1
|
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.
Collapse
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
| |
Collapse
|
2
|
Casares-Marfil D, Martínez-Bueno M, Borghi MO, Pons-Estel G, Reales G, Zuo Y, Espinosa G, Radstake T, van den Hoogen LL, Wallace C, Guthridge J, James JA, Cervera R, Meroni PL, Martin J, Knight JS, Alarcón-Riquelme ME, Sawalha AH. A genome-wide association study suggests new susceptibility loci for primary antiphospholipid syndrome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.05.23299396. [PMID: 38405993 PMCID: PMC10889036 DOI: 10.1101/2023.12.05.23299396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Objectives Primary antiphospholipid syndrome (PAPS) is a rare autoimmune disease characterized by the presence of antiphospholipid antibodies and the occurrence of thrombotic events and pregnancy complications. Our study aimed to identify novel genetic susceptibility loci associated with PAPS. Methods We performed a genome-wide association study comprising 5,485 individuals (482 affected individuals) of European ancestry. Significant and suggestive independent variants from a meta-analysis of approximately 7 million variants were evaluated for functional and biological process enrichment. The genetic risk variability for PAPS in different populations was also assessed. Hierarchical clustering, Mahalanobis distance, and Dirichlet Process Mixtures with uncertainty clustering methods were used to assess genetic similarities between PAPS and other immune-mediated diseases. Results We revealed genetic associations with PAPS in a regulatory locus within the HLA class II region near HLA-DRA and in STAT4 with a genome-wide level of significance. 34 additional suggestive genetic susceptibility loci for PAPS were also identified. The disease risk allele in the HLA class II locus is associated with overexpression of HLA-DRB6 , HLA-DRB9 , HLA-DPB2 , HLA-DQA2 and HLA-DQB2 , and is independent of the association between PAPS and HLA-DRB1*1302 . Functional analyses highlighted immune and nervous system related pathways in PAPS-associated loci. The comparison with other immune-mediated diseases revealed a close genetic relatedness to neuromyelitis optica, systemic sclerosis, and Sjögren's syndrome, suggesting colocalized causal variations close to STAT4 , TNPO3 , and BLK . Conclusions This study represents a comprehensive large-scale genetic analysis for PAPS and provides new insights into the genetic basis and pathophysiology of this rare disease.
Collapse
|
3
|
Vinuesa CG, Shen N, Ware T. Genetics of SLE: mechanistic insights from monogenic disease and disease-associated variants. Nat Rev Nephrol 2023; 19:558-572. [PMID: 37438615 DOI: 10.1038/s41581-023-00732-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2023] [Indexed: 07/14/2023]
Abstract
The past few years have provided important insights into the genetic architecture of systemic autoimmunity through aggregation of findings from genome-wide association studies (GWAS) and whole-exome or whole-genome sequencing studies. In the prototypic systemic autoimmune disease systemic lupus erythematosus (SLE), monogenic disease accounts for a small fraction of cases but has been instrumental in the elucidation of disease mechanisms. Defects in the clearance or digestion of extracellular or intracellular DNA or RNA lead to increased sensing of nucleic acids, which can break B cell tolerance and induce the production of type I interferons leading to tissue damage. Current data suggest that multiple GWAS SLE risk alleles act in concert with rare functional variants to promote SLE development. Moreover, introduction of orthologous variant alleles into mice has revealed that pathogenic X-linked dominant and recessive SLE can be caused by novel variants in TLR7 and SAT1, respectively. Such bespoke models of disease help to unravel pathogenic pathways and can be used to test targeted therapies. Cell type-specific expression data revealed that most GWAS SLE risk genes are highly expressed in age-associated B cells (ABCs), which supports the view that ABCs produce lupus autoantibodies and contribute to end-organ damage by persisting in inflamed tissues, including the kidneys. ABCs have thus emerged as key targets of promising precision therapeutics.
Collapse
Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK.
- University College London, London, UK.
- China Australia Centre for Personalized Immunology (CACPI), Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China.
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine (SJTUSM), Shanghai, China
- Center for Autoimmune Genomics and Aetiology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Paediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Thuvaraka Ware
- The Francis Crick Institute, London, UK
- University College London, London, UK
| |
Collapse
|
4
|
Calvin DJD, Steve RJ, Kannangai R, Abraham P, Udhaya Kumar S, Balasundaram A, George Priya Doss C, Thomas V, Thomas A, Danda D, Fletcher JG. HPV and molecular mimicry in systemic lupus erythematosus and an impact of compiling B-cell epitopes and MHC-class II binding profiles with in silico evidence. J Biomol Struct Dyn 2023; 41:12338-12346. [PMID: 36744526 DOI: 10.1080/07391102.2023.2175261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 01/01/2023] [Indexed: 02/07/2023]
Abstract
Epidemiological link between HPV and SLE is evolving. The possibility of HPV infection-induced molecular mimicry and systemic lupus erythematosus (SLE) was elucidated through detailed in silico analyses. Conserved regions in the structural protein sequences of high-risk HPV types were inferred, and sequence homologies between viral and human peptides were identified to delineate proteins implicated in SLE. B-cell epitopes and MHC-class II binding were compiled using Immune Epitope Database and ProPred II analysis tool. Molecular modeling and molecular dynamics/simulation (MDS) were performed using AutoDock Vina and GROMACS, respectively. Sequence alignment revealed 32 conserved regions, and 27/32 viral peptides showed varying similarities to human peptides, rich in B-cell epitopes with superior accessibility, high hydrophilicity, antigenicity and disposition to bind many class-II HLA alleles. Molecular docking of 13 viral peptides homologous (100%) to human peptides implicated in SLE showed that VIR-PEP1 (QLFNKPYWL) and VIR-PEP2 (DTYRFVTS) exhibited higher binding affinities than corresponding human peptides to SLE predisposing HLA-DRB1 allele. MDS of these peptides showed that the viral peptides had superior folding, compactness, and a higher number of hydrogen bonds than human peptides throughout the simulation period. SASA analysis revealed that the VIR-PEP1&2 fluctuated less frequently than corresponding human peptides. MM-PBSA revealed that the VIR-PEP2 complex exhibited higher binding energy than the human peptide complex. This suggests that highly conserved structural peptides of high-risk HPV types homologous to human peptides could compete and bind avidly to the HLA allele associated with SLE and predispose HPV-infected individuals to SLE through molecular mimicry.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- D John Dickson Calvin
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Runal John Steve
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rajesh Kannangai
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Priya Abraham
- Department of Clinical Virology, Christian Medical College, Vellore, Tamil Nadu, India
| | - S Udhaya Kumar
- Laboratory of Integrative Genomics, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Ambritha Balasundaram
- Laboratory of Integrative Genomics, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - C George Priya Doss
- Laboratory of Integrative Genomics, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu, India
| | - Vinotha Thomas
- Department of Gynecologic Oncology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Anitha Thomas
- Department of Gynecologic Oncology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Debashish Danda
- Department of Clinical Immunology and Rheumatology, Christian Medical College, Vellore, Tamil Nadu, India
| | | |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
Harley ITW, Allison K, Scofield RH. Polygenic autoimmune disease risk alleles impacting B cell tolerance act in concert across shared molecular networks in mouse and in humans. Front Immunol 2022; 13:953439. [PMID: 36090990 PMCID: PMC9450536 DOI: 10.3389/fimmu.2022.953439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Abstract
Most B cells produced in the bone marrow have some level of autoreactivity. Despite efforts of central tolerance to eliminate these cells, many escape to periphery, where in healthy individuals, they are rendered functionally non-responsive to restimulation through their antigen receptor via a process termed anergy. Broad repertoire autoreactivity may reflect the chances of generating autoreactivity by stochastic use of germline immunoglobulin gene segments or active mechanisms may select autoreactive cells during egress to the naïve peripheral B cell pool. Likewise, it is unclear why in some individuals autoreactive B cell clones become activated and drive pathophysiologic changes in autoimmune diseases. Both of these remain central questions in the study of the immune system(s). In most individuals, autoimmune diseases arise from complex interplay of genetic risk factors and environmental influences. Advances in genome sequencing and increased statistical power from large autoimmune disease cohorts has led to identification of more than 200 autoimmune disease risk loci. It has been observed that autoantibodies are detectable in the serum years to decades prior to the diagnosis of autoimmune disease. Thus, current models hold that genetic defects in the pathways that control autoreactive B cell tolerance set genetic liability thresholds across multiple autoimmune diseases. Despite the fact these seminal concepts were developed in animal (especially murine) models of autoimmune disease, some perceive a disconnect between human risk alleles and those identified in murine models of autoimmune disease. Here, we synthesize the current state of the art in our understanding of human risk alleles in two prototypical autoimmune diseases – systemic lupus erythematosus (SLE) and type 1 diabetes (T1D) along with spontaneous murine disease models. We compare these risk networks to those reported in murine models of these diseases, focusing on pathways relevant to anergy and central tolerance. We highlight some differences between murine and human environmental and genetic factors that may impact autoimmune disease development and expression and may, in turn, explain some of this discrepancy. Finally, we show that there is substantial overlap between the molecular networks that define these disease states across species. Our synthesis and analysis of the current state of the field are consistent with the idea that the same molecular networks are perturbed in murine and human autoimmune disease. Based on these analyses, we anticipate that murine autoimmune disease models will continue to yield novel insights into how best to diagnose, prognose, prevent and treat human autoimmune diseases.
Collapse
Affiliation(s)
- Isaac T. W. Harley
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
- Rheumatology Section, Medicine Service, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, United States
- *Correspondence: Isaac T. W. Harley,
| | - Kristen Allison
- Division of Rheumatology, Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
- Human Immunology and Immunotherapy Initiative (HI3), Department of Immunology, University of Colorado School of Medicine, Aurora, CO, United States
| | - R. Hal Scofield
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
- Arthritis & Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States
- Medical/Research Service, US Department of Veterans Affairs Medical Center, Oklahoma City, OK, United States
| |
Collapse
|
7
|
Rabiu Abubakar A, Ahmad R, Rowaiye AB, Rahman S, Iskandar K, Dutta S, Oli AN, Dhingra S, Tor MA, Etando A, Kumar S, Irfan M, Gowere M, Chowdhury K, Akter F, Jahan D, Schellack N, Haque M. Targeting Specific Checkpoints in the Management of SARS-CoV-2 Induced Cytokine Storm. Life (Basel) 2022; 12:life12040478. [PMID: 35454970 PMCID: PMC9031737 DOI: 10.3390/life12040478] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/07/2023] Open
Abstract
COVID-19-infected patients require an intact immune system to suppress viral replication and prevent complications. However, the complications of SARS-CoV-2 infection that led to death were linked to the overproduction of proinflammatory cytokines known as cytokine storm syndrome. This article reported the various checkpoints targeted to manage the SARS-CoV-2-induced cytokine storm. The literature search was carried out using PubMed, Embase, MEDLINE, and China National Knowledge Infrastructure (CNKI) databases. Journal articles that discussed SARS-CoV-2 infection and cytokine storm were retrieved and appraised. Specific checkpoints identified in managing SARS-CoV-2 induced cytokine storm include a decrease in the level of Nod-Like Receptor 3 (NLRP3) inflammasome where drugs such as quercetin and anakinra were effective. Janus kinase-2 and signal transducer and activator of transcription-1 (JAK2/STAT1) signaling pathways were blocked by medicines such as tocilizumab, baricitinib, and quercetin. In addition, inhibition of interleukin (IL)-6 with dexamethasone, tocilizumab, and sarilumab effectively treats cytokine storm and significantly reduces mortality caused by COVID-19. Blockade of IL-1 with drugs such as canakinumab and anakinra, and inhibition of Bruton tyrosine kinase (BTK) with zanubrutinib and ibrutinib was also beneficial. These agents' overall mechanisms of action involve a decrease in circulating proinflammatory chemokines and cytokines and or blockade of their receptors. Consequently, the actions of these drugs significantly improve respiration and raise lymphocyte count and PaO2/FiO2 ratio. Targeting cytokine storms' pathogenesis genetic and molecular apparatus will substantially enhance lung function and reduce mortality due to the COVID-19 pandemic.
Collapse
Affiliation(s)
- Abdullahi Rabiu Abubakar
- Department of Pharmacology and Therapeutics, Faculty of Pharmaceutical Sciences, Bayero University, PMB 3452, Kano 700233, Nigeria;
| | - Rahnuma Ahmad
- Department of Physiology, Medical College for Women and Hospital, Dhaka 1230, Bangladesh;
| | | | - Sayeeda Rahman
- School of Medicine, American University of Integrative Sciences, Bridgetown BB11114, Barbados;
| | - Katia Iskandar
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Lebanese University, Beirut P.O. Box 6573/14, Lebanon;
| | - Siddhartha Dutta
- Department of Pharmacology, All India Institute of Medical Sciences, Rajkot 360001, Gujrat, India;
| | - Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Nnamdi Azikiwe University, PMB 5025, Awka 420110, Nigeria;
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, Bihar, India;
| | - Maryam Abba Tor
- Department of Health and Biosciences, University of East London, University Way, London E16 2RD, UK;
| | - Ayukafangha Etando
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Eswatini Medical Christian University, P.O. Box A624 Swazi Plaza Mbabane, Mbabane H101, Hhohho, Eswatini;
| | - Santosh Kumar
- Department of Periodontology and Implantology, Karnavati School of Dentistry, Karnavati University, 907/A, Adalaj Uvarsad Road, Gandhinagar 382422, Gujarat, India;
| | - Mohammed Irfan
- Department of Forensics, Federal University of Pelotas, R. Gomes Carneiro, 1-Centro, Pelotas 96010-610, RS, Brazil;
| | - Marshall Gowere
- Department of Pharmacology, Faculty of Health Sciences, Basic Medical Sciences Building, Prinshof Campus, University of Pretoria, Arcadia 0083, South Africa; (M.G.); (N.S.)
| | - Kona Chowdhury
- Department of Paediatrics, Gonoshasthaya Samaj Vittik Medical College and Hospital, Dhaka 1344, Bangladesh;
| | - Farhana Akter
- Department of Endocrinology, Chittagong Medical College, Chattogram 4203, Bangladesh;
| | - Dilshad Jahan
- Department of Hematology, Asgar Ali Hospital, 111/1/A Distillery Road, Gandaria Beside Dhupkhola, Dhaka 1204, Bangladesh;
| | - Natalie Schellack
- Department of Pharmacology, Faculty of Health Sciences, Basic Medical Sciences Building, Prinshof Campus, University of Pretoria, Arcadia 0083, South Africa; (M.G.); (N.S.)
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defense Health, Universiti Pertahanan Nasional Malaysia (National Defense University of Malaysia), Kem Perdana Sungai Besi, Kuala Lumpur 57000, Malaysia
- Correspondence: or
| |
Collapse
|
8
|
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.
Collapse
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)
| |
Collapse
|
9
|
Wajda A, Sivitskaya L, Paradowska-Gorycka A. Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases. J Clin Med 2021; 10:3334. [PMID: 34362117 PMCID: PMC8348854 DOI: 10.3390/jcm10153334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
NGS technologies have transformed clinical diagnostics and broadly used from neonatal emergencies to adult conditions where the diagnosis cannot be made based on clinical symptoms. Autoimmune diseases reveal complicate molecular background and traditional methods could not fully capture them. Certainly, NGS technologies meet the needs of modern exploratory research, diagnostic and pharmacotherapy. Therefore, the main purpose of this review was to briefly present the application of NGS technology used in recent years in the understanding of autoimmune diseases paying particular attention to autoimmune connective tissue diseases. The main issues are presented in four parts: (a) panels, whole-genome and -exome sequencing (WGS and WES) in diagnostic, (b) Human leukocyte antigens (HLA) as a diagnostic tool, (c) RNAseq, (d) microRNA and (f) microbiome. Although all these areas of research are extensive, it seems that epigenetic impact on the development of systemic autoimmune diseases will set trends for future studies on this area.
Collapse
Affiliation(s)
- Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
| | - Larysa Sivitskaya
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072 Minsk, Belarus
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
| |
Collapse
|
10
|
Luo J, Meng Y, Zhai J, Zhu Y, Li Y, Wu Y. Screening of SLE-susceptible SNPs in One Chinese Family with Systemic Lupus Erythematosus. Curr Bioinform 2020. [DOI: 10.2174/1574893615666200120105153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background:
Systemic lupus erythematosus (SLE) is a complex autoimmune disease,
which mainly affects childbearing-aged women. Although its pathogenesis is not fully clear yet,
studies have shown that genetic factors are vital in exploring SLE pathogenic mechanisms.
Objective:
The purpose of this study is to predict and screen potential pathogenic single nucleotide
polymorphisms (SNPs). By comparing the genomes of members of a family with SLE and
performing functional analysis on mutation loci, possible pathogenic polymorphisms are screened.
These analyses lay the foundation for further research mechanisms.
Method:
Genomic alignment, variant calling and functional annotation were performed and then
~92,778 original SNPs were obtained for each specimen. We found that the patient/healthyspecific
SNPs show different conservative score distribution. Many patient-specific SNPs were
detected in SLE-related pathways. We therefore investigated the patient-specific SNPs from four
diverse perspectives, including nonsynonymous variations in exon regions, expression quantitative
trait loci (eQTLs), RNA binding sites and RNA-binding protein (RBP) binding sites.
Results:
18 potential pathogenic SNPs were identified in SLE risk genes, which were associated
with functional loci. Systematic literature study was then performed to verify these potential
pathogenic SNPs.
Conclusion:
This study could help to better explain possible genetic mechanisms of SLE from the
perspective of variation. It could provide effective strategy for the accurate diagnosis and
personalized treatment of SLE patients.
Collapse
Affiliation(s)
- Juan Luo
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yanming Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jianzhao Zhai
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Zhu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Yongkang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
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.
| |
Collapse
|
13
|
DNA Damage Response and Oxidative Stress in Systemic Autoimmunity. Int J Mol Sci 2019; 21:ijms21010055. [PMID: 31861764 PMCID: PMC6982230 DOI: 10.3390/ijms21010055] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 02/08/2023] Open
Abstract
The DNA damage response and repair (DDR/R) network, a sum of hierarchically structured signaling pathways that recognize and repair DNA damage, and the immune response to endogenous and/or exogenous threats, act synergistically to enhance cellular defense. On the other hand, a deregulated interplay between these systems underlines inflammatory diseases including malignancies and chronic systemic autoimmune diseases, such as systemic lupus erythematosus, systemic sclerosis, and rheumatoid arthritis. Patients with these diseases are characterized by aberrant immune response to self-antigens with widespread production of autoantibodies and multiple-tissue injury, as well as by the presence of increased oxidative stress. Recent data demonstrate accumulation of endogenous DNA damage in peripheral blood mononuclear cells from these patients, which is related to (a) augmented DNA damage formation, at least partly due to the induction of oxidative stress, and (b) epigenetically regulated functional abnormalities of fundamental DNA repair mechanisms. Because endogenous DNA damage accumulation has serious consequences for cellular health, including genomic instability and enhancement of an aberrant immune response, these results can be exploited for understanding pathogenesis and progression of systemic autoimmune diseases, as well as for the development of new treatments.
Collapse
|
14
|
Polymorphisms of MFGE8 are associated with susceptibility and clinical manifestations through gene expression modulation in Koreans with systemic lupus erythematosus. Sci Rep 2019; 9:18565. [PMID: 31811237 PMCID: PMC6897915 DOI: 10.1038/s41598-019-55061-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 11/20/2019] [Indexed: 12/22/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is characterized by impaired clearance of apoptotic cells. Milk fat globule epidermal growth factor 8 (MFGE8) is a protein that connects αvβ3 integrin on phagocytic macrophages with phosphatidylserine on apoptotic cells. We investigated whether genetic variation of the MFGE8 gene and serum MFGE8 concentration are associated with SLE. Single nucleotide polymorphisms (SNPs) were genotyped and serum concentrations were analyzed. The rs2271715 C allele and rs3743388 G allele showed higher frequency in SLE than in healthy subjects (HSs). Three haplotypes were found among 4 SNPs (rs4945, rs1878327, rs2271715, and rs3743388): AACG, CGCG, and CGTC. CGCG haplotype was significantly more common in SLE than in HSs. rs4945 was associated with the erythrocyte sedimentation rate and rs1878327 was associated with alopecia, C-reactive protein, complement 3, anti-dsDNA antibody, and high disease activity. rs2271715 and rs3743388 were associated with renal disease, cumulative glucocorticoid dose, and cyclophosphamide and mycophenolate mofetil use. Serum MFGE8 concentrations were significantly higher in SLE than in HSs. Furthermore, the levels of MFGE8 were significantly higher in SLE than HSs of the rs2271715 CC genotype. In conclusion, MFGE8 genetic polymorphisms are associated not only with susceptibility to SLE but also with disease activity through modulation of gene expression.
Collapse
|
15
|
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.
Collapse
|
16
|
|
17
|
Abstract
Purpose of Review The purpose is to discuss the advances that genetics and genomics have provided to better understand the molecular mechanisms behind SLE and how to solve its heterogeneity. I propose new ideas that can help us stratify lupus in order to find the best therapies for each patient, and the idea of substituting clinical diagnosis with molecular diagnosis according to their molecular patterns, an idea that may not only include lupus but also other diseases. Recent Findings The study of rare mutations may provide insight into groups of lupus patients where type I interferon signature is important and help understand those with an atypical clinical presentation. Recent papers used longitudinal blood transcriptome data correlating with disease activity scores to stratify lupus into molecular clusters. The implication of neutrophils in the risk to develop nephritis was established, but also that neutrophils and lymphocytes may correlate with activity differentiating the mechanisms of flares and separating patients into clinically separate groups. Summary The role of type I interferon signature is important; however, the stratification of SLE patients according to the genes and cellular compartments being modulated during disease activity may be even more important to define those patients who may benefit the most with new anti-type I IFN receptor therapies.
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Exploring the etiopathogenesis of systemic lupus erythematosus: a genetic perspective. Immunogenetics 2019; 71:283-297. [DOI: 10.1007/s00251-019-01103-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/07/2019] [Indexed: 12/27/2022]
|