diseases: the data of a retrospective cohort two-centered study. Front Med (Lausanne) 2023; 10:1257045. [PMID: 38034538 PMCID: PMC10685903 DOI: 10.3389/fmed.2023.1257045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/13/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction The blockade of interleukine-1 (anakinra and canakinumab) is a well-known highly effective tool for monogenic autoinflammatory diseases (AIDs), such as familial Mediterranean fever, tumor necrosis factor receptor-associated periodic syndrome, hyperimmunoglobulinaemia D syndrome, and cryopyrin-associated periodic syndrome, but this treatment has not been assessed for patients with undifferentiated AIDs (uAIDs). Our study aimed to assess the safety and efficacy of canakinumab for patients with uAIDs. Methods Information on 32 patients with uAIDs was retrospectively collected and analyzed. Next-generation sequencing and Federici criteria were used for the exclusion of the known monogenic AID. Results The median age of the first episode was 2.5 years (IQR: 1.3; 5.5), that of the disease diagnosis was 5.7 years (IQR: 2.5;12.7), and that of diagnostic delay was 1.1 years (IQR: 0.4; 6.1). Patients had variations in the following genes: IL10, NLRP12, STAT2, C8B, LPIN2, NLRC4, PSMB8, PRF1, CARD14, IFIH1, LYST, NFAT5, PLCG2, COPA, IL23R, STXBP2, IL36RN, JAK1, DDX58, LACC1, LRBA, TNFRSF11A, PTHR1, STAT4, TNFRSF1B, TNFAIP3, TREX1, and SLC7A7. The main clinical features were fever (100%), rash (91%; maculopapular predominantly), joint involvement (72%), splenomegaly (66%), hepatomegaly (59%), lymphadenopathy (50%), myalgia (28%), heart involvement (31%), intestinal involvement (19%); eye involvement (9%), pleuritis (16%), ascites (6%), deafness, hydrocephalia (3%), and failure to thrive (25%). Initial treatment before canakinumab consisted of non-biologic therapies: non-steroidal anti-inflammatory drugs (NSAID) (91%), corticosteroids (88%), methotrexate (38%), intravenous immunoglobulin (IVIG) (34%), cyclosporine A (25%), colchicine (6%) cyclophosphamide (6%), sulfasalazine (3%), mycophenolate mofetil (3%), hydroxychloroquine (3%), and biologic drugs: tocilizumab (62%), sarilumab, etanercept, adalimumab, rituximab, and infliximab (all 3%). Canakinumab induced complete remission in 27 patients (84%) and partial remission in one patient (3%). Two patients (6%) were primary non-responders, and two patients (6%) further developed secondary inefficacy. All patients with partial efficacy or inefficacy were switched to tocilizumab (n = 4) and sarilumab (n = 1). The total duration of canakinumab treatment was 3.6 (0.1; 8.7) years. During the study, there were no reported Serious Adverse Events (SAEs). The patients experienced non-frequent mild respiratory infections at a rate that is similar as before canakinumab is administered. Additionally, one patient developed leucopenia, but it was not necessary to stop canakinumab for this patient. Conclusion The treatment of patients with uAIDs using canakinumab was safe and effective. Further randomized clinical trials are required to confirm the efficacy and safety.
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Affiliation(s)
- Ekaterina Alexeeva
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
- Clinical Institute of Children's Health named after N.F. Filatov, Chair of Pediatrics and Pediatric Rheumatology of the Sechenov First Moscow State Medical University, Sechenov University, Moscow, Russia
| | - Meiri Shingarova
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
- Clinical Institute of Children's Health named after N.F. Filatov, Chair of Pediatrics and Pediatric Rheumatology of the Sechenov First Moscow State Medical University, Sechenov University, Moscow, Russia
| | - Tatyana Dvoryakovskaya
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
- Clinical Institute of Children's Health named after N.F. Filatov, Chair of Pediatrics and Pediatric Rheumatology of the Sechenov First Moscow State Medical University, Sechenov University, Moscow, Russia
| | - Olga Lomakina
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Anna Fetisova
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Ksenia Isaeva
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Aleksandra Chomakhidze
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Kristina Chibisova
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Elizaveta Krekhova
- Department of Pediatric Rheumatology, National Medical Research Center of Children's Health, Moscow, Russia
| | - Aleksandra Kozodaeva
- Clinical Institute of Children's Health named after N.F. Filatov, Chair of Pediatrics and Pediatric Rheumatology of the Sechenov First Moscow State Medical University, Sechenov University, Moscow, Russia
| | - Kirill Savostyanov
- Department of Medical Genetics of the Medical and Genetic Center, National Medical Research Center of Children's Health, Moscow, Russia
| | - Aleksandr Pushkov
- Department of Medical Genetics of the Medical and Genetic Center, National Medical Research Center of Children's Health, Moscow, Russia
| | - Ilya Zhanin
- Department of Medical Genetics of the Medical and Genetic Center, National Medical Research Center of Children's Health, Moscow, Russia
| | - Dmitry Demyanov
- Department of Medical Genetics of the Medical and Genetic Center, National Medical Research Center of Children's Health, Moscow, Russia
| | - Evgeny Suspitsin
- Department of Medical Genetics, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg, Russia
- Department of Tumor Growth Biology, N.N. Petrov National Research Center of Oncology, Saint-Petersburg, Russia
| | - Konstantin Belozerov
- Hospital Pediatry, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg, Russia
| | - Mikhail Kostik
- Hospital Pediatry, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg, Russia
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Al-Mayouf SM, Alkhars F, AlSaleem A. Phenotype and disease course differences in monogenic and sporadic childhood lupus. Lupus 2023; 32:1548-1554. [PMID: 37878993 DOI: 10.1177/09612033231211065] [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] [Indexed: 10/27/2023]
Abstract
OBJECTIVE To report the differences in phenotypic characteristics, disease course, and outcome in monogenic and sporadic childhood lupus (SC-lupus) from a single tertiary childhood lupus clinic. METHODS A descriptive, observational, cross-sectional study was conducted. Data were retrospectively collected at the last follow-up visit on patients with monogenic lupus proven by genetic variants and SC-lupus seen between June 1997 and July 2022. SC-lupus patients were selected by systematic sampling from lupus patients presenting to our lupus clinic; the first patient was chosen randomly, and the subsequent patients were chosen at intervals of three. Data comprised the clinical and laboratory findings, disease activity using the SLEDAI, and damage measured by the pSDI. RESULTS A total of 54 patients with a median disease duration of 6.8 (IQR 3.5-10.5) years were included. There were 27 patients with monogenic lupus and 27 patients with SC-lupus, with a median age at disease onset of 3.5 (IQR 1.0-6.0), and 9.5 (IQR 7.0-11.8), respectively. (p < 0.05). The rate of consanguinity and family history of lupus were higher in monogenic lupus patients. The two groups were comparable. However, monogenic lupus patients showed more gastrointestinal tract symptoms, and failure to thrive (p < 0.05). They also had more infections. The frequency of the autoantibody profile was higher in monogenic lupus patients. Belimumab was more frequently used in monogenic lupus while rituximab in SC-lupus patients. Monogenic lupus patients had a higher mean SLEDAI, but statistically, it was insignificant. Patients with monogenic lupus had greater disease damage, with a higher mean pSDI and a higher mortality rate (p < 0.05). CONCLUSION Patients with monogenic lupus are likely to have an early disease onset and a strong family history of lupus, as well as a guarded prognosis, which is likely due to the disease's severity and frequent infections. These differences may be related to the high consanguinity rate and underlying genetic variants.
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Affiliation(s)
- Sulaiman M Al-Mayouf
- Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Fatima Alkhars
- Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Alhanouf AlSaleem
- Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
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Vinuesa CG, Shen N, Ware T. Genetics of SLE: mechanistic insights from monogenic disease and disease-associated variants. Nat Rev Nephrol 2023; 19:558-572. [PMID: 37438615 DOI: 10.1038/s41581-023-00732-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 07/14/2023]
Abstract
The past few years have provided important insights into the genetic architecture of systemic autoimmunity through aggregation of findings from genome-wide association studies (GWAS) and whole-exome or whole-genome sequencing studies. In the prototypic systemic autoimmune disease systemic lupus erythematosus (SLE), monogenic disease accounts for a small fraction of cases but has been instrumental in the elucidation of disease mechanisms. Defects in the clearance or digestion of extracellular or intracellular DNA or RNA lead to increased sensing of nucleic acids, which can break B cell tolerance and induce the production of type I interferons leading to tissue damage. Current data suggest that multiple GWAS SLE risk alleles act in concert with rare functional variants to promote SLE development. Moreover, introduction of orthologous variant alleles into mice has revealed that pathogenic X-linked dominant and recessive SLE can be caused by novel variants in TLR7 and SAT1, respectively. Such bespoke models of disease help to unravel pathogenic pathways and can be used to test targeted therapies. Cell type-specific expression data revealed that most GWAS SLE risk genes are highly expressed in age-associated B cells (ABCs), which supports the view that ABCs produce lupus autoantibodies and contribute to end-organ damage by persisting in inflamed tissues, including the kidneys. ABCs have thus emerged as key targets of promising precision therapeutics.
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Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- China Australia Centre for Personalized Immunology (CACPI), Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- Center for Autoimmune Genomics and Aetiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Paediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Thuvaraka Ware
- The Francis Crick Institute, London, UK
- University College London, London, UK
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11
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Crow MK. Pathogenesis of systemic lupus erythematosus: risks, mechanisms and therapeutic targets. Ann Rheum Dis 2023; 82:999-1014. [PMID: 36792346 DOI: 10.1136/ard-2022-223741] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 02/01/2023] [Indexed: 02/17/2023]
Abstract
Research elucidating the pathogenesis of systemic lupus erythematosus (SLE) has defined two critical families of mediators, type I interferon (IFN-I) and autoantibodies targeting nucleic acids and nucleic acid-binding proteins, as fundamental contributors to the disease. On the fertile background of significant genetic risk, a triggering stimulus, perhaps microbial, induces IFN-I, autoantibody production or most likely both. When innate and adaptive immune system cells are engaged and collaborate in the autoimmune response, clinical SLE can develop. This review describes recent data from genetic analyses of patients with SLE, along with current studies of innate and adaptive immune function that contribute to sustained IFN-I pathway activation, immune activation and autoantibody production, generation of inflammatory mediators and tissue damage. The goal of these studies is to understand disease mechanisms, identify therapeutic targets and stimulate development of therapeutics that can achieve improved outcomes for patients.
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Affiliation(s)
- Mary K Crow
- Mary Kirkland Center for Lupus Research, Hospital for Special Surgery, New York, New York, USA
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12
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Raupov R, Suspitsin E, Belozerov K, Gabrusskaya T, Kostik M. IFIH1 and DDX58 gene variants in pediatric rheumatic diseases. World J Clin Pediatr 2023; 12:107-114. [PMID: 37342449 PMCID: PMC10278078 DOI: 10.5409/wjcp.v12.i3.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 04/24/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND The IFIH1 gene codes the MDA5 protein and the DDX58 gene codes the RIG-I receptor. Both proteins are parts of the interferon (IFN) I signaling pathway and are responsible for antiviral defense and innate immune response. IFIH1 and DDX58 polymorphisms are associated with a spectrum of autoimmune diseases. Rare gain-of-function IFIH1 mutations have been found in Singleton-Merten and Aicardi-Goutières syndrome, while DDX58 mutation can cause atypical Singleton-Merten syndrome.
AIM To characterize children with pediatric rheumatic diseases (PRD) carrying DDX58 or IFIH1 variants.
METHODS Clinical exome sequencing was performed on 92 children with different PRD. IFIH1 and DDX58 variants have been detected in 14 children. IFN-I score has been analyzed and the clinical characteristics of patients have been studied.
RESULTS A total of seven patients with systemic lupus erythematosus (SLE) (n = 2), myelodysplastic syndrome with SLE features at the onset of the disease (n = 1), mixed connective tissue disease (MCTD) (n = 1), undifferentiated systemic autoinflammatory disease (uSAID) (n = 3) have 5 different variants of the DDX58 gene. A common non-pathogenic variant p.D580E has been found in five children. A rare variant of uncertain significance (VUS) p.N354S was found in one patient with uSAID, a rare likely non-pathogenic variant p.E37K in one patient with uSAID, and a rare likely pathogenic variant p.Cys864fs in a patient with SLE. Elevated IFN-I score was detected in 6 of 7 patients with DDX58 variants. Seven patients had six different IFIH1 variants. They were presented with uSAID (n = 2), juvenile dermatomyositis (JDM) (n = 1), SLE-like disease (n = 1), Periodic fever with aphthous stomatitis, pharyngitis, and adenitis syndrome (n = 1), and systemic onset juvenile idiopathic arthritis (n = 1). Three patients have VUS p.E627X, one patient has benign variant p.I923V. Rare VUS p.R595H was detected in the JDM patient. Another rare VUS p.L679Ifs*2 and previously not reported variant p.V599Ffs*5 were detected in the patient with uSAID. One patient with uSAID has rare VUS p.T520A. All patients had elevated IFN-I scores.
CONCLUSION Rare compound-heterozygous IFIH1 variant (p.L679Ifs*2 and p.V599Ffs*5), heterozygous IFIH1 variant (p.T520A) and heterozygous DDX58 variant (p.Cys864fs) are probably disease causative for uSAID and SLE. The majority of patients with different DDX58 and IFI1 variants had hyperactivation of the IFN I signaling pathway.
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Affiliation(s)
- Rinat Raupov
- Department of Pediatry, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg 194100, Russia
| | - Evgeny Suspitsin
- Department of Genetics, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg 194100, Russia
| | - Konstantin Belozerov
- Department of Pediatry, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg 194100, Russia
| | - Tatiana Gabrusskaya
- Department of Gastrointestinal Diseases, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg 194100, Russia
| | - Mikhail Kostik
- Department of Pediatry, Saint-Petersburg State Pediatric Medical University, Saint-Petersburg 194100, Russia
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13
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Englert H, Göbel J, Khong D, Omidi M, Wolska N, Konrath S, Frye M, Mailer RK, Beerens M, Gerwers JC, Preston RJS, Odeberg J, Butler LM, Maas C, Stavrou EX, Fuchs TA, Renné T. Targeting NETs using dual-active DNase1 variants. Front Immunol 2023; 14:1181761. [PMID: 37287977 PMCID: PMC10242134 DOI: 10.3389/fimmu.2023.1181761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/09/2023] [Indexed: 06/09/2023] Open
Abstract
Background Neutrophil Extracellular Traps (NETs) are key mediators of immunothrombotic mechanisms and defective clearance of NETs from the circulation underlies an array of thrombotic, inflammatory, infectious, and autoimmune diseases. Efficient NET degradation depends on the combined activity of two distinct DNases, DNase1 and DNase1-like 3 (DNase1L3) that preferentially digest double-stranded DNA (dsDNA) and chromatin, respectively. Methods Here, we engineered a dual-active DNase with combined DNase1 and DNase1L3 activities and characterized the enzyme for its NET degrading potential in vitro. Furthermore, we produced a mouse model with transgenic expression of the dual-active DNase and analyzed body fluids of these animals for DNase1 and DNase 1L3 activities. We systematically substituted 20 amino acid stretches in DNase1 that were not conserved among DNase1 and DNase1L3 with homologous DNase1L3 sequences. Results We found that the ability of DNase1L3 to degrade chromatin is embedded into three discrete areas of the enzyme's core body, not the C-terminal domain as suggested by the state-of-the-art. Further, combined transfer of the aforementioned areas of DNase1L3 to DNase1 generated a dual-active DNase1 enzyme with additional chromatin degrading activity. The dual-active DNase1 mutant was superior to native DNase1 and DNase1L3 in degrading dsDNA and chromatin, respectively. Transgenic expression of the dual-active DNase1 mutant in hepatocytes of mice lacking endogenous DNases revealed that the engineered enzyme was stable in the circulation, released into serum and filtered to the bile but not into the urine. Conclusion Therefore, the dual-active DNase1 mutant is a promising tool for neutralization of DNA and NETs with potential therapeutic applications for interference with thromboinflammatory disease states.
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Affiliation(s)
- Hanna Englert
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Josephine Göbel
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Danika Khong
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maryam Omidi
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nina Wolska
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sandra Konrath
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Reiner K. Mailer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manu Beerens
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian C. Gerwers
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Roger J. S. Preston
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Jacob Odeberg
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lynn M. Butler
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, The Arctic University of Norway, Tromsø, Norway
- Science for Life Laboratory, Department of Protein Science, CBH, KTH Royal Institute of Technology, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Evi X. Stavrou
- Medicine Service, Section of Hematology-Oncology, Louis Stokes Veterans Administration Medical Center, Cleveland, OH, United States
- Department of Medicine, Hematology and Oncology Division, Case Western Reserve University School of Medicine, Cleveland, OH, United States
| | - Tobias A. Fuchs
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Neutrolis, Inc., Cambridge, MA, United States
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany
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14
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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: 17] [Impact Index Per Article: 17.0] [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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15
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Engavale M, Hernandez CJ, Infante A, LeRoith T, Radovan E, Evans L, Villarreal J, Reilly CM, Sutton RB, Keyel PA. Deficiency of macrophage-derived Dnase1L3 causes lupus-like phenotypes in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537232. [PMID: 37131692 PMCID: PMC10153119 DOI: 10.1101/2023.04.17.537232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease caused by environmental factors and loss of key proteins. One such protein is a serum endonuclease secreted by macrophages and dendritic cells, Dnase1L3. Loss of Dnase1L3 causes pediatric-onset lupus in humans is Dnase1L3. Reduction in Dnase1L3 activity occurs in adult-onset human SLE. However, the amount of Dnase1L3 necessary to prevent lupus onset, if the impact is continuous or requires a threshold, and which phenotypes are most impacted by Dnase1L3 remain unknown. To reduce Dnase1L3 protein levels, we developed a genetic mouse model with reduced Dnase1L3 activity by deleting Dnase1L3 from macrophages (cKO). Serum Dnase1L3 levels were reduced 67%, though Dnase1 activity remained constant. Sera were collected weekly from cKO and littermate controls until 50 weeks of age. Homogeneous and peripheral anti-nuclear antibodies were detected by immunofluorescence, consistent with anti-dsDNA antibodies. Total IgM, total IgG, and anti-dsDNA antibody levels increased in cKO mice with increasing age. In contrast to global Dnase1L3 -/- mice, anti-dsDNA antibodies were not elevated until 30 weeks of age. The cKO mice had minimal kidney pathology, except for deposition of immune complexes and C3. Based on these findings, we conclude that an intermediate reduction in serum Dnase1L3 causes mild lupus phenotypes. This suggest that macrophage-derived DnaselL3 is critical to limiting lupus.
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16
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Stankey CT, Lee JC. Translating non-coding genetic associations into a better understanding of immune-mediated disease. Dis Model Mech 2023; 16:297044. [PMID: 36897113 PMCID: PMC10040244 DOI: 10.1242/dmm.049790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Genome-wide association studies have identified hundreds of genetic loci that are associated with immune-mediated diseases. Most disease-associated variants are non-coding, and a large proportion of these variants lie within enhancers. As a result, there is a pressing need to understand how common genetic variation might affect enhancer function and thereby contribute to immune-mediated (and other) diseases. In this Review, we first describe statistical and experimental methods to identify causal genetic variants that modulate gene expression, including statistical fine-mapping and massively parallel reporter assays. We then discuss approaches to characterise the mechanisms by which these variants modulate immune function, such as clustered regularly interspaced short palindromic repeats (CRISPR)-based screens. We highlight examples of studies that, by elucidating the effects of disease variants within enhancers, have provided important insights into immune function and uncovered key pathways of disease.
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Affiliation(s)
- Christina T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London NW3 2PF, UK
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17
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Virolainen SJ, VonHandorf A, Viel KCMF, Weirauch MT, Kottyan LC. Gene-environment interactions and their impact on human health. Genes Immun 2023; 24:1-11. [PMID: 36585519 PMCID: PMC9801363 DOI: 10.1038/s41435-022-00192-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/31/2022]
Abstract
The molecular processes underlying human health and disease are highly complex. Often, genetic and environmental factors contribute to a given disease or phenotype in a non-additive manner, yielding a gene-environment (G × E) interaction. In this work, we broadly review current knowledge on the impact of gene-environment interactions on human health. We first explain the independent impact of genetic variation and the environment. We next detail well-established G × E interactions that impact human health involving environmental toxicants, pollution, viruses, and sex chromosome composition. We conclude with possibilities and challenges for studying G × E interactions.
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Affiliation(s)
- Samuel J Virolainen
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA
| | - Andrew VonHandorf
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
| | - Kenyatta C M F Viel
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA
| | - Matthew T Weirauch
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
| | - Leah C Kottyan
- Division of Human Genetics, Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., Cincinnati, OH, 45229, USA.
- Immunology Graduate Program, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, 3230 Eden Ave, Cincinnati, OH, 45229, USA.
- Division of Allergy and Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Ave., MLC 15012, Cincinnati, OH, 45229, USA.
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18
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Rekvig OP. SLE classification criteria: Science-based icons or algorithmic distractions – an intellectually demanding dilemma. Front Immunol 2022; 13:1011591. [PMID: 36248792 PMCID: PMC9555175 DOI: 10.3389/fimmu.2022.1011591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 12/01/2022] Open
Abstract
It is, so to say, not a prerogative authority assigned to SLE classification criteria that allow them to declare something definitively important about SLE. This is particularly true as criteria-based classification processes overrule the highly needed evolution of concise diagnostic criteria. It is classification criteria that allocate SLE patients into cohorts intended to describe the nature of their disease. Therefore, all major SLE classification criteria since the 1971 preliminary criteria usurp the role of diagnostic criteria. Today´s practice silently accept that the SLE classification process “diagnose” SLE patients despite the fact that classification criteria are not accepted as diagnostic criteria! This is a central paradox in contemporary SLE research strategies. Contemporary SLE cohorts are designed to investigate SLE´s etiological features. However, each cohort that is categorized by classification criteria has one central inherent problem. From theoretical and practical arguments, they embody multiple distinct clinical phenotypes. This raises the critical and principal question if phenotypically heterogenic SLE cohorts are useful to identify basic SLE-specific etiology(ies) and disease process(es). In times to come, we must prioritize development of firm diagnostic criteria for SLE, as the classification criteria have not contributed to reduce the enigmatic character of the syndrome. No radical improvements are visible in the horizon that may lead to concise investigations of SLE in well-defined homogenous SLE cohorts. We must develop new strategies where studies of phenotypically standardized cohorts of SLE must be central elements. Problems related to contemporary SLE classification criteria are contemplated, analyzed, and critically discussed in this study.
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Affiliation(s)
- Ole Petter Rekvig
- Fürst Medical Laboratory, Oslo, Norway
- Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Ole Petter Rekvig,
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19
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Harley ITW, Allison K, Scofield RH. Polygenic autoimmune disease risk alleles impacting B cell tolerance act in concert across shared molecular networks in mouse and in humans. Front Immunol 2022; 13:953439. [PMID: 36090990 PMCID: PMC9450536 DOI: 10.3389/fimmu.2022.953439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Most B cells produced in the bone marrow have some level of autoreactivity. Despite efforts of central tolerance to eliminate these cells, many escape to periphery, where in healthy individuals, they are rendered functionally non-responsive to restimulation through their antigen receptor via a process termed anergy. Broad repertoire autoreactivity may reflect the chances of generating autoreactivity by stochastic use of germline immunoglobulin gene segments or active mechanisms may select autoreactive cells during egress to the naïve peripheral B cell pool. Likewise, it is unclear why in some individuals autoreactive B cell clones become activated and drive pathophysiologic changes in autoimmune diseases. Both of these remain central questions in the study of the immune system(s). In most individuals, autoimmune diseases arise from complex interplay of genetic risk factors and environmental influences. Advances in genome sequencing and increased statistical power from large autoimmune disease cohorts has led to identification of more than 200 autoimmune disease risk loci. It has been observed that autoantibodies are detectable in the serum years to decades prior to the diagnosis of autoimmune disease. Thus, current models hold that genetic defects in the pathways that control autoreactive B cell tolerance set genetic liability thresholds across multiple autoimmune diseases. Despite the fact these seminal concepts were developed in animal (especially murine) models of autoimmune disease, some perceive a disconnect between human risk alleles and those identified in murine models of autoimmune disease. Here, we synthesize the current state of the art in our understanding of human risk alleles in two prototypical autoimmune diseases – systemic lupus erythematosus (SLE) and type 1 diabetes (T1D) along with spontaneous murine disease models. We compare these risk networks to those reported in murine models of these diseases, focusing on pathways relevant to anergy and central tolerance. We highlight some differences between murine and human environmental and genetic factors that may impact autoimmune disease development and expression and may, in turn, explain some of this discrepancy. Finally, we show that there is substantial overlap between the molecular networks that define these disease states across species. Our synthesis and analysis of the current state of the field are consistent with the idea that the same molecular networks are perturbed in murine and human autoimmune disease. Based on these analyses, we anticipate that murine autoimmune disease models will continue to yield novel insights into how best to diagnose, prognose, prevent and treat human autoimmune diseases.
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Affiliation(s)
- Isaac T. W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
- Rheumatology Section, Medicine Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
- *Correspondence: Isaac T. W. Harley,
| | - Kristen Allison
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
| | - R. Hal Scofield
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Medical/Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
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20
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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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Balamanikandan P, Bharathi SJ. A mathematical modelling to detect sickle cell anemia using Quantum graph theory and Aquila optimization classifier. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:10060-10077. [PMID: 36031983 DOI: 10.3934/mbe.2022470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recently genetic disorders are the most common reason for human fatality. Sickle Cell anemia is a monogenic disorder caused by A-to-T point mutations in the β-globin gene which produces abnormal hemoglobin S (Hgb S) that polymerizes at the state of deoxygenation thus resulting in the physical deformation or erythrocytes sickling. This shortens the expectancy of human life. Thus, the early diagnosis and identification of sickle cell will aid the people in recognizing signs and to take treatments. The manual identification is a time consuming one and might outcome in the misclassification of count as there is millions of red blood cells in one spell. So as to overcome this, data mining approaches like Quantum graph theory model and classifier is effective in detecting sickle cell anemia with high precision rate. The proposed work aims at presenting a mathematical modeling using Quantum graph theory to extract elasticity properties and to distinguish them as normal cells and sickle cell anemia (SCA) in red blood cells. Initially, input DNA sequence is taken and the elasticity property features are extracted by using Quantum graph theory model at which the formation of spanning tree is made followed by graph construction and Hemoglobin quantization. After which, the extracted properties are optimized using Aquila optimization and classified using cascaded Long Short-Term memory (LSTM) to attain the classified outcome of sickle cell and normal cells. Finally, the performance assessment is made and the outcomes attained in terms of accuracy, precision, sensitivity, specificity, and AUC are compared with existing classifier to validate the proposed system effectiveness.
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Affiliation(s)
- P Balamanikandan
- Department of Mathematics, Thiagarajar College of Engineering, Madurai, Tamilnadu, India
| | - S Jeya Bharathi
- Department of Mathematics, Thiagarajar College of Engineering, Madurai, Tamilnadu, India
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22
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Basmanav FB, Betz RC. Translational impact of omics studies in alopecia areata: recent advances and future perspectives. Expert Rev Clin Immunol 2022; 18:845-857. [PMID: 35770930 DOI: 10.1080/1744666x.2022.2096590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Alopecia areata (AA) is a non-scarring, hair loss disorder and a common autoimmune-mediated disease with an estimated lifetime risk of about 2%. To date, the treatment of AA is mainly based on suppression or stimulation of the immune response. Genomics and transcriptomics studies generated important insights into the underlying pathophysiology, enabled discovery of molecular disease signatures, which were used in some of the recent clinical trials to monitor drug response and substantiated the consideration of new therapeutic modalities for the treatment of AA such as abatacept, dupilumab, ustekinumab and Janus Kinase (JAK) inhibitors. AREAS COVERED In this review, genomics and transcriptomics studies in AA are discussed in detail with particular emphasis on their past and prospective translational impacts. Microbiome studies are also briefly introduced. EXPERT OPINION The generation of large datasets using the new high-throughput technologies has revolutionized medical research and AA has also benefited from the wave of omics studies. However, the limitations associated with JAK inhibitors and clinical heterogeneity in AA patients underscore the necessity for continuing omics research in AA for discovery of novel therapeutic modalities and development of clinical tools for precision medicine.
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Affiliation(s)
- F Buket Basmanav
- Medical Faculty & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Regina C Betz
- Medical Faculty & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
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Performance of the EULAR/ACR 2019 classification criteria for systemic lupus erythematous in monogenic lupus. Clin Rheumatol 2022; 41:2721-2727. [PMID: 35590114 DOI: 10.1007/s10067-022-06209-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/10/2022] [Accepted: 04/30/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To evaluate the application of the EULAR/ACR-2019 criteria to monogenic lupus patients and compare its performance against the SLICC-2012 criteria. METHODS In a multicenter retrospective cohort study, consecutive patients with monogenic lupus from three tertiary lupus clinics were enrolled. The diagnosis of monogenic lupus was based on the expert physician's opinion or fulfilling the SLICC-2012 criteria. All enrolled patients had genetic variants. A control group of sporadic childhood SLE (cSLE) and non-SLE patients, were included. A descriptive data analysis was conducted, and the EULAR/ACR-2019 and SLICC-2012 criteria were applied to both groups. RESULTS Forty-nine patients with monogenic lupus with a median age at diagnosis of 6.0 (IQR 3.0-10.8) years and 104 controls (55 patients with cSLE and 49 non-lupus patients with a median age at diagnosis of 10.0 and 5.0 respectively) were included. Forty-four (89.8%) patients with monogenic lupus fulfilled the EULAR/ACR-2019 with a mean score of 22.3±8.9. The most frequent domains were immunologic (93.9%), musculoskeletal and renal (each 57.1%), and mucocutaneous (55.1%). Fifty-four (98.2%) cSLE patients and six (12.2%) non-lupus patients met the EULAR/ACR-2019 criteria with a mean score of 22.5±9.2 and 8.5±5.2, respectively. The sensitivity of the EULAR/ACR-2019 criteria in monogenic lupus was 89.9% (95% CI: 78.3-90.2), while the specificity was 87.6% (95% CI: 75.2-88.7). CONCLUSION This is the first and largest cohort of monogenic lupus patients testing the performance of the 2019-EULAR/ACR criteria. It efficiently classifies monogenic lupus patients, irrespective of the underlying genetic variants. Further studies are needed before these criteria are adopted worldwide. Key Points • Typically, patients with monogenic lupus have early onset severe disease, especially with mucocutaneous manifestations and a strong family history of SLE. • Monogenic lupus is a distinctive entity and might differ from the sporadic childhood SLE. • Our study includes a large multinational cohort of monogenic lupus with heterogeneous phenotypic features and underlying genetic variants. • Our study demonstrates that the EULAR/ACR-2019 criteria efficiently classified monogenic lupus patients, irrespective of the diversity of the underlying genetic variants.
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Chen J, Zhang P, Chen H, Wang X, He X, Zhong J, Zheng H, Li X, Jakovlić I, Zhang Y, Chen Y, Shen B, Deng C, Wu Y. Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus. Genomics 2022; 114:110332. [PMID: 35283196 DOI: 10.1016/j.ygeno.2022.110332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/27/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
Systemic lupus erythematosus (SLE, OMIM 152700) is a rare autoimmune disease with high heritability that affects ~0.1% of the population. Previous studies have revealed several common variants with small effects in European and East Asian SLE patients. However, there is still no rare variant study on Chinese SLE patients using the whole-genome sequencing technology (WGS). Here, we designed a family based WGS study to identify novel rare variants with large effects. Based on large-scale allele frequency data from the gnomAD database, we identified rare protein-coding gene variants with disruptive and sequence-altering impacts in SLE patients. We found that the burden of rare variants was significantly higher than that of common variants in patients, suggesting a larger effect of rare variants on the SLE pathogenesis. We identified the pathogenic risk of rare missense variants with significant odds ratios (p < 0.05) in two genes, including WNT16 (NC_000007.14:g.121329757G > C, NP_057171.2:p.(Ala86Pro) and 7 g.121329760G > C, NP_057171.2:p.(Ala87Pro)), which explains five out of seven patients covering all three families but are absent from all controls, and ERVW-1 (NC_000007.14:g.92469882A > G, NP_001124397.1:p.(Leu167Pro), rs74545114; NC_000007.14:g.92469907G > A, NP_001124397.1:p.(Arg159Cys), rs201142302; NC_000007.14:g.92469919G > A, NP_001124397.1:p.(His155Tyr), rs199552228), which explains the other two patients. None of these variants were identified in any of the controls. These associations are supported by known gene expression studies in SLE patients based on literature review. We further tested the wild and mutant types using the luciferase assays and qPCR in cells. We found that WNT16 can activate the canonical Wnt/β-catenin pathway while the mutant cannot. Additionally, the wild ERVW-1 expression can be significantly up-regulated by cAMP while the mutant cannot. Our study provides the first direct genetic and in vitro evidence for the pathogenic risk of mutant WNT16 and ERVW-1, which may facilitate the design of precision therapy for SLE.
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Affiliation(s)
- Jianhai Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haidi Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - HuaPing Zheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | | | - Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Younan Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cheng Deng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongkang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Shang S, Zhou Y, Chen K, Chen L, Li P, Li D, Cui S, Zhang MJ, Chen X, Li Q. A Novel Gene CDC27 Causes SLE and Is Associated With the Disease Activity. Front Immunol 2022; 13:876963. [PMID: 35418986 PMCID: PMC8996071 DOI: 10.3389/fimmu.2022.876963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022] Open
Abstract
Background As genetic genetic factors are important in SLE, so screening causative genes is of great significance for the prediction and early prevention in people who may develop SLE. At present, it is very difficult to screen causative genes through pedigrees. The analytical method described herein can be used to screen causative genes for SLE and other complex diseases through pedigrees. Methods For the first time, 24 lupus pedigrees were analyzed by combining whole exon sequencing and a variety of biological information tools including common-specific analysis, pVAAST (pedigree variant annotation, analysis and search tool), Exomiser (Combining phenotype and PPI associated analysis), and FARVAT (family based gene burden), and the causative genes of these families with lupus identified. Selected causative genes in peripheral-blood mononuclear cells (PBMCs) were evaluated by quantitative polymerase chain reaction (qPCR). Results Cell division cycle 27 (CDC27) was screened out by common-specific analysis and Exomiser causative gene screening. FARVAT analysis on these families detected only CDC27 at the extremely significant level (false discovery rate <0.05) by three family-based burden analyses (BURDEN, CALPHA, and SKATO). QPCR was performed to detect for CDC27 in the PBMCs of the SLE family patients, sporadic lupus patients, and healthy people. Compared with the healthy control group, CDC27 expression was low in lupus patients (familial and sporadic patients) (P<0.05) and correlated with lupus activity indicators: negatively with C-reactive protein (CRP) (P<0.05) and erythrocyte sedimentation rate (P<0.05) and positively with complement C3 and C4 (P<0.05). The CDC27 expression was upregulated in PBMCs from SLE patients with reduced lupus activity after immunotherapy (P<0.05). Based on Receiver operating characteristic (ROC) curve analysis, the sensitivity and specificity of CDC27 in diagnosing SLE were 82.30% and 94.40%. Conclusion The CDC27 gene, as found through WES combined with multiple analytical method may be a causative gene of lupus. CDC27 may serve as a marker for the diagnosis of SLE and is closely related to the lupus activity. We hope that the analytical method in this study will be used to screen causative genes for other diseases through small pedigrees, especially among non-close relatives.
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Affiliation(s)
- Shunlai Shang
- School of Medicine, Nankai University, Tianjin, China.,Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Yena Zhou
- School of Medicine, Nankai University, Tianjin, China
| | - Keng Chen
- Clinical Medical School, Guangdong Pharmaceutical University, Guangzhou, China
| | - Lang Chen
- Medical Technology & Bioinformatics Department, Beijing Mygenostics co., LTD, Beijing, China
| | - Ping Li
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Diangeng Li
- Department of Academic Research, Beijing-Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Shaoyuan Cui
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Mei-Jun Zhang
- Bioinformation Department, Geneis (Beijing) Co., Ltd., Beijing, China
| | - Xiangmei Chen
- School of Medicine, Nankai University, Tianjin, China.,Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
| | - Qinggang Li
- Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, China
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26
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Concepts in lupus pathophysiology: Lessons learned from disease across the spectrum. Clin Immunol 2022; 238:109021. [DOI: 10.1016/j.clim.2022.109021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/22/2022]
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Harley IT, Sawalha AH. Systemic lupus erythematosus as a genetic disease. Clin Immunol 2022; 236:108953. [PMID: 35149194 PMCID: PMC9167620 DOI: 10.1016/j.clim.2022.108953] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus is the prototypical systemic autoimmune disease, as it is characterized both by protean multi-organ system manifestations and by the uniform presence of pathogenic autoantibodies directed against components of the nucleus. Prior to the modern genetic era, the diverse clinical manifestations of SLE suggested to many that SLE patients were unlikely to share a common genetic risk basis. However, modern genetic studies have revealed that SLE usually arises when an environmental exposure occurs in an individual with a collection of genetic risk variants passing a liability threshold. Here, we summarize the current state of the field aimed at: (1) understanding the genetic architecture of this complex disease, (2) synthesizing how this genetic risk architecture impacts cellular and molecular disease pathophysiology, (3) providing illustrative examples that highlight the rich complexity of the pathobiology of this prototypical autoimmune disease and (4) communicating this complex etiopathogenesis to patients.
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Affiliation(s)
- Isaac T.W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA,Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, USA,Rocky Mountain Regional Veteran’s Administration Medical Center (VAMC), Medicine Service, Rheumatology Section, Aurora, CO, USA,Corresponding author at: Isaac TW Harley, MD, PhD, MS, Division of Rheumatology, University of Colorado Anschutz Medical Campus, Barbara Davis Center, Mail Stop B115, 1775 Aurora Court, Aurora, CO 80045, USA, (I.T.W. Harley)
| | - Amr H. Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA,Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA,Corresponding author at: Amr H. Sawalha, MD, University of Pittsburgh, 7123 Rangos Research Center, 4401 Penn Avenue, Pittsburgh, PA 15224, USA, (A.H. Sawalha)
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Mathapathi S, Chu CQ. Contribution of Impaired DNASE1L3 Activity to Anti-DNA Autoantibody Production in Systemic Lupus Erythematosus. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:17-22. [PMID: 36467024 PMCID: PMC9524810 DOI: 10.2478/rir-2022-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 03/05/2022] [Indexed: 06/17/2023]
Abstract
Anti-DNA autoantibodies are pathogenic in systemic lupus erythematosus (SLE). Cell-free chromatin associated long DNA fragments are antigens for anti-DNA antibodies. In health state, released by cell death and actively secreted by live cells, these cell-free DNA are cleared by deoxyribonucleases (DNASES). In SLE, cell-free DNA are accumulated. The defective clearance of long fragments of cell-free DNA in SLE is largely attributed to impaired deoxyribonuclease 1 like 3 (DNASE1L3). DNASE1L3 null mutation results in monogenic SLE. The SLE risk single-nucleotide polymorphism (rs35677470) encodes R260C variant DNASE1L3, which is defective in secretion, leading to reduced levels of DNASE1L3. In addition, neutralizing autoantibodies to DNASE1L3 are produced in SLE to inhibit its enzymatic activity.
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Affiliation(s)
- Samarth Mathapathi
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Section of Rheumatology, VA Portland Health Care System, Portland, Oregon, USA
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Section of Rheumatology, VA Portland Health Care System, Portland, Oregon, USA
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Da BB, Luo S, Huang M, Song F, Ding R, Xiao Y, Fu Y, Yang YS, Wang HL. Prediction of Hepatocellular Carcinoma Prognosis and Immune Cell Infiltration Using Gene Signature Associated with Inflammatory Response. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2415129. [PMID: 35035517 PMCID: PMC8759924 DOI: 10.1155/2022/2415129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/24/2022]
Abstract
It has been demonstrated that the inflammatory response influences cancer development and can be used as a prognostic biomarker in various tumors. However, the relevance of genes associated with inflammatory responses in hepatocellular carcinoma (HCC) remains unknown. The Cancer Genome Atlas (TCGA) database was analyzed using weighted gene coexpression network analysis (WGCNA) and differential analysis to discover essential inflammatory response-related genes (IFRGs). Cox regression studies, both univariate and multivariate, were employed to develop a prognostic IFRGs signature. Additionally, Gene Set Enrichment Analysis (GSEA) was used to deduce the biological function of the IFRGs signature. Finally, we estimated immune cell infiltration using a single sample GSEA (ssGSEA) and x-cell. Our results revealed that, among the major HCC IFRGs, two (DNASE1L3 and KLKB1) were employed to create a predictive IFRG signature. The IFRG signature could correctly predict overall survival (O.S) as per Kaplan-Meier time-dependent roc curves analysis. It was also linked to pathological tumor stage and T stage and might be used as a prognostic predictor in HCC. GSEA analysis concluded that the IFRG signature might influence the immune response in HCC. Immunological cell infiltration and immune checkpoint molecule expression differed in the high-risk and low-risk groups. As a result of our findings, DNASILE may play a role in the tumor microenvironment. However, more research is necessary to confirm the role of DNASE1L3 and KLKB1.
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Affiliation(s)
- Bin-Bin Da
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Shuai Luo
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Ming Huang
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Fei Song
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Rong Ding
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Yao Xiao
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Yang Fu
- CT Room, Kunming First People's Hospital, Kunming 650000, China
| | - Yin-Shan Yang
- Department of Minimally Invasive Interventional Medicine Yunnan Cancer Hospital, Kunming 650118, China
| | - Hai-Lei Wang
- Hepatobiliary Pancreatic Vascular Surgery, Kunming First People's Hospital, Kunming 650031, China
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He Y, Gallman AE, Xie C, Shen Q, Ma J, Wolfreys FD, Sandy M, Arsov T, Wu X, Qin Y, Zhang P, Jiang S, Stanley M, Wu P, Tan J, Ding H, Xue H, Chen W, Xu J, Criswell LA, Nititham J, Adamski M, Kitching AR, Cook MC, Cao L, Shen N, Cyster JG, Vinuesa CG. P2RY8 variants in lupus patients uncover a role for the receptor in immunological tolerance. J Exp Med 2022; 219:e20211004. [PMID: 34889940 PMCID: PMC8669517 DOI: 10.1084/jem.20211004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/26/2021] [Accepted: 11/18/2021] [Indexed: 12/30/2022] Open
Abstract
B cell self-tolerance is maintained through multiple checkpoints, including restraints on intracellular signaling and cell trafficking. P2RY8 is a receptor with established roles in germinal center (GC) B cell migration inhibition and growth regulation. Somatic P2RY8 variants are common in GC-derived B cell lymphomas. Here, we identify germline novel or rare P2RY8 missense variants in lupus kindreds or the related antiphospholipid syndrome, including a "de novo" variant in a child with severe nephritis. All variants decreased protein expression, F-actin abundance, and GPCR-RhoA signaling, and those with stronger effects increased AKT and ERK activity and cell migration. Remarkably, P2RY8 was reduced in B cell subsets from some SLE patients lacking P2RY8 gene variants. Low P2RY8 correlated with lupus nephritis and increased age-associated B cells and plasma cells. By contrast, P2RY8 overexpression in cells and mice restrained plasma cell development and reinforced negative selection of DNA-reactive developing B cells. These findings uncover a role of P2RY8 in immunological tolerance and lupus pathogenesis.
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MESH Headings
- Animals
- Antiphospholipid Syndrome/genetics
- Antiphospholipid Syndrome/immunology
- Antiphospholipid Syndrome/metabolism
- B-Lymphocyte Subsets/immunology
- B-Lymphocyte Subsets/metabolism
- Cell Line, Tumor
- Female
- HEK293 Cells
- Humans
- Immune Tolerance/genetics
- Immune Tolerance/immunology
- Lupus Erythematosus, Systemic/genetics
- Lupus Erythematosus, Systemic/immunology
- Lupus Erythematosus, Systemic/metabolism
- Lupus Nephritis/genetics
- Lupus Nephritis/immunology
- Lupus Nephritis/metabolism
- Male
- Mice, Inbred C57BL
- Mutation, Missense/genetics
- Mutation, Missense/immunology
- Pedigree
- Plasma Cells/immunology
- Plasma Cells/metabolism
- Receptors, Purinergic P2Y/genetics
- Receptors, Purinergic P2Y/immunology
- Receptors, Purinergic P2Y/metabolism
- Signal Transduction/genetics
- Signal Transduction/immunology
- Mice
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Affiliation(s)
- Yuke He
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Antonia E. Gallman
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Chengmei Xie
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Shen
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Jianyang Ma
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Finn D. Wolfreys
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Moriah Sandy
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Todor Arsov
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Xiaoqian Wu
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Qin
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Pingjing Zhang
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Simon Jiang
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Maurice Stanley
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Philip Wu
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Jingjing Tan
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Huihua Ding
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haiyan Xue
- Department of Pediatrics, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Chen
- Department of Pediatrics, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jinping Xu
- Department of Pediatrics, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lindsey A. Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Marcin Adamski
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - A. Richard Kitching
- Centre for Personalised Immunology, Centre for Inflammatory Diseases, Monash University Department of Medicine, Clayton, Victoria, Australia
| | - Matthew C. Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
| | - Lanfang Cao
- Department of Pediatrics, Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Shen
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jason G. Cyster
- Howard Hughes Medical Institute and Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA
| | - Carola G. Vinuesa
- Centre for Personalised Immunology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Australia
- Francis Crick Institute, London, UK
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Raupov RK, Suspitsin EN, Imelbaev AI, Kostik MM. Simultaneous Onset of Pediatric Systemic Lupus Erythematosus in Twin Brothers: Case Report. Front Pediatr 2022; 10:929358. [PMID: 35783307 PMCID: PMC9243501 DOI: 10.3389/fped.2022.929358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 11/27/2022] Open
Abstract
UNLABELLED There are hundreds of twin adult patients with systemic lupus erythematosus (SLE), but male children with SLE are rarely affected. Two monozygotic twin brothers developed SLE at the age of 11 years during 1 month. The index brother manifested with Henoch-Shonlein purpura, accompanied by ANA positivity, and later developed critical left femoral arterial stenosis with high levels of anti-dsDNA, antiphospholipid antibodies, hypocomplementemia, and Coombs-positive hemolytic anemia. At that time his twin brother had only identical autoimmune findings and developed clinical manifestation (myositis and fasciitis) a month later. Both twins had increased IFN-score and shared a heterozygous variant in the RNASEL gene. Index patients developed scalp rash and nephritis 6 months after their parents refused the treatment which has been lasted for 1 year after disease diagnostics. CONCLUSION The simultaneous onset of the pediatric SLE in the male twin is a very rare situation suspected monogenic origin of the disease. Further functional studies are required to confirm the causative role of the mutation.
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Affiliation(s)
- Rinat K Raupov
- Hospital Pediatry Department, St. Petersburg State Pediatric Medical University, Saint Petersburg, Russia.,H. Turner National Medical Research Center for Children's Orthopedics and Trauma Surgery, Saint Petersburg, Russia.,City Hospital, Saint Petersburg, Russia
| | - Evgeny N Suspitsin
- N. N. Petrov Institute of Oncology, Molecular Diagnostics, Saint Petersburg, Russia.,Molecular Genetics Department, St. Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Artur I Imelbaev
- Radiology Department, St. Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Mikhail M Kostik
- Hospital Pediatry Department, St. Petersburg State Pediatric Medical University, Saint Petersburg, Russia
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32
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Su G, Lai J, Zhu J, Zhang D, Hou J, Xu Y, Zhou Z. Analysis of five cases of monogenic lupus related to primary immunodeficiency diseases. Inflamm Res 2021; 70:1211-1216. [PMID: 34559261 DOI: 10.1007/s00011-021-01479-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVE AND DESIGN We studied five cases of PID-related monogenic lupus to explore the characteristics. MATERIAL OR SUBJECTS Among 42 cases of PID patients between 2017-2020, 5 patients were diagnosed as PID-related monogenic lupus, including 2 males and 3 females, with age range from 2 years 3 months to 13 years old. TREATMENTS DMARDs, biological agents and stem cell transplantation were used to treat different patients. METHODS We collected the clinical observation indicators, auxiliary examination and treatment of the five patients. RESULTS Patient 1 was diagnosed with monogenic lupus secondary to severe combined immunodeficiency and received prednisone and methotrexate treatment. Patient 2 was diagnosed with monogenic lupus secondary to activated phosphoinositide 3-kinase δ syndrome. Allogeneic stem cell transplantation was conducted. Patient 3 was diagnosed with monogenic lupus secondary to RAS-associated lymphoproliferative disease. The child was treated with prednisone and rituximab. Patient 4 was diagnosed with monogenic lupus secondary to PSTPIP1-associated myeloid-related proteinaemia inflammatory syndrome. The child was given methylprednisolone, methotrexate, and infliximab. Patient 5 was diagnosed with monogenic lupus secondary to A20 haploinsufficiency. The child was treated with methylprednisolone and infliximab. CONCLUSIONS Multiple PIDs can lead to monogenic lupus. Different PID-related monogenic lupus has different suitable targeted drugs.
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Affiliation(s)
- Gaixiu Su
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Jianming Lai
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China.
| | - Jia Zhu
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Dan Zhang
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Jun Hou
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Yingjie Xu
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
| | - Zhixuan Zhou
- Department of Rheumatology and Immunology, Capital Institute of Pediatrics, No.2 Yabao Road, Chaoyang District, Beijing, 100020, China
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33
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Critical evaluation of CNA estimators for DNA data using matching confidence masks and WGS technology. Biomed Signal Process Control 2021. [DOI: 10.1016/j.bspc.2021.103004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Abstract
Skewing of type I interferon (IFN) production and responses is a hallmark of systemic lupus erythematosus (SLE). Genetic and environmental contributions to IFN production lead to aberrant innate and adaptive immune activation even before clinical development of disease. Basic and translational research in this arena continues to identify contributions of IFNs to disease pathogenesis, and several promising therapeutic options for targeting of type I IFNs and their signaling pathways are in development for treatment of SLE patients.
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Affiliation(s)
- Sirisha Sirobhushanam
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5568 MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA
| | - Stephanie Lazar
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5568 MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, 5570A MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA; Department of Dermatology, University of Michigan, 5570A MSRB 2, 1150 West Medical Center Drive, Ann Arbor, MI 49109, USA.
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35
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Wajda A, Sivitskaya L, Paradowska-Gorycka A. Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases. J Clin Med 2021; 10:3334. [PMID: 34362117 PMCID: PMC8348854 DOI: 10.3390/jcm10153334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
NGS technologies have transformed clinical diagnostics and broadly used from neonatal emergencies to adult conditions where the diagnosis cannot be made based on clinical symptoms. Autoimmune diseases reveal complicate molecular background and traditional methods could not fully capture them. Certainly, NGS technologies meet the needs of modern exploratory research, diagnostic and pharmacotherapy. Therefore, the main purpose of this review was to briefly present the application of NGS technology used in recent years in the understanding of autoimmune diseases paying particular attention to autoimmune connective tissue diseases. The main issues are presented in four parts: (a) panels, whole-genome and -exome sequencing (WGS and WES) in diagnostic, (b) Human leukocyte antigens (HLA) as a diagnostic tool, (c) RNAseq, (d) microRNA and (f) microbiome. Although all these areas of research are extensive, it seems that epigenetic impact on the development of systemic autoimmune diseases will set trends for future studies on this area.
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Affiliation(s)
- Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
| | - Larysa Sivitskaya
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072 Minsk, Belarus
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
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36
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Peng L, Yuan X, Chen L, Chen S, Chen K. Identification and functional analysis of a novel phospholipase D2 gene mutation associated with familial systemic lupus erythematosus. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2021; 46:234-239. [PMID: 33927069 PMCID: PMC10929931 DOI: 10.11817/j.issn.1672-7347.2021.190589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a kind of autoimmune inflammatory connective tissue disease which seriously endangers human health. Genetic factors play a key role in the pathogenesis of SLE. This study aims to investigate a novel phospholipase D2 (PLD2) mutation associated with familial SLE, and further explore the underlying mechanism of the mutation in SLE. METHODS The blood samples from a SLE patient, the patient's parents, and 147 normal controls were collected and DNA was extracted. Whole genome high-throughput sequencing was performed in the patient and her parents and the results were further analyzed by various bioinformatics methods. The wild type (wt), mutant type (mu), and negative control PLD2 plasmids were further constructed and transfected into 293 cells. The expression level of HRAS protein in 293 cells was detected by Western blotting. RESULTS In this SLE family, the female SLE patient and her mother, 1 in generation II and 1 in generation III had typical clinical manifestations of SLE, and all of them had lupus nephritis at early stage. The genetic characteristics are consistent with autosomal dominant inheritance. A novel PLD2 heterozygous mutation (c.2722C>T) was found in the patient and her mother, but not in her father and other normal controls. Compared with wtPLD2 plasmid and negative control PLD2 plasmid, the expression of HRAS in 293 cells transfected with muPLD2 plasmid was significantly up-regulated (both P<0.05). CONCLUSIONS PLD2 c.2722C>T mutation may be one of the pathogeny of SLE in this family.
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Affiliation(s)
- Lin Peng
- Department of Nephrology, First Hospital of Changsha, Changsha 410005.
| | - Xinke Yuan
- Department of Nephrology, First Hospital of Changsha, Changsha 410005
| | - Lixiao Chen
- Department of Nephrology, First Hospital of Changsha, Changsha 410005
| | - Sijia Chen
- Department of Nephrology, First Hospital of Changsha, Changsha 410005
| | - Ke Chen
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha 410013, China.
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37
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Deng Z, Xiao M, Du D, Luo N, Liu D, Liu T, Lian D, Peng J. DNASE1L3 as a Prognostic Biomarker Associated with Immune Cell Infiltration in Cancer. Onco Targets Ther 2021; 14:2003-2017. [PMID: 33776450 PMCID: PMC7987320 DOI: 10.2147/ott.s294332] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/19/2021] [Indexed: 01/06/2023] Open
Abstract
Objectives Deoxyribonuclease 1 like 3 (DNASE1L3) is critically involved in apoptosis and immune response, however, its role in cancer has yet to be deciphered. We aimed to explore the prognostic value of DNASE1L3 across a series of malignancies. Methods Based on Oncomine database and Tumor Immune Estimation Resource (TIMER), expression profiling of DNASE1L3 was detailed in malignancies. Using PrognoScan, Kaplan-Meier Plotter, GEPIA2, and bc-GenEcMiner v4.5, prognostic value of DNASE1L3 was estimated in diverse cancers. Based on TIMER, association between DNASEL13 expression and immune infiltration was examined in various cancers. Then, mRNA level of DNASE1L3 in hepatocellular carcinoma (HCC) samples (n=22) and stomach adenocarcinoma (STAD) samples (n=17) was measured with qRT-PCR. Immunohistochemistry was performed to confirm expression of DNASE1L3 in paraffin-embedded tissues of HCC (n=9) and lung adenocarcinoma (n=20). Results DNASE1L3 was downregulated in multiple cancers, including breast invasive carcinoma (BRCA), cholangiocarcinoma (CHOL), liver hepatocellular carcinoma (LIHC), and lung adenocarcinoma (LUAD). A lower level of DNASE1L3 correlated with poorer prognosis in various cancers, especially in breast, liver, kidney, stomach, lung adenocarcinoma and sarcoma (SARC). Moreover, DNASE1L3 was positively related to immune cell infiltration in many cancers, including BRCA, LIHC, STAD, LUAD, and SARC. DNASE1L3 was significantly associated with CCR7/CCL19 in cancers. DNASE1L3 was downregulated in HCC and STAD tissues as demonstrated by qRT-PCR, as well as in HCC and LUAD samples, as shown by immunohistochemistry. Conclusion DNASE1L3 has potential to serve as a prognostic biomarker in cancer of the breast, kidney, liver, stomach, lung adenocarcinoma and sarcoma. Down-regulation of DNASE1L3 may participate in immune escape via CCR7/CCL19 axis.
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Affiliation(s)
- Zenghua Deng
- Ninth School of Clinical Medicine, Peking University, Beijing, 100038, People's Republic of China.,Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Mengmeng Xiao
- Peking University International Hospital, Beijing, 102206, People's Republic of China.,Eighth School of Clinical Medicine, Peking University, Beijing, 102206, People's Republic of China
| | - Dexiao Du
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Nan Luo
- Ninth School of Clinical Medicine, Peking University, Beijing, 100038, People's Republic of China.,Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Dongfang Liu
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Tingting Liu
- Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Dongbo Lian
- Ninth School of Clinical Medicine, Peking University, Beijing, 100038, People's Republic of China.,Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Jirun Peng
- Ninth School of Clinical Medicine, Peking University, Beijing, 100038, People's Republic of China.,Department of Surgery, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
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38
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Santa P, Garreau A, Serpas L, Ferriere A, Blanco P, Soni C, Sisirak V. The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing. Front Immunol 2021; 12:629922. [PMID: 33717156 PMCID: PMC7952454 DOI: 10.3389/fimmu.2021.629922] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.
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Affiliation(s)
- Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | | | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Immunology and Immunogenetic Department, Bordeaux University Hospital, Bordeaux, France
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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39
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Al-Mayouf SM, Alreefi HA, Alsinan TA, AlSalmi G, AlRowais A, Al-Herz W, Alazami AM, Alsonbul A, Al-Mousa H. Lupus manifestations in children with primary immunodeficiency diseases: Comprehensive phenotypic and genetic features and outcome. Mod Rheumatol 2021; 31:1171-1178. [PMID: 33563058 DOI: 10.1080/14397595.2021.1886627] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
OBJECTIVES To report the phenotypic, genetic findings and outcome of children with lupus manifestations associated with primary immunodeficiency diseases (PIDs). METHODS Data are retrospectively collected on patients with lupus manifestations and PIDs seen between 1998 and 2019. Data comprised the clinical findings and genetic testing, the response to treatment and the accrual damage related to SLE. RESULTS A total of 39 patients (22 female) were reviewed. Thirty-four patients had lupus manifestations and six patients with SLE-like manifestations. Genetic analysis was performed in 25 patients. Complement deficiency was the most frequent PIDs; 26 patients were C1q deficient, three patients had C3 deficiency, two patients had C4 deficiency and one patient with heterozygous C8b variant. The other seven patients had different PIDs genetic defects that include SCID caused by PNP deficiency, CGD, CVID (PIK3CD), IL-2RB mutation, DNase II deficiency, STAT1 mutation, ISG15 mutation and Griscelli syndrome type 3. Mucocutaneous lesions, arthritis and lung involvement were the main clinical features. 84.1% experienced recurrent infections. The mean accrual damage was 2.7 ± 2.2. There were five deaths because of infection. CONCLUSION This study suggests that patients with lupus manifestations and early onset disease, family history of SLE or recurrent infections should undergo immunological work-up and genetic testing to rule out PIDs.
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Affiliation(s)
- Sulaiman M Al-Mayouf
- Department of Pediatrics, Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia.,College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hajar A Alreefi
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Tuqa A Alsinan
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Ghada AlSalmi
- Department of Pediatrics, Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Abdulaziz AlRowais
- Department of Pediatrics, Pediatric Rheumatology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait.,Pediatric Department, Allergy & Clinical Immunology Unit, Al-Sabah Hospital, Kuwait City, Kuwait
| | - Anas M Alazami
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Abdullah Alsonbul
- Department of Pediatrics, Pediatric Rheumatology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
| | - Hamoud Al-Mousa
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Department of Pediatrics, Allergy & Immunology, King Faisal Specialist Hospital & Research Center, Riyadh, Saudi Arabia
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40
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Kanzi AM, San JE, Chimukangara B, Wilkinson E, Fish M, Ramsuran V, de Oliveira T. Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Front Genet 2020; 11:544162. [PMID: 33193618 PMCID: PMC7649788 DOI: 10.3389/fgene.2020.544162] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/21/2020] [Indexed: 12/29/2022] Open
Abstract
Mendelian and complex genetic trait diseases continue to burden and affect society both socially and economically. The lack of effective tests has hampered diagnosis thus, the affected lack proper prognosis. Mendelian diseases are caused by genetic mutations in a singular gene while complex trait diseases are caused by the accumulation of mutations in either linked or unlinked genomic regions. Significant advances have been made in identifying novel diseases associated mutations especially with the introduction of next generation and third generation sequencing. Regardless, some diseases are still without diagnosis as most tests rely on SNP genotyping panels developed from population based genetic analyses. Analysis of family genetic inheritance using whole genomes, whole exomes or a panel of genes has been shown to be effective in identifying disease-causing mutations. In this review, we discuss next generation and third generation sequencing platforms, bioinformatic tools and genetic resources commonly used to analyze family based genomic data with a focus on identifying inherited or novel disease-causing mutations. Additionally, we also highlight the analytical, ethical and regulatory challenges associated with analyzing personal genomes which constitute the data used for family genetic inheritance.
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Affiliation(s)
- Aquillah M. Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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Sandling JK, Pucholt P, Hultin Rosenberg L, Farias FHG, Kozyrev SV, Eloranta ML, Alexsson A, Bianchi M, Padyukov L, Bengtsson C, Jonsson R, Omdal R, Lie BA, Massarenti L, Steffensen R, Jakobsen MA, Lillevang ST, Lerang K, Molberg Ø, Voss A, Troldborg A, Jacobsen S, Syvänen AC, Jönsen A, Gunnarsson I, Svenungsson E, Rantapää-Dahlqvist S, Bengtsson AA, Sjöwall C, Leonard D, Lindblad-Toh K, Rönnblom L. Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing. Ann Rheum Dis 2020; 80:109-117. [PMID: 33037003 PMCID: PMC7788061 DOI: 10.1136/annrheumdis-2020-218636] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 01/02/2023]
Abstract
Objectives Systemic lupus erythematosus (SLE) is an autoimmune disease with extensive heterogeneity in disease presentation between patients, which is likely due to an underlying molecular diversity. Here, we aimed at elucidating the genetic aetiology of SLE from the immunity pathway level to the single variant level, and stratify patients with SLE into distinguishable molecular subgroups, which could inform treatment choices in SLE. Methods We undertook a pathway-centred approach, using sequencing of immunological pathway genes. Altogether 1832 candidate genes were analysed in 958 Swedish patients with SLE and 1026 healthy individuals. Aggregate and single variant association testing was performed, and we generated pathway polygenic risk scores (PRS). Results We identified two main independent pathways involved in SLE susceptibility: T lymphocyte differentiation and innate immunity, characterised by HLA and interferon, respectively. Pathway PRS defined pathways in individual patients, who on average were positive for seven pathways. We found that SLE organ damage was more pronounced in patients positive for the T or B cell receptor signalling pathways. Further, pathway PRS-based clustering allowed stratification of patients into four groups with different risk score profiles. Studying sets of genes with priors for involvement in SLE, we observed an aggregate common variant contribution to SLE at genes previously reported for monogenic SLE as well as at interferonopathy genes. Conclusions Our results show that pathway risk scores have the potential to stratify patients with SLE beyond clinical manifestations into molecular subsets, which may have implications for clinical follow-up and therapy selection.
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Affiliation(s)
- Johanna K Sandling
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Pascal Pucholt
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Lina Hultin Rosenberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Fabiana H G Farias
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Psychiatry, Washington University, St. Louis, Missouri, USA
| | - Sergey V Kozyrev
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Andrei Alexsson
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Leonid Padyukov
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Christine Bengtsson
- Department of Public Health and Clinical Medicine/Rheumatology, Umeå University, Umeå, Sweden
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roald Omdal
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Clinical Immunology unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo, Oslo, Norway
| | - Laura Massarenti
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Rudi Steffensen
- Department of Clinical Immunology, Aalborg University, Aalborg, Denmark
| | - Marianne A Jakobsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Søren T Lillevang
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | | | - Karoline Lerang
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Øyvind Molberg
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anne Voss
- Department of Rheumatology, Odense University Hospital, Odense, Denmark
| | - Anne Troldborg
- Department of Rheumatology, Aarhus University Hospital, Aarhus, Denmark.,Institute of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Søren Jacobsen
- Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Iva Gunnarsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Division of Rheumatology, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | | | - Anders A Bengtsson
- Department of Clinical Sciences Lund, Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Christopher Sjöwall
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology, Uppsala University, Uppsala, Sweden
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42
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Hagberg N, Lundtoft C, Rönnblom L. Immunogenetics in systemic lupus erythematosus: Transitioning from genetic associations to cellular effects. Scand J Immunol 2020; 92:e12894. [DOI: 10.1111/sji.12894] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Niklas Hagberg
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
| | - Christian Lundtoft
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
| | - Lars Rönnblom
- Rheumatology and Science for Life Laboratories Department of Medical Sciences Uppsala University Uppsala Sweden
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43
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Akbar L, Alsagheir R, Al-Mayouf SM. Efficacy of a sequential treatment by belimumab in monogenic systemic lupus erythematosus. Eur J Rheumatol 2020; 7:eurjrheum.2020.20087. [PMID: 32910770 PMCID: PMC7574768 DOI: 10.5152/eurjrheum.2020.20087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 07/17/2020] [Indexed: 02/02/2023] Open
Abstract
The objective of the study was to report the safety and potential therapeutic effect of belimumab in monogenic systemic lupus erythematosus (SLE). Consecutive children with monogenic SLE treated with belimumab were evaluated retrospectively. Response parameters assessment was completed at the time of initiation of belimumab, at 6 months, and last follow-up visit. Response parameters comprised physician global assessment (physician GA) and parent global assessment (parent GA), global disease activity as measured by SLE disease activity index (SLEDAI), and daily glucocorticoids dose. Undesirable events affecting patients during treatment were also collected. Six children with monogenic SLE proved by genetic testing (five patients with C1q deficiency and one patient with deoxyribonuclease II (DNase II) deficiency), failed glucocorticoids and sequential immunosuppressive medications. Belimumab was added to glucocorticoids and current immunosuppressive medications. The main indications for belimumab initiation were mucocutaneous disease, arthritis, and inability to taper glucocorticoids. All patients tolerated belimumab infusion. No serious events were reported. However, one patient was lost to follow-up and died because of sepsis. Compared to the baseline values, there was an improvement in physician GA, parent GA, and SLEDAI, and a notable reduction in the need of daily corticosteroids. However, there were no significant changes in the complement and ds-DNA antibody levels. Belimumab can be considered as an adjunctive therapeutic option for patients with refractory monogenic SLE. Further follow-up and more patients needed to confirm this finding and a larger prospective study is required for more definitive conclusions.
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Affiliation(s)
- Lujayn Akbar
- Department of Pediatric Rheumatology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Razan Alsagheir
- Department of Pediatric Rheumatology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sulaiman M Al-Mayouf
- Department of Pediatric Rheumatology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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44
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Almlöf JC, Nystedt S, Mechtidou A, Leonard D, Eloranta ML, Grosso G, Sjöwall C, Bengtsson AA, Jönsen A, Gunnarsson I, Svenungsson E, Rönnblom L, Sandling JK, Syvänen AC. Contributions of de novo variants to systemic lupus erythematosus. Eur J Hum Genet 2020; 29:184-193. [PMID: 32724065 PMCID: PMC7852530 DOI: 10.1038/s41431-020-0698-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/04/2020] [Accepted: 07/14/2020] [Indexed: 12/21/2022] Open
Abstract
By performing whole-genome sequencing in a Swedish cohort of 71 parent-offspring trios, in which the child in each family is affected by systemic lupus erythematosus (SLE, OMIM 152700), we investigated the contribution of de novo variants to risk of SLE. We found de novo single nucleotide variants (SNVs) to be significantly enriched in gene promoters in SLE patients compared with healthy controls at a level corresponding to 26 de novo promoter SNVs more in each patient than expected. We identified 12 de novo SNVs in promoter regions of genes that have been previously implicated in SLE, or that have functions that could be of relevance to SLE. Furthermore, we detected three missense de novo SNVs, five de novo insertion-deletions, and three de novo structural variants with potential to affect the expression of genes that are relevant for SLE. Based on enrichment analysis, disease-affecting de novo SNVs are expected to occur in one-third of SLE patients. This study shows that de novo variants in promoters commonly contribute to the genetic risk of SLE. The fact that de novo SNVs in SLE were enriched to promoter regions highlights the importance of using whole-genome sequencing for identification of de novo variants.
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Affiliation(s)
- Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 23, Uppsala, Sweden.
| | - Sara Nystedt
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 23, Uppsala, Sweden
| | - Aikaterini Mechtidou
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 23, Uppsala, Sweden
| | - Dag Leonard
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Maija-Leena Eloranta
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Giorgia Grosso
- Department of Medicine, Karolinska Institutet, Rheumatology, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Christopher Sjöwall
- Department of Clinical and Experimental Medicine, Rheumatology/Division of Neuro and Inflammation Sciences, Linköping University, 581 83, Linköping, Sweden
| | - Anders A Bengtsson
- Department of Clinical Sciences, Rheumatology, Lund University, Skåne University Hospital, 222 42, Lund, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences, Rheumatology, Lund University, Skåne University Hospital, 222 42, Lund, Sweden
| | - Iva Gunnarsson
- Department of Medicine, Karolinska Institutet, Rheumatology, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Elisabet Svenungsson
- Department of Medicine, Karolinska Institutet, Rheumatology, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Lars Rönnblom
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Rheumatology and Science for Life Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, 751 23, Uppsala, Sweden
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45
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From hepatitis C virus immunoproteomics to rheumatology via cross-reactivity in one table. Curr Opin Rheumatol 2020; 31:488-492. [PMID: 31356379 DOI: 10.1097/bor.0000000000000606] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW To give an overview of molecular and immunologic data that link hepatitis C virus (HCV) infection to rheumatic diseases in the human host. RECENT FINDINGS A high level of peptide sharing exists between immunopositive HCV epitopes and human proteins that, when altered, associate with rheumatic manifestations. SUMMARY The findings suggest the involvement of HCV infection in the induction of most rheumatic diseases via a mechanism of autoimmune cross-reactivity.
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46
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Jiang SH, Stanley M, Vinuesa CG. Rare genetic variants in systemic autoimmunity. Immunol Cell Biol 2020; 98:490-499. [PMID: 32315078 DOI: 10.1111/imcb.12339] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/15/2020] [Accepted: 04/15/2020] [Indexed: 01/03/2023]
Abstract
Autoimmune disease is a substantial cause of morbidity and is strongly influenced by genetic risk. Extensive efforts have characterized the overall genetic basis of many autoimmune diseases, typically by investigation of common variants. While these common variants have modest effects and may cumulatively predispose to disease, it is also increasingly apparent that rare variants have significantly greater effect on phenotype and are likely to contribute to autoimmune disease. Recent advances have illustrated the next fundamental step in elucidating the genetic basis of autoimmunity, moving beyond association to demonstrate the functional consequences of these variants.
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Affiliation(s)
- Simon H Jiang
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Acton, ACT, 2601, Australia.,Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Acton, ACT, 2601, Australia.,Department of Renal Medicine, The Canberra Hospital, Garran, ACT, 2601, Australia
| | - Maurice Stanley
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Acton, ACT, 2601, Australia.,Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Acton, ACT, 2601, Australia
| | - Carola G Vinuesa
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Acton, ACT, 2601, Australia.,Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Acton, ACT, 2601, Australia.,China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, Jiao Tong University Shanghai, Huangpu Qu, 200333, China
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47
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Abstract
Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are two common autoimmune rheumatic diseases that vary in severity, clinical presentation, and disease course between individuals. Molecular and genetic studies of both diseases have identified candidate genes and molecular pathways that are linked to various disease outcomes and treatment responses. Currently, patients can be grouped into molecular subsets in each disease, and these molecular categories should enable precision medicine approaches to be applied in rheumatic diseases. In this article, we will review key lessons learned about disease heterogeneity and molecular characterization in rheumatology, which we hope will lead to personalized therapeutic strategies.
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Affiliation(s)
| | - Jaqueline L. Paredes
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
| | - Simone Appenzeller
- Rheumatology Unit, Department of Medicine, Faculty of Medical Science, State University of Campinas, Campinas, Brazil
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, New York University School of Medicine, New York, NY, USA
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48
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Song W, Tang D, Chen D, Zheng F, Huang S, Xu Y, Yu H, He J, Hong X, Yin L, Liu D, Dai W, Dai Y. Advances in applying of multi-omics approaches in the research of systemic lupus erythematosus. Int Rev Immunol 2020; 39:163-173. [PMID: 32138562 DOI: 10.1080/08830185.2020.1736058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wencong Song
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Deheng Chen
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Shaoying Huang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Yong Xu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Haiyan Yu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Jingquan He
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, USA
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
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49
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Alarcón-Riquelme ME. Expanding the inventory of rare variants in SLE. THE LANCET. RHEUMATOLOGY 2020; 2:e67-e69. [PMID: 38263662 DOI: 10.1016/s2665-9913(19)30162-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 01/25/2024]
Affiliation(s)
- Marta E Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Regional Government Center for Genomics and Oncological Research (GENYO), Parque Tecnológico de la Salud, 18016, Granada, Spain.
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50
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Belot A, Rice GI, Omarjee SO, Rouchon Q, Smith EMD, Moreews M, Tusseau M, Frachette C, Bournhonesque R, Thielens N, Gaboriaud C, Rouvet I, Chopin E, Hoshino A, Latour S, Ranchin B, Cimaz R, Romagnani P, Malcus C, Fabien N, Sarda MN, Kassai B, Lega JC, Decramer S, Abou-Jaoude P, Bruce IN, Simonet T, Bardel C, Rollat-Farnier PA, Viel S, Reumaux H, O'Sullivan J, Walzer T, Mathieu AL, Marenne G, Ludwig T, Genin E, Ellingford J, Bader-Meunier B, Briggs TA, Beresford MW, Crow YJ. Contribution of rare and predicted pathogenic gene variants to childhood-onset lupus: a large, genetic panel analysis of British and French cohorts. THE LANCET. RHEUMATOLOGY 2020; 2:e99-e109. [PMID: 38263665 DOI: 10.1016/s2665-9913(19)30142-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/09/2019] [Accepted: 12/10/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a rare immunological disorder and genetic factors are considered important in its causation. Monogenic lupus has been associated with around 30 genotypes in humans and 60 in mice, while genome-wide association studies have identified more than 90 risk loci. We aimed to analyse the contribution of rare and predicted pathogenic gene variants in a population of unselected cases of childhood-onset SLE. METHODS For this genetic panel analysis we designed a next-generation sequencing panel comprising 147 genes, including all known lupus-causing genes in humans, and potentially lupus-causing genes identified through GWAS and animal models. We screened 117 probands fulfilling American College of Rheumatology (ACR) criteria for SLE, ascertained through British and French cohorts of childhood-onset SLE, and compared these data with those of 791 ethnically matched controls from the 1000 Genomes Project and 574 controls from the FREX Consortium. FINDINGS After filtering, mendelian genotypes were confirmed in eight probands, involving variants in C1QA, C1QC, C2, DNASE1L3, and IKZF1. Seven additional patients carried heterozygous variants in complement or type I interferon-associated autosomal recessive genes, with decreased concentrations of the encoded proteins C3 and C9 recorded in two patients. Rare variants that were predicted to be damaging were significantly enriched in the childhood-onset SLE cohort compared with controls; 25% of SLE probands versus 5% of controls were identified to harbour at least one rare, predicted damaging variant (p=2·98 × 10-11). Inborn errors of immunity were estimated to account for 7% of cases of childhood-onset SLE, with defects in innate immunity representing the main monogenic contribution. INTERPRETATION An accumulation of rare variants that are predicted to be damaging in SLE-associated genes might contribute to disease expression and clinical heterogeneity. FUNDING European Research Council.
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Affiliation(s)
- Alexandre Belot
- Paediatric Nephrology, Rheumatology, Dermatology Unit, Femme Mere Enfant Hospital, Hospices Civils de Lyon, France; CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.
| | - Gillian I Rice
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Sulliman Ommar Omarjee
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Quentin Rouchon
- Data Mining and Modelling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Eve M D Smith
- Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK; Department of Women and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Marion Moreews
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Maud Tusseau
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Cécile Frachette
- Paediatric Nephrology, Rheumatology, Dermatology Unit, Femme Mere Enfant Hospital, Hospices Civils de Lyon, France; CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Raphael Bournhonesque
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Nicole Thielens
- University of Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | | | - Isabelle Rouvet
- Centre de biotechnologie cellulaire et Biothèque, Groupe Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France
| | - Emilie Chopin
- Centre de biotechnologie cellulaire et Biothèque, Groupe Hospitalier Est, Hospices Civils de Lyon, 69677 Bron, France
| | - Akihiro Hoshino
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Paris, France
| | - Sylvain Latour
- Laboratory of Lymphocyte Activation and Susceptibility to EBV infection, INSERM UMR 1163, Paris, France; University Paris Descartes Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Bruno Ranchin
- Paediatric Nephrology, Rheumatology, Dermatology Unit, Femme Mere Enfant Hospital, Hospices Civils de Lyon, France
| | - Rolando Cimaz
- Rheumatology Unit, Anna Meyer Children Hospital and University of Florence, University of Florence, Florence, Italy
| | - Paula Romagnani
- Nephrology Unit, Anna Meyer Children Hospital and University of Florence, University of Florence, Florence, Italy
| | - Christophe Malcus
- Service d'Immunologie, Hôpital Edouard Herriot, Hospices Civils de Lyon, 69437 Lyon, France
| | - Nicole Fabien
- Service d'immunologie, Hospices Civils de Lyon, CHLS, 69495 Pierre-Bénite, France
| | - Marie-Nathalie Sarda
- Service d'immunologie, Hospices Civils de Lyon, CHLS, 69495 Pierre-Bénite, France
| | - Behrouz Kassai
- EPICIME-CIC 1407 de Lyon, Inserm, Service de Pharmacotoxicologie, Hospices Civils de Lyon & Université Lyon 1, 69677, Bron, France
| | - Jean-Christophe Lega
- Internal Medicine Unit, CHLS, Hospices Civils de Lyon, Pierre Benite, Université de Lyon 1, Lyon, France
| | - Stéphane Decramer
- Department of Pediatric Nephrology, Centre Hospitalier Universitaire de Toulouse, Toulouse, France; Centre De Référence des Maladies Rénales Rares du Sud Ouest & Inserm U1048, France
| | - Pauline Abou-Jaoude
- Department of Paediatric Nephrology, St George Hospital, University Medical Center, Beirut, Lebanon
| | - Ian N Bruce
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, University of Manchester, Manchester, UK; NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Thomas Simonet
- Department of Biostatistics-bioinformatics, Hospices Civils de Lyon, 69677, Bron, France
| | - Claire Bardel
- Department of Biostatistics-bioinformatics, Hospices Civils de Lyon, 69677, Bron, France; CNRS UMR5558, Biometry and evolutionary biology lab, Lyon University, Lyon 1 University, F-69622 Villeurbanne, France
| | - Pierre Antoine Rollat-Farnier
- CNRS UMR5558, Biometry and evolutionary biology lab, Lyon University, Lyon 1 University, F-69622 Villeurbanne, France
| | - Sebastien Viel
- Service d'immunologie, Hospices Civils de Lyon, CHLS, 69495 Pierre-Bénite, France
| | | | - James O'Sullivan
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Thierry Walzer
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Anne-Laure Mathieu
- CIRI, Centre International de Recherche en Infectiologie/ International Center for Infectiology Research, Inserm, U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | - Gaelle Marenne
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Thomas Ludwig
- Inserm, Univ Brest, EFS, UMR 1078, GGB, F-29200 Brest, France; CHU Brest, Brest, France
| | | | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Brigitte Bader-Meunier
- Paediatric Rheumatology and Immunology Unit, Necker Hospital, Imagine Institution, Paris, France
| | - Tracy A Briggs
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michael W Beresford
- Paediatric Rheumatology, Alder Hey Children's NHS Foundation Trust, Liverpool, UK; Department of Women and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Yanick J Crow
- Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Paris, France; Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France; Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
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