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Jin C, Tao X, Zhang W, Xu H, Wu Y, Chen Q, Li S, Ning A, Wang W, Wu Q, Chu M. Multi-omics and multi-stages integration identified a novel variant associated with silicosis risk. Arch Toxicol 2024; 98:2907-2918. [PMID: 38811393 DOI: 10.1007/s00204-024-03795-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Assessing the association between candidate single-nucleotide polymorphisms (SNPs) identified by multi-omics approaches and susceptibility to silicosis. RNA-seq analysis was performed to screen the differentially expressed mRNAs in the fibrotic lung tissues of mice exposed to silica particles. Following this, we integrated the SNPs located in the above human homologenes with the silicosis-related genome-wide association study (GWAS) data to select the candidate SNPs. Then, expression quantitative trait locus (eQTL)-SNPs were identified by the GTEx database. Next, we validated the associations between the functional eQTL-SNPs and silicosis susceptibility by additional case-control study. And the contribution of the identified SNP and its host gene in the fibrosis process was further validated by functional experiments. A total of 12 eQTL-SNPs were identified in the screening stage. The results of the validation stage suggested that the variant T allele of rs419540 located in IL12RB1 significantly increased the risk of developing silicosis [additive model: odds ratio (OR) = 1.78, 95% confidence interval (CI) 1.11-2.85, P = 0.017]. Furthermore, the combination of GWAS and the results of validation stage also indicated that the variant T allele of rs419540 in IL12RB1 was associated with increased silicosis risk (additive model: OR = 2.07, 95% CI 1.38-3.12, P < 0.001). Additionally, after knockdown or overexpression of IL12RB1, the levels of pro-inflammatory factors, such as IL-12, IFN-γ, and other pro-inflammatory factors, were correspondingly decreased or increased. The novel eQTL-SNP, rs419540, might increase the risk of silicosis by modulating the expression levels of IL12RB1.
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Affiliation(s)
- Chunmeng Jin
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Wendi Zhang
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Huiwen Xu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Siqi Li
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China
| | - Wei Wang
- Department of Occupational Health, Center for Disease Control and Prevention of Wuxi, Wuxi, Jiangsu, China.
| | - Qiuyun Wu
- School of Public Health, Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, Nantong, Jiangsu, China.
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2
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El-Halwagi A, Agarwal SK. Insights into the genetic landscape of systemic sclerosis. Best Pract Res Clin Rheumatol 2024:101981. [PMID: 39068103 DOI: 10.1016/j.berh.2024.101981] [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: 04/30/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]
Abstract
Systemic sclerosis (SSc) is a complex autoimmune disease that clinically manifests as progressive fibrosis of the skin and internal organs. Autoimmunity and endothelial dysfunction play important roles in the development of SSc but the causes of SSc remain unknown. Accumulating evidence, first from familial aggregation studies and subsequently from candidate gene association studies and genome wide association studies underscore the crucial contributions of genetics to the development of SSc. The identification of polymorphisms in the HLA region as well as non-HLA loci is important for understanding the risks of developing SSc but can also provide important pathogenic insight in SSc. While not translating into clinic practice yet, understanding the genetic landscape of SSc will hopefully assist in the diagnosis and management of patients with and/or at risk of developing SSc in the future. Herein we review the studies that investigate genetic risks of SSc susceptibility.
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Affiliation(s)
- Ali El-Halwagi
- Section of Immunology, Allergy and Rheumatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sandeep K Agarwal
- Section of Immunology, Allergy and Rheumatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
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3
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Stabach PR, Sims D, Gomez-Bañuelos E, Zehentmeier S, Dammen-Brower K, Bernhisel A, Kujawski S, Lopez SG, Petri M, Goldman DW, Lester ER, Le Q, Ishaq T, Kim H, Srivastava S, Kumar D, Pereira JP, Yarema KJ, Koumpouras F, Andrade F, Braddock DT. A dual-acting DNASE1/DNASE1L3 biologic prevents autoimmunity and death in genetic and induced lupus models. JCI Insight 2024; 9:e177003. [PMID: 38888971 DOI: 10.1172/jci.insight.177003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
A defining feature of systemic lupus erythematosus (SLE) is loss of tolerance to self-DNA, and deficiency of DNASE1L3, the main enzyme responsible for chromatin degradation in blood, is also associated with SLE. This association can be found in an ultrarare population of pediatric patients with DNASE1L3 deficiency who develop SLE, adult patients with loss-of-function variants of DNASE1L3 who are at a higher risk for SLE, and patients with sporadic SLE who have neutralizing autoantibodies against DNASE1L3. To mitigate the pathogenic effects of inherited and acquired DNASE1L3 deficiencies, we engineered a long-acting enzyme biologic with dual DNASE1/DNASE1L3 activity that is resistant to DNASE1 and DNASE1L3 inhibitors. Notably, we found that the biologic prevented the development of lupus in Dnase1-/-Dnase1L3-/- double-knockout mice and rescued animals from death in pristane-induced lupus. Finally, we confirmed that the human isoform of the enzyme biologic was not recognized by autoantibodies in SLE and efficiently degraded genomic and mitochondrial cell-free DNA, as well as microparticle DNA, in SLE plasma. Our findings suggest that autoimmune diseases characterized by aberrant DNA accumulation, such as SLE, can be effectively treated with a replacement DNASE tailored to bypass pathogenic mechanisms, both genetic and acquired, that restrict DNASE1L3 activity.
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Affiliation(s)
- Paul R Stabach
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Dominique Sims
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eduardo Gomez-Bañuelos
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sandra Zehentmeier
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kris Dammen-Brower
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Bernhisel
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sophia Kujawski
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sam G Lopez
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel W Goldman
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ethan R Lester
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Quan Le
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tayyaba Ishaq
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hana Kim
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shivani Srivastava
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepika Kumar
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joao P Pereira
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kevin J Yarema
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Fotios Koumpouras
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Felipe Andrade
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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4
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Jandali B, Lyons M, Charles J, Zhang M, Theodore S, Pedroza C, Mayes MD, Assassi S. A Prospective Observational Study of Disease Severity and Mortality in Hispanic American Patients With Systemic Sclerosis. Arthritis Care Res (Hoboken) 2024; 76:768-776. [PMID: 38221717 PMCID: PMC11132947 DOI: 10.1002/acr.25300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 12/10/2023] [Accepted: 01/10/2023] [Indexed: 01/16/2024]
Abstract
OBJECTIVE To characterize disease manifestations in Hispanic American patients with systemic sclerosis (SSc) in comparison with non-Hispanic White and Black patients. METHODS Longitudinal clinical characteristics were collected prospectively in the Genetics versus Environment in Scleroderma Outcome Study cohort. All patients fulfilled the classification criteria for SSc and had a disease duration less than five years at enrollment. RESULTS A cohort of 427 patients, consisting of 124 Hispanic, 220 non-Hispanic White, and 83 non-Hispanic Black participants were examined. At enrollment, Hispanic patients were significantly younger but had longer disease duration, higher frequency of U1-RNP positivity as well as concurrent systemic lupus erythematosus (SLE) diagnosis, and lower income and educational levels in comparison to non-Hispanic White patients. Compared with non-Hispanic Black patients, Hispanic patients had more frequently limited cutaneous involvement and anticentromere antibodies. In the longitudinal analysis, Hispanic patients had significantly lower forced vital capacity percents predicted (point estimate, -9.3%; P < 0.001) than non-Hispanic White but not Black patients. Hispanic patients had similar longitudinal modified Rodnan Skin Scores like non-Hispanic White patients but lower measurements than non-Hispanic Black patients (point estimate, -3.2; P = 0.029). Hispanic patients had significantly higher serially obtained perceived functional disability scores than White patients (point estimate, 0.29; P < 0.001). Hispanic patients also had higher mortality rates than White Americans even after adjustment for age, gender, and socioeconomic statuses. CONCLUSION Hispanic patients have higher likelihood of having U1-RNP positivity and SLE overlap, more severe restrictive lung disease, as well as higher rate of mortality than non-Hispanic White patients.
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Affiliation(s)
- Bochra Jandali
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Marka Lyons
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Julio Charles
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Meng Zhang
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Samuel Theodore
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Claudia Pedroza
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Maureen D. Mayes
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
| | - Shervin Assassi
- McGovern Medical School at the University of Texas Health Science Center at Houston, TX, USA
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5
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Garreau A, Santa P, Dubois M, Brisou D, Levionnois É, Laurent P, Ferriere A, Roubertie A, Loizon S, Duluc D, Blanco P, Contin-Bordes C, Truchetet ME, Sisirak V. The deficiency of DNASE1L3 does not affect systemic sclerosis pathogenesis in two inducible murine models of the disease. Eur J Immunol 2024; 54:e2350903. [PMID: 38576111 DOI: 10.1002/eji.202350903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/06/2024]
Abstract
We induced systemic sclerosis (SSc)-like disease in both wild-type and Dnase1l3-deficient mice using two distinct approaches involving bleomycin and hypochlorous acid injections. Our observations revealed that the deficiency in DNASE1L3 did not affect tissue fibrosis or inflammation caused by these treatments. Despite the association of single nucleotide polymorphisms in humans with SSc pathogenesis, our study demonstrates that DNASE1L3 is dispensable in two inducible murine models of SSc-like pathogenesis.
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Affiliation(s)
- Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Maxime Dubois
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Damien Brisou
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | | | - Paôline Laurent
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | | | - Anaïs Roubertie
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Séverine Loizon
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Dorothée Duluc
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - Cécile Contin-Bordes
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
| | - Marie-Elise Truchetet
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Department of Immunology and Immunogenetics, Bordeaux University Hospital, Bordeaux, France
- Department of Rheumatology, Bordeaux University Hospital, Bordeaux, France
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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6
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Gumkowska-Sroka O, Kotyla K, Kotyla P. Immunogenetics of Systemic Sclerosis. Genes (Basel) 2024; 15:586. [PMID: 38790215 PMCID: PMC11121022 DOI: 10.3390/genes15050586] [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: 04/07/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/26/2024] Open
Abstract
Systemic sclerosis (SSc) is a rare autoimmune connective tissue disorder characterized by massive fibrosis, vascular damage, and immune imbalance. Advances in rheumatology and immunology over the past two decades have led to a redefinition of systemic sclerosis, shifting from its initial perception as primarily a "hyperfibrotic" state towards a recognition of systemic sclerosis as an immune-mediated disease. Consequently, the search for genetic markers has transitioned from focusing on fibrotic mechanisms to exploring immune regulatory pathways. Immunogenetics, an emerging field at the intersection of immunology, molecular biology, and genetics has provided valuable insights into inherited factors that influence immunity. Data from genetic studies conducted thus far indicate that alterations in genetic messages can significantly impact disease risk and progression. While certain genetic variations may confer protective effects, others may exacerbate disease susceptibility. This paper presents a comprehensive review of the most relevant genetic changes that influence both the risk and course of systemic sclerosis. Special emphasis is placed on factors regulating the immune response, recognizing their pivotal role in the pathogenesis of the disease.
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Affiliation(s)
| | | | - Przemysław Kotyla
- Department of Rheumatology and Clinical Immunology, Medical University of Silesia, Voivodeship Hospital No. 5, 41-200 Sosnowiec, Poland; (O.G.-S.); (K.K.)
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7
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Engavale M, Hernandez CJ, Infante A, LeRoith T, Radovan E, Evans L, Villarreal J, Reilly CM, Sutton RB, Keyel PA. Deficiency of macrophage-derived Dnase1L3 causes lupus-like phenotypes in mice. J Leukoc Biol 2023; 114:547-556. [PMID: 37804110 PMCID: PMC10843819 DOI: 10.1093/jleuko/qiad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 08/01/2023] [Accepted: 09/07/2023] [Indexed: 10/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease caused by environmental factors and loss of key proteins, including the endonuclease Dnase1L3. Dnase1L3 absence causes pediatric-onset lupus in humans, while reduced activity occurs in adult-onset SLE. The amount of Dnase1L3 that prevents lupus remains unknown. To genetically reduce Dnase1L3 levels, we developed a mouse model lacking Dnase1L3 in macrophages (conditional knockout [cKO]). Serum Dnase1L3 levels were reduced 67%, though Dnase1 activity remained constant. Homogeneous and peripheral antinuclear antibodies were detected in the sera by immunofluorescence, consistent with anti-double-stranded DNA (anti-dsDNA) antibodies. Total immunoglobulin M, total immunoglobulin G, and anti-dsDNA antibody levels increased in cKO mice with age. The cKO mice developed anti-Dnase1L3 antibodies. In contrast to global Dnase1L3-/- mice, anti-dsDNA antibodies were not elevated early in life. The cKO mice had minimal kidney pathology. Therefore, we conclude that an intermediate reduction in serum Dnase1L3 causes mild lupus phenotypes, and macrophage-derived DnaselL3 helps limit lupus.
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Affiliation(s)
- Minal Engavale
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Colton J. Hernandez
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Angelica Infante
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Tanya LeRoith
- Department of Cell Biology and Physiology, Virginia Tech, Blacksburg, VA 24061, United States
| | - Elliott Radovan
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Lauryn Evans
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
| | - Johanna Villarreal
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, United States
| | - Christopher M. Reilly
- Department of Cell Biology and Physiology, Virginia Tech, Blacksburg, VA 24061, United States
| | - R. Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, United States
| | - Peter A. Keyel
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, United States
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8
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Rodriguez-Martin I, Villanueva-Martin G, Guillen-Del-Castillo A, Ortego-Centeno N, Callejas JL, Simeón-Aznar CP, Martin J, Acosta-Herrera M. Contribution of Telomere Length to Systemic Sclerosis Onset: A Mendelian Randomization Study. Int J Mol Sci 2023; 24:15589. [PMID: 37958573 PMCID: PMC10648506 DOI: 10.3390/ijms242115589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Although previous studies have suggested a relationship between telomere shortening and systemic sclerosis (SSc), the association between these two traits remains poorly understood. The objective of this study was to assess the causal relationship between telomere length in leukocytes (LTL) and SSc using the two-sample Mendelian randomization approach, with the genome-wide association study data for both LTL and SSc. The results of inverse-variance weighted regression (OR = 0.716 [95% CI 0.528-0.970], p = 0.031) and the Mendelian randomization pleiotropy residual sum and outlier method (OR = 0.716 [95% CI 0.563-0.911], p = 0.035) indicate an association between telomere length and SSc. Specifically, longer genetically predicted LTL is associated with a reduced risk of SSc. Sensitivity tests highlight the significant roles of the variants rs10936599 and rs2736100 annotated to the TERC and TERT genes, respectively. Our findings suggest an influence of telomere length in leukocytes on the development of SSc.
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Affiliation(s)
| | | | | | - Norberto Ortego-Centeno
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
- Department of Medicine, University of Granada, 18016 Granada, Spain
| | - José L. Callejas
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
| | - Carmen P. Simeón-Aznar
- Department of Internal Medicine, Hospital Universitari Vall d’Hebron, 08035 Barcelona, Spain
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, 18016 Granada, Spain
| | - Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, 18016 Granada, Spain
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, 18012 Granada, Spain
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9
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Li W, Nakano H, Fan W, Li Y, Sil P, Nakano K, Zhao F, Karmaus PW, Grimm SA, Shi M, Xu X, Mizuta R, Kitamura D, Wan Y, Fessler MB, Cook DN, Shats I, Li X, Li L. DNASE1L3 enhances antitumor immunity and suppresses tumor progression in colon cancer. JCI Insight 2023; 8:e168161. [PMID: 37581941 PMCID: PMC10544201 DOI: 10.1172/jci.insight.168161] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 08/02/2023] [Indexed: 08/17/2023] Open
Abstract
DNASE1L3, an enzyme highly expressed in DCs, is functionally important for regulating autoimmune responses to self-DNA and chromatin. Deficiency of DNASE1L3 leads to development of autoimmune diseases in both humans and mice. However, despite the well-established causal relationship between DNASE1L3 and immunity, little is known about the involvement of DNASE1L3 in regulation of antitumor immunity, the foundation of modern antitumor immunotherapy. In this study, we identify DNASE1L3 as a potentially new regulator of antitumor immunity and a tumor suppressor in colon cancer. In humans, DNASE1L3 is downregulated in tumor-infiltrating DCs, and this downregulation is associated with poor patient prognosis and reduced tumor immune cell infiltration in many cancer types. In mice, Dnase1l3 deficiency in the tumor microenvironment enhances tumor formation and growth in several colon cancer models. Notably, the increased tumor formation and growth in Dnase1l3-deficient mice are associated with impaired antitumor immunity, as evidenced by a substantial reduction of cytotoxic T cells and a unique subset of DCs. Consistently, Dnase1l3-deficient DCs directly modulate cytotoxic T cells in vitro. To our knowledge, our study unveils a previously unknown link between DNASE1L3 and antitumor immunity and further suggests that restoration of DNASE1L3 activity may represent a potential therapeutic approach for anticancer therapy.
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Affiliation(s)
- Wenling Li
- Biostatistics and Computational Biology Branch
- Signal Transduction Laboratory
| | | | - Wei Fan
- Biostatistics and Computational Biology Branch
- Signal Transduction Laboratory
| | - Yuanyuan Li
- Biostatistics and Computational Biology Branch
| | - Payel Sil
- Biostatistics and Computational Biology Branch
| | | | - Fei Zhao
- Immunity, Inflammation, and Disease Laboratory
| | | | | | - Min Shi
- Biostatistics and Computational Biology Branch
| | - Xin Xu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, North Carolina, USA
| | - Ryushin Mizuta
- Division of Cancer Cell Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Daisuke Kitamura
- Division of Cancer Cell Biology, Research Institute for Biomedical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yisong Wan
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, North Carolina, USA
| | | | | | | | | | - Leping Li
- Biostatistics and Computational Biology Branch
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10
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Skaug B, Guo X, Li YJ, Charles J, Pham KT, Couturier J, Lewis DE, Bracaglia C, Caiello I, Mayes MD, Assassi S. Reduced digestion of circulating genomic DNA in systemic sclerosis patients with the DNASE1L3 R206C variant. Rheumatology (Oxford) 2023; 62:3197-3204. [PMID: 36708011 PMCID: PMC10473277 DOI: 10.1093/rheumatology/kead050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/01/2023] [Accepted: 01/17/2023] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES Polymorphism in a coding region of deoxyribonuclease I-like III (DNASE1L3), causing amino acid substitution of Arg-206 to Cys (R206C), is a robustly replicated heritable risk factor for SSc and other autoimmune diseases. DNASE1L3 is secreted into the circulation, where it can digest genomic DNA (gDNA) in apoptosis-derived membrane vesicles (AdMVs). We sought to determine the impact of DNASE1L3 R206C on digestion of circulating gDNA in SSc patients and healthy controls (HCs). METHODS The ability of DNASE1L3 to digest AdMV-associated gDNA was tested in vitro. The effect of R206C substitution on extracellular secretion of DNASE1L3 was determined using a transfected cell line and primary monocyte-derived dendritic cells from SSc patients. Plasma samples from SSc patients and HCs with DNASE1L3 R206C or R206 wild type were compared for their ability to digest AdMV-associated gDNA. The digestion status of endogenous gDNA in plasma samples from 123 SSc patients and 74 HCs was determined by measuring the proportion of relatively long to short gDNA fragments. RESULTS The unique ability of DNASE1L3 to digest AdMV-associated gDNA was confirmed. Extracellular secretion of DNASE1L3 R206C was impaired. Plasma from individuals with DNASE1L3 R206C had reduced ability to digest AdMV-associated gDNA. The ratio of long: short gDNA fragments was increased in plasma from SSc patients with DNASE1L3 R206C, and this ratio correlated inversely with DNase activity. CONCLUSION Our results confirm that circulating gDNA is a physiological DNASE1L3 substrate and show that its digestion is reduced in SSc patients with the DNASE1L3 R206C variant.
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Affiliation(s)
- Brian Skaug
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Xinjian Guo
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Yuanteng Jeff Li
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Julio Charles
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Kay T Pham
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Jacob Couturier
- Division of Infectious Diseases, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Dorothy E Lewis
- Division of Infectious Diseases, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Claudia Bracaglia
- Division of Rheumatology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Ivan Caiello
- Division of Rheumatology, IRCCS Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Maureen D Mayes
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Shervin Assassi
- Division of Rheumatology, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
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11
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Spasovski V, Andjelkovic M, Parezanovic M, Komazec J, Ugrin M, Klaassen K, Stojiljkovic M. The Role of Autophagy and Apoptosis in Affected Skin and Lungs in Patients with Systemic Sclerosis. Int J Mol Sci 2023; 24:11212. [PMID: 37446389 DOI: 10.3390/ijms241311212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Systemic sclerosis (SSc) is a complex autoimmune inflammatory disorder with multiple organ involvement. Skin changes present the hallmark of SSc and coincide with poor prognosis. Interstitial lung diseases (ILD) are the most widely reported complications in SSc patients and the primary cause of death. It has been proposed that the processes of autophagy and apoptosis could play a significant role in the pathogenesis and clinical course of different autoimmune diseases, and accordingly in SSc. In this manuscript, we review the current knowledge of autophagy and apoptosis processes in the skin and lungs of patients with SSc. Profiling of markers involved in these processes in skin cells can be useful to recognize the stage of fibrosis and can be used in the clinical stratification of patients. Furthermore, the knowledge of the molecular mechanisms underlying these processes enables the repurposing of already known drugs and the development of new biological therapeutics that aim to reverse fibrosis by promoting apoptosis and regulate autophagy in personalized treatment approach. In SSc-ILD patients, the molecular signature of the lung tissues of each patient could be a distinctive criterion in order to establish the correct lung pattern, which directly impacts the course and prognosis of the disease. In this case, resolving the role of tissue-specific markers, which could be detected in the circulation using sensitive molecular methods, would be an important step toward development of non-invasive diagnostic procedures that enable early and precise diagnosis and preventing the high mortality of this rare disease.
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Affiliation(s)
- Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Marina Andjelkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Marina Parezanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Jovana Komazec
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
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12
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Engavale M, Hernandez CJ, Infante A, LeRoith T, Radovan E, Evans L, Villarreal J, Reilly CM, Sutton RB, Keyel PA. Deficiency of macrophage-derived Dnase1L3 causes lupus-like phenotypes in mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537232. [PMID: 37131692 PMCID: PMC10153119 DOI: 10.1101/2023.04.17.537232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Systemic Lupus Erythematosus (SLE) is a chronic autoimmune disease caused by environmental factors and loss of key proteins. One such protein is a serum endonuclease secreted by macrophages and dendritic cells, Dnase1L3. Loss of Dnase1L3 causes pediatric-onset lupus in humans is Dnase1L3. Reduction in Dnase1L3 activity occurs in adult-onset human SLE. However, the amount of Dnase1L3 necessary to prevent lupus onset, if the impact is continuous or requires a threshold, and which phenotypes are most impacted by Dnase1L3 remain unknown. To reduce Dnase1L3 protein levels, we developed a genetic mouse model with reduced Dnase1L3 activity by deleting Dnase1L3 from macrophages (cKO). Serum Dnase1L3 levels were reduced 67%, though Dnase1 activity remained constant. Sera were collected weekly from cKO and littermate controls until 50 weeks of age. Homogeneous and peripheral anti-nuclear antibodies were detected by immunofluorescence, consistent with anti-dsDNA antibodies. Total IgM, total IgG, and anti-dsDNA antibody levels increased in cKO mice with increasing age. In contrast to global Dnase1L3 -/- mice, anti-dsDNA antibodies were not elevated until 30 weeks of age. The cKO mice had minimal kidney pathology, except for deposition of immune complexes and C3. Based on these findings, we conclude that an intermediate reduction in serum Dnase1L3 causes mild lupus phenotypes. This suggest that macrophage-derived DnaselL3 is critical to limiting lupus.
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13
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Molecular Mechanisms Behind the Role of Plasmacytoid Dendritic Cells in Systemic Sclerosis. BIOLOGY 2023; 12:biology12020285. [PMID: 36829561 PMCID: PMC9953616 DOI: 10.3390/biology12020285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Systemic sclerosis (SSc) is a debilitating autoimmune disease that affects multiple systems. It is characterized by immunological deregulation, functional and structural abnormalities of small blood vessels, and fibrosis of the skin, and, in some cases, internal organs. Fibrosis has a devastating impact on a patient's life and lung fibrosis is associated with high morbimortality. Several immune populations contribute to the progression of SSc, and plasmacytoid dendritic cells (pDCs) have been identified as crucial mediators of fibrosis. Research on murine models of lung and skin fibrosis has shown that pDCs are essential in the development of fibrosis, and that removing pDCs improves fibrosis. pDCs are a subset of dendritic cells (DCs) that are specialized in anti-viral responses and are also involved in autoimmune diseases, such as SSc, systemic lupus erythematosus (SLE) and psoriasis, mostly due to their capacity to produce type I interferon (IFN). A type I IFN signature and high levels of CXCL4, both derived from pDCs, have been associated with poor prognosis in patients with SSc and are correlated with fibrosis. This review will examine the recent research on the molecular mechanisms through which pDCs impact SSc.
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14
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Harsini S, Rezaei N. Autoimmune diseases. Clin Immunol 2023. [DOI: 10.1016/b978-0-12-818006-8.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Purewal JS, Doshi GM. Deciphering the Function of New Therapeutic Targets and Prospective Biomarkers in the Management of Psoriasis. Curr Drug Targets 2023; 24:1224-1238. [PMID: 38037998 DOI: 10.2174/0113894501277656231128060242] [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: 08/17/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023]
Abstract
Psoriasis is an immune-mediated skin condition affecting people worldwide, presenting at any age, and leading to a substantial burden physically and mentally. The innate and adaptive immune systems interact intricately with the pathomechanisms that underlie disease. T cells can interact with keratinocytes, macrophages, and dendritic cells through the cytokines they secrete. According to recent research, psoriasis flare-ups can cause systemic inflammation and various other co-morbidities, including depression, psoriatic arthritis, and cardio-metabolic syndrome. Additionally, several auto-inflammatory and auto-immune illnesses may be linked to psoriasis. Although psoriasis has no proven treatment, care must strive by treating patients as soon as the disease surfaces, finding and preventing concurrent multimorbidity, recognising and reducing bodily and psychological distress, requiring behavioural modifications, and treating each patient individually. Biomarkers are traits that are assessed at any time along the clinical continuum, from the early stages of a disease through the beginning of treatment (the foundation of precision medicine) to the late stages of treatment (outcomes and endpoints). Systemic therapies that are frequently used to treat psoriasis provide a variety of outcomes. Targeted therapy selection, better patient outcomes, and more cost-effective healthcare would be made possible by biomarkers that reliably predict effectiveness and safety. This review is an attempt to understand the role of Antimicrobial peptides (AMP), Interleukin-38 (IL-38), autophagy 5 (ATG5) protein and squamous cell carcinoma antigen (SCCA) as biomarkers of psoriasis.
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Affiliation(s)
- Japneet Singh Purewal
- Department of Pharmacology, Toxicology and Therapeutics, SVKM's Dr Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, India
| | - Gaurav Mahesh Doshi
- Department of Pharmacology, Toxicology and Therapeutics, SVKM's Dr Bhanuben Nanavati College of Pharmacy, V.M. Road, Vile Parle (W), Mumbai, India
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16
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Xiao S, Kuang C. Identification of crucial genes that induce coronary atherosclerosis through endothelial cell dysfunction in AMI-identifying hub genes by WGCNA. Am J Transl Res 2022; 14:8166-8174. [PMID: 36505315 PMCID: PMC9730117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/30/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To identify the most relevant genes of cardiovascular disease in acute myocardial infarction patients using weighted gene co-expression network analysis (WGCNA). METHODS The microarray dataset of GSE66360 was downloaded from the Gene Expression Omnibus (GEO) website. The differential genes with adjusted P < 0.05 and |log2 fold change (FC)| > 0.5 were included in the analysis. The weighed gene co-expression network analysis (WGCNA) was used to build a gene co-expression network and identify the most significant module. Cytoscape was used to filter the hub genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for the hub genes. The key genes were defined as having high statistical and biological significance. RESULTS A total of 4751 differentially expressed genes (DEGs) were screened from the dataset. The purple module had the highest significance in AMI. There were 47 hub genes identified from the module. The GO terms "amyloid beta protein metabolism" and "carbohydrate metabolism" and the KEGG terms "phagosome-related pathways" and "Staphylococcus aureus-associated pathways" were the pathways strongly enriched in AMI. Fatty acid translocase cluster of differentiation (CD36), formyl peptide receptor type 2 (FPR2), integrin subunit alpha M (ITGAM), and oxidized low density lipoprotein receptor 1 (OLR1) were considered key genes in AMI. CONCLUSION Our research suggested that the underlying mechanism was related to inflammation and lipid formation. The hub genes identified were CD36, FPR2, ITGAM, and OLR1.
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17
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Jerjen R, Nikpour M, Krieg T, Denton CP, Saracino AM. Systemic sclerosis in adults. Part I: Clinical features and pathogenesis. J Am Acad Dermatol 2022; 87:937-954. [PMID: 35131402 DOI: 10.1016/j.jaad.2021.10.065] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/06/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
Systemic sclerosis (SSc), also referred to as systemic scleroderma or scleroderma, is a rare, complex immune-mediated connective tissue disease characterized by progressive skin fibrosis and other clinically heterogenous features. The etiopathogenesis of SSc involves vasculopathy and immune system dysregulation occurring on a permissive genetic and epigenetic background, ultimately leading to fibrosis. Recent developments in our understanding of disease-specific autoantibodies and bioinformatic analyses has led to a reconsideration of the purely clinical classification of diffuse and limited cutaneous SSc subgroups. Autoantibody profiles are predictive of skin and internal organ involvement and disease course. Early diagnosis of SSc, with commencement of disease-modifying treatment, has the potential to improve patient outcomes. In SSc, many of the clinical manifestations that present early signs of disease progression and activity are cutaneous, meaning dermatologists can and should play a key role in the diagnosis and management of this significant condition. The first article in this continuing medical education series discusses the epidemiology, clinical characteristics, and pathogenesis of SSc in adults, with an emphasis on skin manifestations, the important role of dermatologists in recognizing these, and their correlation with systemic features and disease course.
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Affiliation(s)
- Rebekka Jerjen
- Department of Dermatology, The Alfred Hospital, Melbourne, Australia
| | - Mandana Nikpour
- Department of Rheumatology, St Vincent's Hospital, Melbourne, Australia; Department of Medicine, The University of Melbourne, Melbourne, Australia
| | - Thomas Krieg
- Department Dermatology and Translational Matrix Biology, CMMC and CECAD, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Christopher P Denton
- Division of Medicine, Centre for Rheumatology and Connective Tissues Diseases, University College London, London, United Kingdom; Department of Rheumatology, Royal Free NHS Foundation Trust, London, United Kingdom
| | - Amanda M Saracino
- Department of Dermatology, The Alfred Hospital, Melbourne, Australia; Department of Medicine, Monash University, Melbourne, Australia.
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18
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Recent advances in elucidating the genetic basis of systemic sclerosis. Curr Opin Rheumatol 2022; 34:295-301. [PMID: 35979692 DOI: 10.1097/bor.0000000000000897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Systemic sclerosis (SSc) is a complex autoimmune disorder that affects the connective tissue and causes severe vascular damage and fibrosis of the skin and internal organs. There are recent advances in the field that apply novel methods to high throughput genotype information of thousands of patients with SSc and provide promising results towards the use of genomic data to help SSc diagnosis and clinical care. RECENT FINDINGS This review addresses the development of the first SSc genomic risk score, which can contribute to differentiating SSc patients from healthy controls and other immune-mediated diseases. Moreover, we explore the implementation of data mining strategies on the results of genome-wide association studies to highlight subtype-specific HLA class II associations and a strong association of the HLA class I locus with SSc for the first time. Finally, the combination of genomic data with transcriptomics informed drug repurposing and genetic association studies in well characterized SSc patient cohorts identified markers of severe complications of the disease. SUMMARY Early diagnosis and clinical management of SSc and SSc-related complications are still challenging for rheumatologists. The development of predictive models and tools using genotype data may help to finally deliver personalized clinical care and treatment for patients with SSc in the near future.
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19
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McCord JJ, Engavale M, Masoumzadeh E, Villarreal J, Mapp B, Latham MP, Keyel PA, Sutton RB. Structural features of Dnase1L3 responsible for serum antigen clearance. Commun Biol 2022; 5:825. [PMID: 35974043 PMCID: PMC9381713 DOI: 10.1038/s42003-022-03755-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/22/2022] [Indexed: 11/09/2022] Open
Abstract
Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 cannot rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are key structural differences between the two enzymes. First, Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. Second, the CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.
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Affiliation(s)
- Jon J McCord
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Minal Engavale
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Elahe Masoumzadeh
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Johanna Villarreal
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA
| | - Britney Mapp
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - Michael P Latham
- Texas Tech University, Dept. of Chemistry & Biochemistry, Lubbock, TX, USA
| | - Peter A Keyel
- Texas Tech University, Dept. of Biological Sciences, Lubbock, TX, USA
| | - R Bryan Sutton
- Texas Tech University Health Sciences Center, Dept of Cell Physiology and Molecular Biophysics, Lubbock, TX, USA.
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20
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Hanson AL, Sahhar J, Ngian GS, Roddy J, Walker J, Stevens W, Nikpour M, Assassi S, Proudman S, Mayes MD, Kenna TJ, Brown MA. Contribution of HLA and KIR Alleles to Systemic Sclerosis Susceptibility and Immunological and Clinical Disease Subtypes. Front Genet 2022; 13:913196. [PMID: 35754823 PMCID: PMC9214260 DOI: 10.3389/fgene.2022.913196] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/03/2022] [Indexed: 01/24/2023] Open
Abstract
Systemic sclerosis (SSc) is an autoinflammatory, fibrotic condition of unknown aetiology. The presence of detectable autoantibodies against diverse nuclear antigens, as well as strong HLA associations with disease, suggest autoimmune involvement, however the links between endogenous and exogenous risk factors and SSc pathology remain undetermined. We have conducted a genetic analysis of HLA inheritance in two independent and meta-analysed cohorts of 1,465 SSc cases and 13,273 controls, including stratified association analyses in clinical and autoantibody positive subgroups of disease. Additionally, we have used patient genotypes to impute gene dosages across the KIR locus, encoding paired activating and inhibitory lymphocyte receptors for Class I HLA ligands, to conduct the largest analysis of KIR-HLA epistatic interactions in SSc to date. We confirm previous Class II HLA associations with SSc risk and report a new Class I association with haplotype HLA-B*44:03-HLA-C*16:01 at genome-wide significance (GWS). We further report statistically significant HLA associations with clinical and serological subtypes of disease through direct case-case comparison, and report a new association of HLA-DRB1*15:01, previously shown to bind topoisomerase-1 derived peptides, with anti-topoisomerase (ATA) positive disease. Finally, we identify genetic epistasis between KIRs and HLA class I ligands, suggesting genetic modulation of lymphocyte activation may further contribute to an individual’s underlying disease risk. Taken together, these findings support future functional investigation into endogenous immunological and environmental stimuli for disrupted immune tolerance in SSc.
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Affiliation(s)
- Aimee L Hanson
- Department of Medicine, University of Queensland, Brisbane, QLD, Australia.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Joanne Sahhar
- Department of Medicine, Clayton and Monash Health, Monash University, Melbourne, VIC, Australia
| | - Gene-Siew Ngian
- Department of Medicine, Clayton and Monash Health, Monash University, Melbourne, VIC, Australia
| | - Janet Roddy
- Department of Rheumatology, Royal Perth Hospital, Perth, WA, Australia
| | - Jennifer Walker
- Rheumatology Unit, Flinders Medical Centre, Adelaide, SA, Australia
| | - Wendy Stevens
- Department of Medicine, University of Melbourne, St Vincent's Hospital, Melbourne, VIC, Australia.,Department of Rheumatology, St Vincent's Hospital, Melbourne, VIC, Australia
| | - Mandana Nikpour
- Department of Medicine, University of Melbourne, St Vincent's Hospital, Melbourne, VIC, Australia.,Department of Rheumatology, St Vincent's Hospital, Melbourne, VIC, Australia
| | - Shervin Assassi
- Division of Rheumatology, University of Texas, Houston, TX, United States
| | - Susanna Proudman
- Rheumtology Unit, Royal Adelaide Hospital, Adelaide, SA, Australia.,Discipline of Medicine, University of Adelaide, Adelaide, SA, Australia
| | - Maureen D Mayes
- Division of Rheumatology, University of Texas, Houston, TX, United States
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Matthew A Brown
- Genomics England, Charterhouse Square, London, United Kingdom.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
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21
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Ortíz-Fernández L, Martín J, Alarcón-Riquelme ME. A Summary on the Genetics of Systemic Lupus Erythematosus, Rheumatoid Arthritis, Systemic Sclerosis, and Sjögren's Syndrome. Clin Rev Allergy Immunol 2022; 64:392-411. [PMID: 35749015 DOI: 10.1007/s12016-022-08951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, and Sjögren's syndrome are four major autoimmune rheumatic diseases characterized by the presence of autoantibodies, caused by a dysregulation of the immune system that leads to a wide variety of clinical manifestations. These conditions present complex etiologies strongly influenced by multiple environmental and genetic factors. The human leukocyte antigen (HLA) region was the first locus identified to be associated and still represents the strongest susceptibility factor for each of these conditions, particularly the HLA class II genes, including DQA1, DQB1, and DRB1, but class I genes have also been associated. Over the last two decades, the genetic component of these disorders has been extensively investigated and hundreds of non-HLA risk genetic variants have been uncovered. Furthermore, it is widely accepted that autoimmune rheumatic diseases share molecular disease pathways, such as the interferon (IFN) type I pathways, which are reflected in a common genetic background. Some examples of well-known pleiotropic loci for autoimmune rheumatic diseases are the HLA region, DNASEL13, TNIP1, and IRF5, among others. The identification of the causal molecular mechanisms behind the genetic associations is still a challenge. However, recent advances have been achieved through mouse models and functional studies of the loci. Here, we provide an updated overview of the genetic architecture underlying these four autoimmune rheumatic diseases, with a special focus on the HLA region.
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Affiliation(s)
- Lourdes Ortíz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av de la Ilustración 114, Parque Tecnológico de La Salud, 18016, Granada, Spain. .,Institute for Environmental Medicine, Karolinska Institutet, 171 77, Solna, Sweden.
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22
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Liu Y, Cheng L, Zhan H, Li H, Li X, Huang Y, Li Y. The Roles of Noncoding RNAs in Systemic Sclerosis. Front Immunol 2022; 13:856036. [PMID: 35464474 PMCID: PMC9024074 DOI: 10.3389/fimmu.2022.856036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Noncoding RNAs (ncRNAs) constitute more than 90% of the RNAs in the human genome. In the past decades, studies have changed our perception of ncRNAs from “junk” transcriptional products to functional regulatory molecules that mediate critical processes, including chromosomal modifications, mRNA splicing and stability, and translation, as well as key signaling pathways. Emerging evidence suggests that ncRNAs are abnormally expressed in not only cancer but also autoimmune diseases, such as systemic sclerosis (SSc), and may serve as novel biomarkers and therapeutic targets for the diagnosis and treatment of SSc. However, the functions and underlying mechanisms of ncRNAs in SSc remain incompletely understood. In this review, we discuss the current findings on the biogenetic processes and functions of ncRNAs, including microRNAs and long noncoding RNAs, as well as explore emerging ncRNA-based diagnostics and therapies for SSc.
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Affiliation(s)
- Yongmei Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linlin Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haoting Zhan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xiaomeng Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yuan Huang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- *Correspondence: Yongzhe Li,
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23
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Scofield RH, Lewis VM, Cavitt J, Kurien BT, Assassi S, Martin J, Gorlova O, Gregersen P, Lee A, Rider LG, O'Hanlon T, Rothwell S, Lilleker J, Kochi Y, Terao C, Igoe A, Stevens W, Sahhar J, Roddy J, Rischmueller M, Lester S, Proudman S, Chen S, Brown MA, Mayes MD, Lamb JA, Miller FW. 47XXY and 47XXX in Scleroderma and Myositis. ACR Open Rheumatol 2022; 4:528-533. [PMID: 35352506 PMCID: PMC9190224 DOI: 10.1002/acr2.11413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 01/05/2023] Open
Abstract
Objective We undertook this study to examine the X chromosome complement in participants with systemic sclerosis (SSc) as well as idiopathic inflammatory myopathies. Methods The participants met classification criteria for the diseases. All participants underwent single‐nucleotide polymorphism typing. We examined X and Y single‐nucleotide polymorphism heterogeneity to determine the number of X chromosomes. For statistical comparisons, we used χ2 analyses with calculation of 95% confidence intervals. Results Three of seventy men with SSc had 47,XXY (P = 0.0001 compared with control men). Among the 435 women with SSc, none had 47,XXX. Among 709 men with polymyositis or dermatomyositis (PM/DM), seven had 47,XXY (P = 0.0016), whereas among the 1783 women with PM/DM, two had 47,XXX. Of 147 men with inclusion body myositis (IBM), six had 47,XXY, and 1 of the 114 women with IBM had 47,XXX. For each of these myositis disease groups, the excess 47,XXY and/or 47,XXX was significantly higher compared with in controls as well as the known birth rate of Klinefelter syndrome or 47,XXX. Conclusion Klinefelter syndrome (47,XXY) is associated with SSc and idiopathic inflammatory myopathies, similar to other autoimmune diseases with type 1 interferon pathogenesis, namely, systemic lupus erythematosus and Sjögren syndrome.
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Affiliation(s)
- R Hal Scofield
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Valerie M Lewis
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Joshua Cavitt
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Biji T Kurien
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Shervin Assassi
- University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, PTS, Granada, Spain
| | - Olga Gorlova
- Geisel School of Medicine, Dartmouth College and Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Peter Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Annette Lee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Lisa G Rider
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
| | - Terrance O'Hanlon
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
| | | | - James Lilleker
- School of Biological Sciences, The University of Manchester, Manchester, UK, and Salford Royal National Health Service Foundation Trust, Salford, UK
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- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Tokyo, Japan, and RIKEN Center for Integrative Medical Sciences, Tokyo Medical and Dental University, Yokohama, Japan
| | - Chikacshi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan, and Shizuoka General Hospital and School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Ann Igoe
- Oklahoma Medical Research Foundation, Oklahoma City
| | - Wendy Stevens
- St. Vincent's Hospital, Melbourne, Victoria, Australia
| | - Joanne Sahhar
- Monash Medical Centre, Melbourne, Victoria, Australia
| | - Janet Roddy
- Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Maureen Rischmueller
- The Queen Elizabeth Hospital and University of Adelaide, Woodville, South Australia, Australia
| | - Sue Lester
- The Queen Elizabeth Hospital and University of Adelaide, Woodville, South Australia, Australia
| | | | - Sixia Chen
- College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City
| | - Matthew A Brown
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Maureen D Mayes
- University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | | | - Frederick W Miller
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
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Harley ITW, 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: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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 (HI(3)), 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.
| | - 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.
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25
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Sun J, Lyu R, Deng L, Li Q, Zhao Y, Zhang Y. SMetABF: A rapid algorithm for Bayesian GWAS meta-analysis with a large number of studies included. PLoS Comput Biol 2022; 18:e1009948. [PMID: 35286307 PMCID: PMC8947622 DOI: 10.1371/journal.pcbi.1009948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 03/24/2022] [Accepted: 02/21/2022] [Indexed: 12/15/2022] Open
Abstract
Bayesian methods are widely used in the GWAS meta-analysis. But the considerable consumption in both computing time and memory space poses great challenges for large-scale meta-analyses. In this research, we propose an algorithm named SMetABF to rapidly obtain the optimal ABF in the GWAS meta-analysis, where shotgun stochastic search (SSS) is introduced to improve the Bayesian GWAS meta-analysis framework, MetABF. Simulation studies confirm that SMetABF performs well in both speed and accuracy, compared to exhaustive methods and MCMC. SMetABF is applied to real GWAS datasets to find several essential loci related to Parkinson's disease (PD) and the results support the underlying relationship between PD and other autoimmune disorders. Developed as an R package and a web tool, SMetABF will become a useful tool to integrate different studies and identify more variants associated with complex traits.
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Affiliation(s)
- Jianle Sun
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ruiqi Lyu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Luojia Deng
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qianwen Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Zhao
- Department of Biostatistics, Nanjing Medical University School of Public Health, Nanjing, Jiangsu, China
- * E-mail: (YAZ); (YUZ)
| | - Yue Zhang
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (YAZ); (YUZ)
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26
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Sirasanagandla SR, Sofin RS, Al-Huseini I, Das S. Role of Bisphenol A in Autophagy Modulation: Understanding the Molecular Concepts and Therapeutic Options. Mini Rev Med Chem 2022; 22:2213-2223. [DOI: 10.2174/1389557522666220214094055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/05/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
Abstract:
Bisphenol A (4,4′-isopropylidenediphenol) is an organic compound, commonly used in the plastic bottles, packaging containers, beverages and resin industry. The adverse effects of bisphenol A were studied in various systems of the body. Autophagy is a lysosomal degradation process meant for the regeneration of new cells. The role of bisphenol A on autophagy modulation in the pathogenesis of diseases is still debatable. Few research studies showed that bisphenol A-induced adverse effects were associated with autophagy dysregulation, while few showed the activation of autophagy by bisphenol A. Such contrasting views make the subject more interesting and debatable. In the present review, we discuss the different steps of autophagy, genes involved, and the effect of bisphenol A in autophagy modulation on different systems of the body. We also discuss the methods for monitoring autophagy and the roles of drugs such as chloroquine, verteporfin, and rapamycin in autophagy. Proper understanding of the role of bisphenol A in the modulation of autophagy may be important for future treatment and drug discovery.
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Affiliation(s)
- Srinivasa Rao Sirasanagandla
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - R.G. Sumesh Sofin
- Department of Physics, College of Science, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - Isehaq Al-Huseini
- Department of Physiology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
| | - Srijit Das
- Department of Human and Clinical Anatomy, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Al-Khodh 123, Oman
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27
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Huang D, Ovcharenko I. Enhancer-silencer transitions in the human genome. Genome Res 2022; 32:437-448. [PMID: 35105669 PMCID: PMC8896465 DOI: 10.1101/gr.275992.121] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/27/2022] [Indexed: 11/24/2022]
Abstract
Dual-function regulatory elements (REs), acting as enhancers in some cellular contexts and as silencers in others, have been reported to facilitate the precise gene regulatory response to developmental signals in Drosophila melanogaster. However, with few isolated examples detected, dual-function REs in mammals have yet to be systematically studied. We herein investigated this class of REs in the human genome and profiled their activity across multiple cell types. Focusing on enhancer–silencer transitions specific to the development of T cells, we built an accurate deep learning classifier of REs and identified about 12,000 silencers active in primary peripheral blood T cells that act as enhancers in embryonic stem cells. Compared with regular silencers, these dual-function REs are evolving under stronger purifying selection and are enriched for mutations associated with disease phenotypes and altered gene expression. In addition, they are enriched in the loci of transcriptional regulators, such as transcription factors (TFs) and chromatin remodeling genes. Dual-function REs consist of two intertwined but largely distinct sets of binding sites bound by either activating or repressing TFs, depending on the type of RE function in a given cell line. This indicates the recruitment of different TFs for different regulatory modes and a complex DNA sequence composition of these REs with dual activating and repressive encoding. With an estimated >6% of cell type–specific human silencers acting as dual-function REs, this overlooked class of REs requires a specific investigation on how their inherent functional plasticity might be a contributing factor to human diseases.
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28
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The Immunogenetics of Systemic Sclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1367:259-298. [DOI: 10.1007/978-3-030-92616-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Pu W, Zhang R, Ma Y, Liu Q, Jiang S, Liu J, Zhao Y, Tu W, Guo G, Zuo X, Wang Q, Chen Y, Wu W, Zhou X, Distler JHW, Reveille JD, Zou H, Jin L, Mayes MD, Wang J. Genetic associations of non-MHC susceptibility loci with systemic sclerosis in a Han Chinese population. J Invest Dermatol 2021; 142:2039-2042.e7. [PMID: 34919939 DOI: 10.1016/j.jid.2021.11.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 11/16/2021] [Accepted: 11/30/2021] [Indexed: 10/19/2022]
Affiliation(s)
- Weilin Pu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences
| | - Rui Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Institute for Six-sector Economy, Fudan University, Shanghai, 200433, China
| | - Yanyun Ma
- Institute for Six-sector Economy, Fudan University, Shanghai, 200433, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences
| | - Qingmei Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China; MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
| | - Shuai Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jing Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yinhuan Zhao
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Wenzhen Tu
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Gang Guo
- Department of Rheumatology, Yiling Hospital, Shijiazhuang, China
| | - Xiaoxia Zuo
- Department of Rheumatology, Xiangya Hospital, Central South University
| | - Qingwen Wang
- Rheumatology and Immunology Department, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuanyuan Chen
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Wenyu Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China; Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Xiaodong Zhou
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, TX, USA
| | - Jörg H W Distler
- Department of Internal Medicine 3 and Institute for Clinical Immunology, University of Erlangen, Nuremberg, Germany
| | - John D Reveille
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, TX, USA
| | - Hejian Zou
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China; Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, TX, USA
| | - Jiucun Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences; Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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30
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Shen CY, Lu CH, Wu CH, Li KJ, Kuo YM, Hsieh SC, Yu CL. Molecular Basis of Accelerated Aging with Immune Dysfunction-Mediated Inflammation (Inflamm-Aging) in Patients with Systemic Sclerosis. Cells 2021; 10:cells10123402. [PMID: 34943909 PMCID: PMC8699891 DOI: 10.3390/cells10123402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/17/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Systemic sclerosis (SSc) is a chronic connective tissue disorder characterized by immune dysregulation, chronic inflammation, vascular endothelial cell dysfunction, and progressive tissue fibrosis of the skin and internal organs. Moreover, increased cancer incidence and accelerated aging are also found. The increased cancer incidence is believed to be a result of chromosome instability. Accelerated cellular senescence has been confirmed by the shortening of telomere length due to increased DNA breakage, abnormal DNA repair response, and telomerase deficiency mediated by enhanced oxidative/nitrative stresses. The immune dysfunctions of SSc patients are manifested by excessive production of proinflammatory cytokines IL-1, IL-6, IL-17, IFN-α, and TNF-α, which can elicit potent tissue inflammation followed by tissue fibrosis. Furthermore, a number of autoantibodies including anti-topoisomerase 1 (anti-TOPO-1), anti-centromere (ACA or anti-CENP-B), anti-RNA polymerase enzyme (anti-RNAP III), anti-ribonuclear proteins (anti-U1, U2, and U11/U12 RNP), anti-nucleolar antigens (anti-Th/T0, anti-NOR90, anti-Ku, anti-RuvBL1/2, and anti-PM/Scl), and anti-telomere-associated proteins were also found. Based on these data, inflamm-aging caused by immune dysfunction-mediated inflammation exists in patients with SSc. Hence, increased cellular senescence is elicited by the interactions among excessive oxidative stress, pro-inflammatory cytokines, and autoantibodies. In the present review, we will discuss in detail the molecular basis of chromosome instability, increased oxidative stress, and functional adaptation by deranged immunome, which are related to inflamm-aging in patients with SSc.
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Affiliation(s)
- Chieh-Yu Shen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Cheng-Hsun Lu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Cheng-Han Wu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Ko-Jen Li
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
| | - Yu-Min Kuo
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Song-Chou Hsieh
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Correspondence: (S.-C.H.); (C.-L.Y.); Tel.: +886-2-23123456 (S.-C.H. & C.-L.Y.)
| | - Chia-Li Yu
- Department of Internal Medicine, National Taiwan University Hospital, Taipei 10002, Taiwan; (C.-Y.S.); (C.-H.L.); (C.-H.W.); (K.-J.L.); (Y.-M.K.)
- Correspondence: (S.-C.H.); (C.-L.Y.); Tel.: +886-2-23123456 (S.-C.H. & C.-L.Y.)
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31
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Wen X, Yang Y, Klionsky DJ. Moments in autophagy and disease: Past and present. Mol Aspects Med 2021; 82:100966. [PMID: 33931245 PMCID: PMC8548407 DOI: 10.1016/j.mam.2021.100966] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/13/2021] [Accepted: 04/19/2021] [Indexed: 01/18/2023]
Abstract
Over the past several decades, research on autophagy, a highly conserved lysosomal degradation pathway, has been advanced by studies in different model organisms, especially in the field of its molecular mechanism and regulation. The malfunction of autophagy is linked to various diseases, among which cancer and neurodegenerative diseases are the major focus. In this review, we cover some other important diseases, including cardiovascular diseases, infectious and inflammatory diseases, and metabolic disorders, as well as rare diseases, with a hope of providing a more complete understanding of the spectrum of autophagy's role in human health.
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Affiliation(s)
- Xin Wen
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ying Yang
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Daniel J Klionsky
- Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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32
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Hinchcliff M, Garcia-Milian R, Di Donato S, Dill K, Bundschuh E, Galdo FD. Cellular and Molecular Diversity in Scleroderma. Semin Immunol 2021; 58:101648. [PMID: 35940960 DOI: 10.1016/j.smim.2022.101648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
With the increasing armamentarium of high-throughput tools available at manageable cost, it is attractive and informative to determine the molecular underpinnings of patient heterogeneity in systemic sclerosis (SSc). Given the highly variable clinical outcomes of patients labelled with the same diagnosis, unravelling the cellular and molecular basis of disease heterogeneity will be crucial to predicting disease risk, stratifying management and ultimately informing a patient-centered precision medicine approach. Herein, we summarise the findings of the past several years in the fields of genomics, transcriptomics, and proteomics that contribute to unraveling the cellular and molecular heterogeneity of SSc. Expansion of these findings and their routine integration with quantitative analysis of histopathology and imaging studies into clinical care promise to inform a scientifically driven patient-centred personalized medicine approach to SSc in the near future.
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Affiliation(s)
- Monique Hinchcliff
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA.
| | | | - Stefano Di Donato
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK
| | | | - Elizabeth Bundschuh
- Yale School of Medicine, Department of Internal Medicine, Section of Rheumatology, Allergy & Immunology, USA
| | - Francesco Del Galdo
- Raynaud's and Scleroderma Programme, Leeds Institute of Rheumatic and Musculoskeletal Medicine and NIHR Biomedical Research Centre, University of Leeds, UK.
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33
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Acosta-Herrera M, Kerick M, Lopéz-Isac E, Assassi S, Beretta L, Simeón-Aznar CP, Ortego-Centeno N, Proudman SM, Hunzelmann N, Moroncini G, de Vries-Bouwstra JK, Orozco G, Barton A, Herrick AL, Terao C, Allanore Y, Brown MA, Radstake TR, Fonseca C, Denton CP, Mayes MD, Martin J. Comprehensive analysis of the major histocompatibility complex in systemic sclerosis identifies differential HLA associations by clinical and serological subtypes. Ann Rheum Dis 2021; 80:1040-1047. [PMID: 34096881 PMCID: PMC8292594 DOI: 10.1136/annrheumdis-2021-219884] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [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: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The greatest genetic effect reported for systemic sclerosis (SSc) lies in the major histocompatibility complex (MHC) locus. Leveraging the largest SSc genome-wide association study, we aimed to fine-map this region to identify novel human leucocyte antigen (HLA) genetic variants associated with SSc susceptibility and its main clinical and serological subtypes. METHODS 9095 patients with SSc and 17 584 controls genome-wide genotyped were used to impute and test single-nucleotide polymorphisms (SNPs) across the MHC, classical HLA alleles and their composite amino acid residues. Additionally, patients were stratified according to their clinical and serological status, namely, limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), anticentromere (ACA), antitopoisomerase (ATA) and anti-RNApolIII autoantibodies (ARA). RESULTS Sequential conditional analyses showed nine SNPs, nine classical alleles and seven amino acids that modelled the observed associations with SSc. This confirmed previously reported associations with HLA-DRB1*11:04 and HLA-DPB1*13:01, and revealed a novel association of HLA-B*08:01. Stratified analyses showed specific associations of HLA-DQA1*02:01 with lcSSc, and an exclusive association of HLA-DQA1*05:01 with dcSSc. Similarly, private associations were detected in HLA-DRB1*08:01 and confirmed the previously reported association of HLA-DRB1*07:01 with ACA-positive patients, as opposed to the HLA-DPA1*02:01 and HLA-DQB1*03:01 alleles associated with ATA presentation. CONCLUSIONS This study confirms the contribution of HLA class II and reveals a novel association of HLA class I with SSc, suggesting novel pathways of disease pathogenesis. Furthermore, we describe specific HLA associations with SSc clinical and serological subtypes that could serve as biomarkers of disease severity and progression.
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Affiliation(s)
- Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Elena Lopéz-Isac
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Shervin Assassi
- Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | | | - Susanna M Proudman
- Department of Rheumatology, Royal Adelaide Hospital, Adelaide, Victoria, Australia
| | | | - Gianluca Moroncini
- Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | | | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ariane L Herrick
- Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yannick Allanore
- Department of Rheumatology A, Hospital Cochin, Paris, Île-de-France, France
| | - Matthew A Brown
- NIHR Biomedical Research Centre, Guy's and Saint Thomas' NHS Foundation Trust and King's College, London, UK
| | - Timothy Rdj Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Maureen D Mayes
- Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
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Liu C, Yan S, Chen H, Wu Z, Li L, Cheng L, Li H, Li Y. Association of GTF2I, NFKB1, and TYK2 Regional Polymorphisms With Systemic Sclerosis in a Chinese Han Population. Front Immunol 2021; 12:640083. [PMID: 34248934 PMCID: PMC8261294 DOI: 10.3389/fimmu.2021.640083] [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: 12/10/2020] [Accepted: 06/07/2021] [Indexed: 12/03/2022] Open
Abstract
Objectives Systemic sclerosis (SSc) is an uncommon autoimmune disease that varies with ethnicity. Single nucleotide polymorphisms (SNPs) in the GTFSI, NFKB1, and TYK2 genes have been reported to be associated with SSc in other populations and in individuals with various autoimmune diseases. This study aimed to investigate the association between these SNPs and susceptibility to SSc in a Chinese Han population. Method A case-control study was performed in 343 patients with SSc and 694 ethnically matched healthy controls. SNPs in GTF2I, NFKB1, and TYK2 were genotyped using a Sequenom MassArray iPLEX system. Association analyses were performed using PLINK v1.90 software. Result Our study demonstrated that the GTF2I rs117026326 T allele and the GTF2I rs73366469 C allele were strongly associated with patients with SSc (P = 6.97E-10 and P = 1.33E-08, respectively). Patients carrying the GTF2I rs117026326 TT genotype and the GTF2I rs73366469 CC genotype had a strongly increased risk of SSc (P = 6.25E-09 and P = 1.67E-08, respectively), and those carrying the NFKB1 rs1599961 AA genotype had a suggestively significantly increased risk of SSc (P = 0.014). Moreover, rs117026326 and rs73366469 were associated with SSc in different genetic models (additive model, dominant model, and recessive model) (P < 0.05) whereas rs1599961 was associated with SSc in the dominant genetic model but not in the addictive and recessive models (P = 0.0026). TYK2 rs2304256 was not significantly associated with SSc in this study. Conclusion GTF2I rs117026326 and rs73366469 SNPs were strongly associated with SSc in this Chinese Han population. NFKB1 rs1599961 showed a suggestive association with SSc, and no significant association was found between TYK2 rs2304256 and SSc in this Chinese Han population.
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Affiliation(s)
- Chenxi Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Songxin Yan
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haizhen Chen
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.,Department of Clinical Laboratory, The First Hospital of Jilin University, Jilin, China
| | - Ziyan Wu
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Liubing Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Linlin Cheng
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Haolong Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yongzhe Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Ota Y, Kuwana M. Updates on genetics in systemic sclerosis. Inflamm Regen 2021; 41:17. [PMID: 34130729 PMCID: PMC8204536 DOI: 10.1186/s41232-021-00167-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/24/2021] [Indexed: 12/15/2022] Open
Abstract
Systemic sclerosis (SSc) is a complex disease, in which an interaction of genetic and environmental factors plays an important role in its development and pathogenesis. A number of genetic studies, including candidate gene analysis and genome-wide association study, have found that the associated genetic variants are mainly localized in noncoding regions in the expression quantitative trait locus and influence corresponding gene expression. The gene variants identified as a risk for SSc susceptibility include those associated with innate immunity, adaptive immune response, and cell death, while there are only few SSc-associated genes involved in the fibrotic process or vascular homeostasis. Human leukocyte antigen class II genes are associated with SSc-related autoantibodies rather than SSc itself. Since the pathways between the associated genotype and phenotype are still poorly understood, further investigations using multi-omics technologies are necessary to characterize the complex molecular architecture of SSc, identify biomarkers useful to predict future outcomes and treatment responses, and discover effective drug targets.
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Affiliation(s)
- Yuko Ota
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8603-8582, Japan
| | - Masataka Kuwana
- Department of Allergy and Rheumatology, Nippon Medical School Graduate School of Medicine, 1-1-5 Sendagi, Bunkyo-ku, Tokyo, 113-8603-8582, Japan.
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A Literature-Derived Knowledge Graph Augments the Interpretation of Single Cell RNA-seq Datasets. Genes (Basel) 2021; 12:genes12060898. [PMID: 34200671 PMCID: PMC8229796 DOI: 10.3390/genes12060898] [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: 03/31/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 01/05/2023] Open
Abstract
Technology to generate single cell RNA-sequencing (scRNA-seq) datasets and tools to annotate them have advanced rapidly in the past several years. Such tools generally rely on existing transcriptomic datasets or curated databases of cell type defining genes, while the application of scalable natural language processing (NLP) methods to enhance analysis workflows has not been adequately explored. Here we deployed an NLP framework to objectively quantify associations between a comprehensive set of over 20,000 human protein-coding genes and over 500 cell type terms across over 26 million biomedical documents. The resultant gene-cell type associations (GCAs) are significantly stronger between a curated set of matched cell type-marker pairs than the complementary set of mismatched pairs (Mann Whitney p = 6.15 × 10−76, r = 0.24; cohen’s D = 2.6). Building on this, we developed an augmented annotation algorithm (single cell Annotation via Literature Encoding, or scALE) that leverages GCAs to categorize cell clusters identified in scRNA-seq datasets, and we tested its ability to predict the cellular identity of 133 clusters from nine datasets of human breast, colon, heart, joint, ovary, prostate, skin, and small intestine tissues. With the optimized settings, the true cellular identity matched the top prediction in 59% of tested clusters and was present among the top five predictions for 91% of clusters. scALE slightly outperformed an existing method for reference data driven automated cluster annotation, and we demonstrate that integration of scALE can meaningfully improve the annotations derived from such methods. Further, contextualization of differential expression analyses with these GCAs highlights poorly characterized markers of well-studied cell types, such as CLIC6 and DNASE1L3 in retinal pigment epithelial cells and endothelial cells, respectively. Taken together, this study illustrates for the first time how the systematic application of a literature-derived knowledge graph can expedite and enhance the annotation and interpretation of scRNA-seq data.
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Kerick M, González-Serna D, Carnero-Montoro E, Teruel M, Acosta-Herrera M, Makowska Z, Buttgereit A, Babaei S, Barturen G, López-Isac E, Lesche R, Beretta L, Alarcon-Riquelme ME, Martin J. Expression Quantitative Trait Locus Analysis in Systemic Sclerosis Identifies New Candidate Genes Associated With Multiple Aspects of Disease Pathology. Arthritis Rheumatol 2021; 73:1288-1300. [PMID: 33455083 DOI: 10.1002/art.41657] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/12/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE To identify the genetic variants that affect gene expression (expression quantitative trait loci [eQTLs]) in systemic sclerosis (SSc) and to investigate their role in the pathogenesis of the disease. METHODS We performed an eQTL analysis using whole-blood sequencing data from 333 SSc patients and 524 controls and integrated them with SSc genome-wide association study (GWAS) data. We integrated our findings from expression modeling, differential expression analysis, and transcription factor binding site enrichment with key clinical features of SSc. RESULTS We detected 49,123 validated cis-eQTLs from 4,539 SSc-associated single-nucleotide polymorphisms (SNPs) (PGWAS < 10-5 ). A total of 1,436 genes were within 1 Mb of the 4,539 SSc-associated SNPs. Of those 1,436 genes, 565 were detected as having ≥1 eQTL with an SSc-associated SNP. We developed a strategy to prioritize disease-associated genes based on their expression variance explained by SSc eQTLs (r2 > 0.05). As a result, 233 candidates were identified, 134 (58%) of them associated with hallmarks of SSc and 105 (45%) of them differentially expressed in the blood cells, skin, or lung tissue of SSc patients. Transcription factor binding site analysis revealed enriched motifs of 24 transcription factors (5%) among SSc eQTLs, 5 of which were found to be differentially regulated in the blood cells (ELF1 and MGA), skin (KLF4 and ID4), and lungs (TBX4) of SSc patients. Ten candidate genes (4%) can be targeted by approved medications for immune-mediated diseases, of which only 3 have been tested in clinical trials in patients with SSc. CONCLUSION The findings of the present study indicate a new layer to the molecular complexity of SSc, contributing to a better understanding of the pathogenesis of the disease.
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Affiliation(s)
- Martin Kerick
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | | | - Elena Carnero-Montoro
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Maria Teruel
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | | | | | | | | | - Guillermo Barturen
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
| | | | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Marta E Alarcon-Riquelme
- Pfizer-University of Granada-Junta de Andalucía Centre for Genomics and Oncological Research, Granada, Spain
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain
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Osoegawa K, Creary LE, Montero-Martín G, Mallempati KC, Gangavarapu S, Caillier SJ, Santaniello A, Isobe N, Hollenbach JA, Hauser SL, Oksenberg JR, Fernández-Viňa MA. High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. Front Immunol 2021; 12:644838. [PMID: 34211458 PMCID: PMC8240666 DOI: 10.3389/fimmu.2021.644838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from 'hitchhiking' alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Lisa E. Creary
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kalyan C. Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J. Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L. Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Marcelo A. Fernández-Viňa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
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Abstract
PURPOSE OF REVIEW To review susceptibility genes and how they could integrate in systemic sclerosis (SSc) pathophysiology providing insight and perspectives for innovative therapies. RECENT FINDINGS SSc is a rare disease characterized by vasculopathy, dysregulated immunity and fibrosis. Genome-Wide association studies and ImmunoChip studies performed in recent years revealed associated genetic variants mainly localized in noncoding regions and mostly affecting the immune system of SSc patients. Gene variants were described in innate immunity (IRF5, IRF7 and TLR2), T and B cells activation (CD247, TNFAIP3, STAT4 and BLK) and NF-κB pathway (TNFAIP3 and TNIP1) confirming previous biological data. In addition to impacting immune response, CSK, DDX6, DNASE1L3 and GSDMA/B could also act in the vascular and fibrotic components of SSc. SUMMARY Although genetic studies highlighted the dysregulated immune response in SSc, future research must focus on a deeper characterization of these variants with determination of their functional effects. Moreover, the role of these genes or others on specific vasculopathy and fibrosis would provide insight. Establishment of polygenic score or integrated genome approaches could identify new targets specific of SSc clinical features. This will allow physicians to propose new therapies to SSc patients.
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Santa P, Garreau A, Serpas L, Ferriere A, Blanco P, Soni C, Sisirak V. The Role of Nucleases and Nucleic Acid Editing Enzymes in the Regulation of Self-Nucleic Acid Sensing. Front Immunol 2021; 12:629922. [PMID: 33717156 PMCID: PMC7952454 DOI: 10.3389/fimmu.2021.629922] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of microbial nucleic acids by the innate immune system is mediated by numerous intracellular nucleic acids sensors. Upon the detection of nucleic acids these sensors induce the production of inflammatory cytokines, and thus play a crucial role in the activation of anti-microbial immunity. In addition to microbial genetic material, nucleic acid sensors can also recognize self-nucleic acids exposed extracellularly during turn-over of cells, inefficient efferocytosis, or intracellularly upon mislocalization. Safeguard mechanisms have evolved to dispose of such self-nucleic acids to impede the development of autoinflammatory and autoimmune responses. These safeguard mechanisms involve nucleases that are either specific to DNA (DNases) or RNA (RNases) as well as nucleic acid editing enzymes, whose biochemical properties, expression profiles, functions and mechanisms of action will be detailed in this review. Fully elucidating the role of these enzymes in degrading and/or processing of self-nucleic acids to thwart their immunostimulatory potential is of utmost importance to develop novel therapeutic strategies for patients affected by inflammatory and autoimmune diseases.
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Affiliation(s)
- Pauline Santa
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Anne Garreau
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
| | - Lee Serpas
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | | | - Patrick Blanco
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
- Immunology and Immunogenetic Department, Bordeaux University Hospital, Bordeaux, France
| | - Chetna Soni
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Vanja Sisirak
- CNRS-UMR 5164, ImmunoConcEpT, Bordeaux University, Bordeaux, France
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Yaseen B, Lopez H, Taki Z, Zafar S, Rosario H, Abdi BA, Vigneswaran S, Xing F, Arumalla N, Black S, Ahmad S, Kumar K, Gul R, Scolamiero L, Morris S, Bowman A, Stainer A, Rice A, Stock C, Renzoni E, Denton CP, Venturini C, Brown M, O'Reilly S, Stratton R. Interleukin-31 promotes pathogenic mechanisms underlying skin and lung fibrosis in scleroderma. Rheumatology (Oxford) 2021; 59:2625-2636. [PMID: 32365362 DOI: 10.1093/rheumatology/keaa195] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 03/19/2020] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Cytokines released by infiltrating T cells may promote mechanisms leading to fibrosis in scleroderma. The aim of this study was to investigate the role of the Th2 cytokine IL-31, and its receptor IL-31RA, in scleroderma skin and lung fibrosis. METHODS IL-31 was measured by ELISA of plasma, and by immunochemistry of fibrotic skin and lung tissue of scleroderma patients. The receptor, IL-31RA, was assayed by qPCR of tissue resident cells. Next-generation sequencing was used to profile the responses of normal skin fibroblasts to IL-31. In wild-type Balb/c mice, IL-31 was administered by subcutaneous mini pump, with or without additional TGFβ, and the fibrotic reaction measured by histology and ELISA of plasma. RESULTS IL-31 was present at high levels in plasma and fibrotic skin and lung lesions in a subset of scleroderma patients, and the receptor overexpressed by downstream cells relevant to the disease process, including skin and lung fibroblasts, through loss of epigenetic regulation by miR326. In skin fibroblasts, IL-31 induced next generation sequencing profiles associated with cellular growth and proliferation, anaerobic metabolism and mineralization, and negatively associated with angiogenesis and vascular repair, as well as promoting phenotype changes including migration and collagen protein release via pSTAT3, resembling the activation state in the disease. In mice, IL-31 induced skin and lung fibrosis. No synergy was seen with TGFβ, which supressed IL-31RA. CONCLUSION IL-31/IL-31RA is confirmed as a candidate pro-fibrotic pathway, which may contribute to skin and lung fibrosis in a subset of scleroderma patients.
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Affiliation(s)
- Bodoor Yaseen
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Henry Lopez
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK.,MuriGenics, Inc, Vallejo, CA, USA
| | - Zeinab Taki
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Sara Zafar
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Henrique Rosario
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Bahja Ahmed Abdi
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Shivanee Vigneswaran
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Fiona Xing
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Nikita Arumalla
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Simon Black
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Sara Ahmad
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Kimti Kumar
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Rabia Gul
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Laura Scolamiero
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Sian Morris
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | - Alex Bowman
- Department of Respiratory Medicine, Imperial College London, Royal Brompton Campus
| | - Anna Stainer
- Department of Respiratory Medicine, Imperial College London, Royal Brompton Campus
| | - Alexandra Rice
- Department of Respiratory Medicine, Imperial College London, Royal Brompton Campus
| | - Carmel Stock
- Department of Respiratory Medicine, Imperial College London, Royal Brompton Campus
| | - Elisabetta Renzoni
- Department of Respiratory Medicine, Imperial College London, Royal Brompton Campus
| | - Christopher P Denton
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
| | | | - Max Brown
- Department of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Steven O'Reilly
- Department of Health and Life Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Richard Stratton
- Centre for Rheumatology and Connective Tissue Diseases, Royal Free Hospital Campus, University College London Medical School, London, UK
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Coke LN, Wen H, Comeau M, Ghanem MH, Shih A, Metz CN, Li W, Langefeld CD, Gregersen PK, Simpfendorfer KR. Arg206Cys substitution in DNASE1L3 causes a defect in DNASE1L3 protein secretion that confers risk of systemic lupus erythematosus. Ann Rheum Dis 2021; 80:782-787. [PMID: 33455918 PMCID: PMC8142439 DOI: 10.1136/annrheumdis-2020-218810] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES To determine if the polymorphism encoding the Arg206Cys substitution in DNASE1L3 explains the association of the DNASE1L3/PXK gene locus with systemic lupus erythematosus (SLE) and to examine the effect of the Arg206Cys sequence change on DNASE1L3 protein function. METHODS Conditional analysis for rs35677470 was performed on cases and controls with European ancestry from the SLE Immunochip study, and genotype and haplotype frequencies were compared. DNASE1L3 protein levels were measured in cells and supernatants of HEK293 cells and monocyte-derived dendritic cells expressing recombinant and endogenous 206Arg and 206Cys protein variants. RESULTS Conditional analysis on rs35677470 eliminated the SLE risk association signal for lead single-nucleotide polymorphisms (SNPs) rs180977001 and rs73081554, which are found to tag the same risk haplotype as rs35677470. The modest effect sizes of the SLE risk genotypes (heterozygous risk OR=1.14 and homozygous risk allele OR=1.68) suggest some DNASE1L3 endonuclease enzyme function is retained. An SLE protective signal in PXK (lead SNP rs11130643) remained following conditioning on rs35677470. The DNASE1L3 206Cys risk variant maintained enzymatic activity, but secretion of the artificial and endogenous DNASE1L3 206Cys protein was substantially reduced. CONCLUSIONS SLE risk association in the DNASE1L3 locus is dependent on the missense SNP rs35677470, which confers a reduction in DNASE1L3 protein secretion but does not eliminate its DNase enzyme function.
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Affiliation(s)
- Latanya N Coke
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Hongxiu Wen
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Mary Comeau
- Department of Biostatistics and Data Science, Division of Public Health Sciences, School of Medicine, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Mustafa H Ghanem
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Andrew Shih
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Christine N Metz
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Wentian Li
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, School of Medicine, Wake Forest University, Winston-Salem, North Carolina, USA
| | - Peter K Gregersen
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA.,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
| | - Kim R Simpfendorfer
- The Institute of Molecular Medicine, Northwell Health Feinstein Institutes for Medical Research, Manhasset, New York, USA .,Department of Molecular Medicine, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, New York, USA
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Bale S, Varga J, Bhattacharyya S. Role of RP105 and A20 in negative regulation of toll-like receptor activity in fibrosis: potential targets for therapeutic intervention. AIMS ALLERGY AND IMMUNOLOGY 2021. [DOI: 10.3934/allergy.2021009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Stone RC, Chen V, Burgess J, Pannu S, Tomic-Canic M. Genomics of Human Fibrotic Diseases: Disordered Wound Healing Response. Int J Mol Sci 2020; 21:ijms21228590. [PMID: 33202590 PMCID: PMC7698326 DOI: 10.3390/ijms21228590] [Citation(s) in RCA: 12] [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: 09/24/2020] [Revised: 11/08/2020] [Accepted: 11/11/2020] [Indexed: 02/06/2023] Open
Abstract
Fibrotic disease, which is implicated in almost half of all deaths worldwide, is the result of an uncontrolled wound healing response to injury in which tissue is replaced by deposition of excess extracellular matrix, leading to fibrosis and loss of organ function. A plethora of genome-wide association studies, microarrays, exome sequencing studies, DNA methylation arrays, next-generation sequencing, and profiling of noncoding RNAs have been performed in patient-derived fibrotic tissue, with the shared goal of utilizing genomics to identify the transcriptional networks and biological pathways underlying the development of fibrotic diseases. In this review, we discuss fibrosing disorders of the skin, liver, kidney, lung, and heart, systematically (1) characterizing the initial acute injury that drives unresolved inflammation, (2) identifying genomic studies that have defined the pathologic gene changes leading to excess matrix deposition and fibrogenesis, and (3) summarizing therapies targeting pro-fibrotic genes and networks identified in the genomic studies. Ultimately, successful bench-to-bedside translation of observations from genomic studies will result in the development of novel anti-fibrotic therapeutics that improve functional quality of life for patients and decrease mortality from fibrotic diseases.
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Affiliation(s)
- Rivka C. Stone
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Correspondence: (R.C.S.); (M.T.-C.)
| | - Vivien Chen
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
| | - Jamie Burgess
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- Medical Scientist Training Program in Biomedical Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Sukhmani Pannu
- Department of Dermatology, Tufts Medical Center, Boston, MA 02116, USA;
| | - Marjana Tomic-Canic
- Wound Healing and Regenerative Medicine Research Program, Dr. Phillip Frost Department of Dermatology and Cutaneous Surgery, University of Miami-Miller School of Medicine, Miami, FL 33136, USA; (V.C.); (J.B.)
- John P. Hussman Institute for Human Genomics, University of Miami-Miller School of Medicine, Miami, FL 33136, USA
- Correspondence: (R.C.S.); (M.T.-C.)
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Tamargo-Gómez I, Fernández ÁF, Mariño G. Pathogenic Single Nucleotide Polymorphisms on Autophagy-Related Genes. Int J Mol Sci 2020; 21:ijms21218196. [PMID: 33147747 PMCID: PMC7672651 DOI: 10.3390/ijms21218196] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 02/06/2023] Open
Abstract
In recent years, the study of single nucleotide polymorphisms (SNPs) has gained increasing importance in biomedical research, as they can either be at the molecular origin of a determined disorder or directly affect the efficiency of a given treatment. In this regard, sequence variations in genes involved in pro-survival cellular pathways are commonly associated with pathologies, as the alteration of these routes compromises cellular homeostasis. This is the case of autophagy, an evolutionarily conserved pathway that counteracts extracellular and intracellular stressors by mediating the turnover of cytosolic components through lysosomal degradation. Accordingly, autophagy dysregulation has been extensively described in a wide range of human pathologies, including cancer, neurodegeneration, or inflammatory alterations. Thus, it is not surprising that pathogenic gene variants in genes encoding crucial effectors of the autophagosome/lysosome axis are increasingly being identified. In this review, we present a comprehensive list of clinically relevant SNPs in autophagy-related genes, highlighting the scope and relevance of autophagy alterations in human disease.
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Affiliation(s)
- Isaac Tamargo-Gómez
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Álvaro F. Fernández
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
| | - Guillermo Mariño
- Instituto de Investigación Sanitaria del Principado de Asturias, 33011 Oviedo, Spain;
- Departamento de Biología Funcional, Universidad de Oviedo, 33011 Oviedo, Spain
- Correspondence: (Á.F.F.); (G.M.); Tel.: +34-985652416 (G.M.)
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Pu W, Wu W, Liu Q, Ma Y, Tu W, Zuo X, Guo G, Jiang S, Zhao Y, Zuo X, Wang Q, Yang L, Xiao R, Chu H, Wang L, Sun L, Cui J, Yu L, Li H, Li Y, Shi Y, Zhang J, Zhang H, Liang M, Chen D, Ding Y, Chen X, Chen Y, Zhang R, Zhao H, Li Y, Qi Q, Bai P, Zhao L, Reveille JD, Mayes MD, Jin L, Lee EB, Zhang X, Xu J, Zhang Z, Zhou X, Zou H, Wang J. Exome-Wide Association Analysis Suggests LRP2BP as a Susceptibility Gene for Endothelial Injury in Systemic Sclerosis in the Han Chinese Population. J Invest Dermatol 2020; 141:1254-1263.e6. [PMID: 33069728 DOI: 10.1016/j.jid.2020.07.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 07/13/2020] [Accepted: 07/24/2020] [Indexed: 11/18/2022]
Abstract
Genetic factors play a key role in the pathogenesis of autoimmune diseases, whereas the disease-causing variants remain largely unknown. Herein, we performed an exome-wide association study of systemic sclerosis in a Han Chinese population. In the discovery stage, 527 patients with systemic sclerosis and 5,024 controls were recruited and genotyped. In the validation study, an independent sample set of 479 patients and 1,096 controls were examined. In total, we found that four independent signals reached genome-wide significance. Among them, rs7574865 (Pcombined = 3.87 × 10-12) located within signal transducer and activator of transcription 4 gene was identified previously using samples of European ancestry. Additionally, another signal including three SNPs in linkage disequilibrium might be unreported susceptibility loci located in the epidermis differentiation complex region. Furthermore, two SNPs located within exon 3 of IGHM (rs45471499, Pcombined = 1.15 × 10-9) and upstream of LRP2BP (rs4317244, Pcombined = 4.17 × 10-8) were found. Moreover, rs4317244 was identified as an expression quantitative trait locus for LRP2BP that regulates tight junctions, cell cycle, and apoptosis in endothelial cell lines. Collectively, our results revealed three signals associated with systemic sclerosis in Han Chinese and suggested the importance of LRP2BP in systemic sclerosis pathogenesis. Given the limited sample size and discrepancies between previous results and our study, further studies in multiethnic populations are required for verification.
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Affiliation(s)
- Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China
| | - Wenyu Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingmei Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yanyun Ma
- Human Phenome Institute, Fudan University, Shanghai, China; Six-sector Industrial Research Institute, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenzhen Tu
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Xianbo Zuo
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Gang Guo
- Department of Rheumatology, Yiling Hospital, Shijiazhuang, China
| | - Shuai Jiang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China; Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yinhuan Zhao
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Xiaoxia Zuo
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Qingwen Wang
- Rheumatology and Immunology Department, Peking University Shenzhen Hospital, Shenzhen, China
| | - Li Yang
- Department of Rheumatology, The Affiliated Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Rong Xiao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Haiyan Chu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Lei Wang
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Liangdan Sun
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Jimin Cui
- Department of Rheumatology, Yiling Hospital, Shijiazhuang, China
| | - Ling Yu
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Huiyun Li
- Department of Rheumatology, Yiling Hospital, Shijiazhuang, China
| | - Yisha Li
- Department of Rheumatology, Xiangya Hospital, Central South University, Changsha, China
| | - Yaqian Shi
- Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
| | - Jiaqian Zhang
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Haishun Zhang
- Department of Rheumatology, Yiling Hospital, Shijiazhuang, China
| | - Minrui Liang
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dongdong Chen
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Yue Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiangxiang Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuanyuan Chen
- Division of Rheumatology, Shanghai TCM-integrated Hospital, Shanghai, China
| | - Rui Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Han Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Yuan Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Qing Qi
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China; Department of Dermatology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Bai
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Liang Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - John D Reveille
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, Texas, USA
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, Texas, USA
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China
| | - Eun Bong Lee
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Xuejun Zhang
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zheng Zhang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaodong Zhou
- Division of Rheumatology and Clinical Immunogenetics, the University of Texas-McGovern Medical School, Houston, Texas, USA
| | - Hejian Zou
- Department of Rheumatology, Huashan Hospital, Fudan University, Shanghai, China; Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Human Phenome Institute, Fudan University, Shanghai, China; Research Unit of dissecting the population genetics and developing new technologies for treatment and prevention of skin phenotypes and dermatological diseases (2019RU058), Chinese Academy of Medical Sciences, Beijing, China; Institute of Rheumatology, Immunology and Allergy, Fudan University, Shanghai, China.
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Bossini-Castillo L, Villanueva-Martin G, Kerick M, Acosta-Herrera M, López-Isac E, Simeón CP, Ortego-Centeno N, Assassi S, Hunzelmann N, Gabrielli A, de Vries-Bouwstra JK, Allanore Y, Fonseca C, Denton CP, Radstake TR, Alarcón-Riquelme ME, Beretta L, Mayes MD, Martin J. Genomic Risk Score impact on susceptibility to systemic sclerosis. Ann Rheum Dis 2020; 80:118-127. [PMID: 33004331 DOI: 10.1136/annrheumdis-2020-218558] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Genomic Risk Scores (GRS) successfully demonstrated the ability of genetics to identify those individuals at high risk for complex traits including immune-mediated inflammatory diseases (IMIDs). We aimed to test the performance of GRS in the prediction of risk for systemic sclerosis (SSc) for the first time. METHODS Allelic effects were obtained from the largest SSc Genome-Wide Association Study (GWAS) to date (9 095 SSc and 17 584 healthy controls with European ancestry). The best-fitting GRS was identified under the additive model in an independent cohort that comprised 400 patients with SSc and 571 controls. Additionally, GRS for clinical subtypes (limited cutaneous SSc and diffuse cutaneous SSc) and serological subtypes (anti-topoisomerase positive (ATA+) and anti-centromere positive (ACA+)) were generated. We combined the estimated GRS with demographic and immunological parameters in a multivariate generalised linear model. RESULTS The best-fitting SSc GRS included 33 single nucleotide polymorphisms (SNPs) and discriminated between patients with SSc and controls (area under the receiver operating characteristic (ROC) curve (AUC)=0.673). Moreover, the GRS differentiated between SSc and other IMIDs, such as rheumatoid arthritis and Sjögren's syndrome. Finally, the combination of GRS with age and immune cell counts significantly increased the performance of the model (AUC=0.787). While the SSc GRS was not able to discriminate between ATA+ and ACA+ patients (AUC<0.5), the serological subtype GRS, which was based on the allelic effects observed for the comparison between ACA+ and ATA+ patients, reached an AUC=0.693. CONCLUSIONS GRS was successfully implemented in SSc. The model discriminated between patients with SSc and controls or other IMIDs, confirming the potential of GRS to support early and differential diagnosis for SSc.
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Affiliation(s)
- Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Universidad de Granada, Granada, Andalucía, Spain
| | | | - Martin Kerick
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Andalucía, Spain
| | | | - Elena López-Isac
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Andalucía, Spain
| | - Carmen P Simeón
- Departament of Internal Medicine, Hospital Vall d'Hebron, Barcelona, Catalunya, Spain
| | - Norberto Ortego-Centeno
- Departament of Internal Medicine, Hospital Universitario San Cecilio, Granada, Andalucía, Spain
| | - Shervin Assassi
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | | | | | | | | | - Nicolas Hunzelmann
- Department of Dermatology, University of Cologne, Koln, Nordrhein-Westfalen, Germany
| | - Armando Gabrielli
- Istituto di Clinica Medica Generale, Ematologia ed Immunologia Clinica, Università Politecnica delle Marche, Ancona, Marche, Italy
| | | | - Yannick Allanore
- Rheumatology A Department, Hospital Cochin, Paris, Île-de-France, France
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, London, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, London, UK
| | - Timothy Rdj Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, Utrecht, Netherlands
| | - Marta Eugenia Alarcón-Riquelme
- Centre for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Lorenzo Beretta
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, La Fondazione IRCCS Ca' Granda Ospedale Maggiore di Milano Policlinico, Milano, Lombardia, Italy
| | - Maureen D Mayes
- Division of Rheumatology and Clinical Immunogenetics, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Andalucía, Spain
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Ishikawa Y, Terao C. Genetics of systemic sclerosis. JOURNAL OF SCLERODERMA AND RELATED DISORDERS 2020; 5:192-201. [PMID: 35382527 PMCID: PMC8922623 DOI: 10.1177/2397198320913695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/23/2020] [Indexed: 01/05/2024]
Abstract
Systemic sclerosis is an autoimmune disease characterized by generalized fibrosis in connective tissues and internal organs as consequences of microvascular dysfunction and immune dysfunctions, which leads to premature death in affected individuals. The etiology of systemic sclerosis is complex and poorly understood, but as with most autoimmune diseases, it is widely accepted that both environmental and genetic factors contribute to disease risk. During the last decade, the number of genetic markers convincingly associated with systemic sclerosis has exponentially increased. In this article, we briefly mention the genetic components of systemic sclerosis. Then, we review the classical and novel genetic associations with systemic sclerosis, analyzing the firmest and replicated signals within non-human leukocyte antigen genes, identified by both candidate gene approach and genome-wide association studies. We also provide an insight into the future perspectives that will shed more light into the complex genetic background of the disease. Despite the remarkable advance of systemic sclerosis genetics during the last decade, the use of the new genetic technologies such as next-generation sequencing, as well as the deep phenotyping of the study cohorts, to fully characterize the genetic component of this disease is imperative to identify causal variants, which leads to more targeted and effective treatment of systemic sclerosis.
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Affiliation(s)
- Yuki Ishikawa
- Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
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Ding J, Frantzeskos A, Orozco G. Functional genomics in autoimmune diseases. Hum Mol Genet 2020; 29:R59-R65. [PMID: 32420598 PMCID: PMC7530520 DOI: 10.1093/hmg/ddaa097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Associations between genetic loci and increased susceptibility to autoimmune disease have been well characterized, however, translating this knowledge into mechanistic insight and patient benefit remains a challenge. While improvements in the precision, completeness and accuracy of our genetic understanding of autoimmune diseases will undoubtedly be helpful, meeting this challenge will require two interlinked problems to be addressed: first which of the highly correlated variants at an individual locus is responsible for increased disease risk, and second what are the downstream effects of this variant. Given that the majority of loci are thought to affect non-coding regulatory elements, the second question is often reframed as what are the target gene(s) and pathways affected by causal variants. Currently, these questions are being addressed using a wide variety of novel techniques and datasets. In many cases, these approaches are complementary and it is likely that the most accurate picture will be generated by consolidating information relating to transcription, regulatory activity, chromatin accessibility, chromatin conformation and readouts from functional experiments, such as genome editing and reporter assays. It is clear that it will be necessary to gather this information from disease relevant cell types and conditions and that by doing so our understanding of disease etiology will be improved. This review is focused on the field of autoimmune disease functional genomics with a particular focus on the most exciting and significant research to be published within the last couple of years.
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Affiliation(s)
- James Ding
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Antonios Frantzeskos
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9LJ, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
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50
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Zervou MI, Andreou A, Matalliotakis M, Spandidos DA, Goulielmos GN, Eliopoulos EE. Association of the DNASE1L3 rs35677470 polymorphism with systemic lupus erythematosus, rheumatoid arthritis and systemic sclerosis: Structural biological insights. Mol Med Rep 2020; 22:4492-4498. [PMID: 33173951 PMCID: PMC7646740 DOI: 10.3892/mmr.2020.11547] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/30/2020] [Indexed: 01/29/2023] Open
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of autoimmune disease-associated loci, much of the genetics underlying these diseases remains unknown. In an attempt to identify potential causal variants, previous studies have determined that the rs35677470 missense variant of the Deoxyribonuclease I-like 3 (DNASE1L3) gene was associated with the development of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc). DNase1L3 is a member of the human DNase I family, representing a nuclease that cleaves double-stranded DNA during apoptosis and serving a role in the development of autoimmune diseases. The present study aimed to determine the role of the rs35677470 variant at the DNASE1L3 gene leading to the R206C mutation in SLE, RA and SSc. The underlying mechanism potentially affecting protein structure loss of function was also assessed. DNASE1L3 evolution was investigated to define conservation elements in the protein sequence. Additionally, 3D homology modeling and in silico mutagenesis was performed to localize the polymorphism under investigation. Evolutionary analysis revealed heavily conserved sequence elements among species, indicating structural/functional importance. In silico mutagenesis and 3D protein structural analysis also demonstrated the potentially varied impact of the DNASE1L3 (rs35677470) single nucleotide polymorphism (SNP), providing an explanation for its effect on the R206C variant. Structural analysis demonstrated that the rs35677470 SNP encodes a non-conservative amino acid variation, R206C, which disrupted the conserved electrostatic network holding secondary protein structure elements in position. Specifically, the R206 to E170 interaction forming part of a salt bridge network stabilizing two α-helices was interrupted, thereby affecting the molecular architecture. Previous studies on the effect of this SNP in Caucasian populations demonstrated lower DNAse1L3 activity levels, which is consistent with the current results. The present study comprehensively evaluated the shared autoimmune locus of DNASE1L3 (rs35677470), which produced an inactive form of DNaseIL3. Furthermore, structural analysis explained the potential role of the produced mutation by modifying the placement of structural elements and consequently introducing disorder in protein folding, affecting biological function.
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Affiliation(s)
- Maria I Zervou
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Athena Andreou
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Michail Matalliotakis
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George N Goulielmos
- Section of Molecular Pathology and Human Genetics, Department of Internal Medicine, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Elias E Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
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