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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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Cao L, Deng J, Chen W, He M, Zhao N, Huang H, Ling L, Li Q, Zhu X, Wang L. CTRP4/interleukin-6 receptor signaling ameliorates autoimmune encephalomyelitis by suppressing Th17 cell differentiation. J Clin Invest 2023; 134:e168384. [PMID: 38015631 PMCID: PMC10866667 DOI: 10.1172/jci168384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 11/21/2023] [Indexed: 11/30/2023] Open
Abstract
C1q/TNF-related protein 4 (CTRP4) is generally thought to be released extracellularly and plays a critical role in energy metabolism and protecting against sepsis. However, its physiological functions in autoimmune diseases have not been thoroughly explored. In this study, we demonstrate that Th17 cell-associated experimental autoimmune encephalomyelitis was greatly exacerbated in Ctrp4-/- mice compared with WT mice due to increased Th17 cell infiltration. The absence of Ctrp4 promoted the differentiation of naive CD4+ T cells into Th17 cells in vitro. Mechanistically, CTRP4 interfered with the interaction between IL-6 and the IL-6 receptor (IL-6R) by directly competing to bind with IL-6R, leading to suppression of IL-6-induced activation of the STAT3 pathway. Furthermore, the administration of recombinant CTRP4 protein ameliorated disease symptoms. In conclusion, our results indicate that CTRP4, as an endogenous regulator of the IL-6 receptor-signaling pathway, may be a potential therapeutic intervention for Th17-driven autoimmune diseases.
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Affiliation(s)
- Lulu Cao
- Department of Rheumatology and Immunology, Peking University People’s Hospital and Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - Jinhai Deng
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - Wei Chen
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - Minwei He
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - Ning Zhao
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - He Huang
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
| | - Lu Ling
- Department of Clinical Laboratory, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoxin Zhu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lu Wang
- Department of Immunology, School of Basic Medical Sciences, Health Science Center, and
- Key Laboratory of Medical Immunology, Ministry of Health, School of Basic Medical Science, Peking University, Beijing, China
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Pan L, Liu J, Liu C, Guo L, Punaro M, Yang S. Childhood-onset systemic lupus erythematosus: characteristics and the prospect of glucocorticoid pulse therapy. Front Immunol 2023; 14:1128754. [PMID: 37638017 PMCID: PMC10448525 DOI: 10.3389/fimmu.2023.1128754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Childhood-onset systemic lupus erythematosus (cSLE) is an autoimmune disease that results in significant damage and often needs more aggressive treatment. Compared to adult-onset SLE, cSLE has a stronger genetic background and more prevalent elevated type I Interferon expression. The management of cSLE is more challenging because the disease itself and treatment can affect physical, psychological and emotional growth and development. High dose oral glucocorticoid (GC) has become the rule for treating moderate to severe cSLE activity. However, GC-related side effects and potential toxicities are problems that cannot be ignored. Recent studies have suggested that GC pulse therapy can achieve disease remission rapidly and reduce GC-related side effects with a reduction in oral prednisone doses. This article reviews characteristics, including pathogenesis and manifestations of cSLE, and summarized the existing evidence on GC therapy, especially on GC pulse therapy in cSLE, followed by our proposal for GC therapy according to the clinical effects and pathogenesis.
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Affiliation(s)
- Lu Pan
- Department of Pediatric Rheumatology, Immunology and Allergy, The First Hospital, Jilin University, Changchun, China
| | - Jinxiang Liu
- Department of Pediatric Rheumatology, Immunology and Allergy, The First Hospital, Jilin University, Changchun, China
| | - Congcong Liu
- Department of Pediatric Rheumatology, Immunology and Allergy, The First Hospital, Jilin University, Changchun, China
| | - Lishuang Guo
- Department of Pediatric Rheumatology, Immunology and Allergy, The First Hospital, Jilin University, Changchun, China
| | - Marilynn Punaro
- Pediatric Rheumatology, University of Texas Southwestern Medical Center, Dallas, TX, United States
- Rheumatology, Texas Scottish Rite Hospital for Children, Houston, TX, United States
- Pediatric Rheumatology, Children’s Medical Center of Dallas, Dallas, TX, United States
| | - Sirui Yang
- Department of Pediatric Rheumatology, Immunology and Allergy, The First Hospital, Jilin University, Changchun, China
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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: 59] [Impact Index Per Article: 59.0] [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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Khadzhieva MB, Gracheva AS, Belopolskaya OB, Kolobkov DS, Kashatnikova DA, Redkin IV, Kuzovlev AN, Grechko AV, Salnikova LE. COVID-19 severity: does the genetic landscape of rare variants matter? Front Genet 2023; 14:1152768. [PMID: 37456666 PMCID: PMC10339319 DOI: 10.3389/fgene.2023.1152768] [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: 01/28/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Rare variants affecting host defense against pathogens may be involved in COVID-19 severity, but most rare variants are not expected to have a major impact on the course of COVID-19. We hypothesized that the accumulation of weak effects of many rare functional variants throughout the exome may contribute to the overall risk in patients with severe disease. This assumption is consistent with the omnigenic model of the relationship between genetic and phenotypic variation in complex traits, according to which association signals tend to spread across most of the genome through gene regulatory networks from genes outside the major pathways to disease-related genes. We performed whole-exome sequencing and compared the burden of rare variants in 57 patients with severe and 29 patients with mild/moderate COVID-19. At the whole-exome level, we observed an excess of rare, predominantly high-impact (HI) variants in the group with severe COVID-19. Restriction to genes intolerant to HI or damaging missense variants increased enrichment for these classes of variants. Among various sets of genes, an increased signal of rare HI variants was demonstrated predominantly for primary immunodeficiency genes and the entire set of genes associated with immune diseases, as well as for genes associated with respiratory diseases. We advocate taking the ideas of the omnigenic model into account in COVID-19 studies.
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Affiliation(s)
- Maryam B. Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alesya S. Gracheva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Department of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olesya B. Belopolskaya
- The Resource Center “Bio-bank Center”, Research Park of St. Petersburg State University, St. Petersburg, Russia
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry S. Kolobkov
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Darya A. Kashatnikova
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Ivan V. Redkin
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Artem N. Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Lyubov E. Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
- The Laboratory of Ecological Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- The Laboratory of Molecular Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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Costa F, Beltrami E, Mellone S, Sacchetti S, Boggio E, Gigliotti CL, Stoppa I, Dianzani U, Rolla R, Giordano M. Genes and Microbiota Interaction in Monogenic Autoimmune Disorders. Biomedicines 2023; 11:1127. [PMID: 37189745 PMCID: PMC10135656 DOI: 10.3390/biomedicines11041127] [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: 03/10/2023] [Revised: 03/30/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Monogenic autoimmune disorders represent an important tool to understand the mechanisms behind central and peripheral immune tolerance. Multiple factors, both genetic and environmental, are known to be involved in the alteration of the immune activation/immune tolerance homeostasis typical of these disorders, making it difficult to control the disease. The latest advances in genetic analysis have contributed to a better and more rapid diagnosis, although the management remains confined to the treatment of clinical manifestations, as there are limited studies on rare diseases. Recently, the correlation between microbiota composition and the onset of autoimmune disorders has been investigated, thus opening up new perspectives on the cure of monogenic autoimmune diseases. In this review, we will summarize the main genetic features of both organ-specific and systemic monogenic autoimmune diseases, reporting on the available literature data on microbiota alterations in these patients.
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Affiliation(s)
- Federica Costa
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
| | - Eleonora Beltrami
- Maggiore della Carità University Hospital, 28100 Novara, Italy; (E.B.); (S.M.)
| | - Simona Mellone
- Maggiore della Carità University Hospital, 28100 Novara, Italy; (E.B.); (S.M.)
| | - Sara Sacchetti
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
| | - Elena Boggio
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
| | - Casimiro Luca Gigliotti
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
| | - Ian Stoppa
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
| | - Umberto Dianzani
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
- Maggiore della Carità University Hospital, 28100 Novara, Italy; (E.B.); (S.M.)
| | - Roberta Rolla
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
- Maggiore della Carità University Hospital, 28100 Novara, Italy; (E.B.); (S.M.)
| | - Mara Giordano
- Department of Health Sciences, Università del Piemonte Orientale, 28100 Novara, Italy; (F.C.); (S.S.); (E.B.); (C.L.G.); (I.S.); (R.R.); (M.G.)
- Maggiore della Carità University Hospital, 28100 Novara, Italy; (E.B.); (S.M.)
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Zhou C, Cai S, Xie Y, Zeng Z, Zhang J, Su G, Wu Q, Ye X, Cao Q, Yang P, Hu J. Genetic association of PRKCD and CARD9 polymorphisms with Vogt-Koyanagi-Harada disease in the Chinese Han population. Hum Genomics 2023; 17:9. [PMID: 36782298 PMCID: PMC9926551 DOI: 10.1186/s40246-023-00459-7] [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: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Protein kinase C delta (PRKCD) and caspase recruitment domain family member 9 (CARD9) are genes involved in B and T cell activation, and cytokine production, which are vital mechanisms underlying autoimmune disease development. This study aimed to explore the association of the PRKCD and CARD9 genes with Vogt-Koyanagi-Harada disease (VKH) disease. The case-control study was performed to in 912 patients with VKH and 878 normal controls. MassARRAY system, SHEsis online platform, real-time PCR, and enzyme-linked immunosorbent assay were used to detect genotyping, haplotyping, mRNA expression, and cytokine levels, respectively. RESULTS We found that rs74437127 C allele of PRKCD, rs3812555 CC genotype, and C allele of CARD9 were associated with increased susceptibility of VKH (Pc = 0.020, OR = 1.624; Pc = 2.04 × 10-5, OR = 1.810; Pc = 2.76 × 10-5, OR = 1.698, respectively). However, the rs74437127 T allele, and rs3812555 TC genotype and T allele were linked with decreased susceptibility to VKH (Pc = 0.020, OR = 0.616; Pc = 7.85 × 10-5, OR = 0.559; Pc = 2.76 × 10-5, OR = 0.589, respectively). PRKCD ATG and CARD9 GCTTA haplotypes decreased susceptibility to VKH (Pc = 3.11 × 10-3, OR = 0.594; Pc = 5.00 × 10-3, OR = 0.639, respectively). Functional studies on rs3812555 genotyped individuals revealed that CC carriers had significantly higher CARD9 mRNA expression and tumour necrosis factor-α production than TC/TT carriers (P = 1.00 × 10-4; P = 2.00 × 10-3, respectively). CONCLUSIONS We found an association between PRKCD rs74437127 and CARD9 rs3812555 polymorphisms and VKH susceptibility and revealed that the increased susceptibility of rs3812555 for VKH may be mediated by regulating CARD9 gene expression and the production of pro-inflammatory cytokines, such as TNF-α.
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Affiliation(s)
- Chunya Zhou
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Shiya Cai
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Yuhong Xie
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Zhen Zeng
- grid.488542.70000 0004 1758 0435Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000 People’s Republic of China ,grid.256112.30000 0004 1797 9307Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004 People’s Republic of China
| | - Jun Zhang
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Guannan Su
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Qiuying Wu
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Xingsheng Ye
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Qingfeng Cao
- grid.452206.70000 0004 1758 417XThe First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016 China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute, Youyi Road 1, Chongqing, 400016, China.
| | - Jianmin Hu
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Engineering Research Center of Assistive Technology for Visual Impairment, Fujian Province University, Quanzhou, 362000, People's Republic of China. .,Department of Ophthalmology and Optometry, The School of Medical Technology and Engineering, Fujian Medical University, Jiaotong Road 88, Fuzhou, 350004, People's Republic of China.
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Wu CY, Fan WL, Yang HY, Chu PS, Liao PC, Chen LC, Yao TC, Yeh KW, Ou LS, Lin SJ, Lee WI, Huang JL. Contribution of genetic variants associated with primary immunodeficiencies to childhood-onset systemic lupus erythematous. J Allergy Clin Immunol 2022; 151:1123-1131. [PMID: 36586539 DOI: 10.1016/j.jaci.2022.12.807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND A dysregulated immune response is a hallmark of autoimmune disorders. Evidence suggests that systemic autoimmune diseases and primary immunodeficiency disorders (PIDs) may be similar diseases with different clinical phenotypes. OBJECTIVE This study aimed to investigate the burden of PID-associated genetic variants in patients with childhood-onset systemic lupus erythematosus (cSLE). METHODS We enrolled 118 cSLE patients regularly followed at Chang Gung Memorial Hospital. Targeted next-generation sequencing identified PID genetic variants in patients versus 1475 unrelated healthy individuals, which were further filtered by allelic frequency and various functional scores. Customized immune assays tested the functions of the identified variants. RESULTS On filtration, 36 patients (30.5%) harbored rare variants in PID-associated genes predicted to be damaging. One homozygous TREX1 (c.294dupA) mutation and 4 heterozygous variants with possible dominant PID traits, including BCL11B (c.G1040T), NFKB1 (c.T695G), and NFKB2 (c.G1210A, c.G1651A), were discovered. With recessive traits, variants were found across all PID types; one fifth involved phagocyte number or function defects. Predicted pathogenic PID variants were more predominant in those with a family history of lupus, regardless of infection susceptibility. Moreover, mutation loads were greater among cSLE patients than controls despite sex or age at disease onset. While greater mutation loads were observed among cSLE patients with peripubertal disease onset, no significant differences in sex or phenotype were noted among cSLE patients. CONCLUSION cSLE is mostly not monogenic. Gene-specific analysis and mutation load investigations suggested that rare and predicted damaging variants in PID-related genes can potentially contribute to cSLE susceptibility.
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Affiliation(s)
- Chao-Yi Wu
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wen-Lang Fan
- Department of Medical Research, Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Huang-Yu Yang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Pi-Shuang Chu
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Pei-Chun Liao
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Li-Chen Chen
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan
| | - Tsung-Chieh Yao
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Wei Yeh
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Liang-Shiou Ou
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Syh-Jae Lin
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wen-I Lee
- Department of Pediatrics, Division of Allergy, Asthma, and Rheumatology, Chang Gung Memorial Hospital, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Jing-Long Huang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei City, Taiwan.
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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: 18] [Impact Index Per Article: 9.0] [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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10
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Owen KA, Grammer AC, Lipsky PE. Deconvoluting the heterogeneity of SLE: The contribution of ancestry. J Allergy Clin Immunol 2021; 149:12-23. [PMID: 34857396 DOI: 10.1016/j.jaci.2021.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 12/23/2022]
Abstract
Systemic lupus erythematosus (SLE) is a multiorgan autoimmune disorder with a prominent genetic component. Evidence has shown that individuals of non-European ancestry experience the disease more severely, exhibiting an increased incidence of cardiovascular disease, renal involvement, and tissue damage compared with European ancestry populations. Furthermore, there seems to be variability in the response of individuals within different ancestral groups to standard medications, including cyclophosphamide, mycophenolate, rituximab, and belimumab. Although the widespread application of candidate gene, Immunochip, and genome-wide association studies has contributed to our understanding of the link between genetic variation (typically single nucleotide polymorphisms) and SLE, despite decades of research it is still unclear why ancestry remains a key determinant of poorer outcome in non-European-ancestry patients with SLE. Here, we will discuss the impact of ancestry on SLE disease burden in patients from diverse backgrounds and highlight how research efforts using novel bioinformatic and pathway-based approaches have begun to disentangle the complex genetic architecture linking ancestry to SLE susceptibility. Finally, we will illustrate how genomic and gene expression analyses can be combined to help identify novel molecular pathways and drug candidates that might uniquely impact SLE among different ancestral populations.
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11
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Sarver DC, Xu C, Cheng Y, Terrillion CE, Wong GW. CTRP4 ablation impairs associative learning and memory. FASEB J 2021; 35:e21910. [PMID: 34610176 DOI: 10.1096/fj.202100733rr] [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] [Received: 04/29/2021] [Revised: 08/12/2021] [Accepted: 08/24/2021] [Indexed: 11/11/2022]
Abstract
C1q/TNF-related protein (CTRP) family comprises fifteen highly conserved secretory proteins with diverse central and peripheral functions. In zebrafish, mouse, and human, CTRP4 is most highly expressed in the brain. We previously showed that CTRP4 is a metabolically responsive regulator of food intake and energy balance, and mice lacking CTRP4 exhibit sexually dimorphic changes in ingestive behaviors and systemic metabolism. Recent single-cell RNA sequencing also revealed Ctrp4/C1qtnf4 expression in diverse neuronal cell types across distinct anatomical brain regions, hinting at additional roles in the central nervous system not previously characterized. To uncover additional central functions of CTRP4, we subjected Ctrp4 knockout (KO) mice to a battery of behavioral tests. Relative to wild-type (WT) littermates, loss of CTRP4 does not alter exploratory, anxiety-, or depressive-like behaviors, motor function and balance, sensorimotor gating, novel object recognition, and spatial memory. While pain-sensing mechanisms in response to thermal stress and mild shock are intact, both male and female Ctrp4 KO mice have increased sensitivity to pain induced by higher-level shock, suggesting altered nociceptive function. Importantly, CTRP4 deficiency impairs hippocampal-dependent associative learning and memory as assessed by trace fear conditioning paradigm. This deficit is sex-dependent, affects only female mice, and is associated with altered expression of learning and memory genes (Arc, c-fos, and Pde4d) in the hippocampus and cortex. Altogether, our behavioral and gene expression analyses have uncovered novel aspects of the CTRP4 function and provided a physiological context to further investigate its mechanism of action in the central and peripheral nervous system.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Cheng Xu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yi Cheng
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Chantelle E Terrillion
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Rivellese F, Manou-Stathopoulou S, Mauro D, Goldmann K, Pyne D, Rajakariar R, Gordon P, Schafer P, Bombardieri M, Pitzalis C, Lewis MJ. Effects of targeting the transcription factors Ikaros and Aiolos on B cell activation and differentiation in systemic lupus erythematosus. Lupus Sci Med 2021; 8:8/1/e000445. [PMID: 33727237 PMCID: PMC7970264 DOI: 10.1136/lupus-2020-000445] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 12/22/2020] [Accepted: 01/28/2021] [Indexed: 12/11/2022]
Abstract
Objective To evaluate the effects of targeting Ikaros and Aiolos by cereblon modulator iberdomide on the activation and differentiation of B-cells from patients with systemic lupus erythematosus (SLE). Methods CD19+ B-cells isolated from the peripheral blood of patients with SLE (n=41) were cultured with TLR7 ligand resiquimod ±IFNα together with iberdomide or control from day 0 (n=16). Additionally, in vitro B-cell differentiation was induced by stimulation with IL-2/IL-10/IL-15/CD40L/resiquimod with iberdomide or control, given at day 0 or at day 4. At day 5, immunoglobulins were measured by ELISA and cells analysed by flow cytometry. RNA-Seq was performed on fluorescence-activated cell-sorted CD27-IgD+ naïve-B-cells and CD20lowCD27+CD38+ plasmablasts to investigate the transcriptional consequences of iberdomide. Results Iberdomide significantly inhibited the TLR7 and IFNα-mediated production of immunoglobulins from SLE B-cells and the production of antinuclear antibodies as well as significantly reducing the number of CD27+CD38+ plasmablasts (0.3±0.18, vehicle 1.01±0.56, p=0.011) and CD138+ plasma cells (0.12±0.06, vehicle 0.28±0.02, p=0.03). Additionally, treatment with iberdomide from day 0 significantly inhibited the differentiation of SLE B-cells into plasmablasts (6.4±13.5 vs vehicle 34.9±20.1, p=0.013) and antibody production. When given at later stages of differentiation, iberdomide did not affect the numbers of plasmablasts or the production of antibodies; however, it induced a significant modulation of gene expression involving IKZF1 and IKZF3 transcriptional programmes in both naïve B-cells and plasmablasts (400 and 461 differentially modulated genes, respectively, false discovery rate<0.05). Conclusion These results demonstrate the relevance of Ikaros and Aiolos as therapeutic targets in SLE due to their ability to modulate B cell activation and differentiation downstream of TLR7.
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Affiliation(s)
- Felice Rivellese
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sotiria Manou-Stathopoulou
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Daniele Mauro
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Katriona Goldmann
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Debasish Pyne
- Rheumatology Department, Barts Health NHS Trust, London, UK
| | | | - Patrick Gordon
- Rheumatology Department, King's College London, London, UK
| | - Peter Schafer
- Translational Medicine Department, Bristol-Myers Squibb Co, Princeton, New Jersey, USA
| | - Michele Bombardieri
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Costantino Pitzalis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Myles J Lewis
- Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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13
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Iacobas D, Wen J, Iacobas S, Schwartz N, Putterman C. Remodeling of Neurotransmission, Chemokine, and PI3K-AKT Signaling Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus. Genes (Basel) 2021; 12:251. [PMID: 33578738 PMCID: PMC7916450 DOI: 10.3390/genes12020251] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 12/13/2022] Open
Abstract
Cognitive dysfunction and mood changes are prevalent and especially taxing issues for patients with systemic lupus erythematosus (SLE). Tumor necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) and its cognate receptor Fn14 have been shown to play an important role in neurocognitive dysfunction in murine lupus. We profiled and compared gene expression in the cortices of MRL/+, MRL/lpr (that manifest lupus-like phenotype) and MRL/lpr-Fn14 knockout (Fn14ko) adult female mice to determine the transcriptomic impact of TWEAK/Fn14 on cortical gene expression in lupus. We found that the TWEAK/Fn14 pathway strongly affects the expression level, variability and coordination of the genomic fabrics responsible for neurotransmission and chemokine signaling. Dysregulation of the Phosphoinositide 3-kinase (PI3K)-AKT pathway in the MRL/lpr lupus strain compared with the MRL/+ control and Fn14ko mice was particularly prominent and, therefore, promising as a potential therapeutic target, although the complexity of the transcriptomic fabric highlights important considerations in in vivo experimental models.
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Affiliation(s)
- Dumitru Iacobas
- Center for Computational Systems Biology, Personalized Genomics Laboratory, Roy G. Perry College of Engineering, Prairie View A & M University, Prairie View, TX 77446, USA;
- DP Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jing Wen
- Department of Medicine (Rheumatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.W.); (N.S.)
| | - Sanda Iacobas
- Department of Pathology, New York Medical College, Valhalla, NY 10595, USA;
| | - Noa Schwartz
- Department of Medicine (Rheumatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.W.); (N.S.)
| | - Chaim Putterman
- Department of Medicine (Rheumatology), Albert Einstein College of Medicine, Bronx, NY 10461, USA; (J.W.); (N.S.)
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Azrieli Faculty of Medicine, Bar-Ilan University, Zefat 52100, Israel
- Galilee Medical Center, Research Institute, Nahariya 22100, Israel
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14
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Vester SK, Beavil RL, Lynham S, Beavil AJ, Cunninghame Graham DS, McDonnell JM, Vyse TJ. Nucleolin acts as the receptor for C1QTNF4 and supports C1QTNF4-mediated innate immunity modulation. J Biol Chem 2021; 296:100513. [PMID: 33676896 PMCID: PMC8042453 DOI: 10.1016/j.jbc.2021.100513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/16/2022] Open
Abstract
The C1q and TNF related 4 (C1QTNF4) protein is a structurally unique member of the C1QTNF family, a family of secreted proteins that have structural homology with both complement C1q and the tumor necrosis factor superfamily. C1QTNF4 has been linked to the autoimmune disease systemic lupus erythematosus through genetic studies; however, its role in immunity and inflammation remains poorly defined and a cell surface receptor of C1QTNF4 has yet to be identified. Here we report identification of nucleolin as a cell surface receptor of C1QTNF4 using mass spectrometric analysis. Additionally, we present evidence that the interaction between C1QTNF4 and nucleolin is mediated by the second C1q-like domain of C1QTNF4 and the C terminus of nucleolin. We show that monocytes and B cells are target cells of C1QTNF4 and observe extensive binding to dead cells. Imaging flow cytometry experiments in monocytes show that C1QTNF4 becomes actively internalized upon cell binding. Our results suggest that nucleolin may serve as a docking molecule for C1QTNF4 and act in a context-dependent manner through coreceptors. Taken together, these findings further our understanding of C1QTNF4's function in the healthy immune system and how dysfunction may contribute to the development of systemic lupus erythematosus.
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Affiliation(s)
- Susan K Vester
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Rebecca L Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | | | - James M McDonnell
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.
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15
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Sarver DC, Stewart AN, Rodriguez S, Little HC, Aja S, Wong GW. Loss of CTRP4 alters adiposity and food intake behaviors in obese mice. Am J Physiol Endocrinol Metab 2020; 319:E1084-E1100. [PMID: 33017221 PMCID: PMC7792665 DOI: 10.1152/ajpendo.00448.2020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Central and peripheral mechanisms are both required for proper control of energy homeostasis. Among circulating plasma proteins, C1q/TNF-related proteins (CTRPs) have recently emerged as important regulators of sugar and fat metabolism. CTRP4, expressed in brain and adipose tissue, is unique among the family members in having two tandem globular C1q domains. We previously showed that central administration of recombinant CTRP4 suppresses food intake, suggesting a central nervous system role in regulating ingestive physiology. Whether this effect is pharmacological or physiological remains unclear. We used a loss-of-function knockout (KO) mouse model to clarify the physiological role of CTRP4. Under basal conditions, CTRP4 deficiency increased serum cholesterol levels and impaired glucose tolerance in male but not female mice fed a control low-fat diet. When challenged with a high-fat diet, male and female KO mice responded differently to weight gain and had different food intake patterns. On an obesogenic diet, male KO mice had similar weight gain as wild-type littermates. When fed ad libitum, KO male mice had greater meal number, shorter intermeal interval, and reduced satiety ratio. Female KO mice, in contrast, had lower body weight and adiposity. In the refeeding period following food deprivation, female KO mice had significantly higher food intake due to longer meal duration and reduced satiety ratio. Collectively, our data provide genetic evidence for a sex-dependent physiological role of CTRP4 in modulating food intake patterns and systemic energy metabolism.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ashley N Stewart
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susana Rodriguez
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hannah C Little
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan Aja
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Center for Metabolism and Obesity Research, Johns Hopkins University School of Medicine, Baltimore, Maryland
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16
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Swietlik EM, Prapa M, Martin JM, Pandya D, Auckland K, Morrell NW, Gräf S. 'There and Back Again'-Forward Genetics and Reverse Phenotyping in Pulmonary Arterial Hypertension. Genes (Basel) 2020; 11:E1408. [PMID: 33256119 PMCID: PMC7760524 DOI: 10.3390/genes11121408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/17/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023] Open
Abstract
Although the invention of right heart catheterisation in the 1950s enabled accurate clinical diagnosis of pulmonary arterial hypertension (PAH), it was not until 2000 when the landmark discovery of the causative role of bone morphogenetic protein receptor type II (BMPR2) mutations shed new light on the pathogenesis of PAH. Since then several genes have been discovered, which now account for around 25% of cases with the clinical diagnosis of idiopathic PAH. Despite the ongoing efforts, in the majority of patients the cause of the disease remains elusive, a phenomenon often referred to as "missing heritability". In this review, we discuss research approaches to uncover the genetic architecture of PAH starting with forward phenotyping, which in a research setting should focus on stable intermediate phenotypes, forward and reverse genetics, and finally reverse phenotyping. We then discuss potential sources of "missing heritability" and how functional genomics and multi-omics methods are employed to tackle this problem.
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Affiliation(s)
- Emilia M. Swietlik
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matina Prapa
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Jennifer M. Martin
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Divya Pandya
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Kathryn Auckland
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
| | - Nicholas W. Morrell
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- Royal Papworth Hospital NHS Foundation Trust, Cambridge CB2 0AY, UK
- Addenbrooke’s Hospital NHS Foundation Trust, Cambridge CB2 0QQ, UK
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Stefan Gräf
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK; (E.M.S.); (M.P.); (J.M.M.); (D.P.); (K.A.); (N.W.M.)
- NIHR BioResource for Translational Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
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17
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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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18
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Pakzad B, Shirpour R, Mousavi M, Karimzadeh H, Salehi A, Kazemi M, Amini G, Akbari M, Salehi R. C1QTNF4 gene p.His198Gln mutation is correlated with early-onset systemic lupus erythematosus in Iranian patients. Int J Rheum Dis 2020; 23:1594-1598. [PMID: 33009720 DOI: 10.1111/1756-185x.13981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/12/2020] [Accepted: 09/09/2020] [Indexed: 01/20/2023]
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is an autoimmune disease with multifactorial etiology. Several studies show that genetic factors have an important part in the incidence of SLE. The C1QTNF4 gene is involved in the regulation of the inflammatory pathways by pro-inflammatory function. In the present study, we have evaluated the association between C1QTNF4 gene p.His198Gln mutation and risk of SLE. METHODS Forty SLE patients and 40 control subjects were recruited in this case-control study. Genotyping of C1QTNF4 p.His198Gln mutation was performed using real-time polymerase chain reaction high resolution melting method. RESULTS We found a significant association between this mutation (GG + GC) with the risk of SLE (odds ratio = 6.33, 95% CI = 1.28-31.11). Furthermore, we observed that in the patient group, this mutation leads to early-onset SLE (19.7 ± 4.34 years for mutation carriers compared to 27.7 ± 11.4 years for wild type carriers; P = .003). CONCLUSION Our results suggest that this mutation (p.His198Gln) potentially has an important role in SLE risk in the Iranian population.
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Affiliation(s)
- Bahram Pakzad
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Reza Shirpour
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Maryam Mousavi
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Hadi Karimzadeh
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Amirhossein Salehi
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Mehdi Kazemi
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Guilda Amini
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease and Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mojtaba Akbari
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Rasoul Salehi
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-communicable Disease and Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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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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20
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Amanat S, Requena T, Lopez-Escamez JA. A Systematic Review of Extreme Phenotype Strategies to Search for Rare Variants in Genetic Studies of Complex Disorders. Genes (Basel) 2020; 11:genes11090987. [PMID: 32854191 PMCID: PMC7564972 DOI: 10.3390/genes11090987] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Exome sequencing has been commonly used to characterize rare diseases by selecting multiplex families or singletons with an extreme phenotype (EP) and searching for rare variants in coding regions. The EP strategy covers both extreme ends of a disease spectrum and it has been also used to investigate the contribution of rare variants to the heritability of complex clinical traits. We conducted a systematic review to find evidence supporting the use of EP strategies in the search for rare variants in genetic studies of complex diseases and highlight the contribution of rare variations to the genetic structure of polygenic conditions. After assessing the quality of the retrieved records, we selected 19 genetic studies considering EPs to demonstrate genetic association. All studies successfully identified several rare or de novo variants, and many novel candidate genes were also identified by selecting an EP. There is enough evidence to support that the EP approach for patients with an early onset of a disease can contribute to the identification of rare variants in candidate genes or pathways involved in complex diseases. EP patients may contribute to a better understanding of the underlying genetic architecture of common heterogeneous disorders such as tinnitus or age-related hearing loss.
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Affiliation(s)
- Sana Amanat
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
| | - Teresa Requena
- Centre for Discovery Brain Sciences, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9JZ, UK;
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO—Centre for Genomics and Oncological Research—Pfizer/University of Granada/Junta de Andalucía, PTS, 18016 Granada, Spain;
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.GRANADA, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18016 Granada, Spain
- Department of Surgery, Division of Otolaryngology, Universidad de Granada, 18016 Granada, Spain
- Correspondence: ; Tel.: +34-958-715-500-160
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21
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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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22
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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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23
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Demirkaya E, Sahin S, Romano M, Zhou Q, Aksentijevich I. New Horizons in the Genetic Etiology of Systemic Lupus Erythematosus and Lupus-Like Disease: Monogenic Lupus and Beyond. J Clin Med 2020; 9:E712. [PMID: 32151092 PMCID: PMC7141186 DOI: 10.3390/jcm9030712] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/12/2020] [Accepted: 02/21/2020] [Indexed: 02/05/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a clinically and genetically heterogeneous autoimmune disease. The etiology of lupus and the contribution of genetic, environmental, infectious and hormonal factors to this phenotype have yet to be elucidated. The most straightforward approach to unravel the molecular pathogenesis of lupus may rely on studies of patients who present with early-onset severe phenotypes. Typically, they have at least one of the following clinical features: childhood onset of severe disease (<5 years), parental consanguinity, and presence of family history for autoimmune diseases in a first-degree relative. These patients account for a small proportion of patients with lupus but they inform considerable knowledge about cellular pathways contributing to this inflammatory phenotype. In recent years with the aid of new sequencing technologies, novel or rare pathogenic variants have been reported in over 30 genes predisposing to SLE and SLE-like diseases. Future studies will likely discover many more genes with private variants associated to lupus-like phenotypes. In addition, genome-wide association studies (GWAS) have identified a number of common alleles (SNPs), which increase the risk of developing lupus in adult age. Discovery of a possible shared immune pathway in SLE patients, either with rare or common variants, can provide important clues to better understand this complex disorder, it's prognosis and can help guide new therapeutic approaches. The aim of this review is to summarize the current knowledge of the clinical presentation, genetic diagnosis and mechanisms of disease in patents with lupus and lupus-related phenotypes.
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Affiliation(s)
- Erkan Demirkaya
- Schulich School of Medicine & Dentistry, Department of Paediatrics, Division of Paediatric Rheumatology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Sezgin Sahin
- Van Training and Research Hospital, Department of Paediatric Rheumatology, 65000 Van, Turkey;
| | - Micol Romano
- Schulich School of Medicine & Dentistry, Department of Paediatrics, Division of Paediatric Rheumatology, University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Pediatric Rheumatology, ASST-PINI-CTO, 20122 Milano, Italy
| | - Qing Zhou
- Life Sciences Institute, Zhejiang University, Hang Zhou 310058, China;
| | - Ivona Aksentijevich
- Inflammatory Disease Section, National Human Genome Research Institute, Bethesda, MD 20892, USA;
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24
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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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25
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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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26
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The pathogenesis of systemic lupus erythematosus: Harnessing big data to understand the molecular basis of lupus. J Autoimmun 2019; 110:102359. [PMID: 31806421 DOI: 10.1016/j.jaut.2019.102359] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic, systemic autoimmune disease that causes damage to multiple organ systems. Despite decades of research and available murine models that capture some aspects of the human disease, new treatments for SLE lag behind other autoimmune diseases such as Rheumatoid Arthritis and Crohn's disease. Big data genomic assays have transformed our understanding of SLE by providing important insights into the molecular heterogeneity of this multigenic disease. Gene wide association studies have demonstrated more than 100 risk loci, supporting a model of multiple genetic hits increasing SLE risk in a non-linear fashion, and providing evidence of ancestral diversity in susceptibility loci. Epigenetic studies to determine the role of methylation, acetylation and non-coding RNAs have provided new understanding of the modulation of gene expression in SLE patients and identified new drug targets and biomarkers for SLE. Gene expression profiling has led to a greater understanding of the role of myeloid cells in the pathogenesis of SLE, confirmed roles for T and B cells in SLE, promoted clinical trials based on the prominent interferon signature found in SLE patients, and identified candidate biomarkers and cellular signatures to further drug development and drug repurposing. Gene expression studies are advancing our understanding of the underlying molecular heterogeneity in SLE and providing hope that patient stratification will expedite new therapies based on personal molecular signatures. Although big data analyses present unique interpretation challenges, both computationally and biologically, advances in machine learning applications may facilitate the ability to predict changes in SLE disease activity and optimize therapeutic strategies.
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Abstract
Zusammenfassung
Häufige Krankheiten, die sog. Volkskrankheiten, sind in der Regel multifaktoriell verursacht, d. h. zu ihrer Entwicklung tragen sowohl genetische Faktoren als auch nicht-genetische Umgebungseinflüsse bei. Die geschätzte Gesamterblichkeit (‑heritabilität) reicht von moderat bis vergleichsweise hoch. Die genetische Architektur ist komplex und kann das gesamte allelische Spektrum, von häufigen Varianten mit niedriger Penetranz bis hin zu seltenen Varianten mit höherer Penetranz, sowie alle möglichen Kombinationen umfassen. Während häufige Varianten seit mehreren Jahren mit großem Erfolg durch genomweite Assoziationsstudien (GWAS) identifiziert werden, war bisher die Identifizierung seltener Varianten, insbesondere aufgrund der großen Zahl beitragender Gene, nur begrenzt erfolgreich. Dies ändert sich derzeit dank der Anwendung von Hochdurchsatz-Sequenziertechnologien („next-generation sequencing“, NGS) und der daraus resultierenden zunehmenden Verfügbarkeit von exom- und genomweiten Sequenzdaten großer Kollektive. In diesem Artikel geben wir einen Überblick über die Bedeutung seltener Varianten bei häufigen Erkrankungen sowie den aktuellen Stand in Bezug auf deren Identifizierung mittels NGS. Wir betrachten insbesondere die folgenden Fragen: Bei welchen häufigen Krankheiten ist ein Beitrag seltener Varianten zu erwarten, wie können diese Varianten identifiziert werden, und welches Potenzial bieten seltene Varianten für das Verständnis biologischer Prozesse bzw. für die Translation in die klinische Praxis?
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Affiliation(s)
- Kerstin U. Ludwig
- Aff2 0000 0000 8786 803X grid.15090.3d Emmy-Noether-Gruppe „Kraniofaziale Genomik“, Institut für Humangenetik U ni ver si täts kli ni kum Bonn Venusberg-Campus 1, Gebäude 76 53127 Bonn Deutschland
| | - Franziska Degenhardt
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
| | - Markus M. Nöthen
- Aff1 0000 0000 8786 803X grid.15090.3d Institut für Humangenetik Universitätsklinikum Bonn Bonn Deutschland
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29
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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Martínez-Bueno M, Alarcón-Riquelme ME. Exploring Impact of Rare Variation in Systemic Lupus Erythematosus by a Genome Wide Imputation Approach. Front Immunol 2019; 10:258. [PMID: 30863397 PMCID: PMC6399402 DOI: 10.3389/fimmu.2019.00258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/29/2019] [Indexed: 01/31/2023] Open
Abstract
The importance of low frequency and rare variation in complex disease genetics is difficult to estimate in patient populations. Genome-wide association studies are therefore, underpowered to detect rare variation. We have used a combined approach of genome-wide-based imputation with a highly stringent sequence kernel association (SKAT) test and a case-control burden test. We identified 98 candidate genes containing rare variation that in aggregate show association with SLE many of which have recognized immunological function, but also function and expression related to relevant tissues such as the joints, skin, blood or central nervous system. In addition we also find that there is a significant enrichment of genes annotated for disease-causing mutations in the OMIM database, suggesting that in complex diseases such as SLE, such mutations may be involved in subtle or combined phenotypes or could accelerate specific organ abnormalities found in the disease. We here provide an important resource of candidate genes for SLE.
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Affiliation(s)
- Manuel Martínez-Bueno
- Department of Medical Genomics, GENYO, Center for Genomics and Oncological Research Pfizer, University of Granada, Granada, Spain
| | - Marta E Alarcón-Riquelme
- Unit of Chronic Inflammation, Institute for Environmental Medicine, Karolinska Institute, Stockholm, Sweden
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Cheung SG, Goldenthal AR, Uhlemann AC, Mann JJ, Miller JM, Sublette ME. Systematic Review of Gut Microbiota and Major Depression. Front Psychiatry 2019; 10:34. [PMID: 30804820 PMCID: PMC6378305 DOI: 10.3389/fpsyt.2019.00034] [Citation(s) in RCA: 312] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background: Recently discovered relationships between the gastrointestinal microbiome and the brain have implications for psychiatric disorders, including major depressive disorder (MDD). Bacterial transplantation from MDD patients to rodents produces depression-like behaviors. In humans, case-control studies have examined the gut microbiome in healthy and affected individuals. We systematically reviewed existing studies comparing gut microbial composition in MDD and healthy volunteers. Methods: A PubMed literature search combined the terms "depression," "depressive disorder," "stool," "fecal," "gut," and "microbiome" to identify human case-control studies that investigated relationships between MDD and microbiota quantified from stool. We evaluated the resulting studies, focusing on bacterial taxa that were different between MDD and healthy controls. Results: Six eligible studies were found in which 50 taxa exhibited differences (p < 0.05) between patients with MDD and controls. Patient characteristics and methodologies varied widely between studies. Five phyla-Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria, and Protobacteria-were represented; however, divergent results occurred across studies for all phyla. The largest number of differentiating taxa were within phylum Firmicutes, in which nine families and 12 genera differentiated the diagnostic groups. The majority of these families and genera were found to be statistically different between the two groups in two identified studies. Family Lachnospiraceae differentiated the diagnostic groups in four studies (with an even split in directionality). Across all five phyla, nine genera were higher in MDD (Anaerostipes, Blautia, Clostridium, Klebsiella, Lachnospiraceae incertae sedis, Parabacteroides, Parasutterella, Phascolarctobacterium, and Streptococcus), six were lower (Bifidobacterium, Dialister, Escherichia/Shigella, Faecalibacterium, and Ruminococcus), and six were divergent (Alistipes, Bacteroides, Megamonas, Oscillibacter, Prevotella, and Roseburia). We highlight mechanisms and products of bacterial metabolism as they may relate to the etiology of depression. Conclusions: No consensus has emerged from existing human studies of depression and gut microbiome concerning which bacterial taxa are most relevant to depression. This may in part be due to differences in study design. Given that bacterial functions are conserved across taxonomic groups, we propose that studying microbial functioning may be more productive than a purely taxonomic approach to understanding the gut microbiome in depression.
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Affiliation(s)
- Stephanie G. Cheung
- Division of Consultation-Liaison Psychiatry, Columbia University, New York, NY, United States
- Department of Psychiatry, Columbia University, New York, NY, United States
| | - Ariel R. Goldenthal
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, Columbia University, New York, NY, United States
- Microbiome & Pathogen Genomics Core, Columbia University, New York, NY, United States
| | - J. John Mann
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
- Department of Radiology, Columbia University, New York, NY, United States
| | - Jeffrey M. Miller
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
| | - M. Elizabeth Sublette
- Department of Psychiatry, Columbia University, New York, NY, United States
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, New York, NY, United States
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Almlöf JC, Nystedt S, Leonard D, Eloranta ML, Grosso G, Sjöwall C, Bengtsson AA, Jönsen A, Gunnarsson I, Svenungsson E, Rönnblom L, Sandling JK, Syvänen AC. Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus. Hum Genet 2019; 138:141-150. [PMID: 30707351 PMCID: PMC6373277 DOI: 10.1007/s00439-018-01966-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023]
Abstract
Systemic lupus erythematosus (SLE, OMIM 152700) is a systemic autoimmune disease with a complex etiology. The mode of inheritance of the genetic risk beyond familial SLE cases is currently unknown. Additionally, the contribution of heterozygous variants in genes known to cause monogenic SLE is not fully understood. Whole-genome sequencing of DNA samples from 71 Swedish patients with SLE and their healthy biological parents was performed to investigate the general genetic risk of SLE using known SLE GWAS risk loci identified using the ImmunoChip, variants in genes associated to monogenic SLE, and the mode of inheritance of SLE risk alleles in these families. A random forest model for predicting genetic risk for SLE showed that the SLE risk variants were mainly inherited from one of the parents. In the 71 patients, we detected a significant enrichment of ultra-rare ( ≤ 0.1%) missense and nonsense mutations in 22 genes known to cause monogenic forms of SLE. We identified one previously reported homozygous nonsense mutation in the C1QC (Complement C1q C Chain) gene, which explains the immunodeficiency and severe SLE phenotype of that patient. We also identified seven ultra-rare, coding heterozygous variants in five genes (C1S, DNASE1L3, DNASE1, IFIH1, and RNASEH2A) involved in monogenic SLE. Our findings indicate a complex contribution to the overall genetic risk of SLE by rare variants in genes associated with monogenic forms of SLE. The rare variants were inherited from the other parent than the one who passed on the more common risk variants leading to an increased genetic burden for SLE in the child. Higher frequency SLE risk variants are mostly passed from one of the parents to the offspring affected with SLE. In contrast, the other parent, in seven cases, contributed heterozygous rare variants in genes associated with monogenic forms of SLE, suggesting a larger impact of rare variants in SLE than hitherto reported.
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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
| | - 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
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Rheumatology, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Christopher Sjöwall
- Division of Neuro and Inflammation Sciences, Department of Clinical and Experimental Medicine, Rheumatology, 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
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Rheumatology, Karolinska University Hospital, 171 77, Stockholm, Sweden
| | - Elisabet Svenungsson
- Rheumatology Unit, 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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Alperin JM, Ortiz-Fernández L, Sawalha AH. Monogenic Lupus: A Developing Paradigm of Disease. Front Immunol 2018; 9:2496. [PMID: 30459768 PMCID: PMC6232876 DOI: 10.3389/fimmu.2018.02496] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/09/2018] [Indexed: 12/13/2022] Open
Abstract
Monogenic lupus is a form of systemic lupus erythematosus (SLE) that occurs in patients with a single gene defect. This rare variant of lupus generally presents with early onset severe disease, especially affecting the kidneys and central nervous system. To date, a significant number of genes have been implicated in monogenic lupus, providing valuable insights into a very complex disease process. Throughout this review, we will summarize the genes reported to be associated with monogenic lupus or lupus-like diseases, and the pathogenic mechanisms affected by the mutations involved upon inducing autoimmunity.
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Affiliation(s)
- Jessie M Alperin
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Lourdes Ortiz-Fernández
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
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34
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Monogenic systemic lupus erythematosus: insights in pathophysiology. Rheumatol Int 2018; 38:1763-1775. [DOI: 10.1007/s00296-018-4048-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 05/10/2018] [Indexed: 01/02/2023]
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35
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Lancour D, Naj A, Mayeux R, Haines JL, Pericak-Vance MA, Schellenberg GD, Crovella M, Farrer LA, Kasif S. One for all and all for One: Improving replication of genetic studies through network diffusion. PLoS Genet 2018; 14:e1007306. [PMID: 29684019 PMCID: PMC5933817 DOI: 10.1371/journal.pgen.1007306] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 05/03/2018] [Accepted: 03/11/2018] [Indexed: 12/31/2022] Open
Abstract
Improving accuracy in genetic studies would greatly accelerate understanding the genetic basis of complex diseases. One approach to achieve such an improvement for risk variants identified by the genome wide association study (GWAS) approach is to incorporate previously known biology when screening variants across the genome. We developed a simple approach for improving the prioritization of candidate disease genes that incorporates a network diffusion of scores from known disease genes using a protein network and a novel integration with GWAS risk scores, and tested this approach on a large Alzheimer disease (AD) GWAS dataset. Using a statistical bootstrap approach, we cross-validated the method and for the first time showed that a network approach improves the expected replication rates in GWAS studies. Several novel AD genes were predicted including CR2, SHARPIN, and PTPN2. Our re-prioritized results are enriched for established known AD-associated biological pathways including inflammation, immune response, and metabolism, whereas standard non-prioritized results were not. Our findings support a strategy of considering network information when investigating genetic risk factors. Integrating multiple types of -omics data is a rapidly growing research area due in part to the increasing amount of diverse and publicly accessible data. In this study, we demonstrated that integration of genetic association and protein interaction data using a network diffusion approach measurably improves reproducibility of top candidate genes. Application of this approach to Alzheimer disease (AD) using a large dataset assembled by the Alzheimer’s Disease Genetics Consortium identified several novel candidate AD genes that are supported by pre-existing knowledge of AD pathobiology. Our findings support a strategy of considering network information when investigating genetic risk factors. Finally, we developed a transparent and easy-to-use R package that can facilitate the extension of our methodology to other phenotypes for which genetic data are available.
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Affiliation(s)
- Daniel Lancour
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Adam Naj
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Richard Mayeux
- Department of Neurology and Sergievsky Center, Columbia University, New York, New York, United States of America
| | - Jonathan L. Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Margaret A. Pericak-Vance
- Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, United States of America
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Mark Crovella
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
- Department of Computer Science, Boston University, Boston, Massachusetts, United States of America
| | - Lindsay A. Farrer
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Ophthalmology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
| | - Simon Kasif
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
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