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Peng XP, Al-Ddafari MS, Caballero-Oteyza A, El Mezouar C, Mrovecova P, Dib SE, Massen Z, Smahi MCE, Faiza A, Hassaïne RT, Lefranc G, Aribi M, Grimbacher B. Next generation sequencing (NGS)-based approach to diagnosing Algerian patients with suspected inborn errors of immunity (IEIs). Clin Immunol 2023; 256:109758. [PMID: 37678716 DOI: 10.1016/j.clim.2023.109758] [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: 05/04/2023] [Revised: 07/23/2023] [Accepted: 09/02/2023] [Indexed: 09/09/2023]
Abstract
The advent of next-generation sequencing (NGS) technologies has greatly expanded our understanding of both the clinical spectra and genetic landscape of inborn errors of immunity (IEIs). Endogamous populations may be enriched for unique, ancestry-specific disease-causing variants, a consideration that significantly impacts molecular testing and analysis strategies. Herein, we report on the application of a 2-step NGS-based testing approach beginning with targeted gene panels (TGPs) tailored to specific IEI subtypes and reflexing to whole exome sequencing (WES) if negative for Northwest Algerian patients with suspected IEIs. Our overall diagnostic yield of 57% is comparable to others broadly applying short-read NGS to IEI detection, but data from our localized cohort show some similarities and differences from NGS studies performed on larger regional IEI cohorts. This suggests the importance of tailoring diagnostic strategies to local demographics and needs, but also highlights ongoing concerns inherent to the application of genomics for clinical IEI diagnostics.
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Affiliation(s)
- Xiao P Peng
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States of America.
| | - Moudjahed Saleh Al-Ddafari
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Andres Caballero-Oteyza
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany
| | - Chahrazed El Mezouar
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Pavla Mrovecova
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany
| | - Saad Eddin Dib
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Zoheir Massen
- Pediatric Department, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Algeria
| | - Mohammed Chems-Eddine Smahi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria; Specialized Mother-Child Hospital of Tlemcen, Department of Neonatology, Faculty of Medicine, University of Tlemcen, Algeria
| | - Alddafari Faiza
- Department of Internal Medicine, Medical Center University of Tlemcen, Faculty of Medicine, University of Tlemcen, Tlemcen, Algeria
| | | | - Gérard Lefranc
- Institute of Human Genetics, UMR 9002 CNRS-University of Montpellier, France
| | - Mourad Aribi
- Laboratory of Applied Molecular Biology and Immunology, W0414100, University of Tlemcen, Algeria.
| | - Bodo Grimbacher
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, Germany; DZIF - German Center for Infection Research, Satellite Center Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, Albert-Ludwigs University, Freiburg, Germany; RESIST - Cluster of Excellence 2155 to Hanover Medical School, Satellite Center Freiburg, Germany.
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Essouma M, Noubiap JJ, Singwe-Ngandeu M, Hachulla E. Epidemiology of Sjögren Syndrome in Africa: A Scoping Review. J Clin Rheumatol 2022; 28:e240-e244. [PMID: 34941621 DOI: 10.1097/rhu.0000000000001708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND The epidemiology of Sjögren syndrome (SS) has been extensively studied in America, Europe, and Asia. OBJECTIVE To summarize available data on the epidemiology of SS in Africa. METHODS MEDLINE, EMBASE, and African Journals Online were searched from inception up to May 17, 2020, to identify relevant articles. Data gleaned from these reports have been summarized narratively in this review. RESULTS Twenty-one hospital-based studies were included. These studies reported 744 cases of SS. The mean age at diagnosis varied between 28 and 73.6 years, and the female proportion ranged from 83.3% to 100%. There was no population-based incidence or prevalence. Among people with autoimmune and other rheumatic conditions, the frequency of primary SS was in the range 1.9% to 47.6%, whereas that of rheumatoid arthritis-associated secondary SS was in the range 4.3% to 100%. Sicca symptoms were the commonest features, with most frequently involved organs being joints, lungs, and neurological structures. Main autoantibodies were anti-Ro/SS antigen A, anti-La/SS antigen B, and antinuclear antibodies. CONCLUSIONS The epidemiology of SS is poorly characterized in Africa. Available data are broadly consistent with those from other populations. Extensive and high-quality research is urgently needed.
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Affiliation(s)
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | | | - Eric Hachulla
- Department of Internal Medicine and Clinical Immunology, CHRU Lille, Referral Centre for Rare Systemic Autoimmune Diseases North and Northwest of France, Univ. Lille, INSERM U995-LIRIC-Lille Inflammation Research International Centre, Lille, France
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Ueki M, Kimura-Kataoka K, Fujihara J, Iida R, Kawai Y, Kusaka A, Sasaki T, Takeshita H, Yasuda T. Evaluation of the functional effects of genetic variants‒missense and nonsense SNPs, indels and copy number variations‒in the gene encoding human deoxyribonuclease I potentially implicated in autoimmunity. Sci Rep 2019; 9:13660. [PMID: 31541133 PMCID: PMC6754452 DOI: 10.1038/s41598-019-49935-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/29/2019] [Indexed: 01/31/2023] Open
Abstract
Genetic variants, such as single nucleotide polymorphisms (SNPs), in the deoxyribonuclease I (DNase I) gene which remarkably reduce or abolish the activity are assumed to be substantially responsible for the genetic backgrounds determining susceptibility to autoimmune dysfunction. Here, we evaluated many genetic variants, including missense and nonsense SNPs, and indel (inframe) variants in the gene, potentially implicated in autoimmune diseases as functional variants resulting in altered activity levels. Eighteen missense and 7 nonsense SNPs, and 9 indel (inframe) variants were found to result in loss of function and disappearance of DNase I activity. Furthermore, considering the positions in the DNase I protein corresponding to the various nonsense SNPs, all of the other nonsense SNPs and frameshift variants registered in the Ensembl database (https://asia.ensembl.org) appear likely to exert a pathogenetic effect through loss of the activity. Accordingly, a total of 60 genetic variants in the DNase 1 gene (DNASE1) inducing abolishment or marked reduction of the DNase I activity could be identified as genetic risk factors for autoimmunity, irrespective of how sparsely they were distributed in the population. It was noteworthy that SNP p.Gln244Arg, reportedly associated with autoimmunity and reducing the activity to about half of that of the wild type, and SNP p.Arg107Gly, abolishing the activity completely, were distributed worldwide and in African populations at the polymorphic level, respectively. On the other hand, with regard to copy number variations in DNASE1 where loss of copy leads to a reduction of the in vivo enzyme activity, only 2 diploid copy numbers were distributed in Japanese and German populations, demonstrating no loss of copy. These exhaustive data for genetic variants in DNASE1 resulting in loss or marked reduction of the DNase I activity are highly informative when considering genetic predisposition leading to autoimmune dysfunction.
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Affiliation(s)
- Misuzu Ueki
- Department of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui, Japan
| | - Kaori Kimura-Kataoka
- Department of Legal Medicine, Shimane University School of Medicine, Enya, Izumo, Japan
| | - Junko Fujihara
- Department of Legal Medicine, Shimane University School of Medicine, Enya, Izumo, Japan
| | - Reiko Iida
- Department of Life Sciences, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui, Japan
| | - Yasuyuki Kawai
- Department of Cardiology, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Akari Kusaka
- Department of Legal Medicine, Shimane University School of Medicine, Enya, Izumo, Japan
| | - Takamitsu Sasaki
- Department of Legal Medicine, Shimane University School of Medicine, Enya, Izumo, Japan
| | - Haruo Takeshita
- Department of Legal Medicine, Shimane University School of Medicine, Enya, Izumo, Japan.
| | - Toshihiro Yasuda
- Department of Medical Genetics and Biochemistry, Faculty of Medical Sciences, University of Fukui, Eiheiji, Fukui, Japan
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Nikolic A. Pathophysiology and Genetics of Bronchiectasis Unrelated to Cystic Fibrosis. Lung 2018; 196:383-392. [PMID: 29754320 DOI: 10.1007/s00408-018-0121-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/04/2018] [Indexed: 10/16/2022]
Abstract
Bronchiectasis is characterized by deregulated inflammatory response and recurrent bacterial infection resulting in progressive lung damage and an irreversible dilatation of bronchi and bronchioles. Generally accepted model of the development of bronchiectasis is the "vicious cycle hypothesis" that proposes compromising of the mucociliary clearance by an initial event, which leads to the infection of the respiratory tract followed by further impairment of mucociliary function, bacterial proliferation, and more inflammation. Bronchiectasis is a very common symptom in patients with cystic fibrosis (CF), while bronchiectasis unrelated to CF is heterogeneous pathology of unknown cause with a large number of potential contributory factors and poorly understood pathogenesis. It is presumed that bronchiectasis unrelated to CF is a multifactorial condition predisposed by genetic factors. Different molecules have been implicated in the onset and development of idiopathic bronchiectasis, as well as modulation of the disease severity and response to therapy. Most of these molecules are involved in the processes that contribute to the homeostasis of the lung tissue, especially mucociliary clearance, protease-antiprotease balance, and immunomodulation. Evaluation of the studies performed towards investigation of the role these molecules play in bronchiectasis identifies genetic variants that may be of potential importance for clinical management of the disease, and also of interest for future research efforts. This review focuses on the molecules with major roles in lung homeostasis and their involvement in bronchiectasis unrelated to CF.
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Affiliation(s)
- Aleksandra Nikolic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444A, PO Box 23, 11010, Belgrade, Serbia.
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Pérez-Sánchez C, Ruiz-Limón P, Aguirre MA, Jiménez-Gómez Y, Arias-de la Rosa I, Ábalos-Aguilera MC, Rodriguez-Ariza A, Castro-Villegas MC, Ortega-Castro R, Segui P, Martinez C, Gonzalez-Conejero R, Rodríguez-López S, Gonzalez-Reyes JA, Villalba JM, Collantes-Estévez E, Escudero A, Barbarroja N, López-Pedrera C. Diagnostic potential of NETosis-derived products for disease activity, atherosclerosis and therapeutic effectiveness in Rheumatoid Arthritis patients. J Autoimmun 2017; 82:31-40. [PMID: 28465139 DOI: 10.1016/j.jaut.2017.04.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/23/2022]
Abstract
OBJECTIVES 1) To assess the association of NETosis and NETosis-derived products with the activity of the disease and the development of cardiovascular disease in RA; 2) To evaluate the involvement of NETosis on the effects of biologic therapies such as anti-TNF alpha (Infliximab) and anti-IL6R drugs (Tocilizumab). METHODS One hundred and six RA patients and 40 healthy donors were evaluated for the occurrence of NETosis. Carotid-intimae media thickness was analyzed as early atherosclerosis marker. Inflammatory and oxidative stress mediators were quantified in plasma and neutrophils. Two additional cohorts of 75 RA patients, treated either with Infliximab (n = 55) or Tocilizumab (n = 20) for six months, were evaluated. RESULTS NETosis was found increased in RA patients, beside myeloperoxidase and neutrophil elastase protein levels. Cell-free nucleosomes plasma levels were elevated, and strongly correlated with the activity of the disease and the positivity for autoantibodies, alongside inflammatory and oxidative profiles in plasma and neutrophils. Moreover, ROC analyses showed that cell-free nucleosomes levels could identify RA patients showing early atherosclerosis with high specificity. RA patients treated either with IFX or TCZ for six months exhibited decreased generation of NETs. Concomitantly, clinical parameters and serum markers of inflammation were found reduced. Mechanistic in vitro analyses showed that inhibition of NETs extrusion by either DNase, IFX or TCZ, further abridged the endothelial dysfunction and the activation of immune cells, thus influencing the global activity of the vascular system. CONCLUSIONS NETosis-derived products may have diagnostic potential for disease activity and atherosclerosis, as well as for the assessment of therapeutic effectiveness in RA.
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Affiliation(s)
- C Pérez-Sánchez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - P Ruiz-Limón
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Departamento de Medicina (Medicina, Dermatología y Otorrinolaringología), Universidad de Córdoba, Spain
| | - M A Aguirre
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain; Departamento de Medicina (Medicina, Dermatología y Otorrinolaringología), Universidad de Córdoba, Spain
| | - Y Jiménez-Gómez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Departamento de Medicina (Medicina, Dermatología y Otorrinolaringología), Universidad de Córdoba, Spain
| | - I Arias-de la Rosa
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | | | - A Rodriguez-Ariza
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - M C Castro-Villegas
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - R Ortega-Castro
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - P Segui
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - C Martinez
- Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Spain
| | - R Gonzalez-Conejero
- Centro Regional de Hemodonación, Universidad de Murcia, IMIB-Arrixaca, Spain
| | - S Rodríguez-López
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
| | - J A Gonzalez-Reyes
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
| | - J M Villalba
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Córdoba, Spain
| | - E Collantes-Estévez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain; Departamento de Medicina (Medicina, Dermatología y Otorrinolaringología), Universidad de Córdoba, Spain
| | - A Escudero
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - N Barbarroja
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain
| | - Ch López-Pedrera
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Spain; Unidad de Gestión Clínica Reumatología, Hospital Universitario Reina Sofía, Córdoba, Spain.
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Trofimenko AS, Gontar IP, Zborovsky AB, Paramonova OV. Anti-DNase I antibodies in systemic lupus erythematosus: diagnostic value and share in the enzyme inhibition. Rheumatol Int 2016; 36:521-9. [PMID: 26879320 DOI: 10.1007/s00296-016-3437-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/02/2016] [Indexed: 11/25/2022]
Abstract
Diagnostic accuracy of anti-DNase I antibodies measurement in a differentiation between SLE and other autoimmune rheumatic diseases was evaluated. The share of anti-DNase I and actin in the DNase I activity decrease in SLE was established. Serum samples were obtained from 54 patients with verified SLE, 52 control patients with other autoimmune rheumatic diseases, and 44 healthy persons. Anti-DNase I concentrations were measured by ELISA. Free and actin inhibited DNase I activities were evaluated in the fresh serum samples. The appraisal of antibodies and actin effects on DNase I activity was made using multiple regression. Anti-DNase I antibodies were positive in 35 SLE and 8 control patients, without significant difference between the mean antibody concentrations. Sensitivity of this test was 64.81 %, and specificity-84.62 %. Mean free DNase I activity in SLE was somewhat lower than in the control group as a result of augmented frequency of extremely low enzyme activities. On the contrary, after the exclusion of the latter cases we have revealed elevated mean free DNase I activity in the other SLE patients comparing to the similar control subgroup. Unlike the controls, low serum DNase I activity in SLE arose not only from actin and antibody action, but also, in half of the cases, from unidentified factor, related to active SLE. The accuracy of the anti-DNase I antibodies measurement is approximate to the present reference standard of SLE diagnostics. We first demonstrated that neither antibodies nor actin caused DNase I activity decrease in SLE.
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Affiliation(s)
- A S Trofimenko
- FSBSI Research Institute of Clinical and Experimental Rheumatology, 76, Zemlyachki Str., Volgograd, Russia, 400138. .,Hospital Therapy Department, Volgograd State Medical University, 1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131.
| | - I P Gontar
- FSBSI Research Institute of Clinical and Experimental Rheumatology, 76, Zemlyachki Str., Volgograd, Russia, 400138.,Hospital Therapy Department, Volgograd State Medical University, 1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
| | - A B Zborovsky
- FSBSI Research Institute of Clinical and Experimental Rheumatology, 76, Zemlyachki Str., Volgograd, Russia, 400138.,Hospital Therapy Department, Volgograd State Medical University, 1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
| | - O V Paramonova
- Hospital Therapy Department, Volgograd State Medical University, 1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
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James JA. Clinical perspectives on lupus genetics: advances and opportunities. Rheum Dis Clin North Am 2014; 40:413-32, vii. [PMID: 25034154 DOI: 10.1016/j.rdc.2014.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In recent years, genome-wide association studies have led to an expansion in the identification of regions containing confirmed genetic risk variants within complex human diseases, such as systemic lupus erythematosus (SLE). Many of the strongest SLE genetic associations can be divided into groups based on their potential roles in different processes implicated in lupus pathogenesis, including ubiquitination, DNA degradation, innate immunity, cellular immunity, lymphocyte development, and antigen presentation. Recent advances have also shown several genetic associations with SLE subphenotypes and subcriteria. Many areas for further exploration remain to move lupus genetic studies toward clinically informative end points.
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Affiliation(s)
- Judith A James
- Oklahoma Clinical & Translational Science Institute, University of Oklahoma Health Sciences Center, 920 Stanton L Young Boulevard, Oklahoma City, OK 73104, USA; Departments of Medicine, Pathology, Microbiology & Immunology, University of Oklahoma Health Sciences Center, 920 Stanton L Young Boulevard, Oklahoma City, OK 73104, USA.
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Viatte S, Flynn E, Lunt M, Barnes J, Singwe-Ngandeu M, Bas S, Barton A, Gabay C. Investigation of Caucasian rheumatoid arthritis susceptibility loci in African patients with the same disease. Arthritis Res Ther 2012; 14:R239. [PMID: 23121884 PMCID: PMC3674592 DOI: 10.1186/ar4082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 10/30/2012] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION The largest genetic risk to develop rheumatoid arthritis (RA) arises from a group of alleles of the HLA DRB1 locus ('shared epitope', SE). Over 30 non-HLA single nucleotide polymorphisms (SNPs) predisposing to disease have been identified in Caucasians, but they have never been investigated in West/Central Africa. We previously reported a lower prevalence of the SE in RA patients in Cameroon compared to European patients and aimed in the present study to investigate the contribution of Caucasian non-HLA RA SNPs to disease susceptibility in Black Africans. METHODS RA cases and controls from Cameroon were genotyped for Caucasian RA susceptibility SNPs using Sequenom MassArray technology. Genotype data were also available for 5024 UK cases and 4281 UK controls and for 119 Yoruba individuals in Ibadan, Nigeria (YRI, HapMap). A Caucasian aggregate genetic-risk score (GRS) was calculated as the sum of the weighted risk-allele counts. RESULTS After genotyping quality control procedures were performed, data on 28 Caucasian non-HLA susceptibility SNPs were available in 43 Cameroonian RA cases and 44 controls. The minor allele frequencies (MAF) were tightly correlated between Cameroonian controls and YRI individuals (correlation coefficient 93.8%, p = 1.7E-13), and they were pooled together. There was no correlation between MAF of UK and African controls; 13 markers differed by more than 20%. The MAF for markers at PTPN22, IL2RA, FCGR2A and IL2/IL21 was below 2% in Africans. The GRS showed a strong association with RA in the UK. However, the GRS did not predict RA in Africans (OR = 0.71, 95% CI 0.29 - 1.74, p = 0.456). Random sampling from the UK cohort showed that this difference in association is unlikely to be explained by small sample size or chance, but is statistically significant with p<0.001. CONCLUSIONS The MAFs of non-HLA Caucasian RA susceptibility SNPs are different between Caucasians and Africans, and several polymorphisms are barely detectable in West/Central Africa. The genetic risk of developing RA conferred by a set of 28 Caucasian susceptibility SNPs is significantly different between the UK and Africa with p<0.001. Taken together, these observations strengthen the hypothesis that the genetic architecture of RA susceptibility is different in different ethnic backgrounds.
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Morgan AR, Lam WJ, Han DY, Fraser AG, Ferguson LR. DNase1: No Association with Crohn's Disease in a New Zealand Population. ISRN GASTROENTEROLOGY 2012; 2012:826323. [PMID: 22701800 PMCID: PMC3373076 DOI: 10.5402/2012/826323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 04/10/2012] [Indexed: 11/23/2022]
Abstract
DNase1 has been implicated in a number of immune disorders and is an excellent candidate gene for Crohn's disease (CD). We investigated whether DNase1 SNPs rs1053874 and rs8176938 were associated with CD in a well-characterized New Zealand dataset consisting of 447 cases and 716 controls. Furthermore, we measured serum DNase1 activity levels in a number of CD patients and controls. We did not find any evidence of association for either DNase1 genetic variation or DNase1 activity levels with CD. The lack of association indicates that DNase1 does not play a significant role in predisposing to CD in the New Zealand population.
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Affiliation(s)
- Angharad R Morgan
- Discipline of Nutrition, Faculty of Medical and Health Sciences (FMHS), The University of Auckland, 85 Park Road, Grafton, 1142 Auckland, New Zealand
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Malíčková K, Ďuricová D, Bortlík M, Hrušková Z, Svobodová B, Machková N, Komárek V, Fučíková T, Janatková I, Zima T, Lukáš M. Impaired deoxyribonuclease I activity in patients with inflammatory bowel diseases. Autoimmune Dis 2011; 2011:945861. [PMID: 21687600 PMCID: PMC3112520 DOI: 10.4061/2011/945861] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 04/05/2011] [Indexed: 11/20/2022] Open
Abstract
Background and Aims. Deoxyribonuclease I (DNaseI) is an endonuclease that facilitates chromatin breakdown and promotes susceptibility to autoimmune disorders. The aim of current study was to investigate serum DNase I activity in patients with inflammatory bowel diseases (IBD). Patients and Methods. A cohort of 110 IBD patients was evaluated, aged 35 ± 12 years, 77 with Crohn's disease (CD) and 33 with ulcerative colitis (UC). 50 SLE patients and 50 healthy blood donors were examined as control groups. Results. DNase I activity in IBD patients was significantly lower than in healthy individuals, but higher than in SLE patients (P < .0001). Patients with UC showed higher DNase I activity than CD patients, P = .21. DNase I activity in female patients with IBD was significantly lower than in males, P = .024; however, no differences in DNase I activity were found in relation to gender in healthy individuals. DNase I activity has shown a strong negative correlation with the serum concentration of anti-nucleosomal antibodies in the autoimmune (SLE + IBD) cohort, as well as in the separate IBD cohort. Conclusions. Reduced serum DNase I activity probably has pathogenetic consequences in IBD. Induction of autoantibodies towards nucleosomes could be a reflection of impaired DNase I activity.
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Affiliation(s)
- Karin Malíčková
- Institute of Clinical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague, First Faculty of Medicine, Charles University in Prague, Karlovo nam. 32, 121 11 Prague 2, Czech Republic
| | - Dana Ďuricová
- Clinical and Research Center for Inflammatory Bowel Disease, ISCARE a.s. and Charles University in Prague, Czech Republic
| | - Martin Bortlík
- Clinical and Research Center for Inflammatory Bowel Disease, ISCARE a.s. and Charles University in Prague, Czech Republic
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Zdenka Hrušková
- Department of Nephrology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Barbora Svobodová
- Department of Nephrology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Naděžda Machková
- Clinical and Research Center for Inflammatory Bowel Disease, ISCARE a.s. and Charles University in Prague, Czech Republic
| | - Viktor Komárek
- Clinical and Research Center for Inflammatory Bowel Disease, ISCARE a.s. and Charles University in Prague, Czech Republic
| | - Terezie Fučíková
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University in Prague and General University Hospital in Prague, Czech Republic
| | - Ivana Janatková
- Institute of Clinical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague, First Faculty of Medicine, Charles University in Prague, Karlovo nam. 32, 121 11 Prague 2, Czech Republic
| | - Tomáš Zima
- Institute of Clinical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague, First Faculty of Medicine, Charles University in Prague, Karlovo nam. 32, 121 11 Prague 2, Czech Republic
| | - Milan Lukáš
- Institute of Clinical Biochemistry and Laboratory Diagnostics, General University Hospital in Prague, First Faculty of Medicine, Charles University in Prague, Karlovo nam. 32, 121 11 Prague 2, Czech Republic
- Clinical and Research Center for Inflammatory Bowel Disease, ISCARE a.s. and Charles University in Prague, Czech Republic
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