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Artaza H, Eriksson D, Lavrichenko K, Aranda-Guillén M, Bratland E, Vaudel M, Knappskog P, Husebye ES, Bensing S, Wolff ASB, Kämpe O, Røyrvik EC, Johansson S. Rare copy number variation in autoimmune Addison's disease. Front Immunol 2024; 15:1374499. [PMID: 38562931 PMCID: PMC10982488 DOI: 10.3389/fimmu.2024.1374499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Autoimmune Addison's disease (AAD) is a rare but life-threatening endocrine disorder caused by an autoimmune destruction of the adrenal cortex. A previous genome-wide association study (GWAS) has shown that common variants near immune-related genes, which mostly encode proteins participating in the immune response, affect the risk of developing this condition. However, little is known about the contribution of copy number variations (CNVs) to AAD susceptibility. We used the genome-wide genotyping data from Norwegian and Swedish individuals (1,182 cases and 3,810 controls) to investigate the putative role of CNVs in the AAD aetiology. Although the frequency of rare CNVs was similar between cases and controls, we observed that larger deletions (>1,000 kb) were more common among patients (OR = 4.23, 95% CI 1.85-9.66, p = 0.0002). Despite this, none of the large case-deletions were conclusively pathogenic, and the clinical presentation and an AAD-polygenic risk score were similar between cases with and without the large CNVs. Among deletions exclusive to individuals with AAD, we highlight two ultra-rare deletions in the genes LRBA and BCL2L11, which we speculate might have contributed to the polygenic risk in these carriers. In conclusion, rare CNVs do not appear to be a major cause of AAD but further studies are needed to ascertain the potential contribution of rare deletions to the polygenic load of AAD susceptibility.
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Affiliation(s)
- Haydee Artaza
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
| | - Daniel Eriksson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Ksenia Lavrichenko
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Maribel Aranda-Guillén
- Center for Molecular Medicine, Department of Medicine (Solna), Karolinska Institutet, Stockholm, Sweden
| | - Eirik Bratland
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Marc Vaudel
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Health Data and Digitalization, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Knappskog
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eystein S. Husebye
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sophie Bensing
- Department of Endocrinology, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anette S. B. Wolff
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Olle Kämpe
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ellen C. Røyrvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- K. G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Bergen, Norway
| | - Stefan Johansson
- Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
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2
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Lorente-Bermúdez R, Pan-Lizcano R, Núñez L, López-Vázquez D, Rebollal-Leal F, Vázquez-Rodríguez JM, Hermida-Prieto M. Analysis of the Association between Copy Number Variation and Ventricular Fibrillation in ST-Elevation Acute Myocardial Infarction. Int J Mol Sci 2024; 25:2548. [PMID: 38473795 DOI: 10.3390/ijms25052548] [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: 12/12/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 03/14/2024] Open
Abstract
Sudden cardiac death due to ventricular fibrillation (VF) during ST-elevation acute myocardial infarction (STEAMI) significantly contributes to cardiovascular-related deaths. Although VF has been linked to genetic factors, variations in copy number variation (CNV), a significant source of genetic variation, have remained largely unexplored in this context. To address this knowledge gap, this study performed whole exome sequencing analysis on a cohort of 39 patients with STEAMI who experienced VF, aiming to elucidate the role of CNVs in this pathology. The analysis revealed CNVs in the form of duplications in the PARP2 and TTC5 genes as well as CNVs in the form of deletions in the MUC15 and PPP6R1 genes, which could potentially serve as risk indicators for VF during STEAMI. The analysis also underscores notable CNVs with an average gene copy number equal to or greater than four in DEFB134, FCGR2C, GREM1, PARM1, SCG5, and UNC79 genes. These findings provide further insight into the role of CNVs in VF in the context of STEAMI.
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Affiliation(s)
- Roberto Lorente-Bermúdez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Ricardo Pan-Lizcano
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Lucía Núñez
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
- GRINCAR Research Group, Departamento de Ciencias de la Salud, Universidade da Coruña, 15403 A Coruña, Spain
| | - Domingo López-Vázquez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - Fernando Rebollal-Leal
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
| | - José Manuel Vázquez-Rodríguez
- Servicio de Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), Universidade da Coruña (UDC), 15006 A Coruña, Spain
- Centro de Investigación Biomédica en Red Enfermedades Cardiovasculares (CIBERCV), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Manuel Hermida-Prieto
- Grupo de Investigación en Cardiología, Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC-SERGAS), GRINCAR-Universidade da Coruña (UDC), 15006 A Coruña, Spain
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3
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Viel KR. Response to 'Reduced Cell Surface Levels of C-C Chemokine Receptor 5 and Immunosuppression in Long Coronavirus Disease 2019 Syndrome'. Clin Infect Dis 2022; 75:1485-1486. [PMID: 35819236 PMCID: PMC9384431 DOI: 10.1093/cid/ciac389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kevin R Viel
- Department of Genomics, Histonis Incorporated, Manchester, New Hampshire, USA
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4
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Kerick M, Acosta-Herrera M, Simeón-Aznar CP, Callejas JL, Assassi S, Proudman SM, Nikpour M, Hunzelmann N, Moroncini G, de Vries-Bouwstra JK, Orozco G, Barton A, Herrick AL, Terao C, Allanore Y, Fonseca C, Alarcón-Riquelme ME, Radstake TRDJ, Beretta L, Denton CP, Mayes MD, Martin J. Complement component C4 structural variation and quantitative traits contribute to sex-biased vulnerability in systemic sclerosis. NPJ Genom Med 2022; 7:57. [PMID: 36198672 PMCID: PMC9534873 DOI: 10.1038/s41525-022-00327-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/22/2022] [Indexed: 11/16/2022] Open
Abstract
Copy number (CN) polymorphisms of complement C4 play distinct roles in many conditions, including immune-mediated diseases. We investigated the association of C4 CN with systemic sclerosis (SSc) risk. Imputed total C4, C4A, C4B, and HERV-K CN were analyzed in 26,633 individuals and validated in an independent cohort. Our results showed that higher C4 CN confers protection to SSc, and deviations from CN parity of C4A and C4B augmented risk. The protection contributed per copy of C4A and C4B differed by sex. Stronger protection was afforded by C4A in men and by C4B in women. C4 CN correlated well with its gene expression and serum protein levels, and less C4 was detected for both in SSc patients. Conditioned analysis suggests that C4 genetics strongly contributes to the SSc association within the major histocompatibility complex locus and highlights classical alleles and amino acid variants of HLA-DRB1 and HLA-DPB1 as C4-independent signals.
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Affiliation(s)
- Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
| | - Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain.
| | | | | | - Shervin Assassi
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susanna M Proudman
- Rheumatology Unit, Royal Adelaide Hospital and University of Adelaide, Adelaide, SA, Australia
| | - Mandana Nikpour
- The University of Melbourne at St. Vincent's Hospital, Melbourne, VIC, Australia
| | | | - Gianluca Moroncini
- Department of Clinical and Molecular Science, Università Politecnica delle Marche e Ospedali Riuniti, Ancona, Italy
| | | | - Gisela Orozco
- Center 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 Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Anne Barton
- Center 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 Center, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ariane L Herrick
- Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Northern care Alliance 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
| | - Carmen Fonseca
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Marta Eugenia Alarcón-Riquelme
- Center for Genomics and Oncological Research (GENYO), Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain
| | - Timothy R D J Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Christopher P Denton
- Center for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Maureen D Mayes
- Department of Rheumatology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Spain.
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5
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Hu X, Li Z, Ji M, Lin Y, Chen Y, Lu J. Identification of cellular heterogeneity and immunogenicity of chondrocytes via single-cell RNA sequencing technique in human osteoarthritis. Front Pharmacol 2022; 13:1004766. [PMID: 36249797 PMCID: PMC9562112 DOI: 10.3389/fphar.2022.1004766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/17/2022] [Indexed: 11/25/2022] Open
Abstract
Background: Osteoarthritis (OA) has placed a heavy burden to the economy and humanistics. To explore the biological functions and markers of chondrocytes contributes significantly to the accurate diagnosis and targeted treatment of OA. Methods: We systematically analyzed the immunogenicity and biological function of varied chondrocytes at single cell resolution, and identified the chondrocyte subtypes and biomarkers involved in the development of OA, which are verified in the bulk sequencing cohort. Results: Based on previous study, we defined eight subtypes of chondrocytes with different biological functions, finding out that effector chondrocytes (ECs) and fibrocartilage chondrocytes (FCs) may promote the development of OA. Compared with other chondrocytes, ECs and FCs show stronger immunogenicity. FCs mainly affects the degeneration of cartilage caused by fibrous degeneration, while ECs mainly exerts immune function and causes tissues inflammation. In addition, the canonical gene markers of EC and FC assist with the prediction of OA, which has been verified in Bulk RNA sequencing data from two GEO datasets. Conclusion: In summary, this study provides a new perspective for the exploration of cellular heterogeneity and pathophysiology in OA and will make contribution to the accurate diagnosis and targeted treatment of OA.
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Affiliation(s)
- Xinyue Hu
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Zhuang Li
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Mingliang Ji
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yucheng Lin
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Yuzhi Chen
- School of Medicine, Southeast University, Nanjing, Jiangsu, China
| | - Jun Lu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu, China
- *Correspondence: Jun Lu,
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6
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Wang H, Liu M. Complement C4, Infections, and Autoimmune Diseases. Front Immunol 2021; 12:694928. [PMID: 34335607 PMCID: PMC8317844 DOI: 10.3389/fimmu.2021.694928] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/21/2021] [Indexed: 02/05/2023] Open
Abstract
Complement C4, a key molecule in the complement system that is one of chief constituents of innate immunity for immediate recognition and elimination of invading microbes, plays an essential role for the functions of both classical (CP) and lectin (LP) complement pathways. Complement C4 is the most polymorphic protein in complement system. A plethora of research data demonstrated that individuals with C4 deficiency are prone to microbial infections and autoimmune disorders. In this review, we will discuss the diversity of complement C4 proteins and its genetic structures. In addition, the current development of the regulation of complement C4 activation and its activation derivatives will be reviewed. Moreover, the review will provide the updates on the molecule interactions of complement C4 under the circumstances of bacterial and viral infections, as well as autoimmune diseases. Lastly, more evidence will be presented to support the paradigm that links microbial infections and autoimmune disorders under the condition of the deficiency of complement C4. We provide such an updated overview that would shed light on current research of complement C4. The newly identified targets of molecular interaction will not only lead to novel hypotheses on the study of complement C4 but also assist to propose new strategies for targeting microbial infections, as well as autoimmune disorders.
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Affiliation(s)
- Hongbin Wang
- Master Program of Pharmaceutical Sciences College of Graduate Studies, California Northstate University, Elk Grove, CA, United States.,Department of Pharmaceutical and Biomedical Sciences College of Pharmacy, California Northstate University, Elk Grove, CA, United States.,Department of Basic Science College of Medicine, California Northstate University, Elk Grove, CA, United States
| | - Mengyao Liu
- Master Program of Pharmaceutical Sciences College of Graduate Studies, California Northstate University, Elk Grove, CA, United States
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7
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Bakry O, Shoeib M, Soliman S, Kamal L. Neutrophil Cytosolic Factor-1 Genotyping in Acne Vulgaris. Skin Pharmacol Physiol 2021; 34:51-56. [PMID: 33596590 DOI: 10.1159/000513053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022]
Abstract
Acne vulgaris (AV) is a very common inflammatory dermatosis. It has a complex pathogenesis in which oxidative stress plays an important role. Neutrophil cytosolic factor (NCF)-1 gene encodes for NCF1 protein which shares in reactive oxygen species (ROS) production. Copy number variation (CNV) is a type of genetic variance in which gene copies are duplicated or deleted. The current work aimed to detect the association between NCF1 CNV and NCF-1 genotypes and AV to explore their possible role in increased disease risk or influencing its clinical presentation. Twenty-five cases with AV and 25 age- and gender-matched healthy volunteers were selected. NCF1 CNV and genotypes were determined using quantitative real-time polymerase chain reaction. NCF1 copy number was significantly increased in patients compared to the control group (p = 0.02). Higher copy number increased the risk of occurrence of AV by about 4-fold. The NCF1 genotype was more prevalent in patients (72%) compared to NCF1B (24%) and NCF1C (4%) variants, while NCF1B and NCF1C variants (68%) were more prevalent in the control group. The NCF1B genotype decreased the risk of occurrence of AV by 0.2-fold. NCF1 was significantly associated with cases more than controls (p = 0.005). It increased the risk of occurrence of acne by 5.4-fold. There was significant association between NCF1 copy number and disease duration where higher number was associated with long disease duration (p = 0.03). Higher copy number was also associated with the NCF1 genotype (p = 0.01). This study suggests that increased copy number of NCF1 gene may be a predisposing factor for AV development. However, the presence of NCF1B and NCF1C variants lowers ROS production and subsequently decreases the risk of development of AV.
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Affiliation(s)
- Ola Bakry
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt,
| | - Mohamed Shoeib
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
| | - Shimaa Soliman
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt.,Medical Biochemistry Unit, Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Lamiaa Kamal
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
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8
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Copy number variation: Characteristics, evolutionary and pathological aspects. Biomed J 2021; 44:548-559. [PMID: 34649833 PMCID: PMC8640565 DOI: 10.1016/j.bj.2021.02.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Copy number variants (CNVs) were the subject of extensive research in the past years. They are common features of the human genome that play an important role in evolution, contribute to population diversity, development of certain diseases, and influence host–microbiome interactions. CNVs have found application in the molecular diagnosis of many diseases and in non-invasive prenatal care, but their full potential is only emerging. CNVs are expected to have a tremendous impact on screening, diagnosis, prognosis, and monitoring of several disorders, including cancer and cardiovascular disease. Here, we comprehensively review basic definitions of the term CNV, outline mechanisms and factors involved in CNV formation, and discuss their evolutionary and pathological aspects. We suggest a need for better defined distinguishing criteria and boundaries between known types of CNVs.
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9
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Aghaei H, Farhadi E, Akhtari M, Shahba S, Mostafaei S, Jamshidi A, Poursani S, Mahmoudi M, Nicknam MH. Copy number variation of IL17RA gene and its association with the ankylosing spondylitis risk in Iranian patients: a case-control study. BMC MEDICAL GENETICS 2020; 21:147. [PMID: 32650733 PMCID: PMC7350761 DOI: 10.1186/s12881-020-01078-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Background Ankylosing spondylitis (AS) is considered as a subtype of spondyloarthritis (SpA) that mainly leads to fatigue, stiffness, spinal ankylosis, and impaired physical functions with reduced quality of life. Interleukin (IL)-17A provokes additional inflammatory mediators and recruits immune cells to the inflamed site. IL17 expression increased in various inflammatory disorders including psoriasis, rheumatoid arthritis, multiple sclerosis, crohn’s disease, and ankylosing spondylitis. The current study aimed to evaluate the association of IL17RA copy number changes with the susceptibility to AS and their correlation to IL17RA expression in Iranian population. Methods IL17RA copy number genotyping assessments were carried out in 455 AS patients and 450 healthy controls, using custom TaqMan CNV assays. TaqMan primers and probe were located in Chr.22:17109553 based on pre-designed IL17RA Copy Number Assay ID, Hs02339506_cn. mRNA expression of IL17RA was also measured by SYBR Green real-time polymerase chain reaction (PCR). Results A IL17RA copy number loss (< 2) was associated with AS compared to 2 copies as reference (OR:2.18, 95% CI: (1.38–3.44), P-value < 0.001) and increased the risk of AS. IL17RA mRNA expression showed a significant increase in peripheral blood mononuclear cells (PBMCs) of all AS individuals than controls. The mRNA expression level of 2 copies was significantly higher in AS patients. Conclusions Our findings revealed that a low copy number of IL17RA might confer a susceptibility risk to AS. However, it is probably not directly involved in the regulation of IL17RA mRNA expression. Epigenetic mechanisms like DNA methylation, post-transcriptional, and -translational modifications that regulate the expression of the genes may contribute in upregulation of IL17RA mRNA expression in the loss of gene copy number condition.
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Affiliation(s)
- Hamideh Aghaei
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Shahba
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shayan Mostafaei
- Department of Biostatistics, School of Health, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Poursani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran. .,Inflammation Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Hossein Nicknam
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran. .,Molecular Immunology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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10
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Zhang M, Gu Y, Huang S, Lou Q, Xie Q, Xu Z, Chen Y, Pan F, Xu S, Liu S, Tao J, Liu S, Cai J, Chen P, Qian L, Wang C, Liang C, Huang H, Pan H, Su H, Cheng J, Zhang Y, Hu W, Zou Y. Copy number variations and polymorphisms in HSP90AB1 and risk of systemic lupus erythematosus and efficacy of glucocorticoids. J Cell Mol Med 2019; 23:5340-5348. [PMID: 31124601 PMCID: PMC6653051 DOI: 10.1111/jcmm.14410] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 05/04/2019] [Accepted: 05/08/2019] [Indexed: 11/26/2022] Open
Abstract
The aim of our study was to assess the associations of HSP90AB1 copy number variations (CNVs) with systemic lupus erythematosus (SLE) risk and glucocorticoids (GCs) efficacy, as well as the relationship between HSP90AB1 single‐nucleotide polymorphisms (SNPs) and GCs efficacy. HSP90AB1 CNVs and SLE risk were analysed in 519 patients and 538 controls. Patients treated with GCs were followed up for 12 weeks and were divided into sensitive and insensitive groups to investigate the effects of CNVs (419 patients) and SNPs (457 patients) on the efficacy of GCs. Health‐related quality of life (HRQoL) was also measured by SF‐36 at baseline and week 12 to explore the relationship between CNVs/SNPs and HRQoL improvements in Chinese SLE patients. Our results indicated a statistically significant association between HSP90AB1 CNVs and SLE (PBH = 0.039), and this association was more pronounced in the female subgroup (PBH = 0.039). However, we did not detect association of HSP90AB1 CNVs/SNPs with efficacy of GCs. But we found a marginal association between SNP rs13296 and improvement in Role‐emotional, while this association was not strong enough to survive in the multiple testing corrections. Collectively, our findings suggest that the copy number of HSP90AB1 is associated with SLE susceptibility. But copy number and polymorphisms of HSP90AB1 may not be associated with efficacy of GCs.
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Affiliation(s)
- Man Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Yuanyuan Gu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Shunwei Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Qiuyue Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Qiaomei Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Zhiwei Xu
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yangfan Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Shengqian Xu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shengxiu Liu
- Institute of Dermatology and Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jinhui Tao
- Department of Rheumatology and Immunology, Anhui Medical University Affiliated Provincial Hospital, Hefei, China
| | - Shuang Liu
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jing Cai
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiling Chen
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Long Qian
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chunhuai Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chunmei Liang
- Department of Laboratory Medicine, School of Public Health, Anhui Medical University, Hefei, China
| | - Hailiang Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Haifeng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Hong Su
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
| | - Jian Cheng
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yuzhou Zhang
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Wenbiao Hu
- School of Public Health and Social Work, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China.,The Key Laboratory of Anhui Medical Autoimmune Diseases, Hefei, China
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11
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Mehra C, Sil A, Hedderly T, Kyriakopoulos M, Lim M, Turnbull J, Happe F, Baird G, Absoud M. Childhood disintegrative disorder and autism spectrum disorder: a systematic review. Dev Med Child Neurol 2019; 61:523-534. [PMID: 30548847 DOI: 10.1111/dmcn.14126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2018] [Indexed: 12/01/2022]
Abstract
AIM In an attempt to clarify the debate surrounding the diagnostic validity of childhood disintegrative disorder (CDD), we systematically reviewed its characteristics and compared it with autism spectrum disorder (ASD). METHOD Four databases were searched (PubMed, PsycINFO, Embase, and Web of Science). Included articles had participants with CDD, as defined by symptoms present in the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision and the International Classification of Diseases, 10th Revision. Comparison groups were those with ASD and ASD with regression. Case studies were excluded. RESULTS Twenty articles, comprising 96 participants with CDD (80 males, 16 females), were included. Most studies were cross-sectional. The prevalence of CDD was 1.1 to 9.2 per 100 000, with a mean age at regression of 3 years 2 months (SD 1y 1mo), with a range of 2 years to 7 years. In addition to core CDD symptoms, most had intellectual impairment, anxiety, challenging behaviours, and regressed in toileting skills. Participants with CDD and ASD shared core diagnostic and extra-diagnostic features. However, participants with CDD seemed to have more severe symptoms and a different symptom profile, including apparently typical development before regression, faster regression, more affective symptoms, and more global developmental deficit. Possible genetic and autoimmune neurobiological mechanisms were identified. INTERPRETATION There is limited high-quality evidence describing the aetiology and outcomes of CDD. However, given the qualitative and prognostic differences between ASD and CDD, we recommend that future diagnostic criteria should distinguish late-onset regression.
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Affiliation(s)
- Chirag Mehra
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Annesha Sil
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Tammy Hedderly
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Marinos Kyriakopoulos
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National and Specialist Acorn Lodge Inpatient Children's Unit, Child and Adolescent Mental Health Clinical Academic Group, South London and the Maudsley NHS Foundation Trust, London, UK
| | - Ming Lim
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Jessica Turnbull
- Evelina London Community Children's Services, Sunshine House Children and Young People's Development Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Francesca Happe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gillian Baird
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Michael Absoud
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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12
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Shahba S, Jafari Shakib R, Jamshidi A, Vojdanian M, Akhtari M, Aslani S, Poursani S, Nikokar I, Mahmoudi M. Association study of copy number variation in BMP8A gene with the risk of ankylosing spondylitis in Iranian population. J Cell Biochem 2019; 120:8359-8365. [PMID: 30485530 DOI: 10.1002/jcb.28120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Copy number variation (CNV) of DNA segments has been considered as an important component of genetic variation, affecting the quality and quantity of gene expression. Bone morphogenic protein 8A (BMP8A) has been reported to function in bone formation. With respect to the bone and joint complications in ankylosing spondylitis (AS), this investigation aimed to study the role of BMP8A gene CNV in impressing the gene expression as well as the disease risk. METHODS A total of 900 individuals, including 450 patients with AS and 450 healthy controls were enrolled. The copy numbers of BMP8A gene were detected by TaqMan real-time polymerase chain reaction (PCR) method. BMP8A messenger RNA (mRNA) transcript level in peripheral blood mononuclear cells (PBMCs) was also measured by SYBR Green real-time gene expression PCR method. RESULTS No significant association of BMP8A copy number was detected with the risk of AS. BMP8A mRNA expression level was significantly downregulated in patients compared with controls. mRNA expression level of BMP8A in both AS patients with and without syndesmophyte was significantly lower than the healthy control group. There was no correlation between the mRNA expression level of BMP8A and both demographic and clinical data of the patients. CONCLUSIONS Although BMP8A gene expression was downregulated in patients with AS, its copy number could not affect the transcript level of BMP8A gene in PBMCs and was not associated with susceptibility to AS in Iranian population. BMP8a may take into account as an indicator of bone formation process in AS, but it seems that mechanisms other than CNV may regulate this protein.
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Affiliation(s)
- Sara Shahba
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran.,Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Jafari Shakib
- Department of Immunology, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ahmadreza Jamshidi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Vojdanian
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Akhtari
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Saeed Aslani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Poursani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Iraj Nikokar
- Laboratory of Microbiology and Immunology of Infectious Diseases, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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13
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Yau ACY, Holmdahl R. Rheumatoid arthritis: identifying and characterising polymorphisms using rat models. Dis Model Mech 2017; 9:1111-1123. [PMID: 27736747 PMCID: PMC5087835 DOI: 10.1242/dmm.026435] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Rheumatoid arthritis is a chronic inflammatory joint disorder characterised by erosive inflammation of the articular cartilage and by destruction of the synovial joints. It is regulated by both genetic and environmental factors, and, currently, there is no preventative treatment or cure for this disease. Genome-wide association studies have identified ∼100 new loci associated with rheumatoid arthritis, in addition to the already known locus within the major histocompatibility complex II region. However, together, these loci account for only a modest fraction of the genetic variance associated with this disease and very little is known about the pathogenic roles of most of the risk loci identified. Here, we discuss how rat models of rheumatoid arthritis are being used to detect quantitative trait loci that regulate different arthritic traits by genetic linkage analysis and to positionally clone the underlying causative genes using congenic strains. By isolating specific loci on a fixed genetic background, congenic strains overcome the challenges of genetic heterogeneity and environmental interactions associated with human studies. Most importantly, congenic strains allow functional experimental studies be performed to investigate the pathological consequences of natural genetic polymorphisms, as illustrated by the discovery of several major disease genes that contribute to arthritis in rats. We discuss how these advances have provided new biological insights into arthritis in humans.
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Affiliation(s)
- Anthony C Y Yau
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Rikard Holmdahl
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77 Stockholm, Sweden Southern Medical University, Guangzhou 510515, China
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14
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Yau ACY, Lönnblom E, Zhong J, Holmdahl R. Influence of hydrocarbon oil structure on adjuvanticity and autoimmunity. Sci Rep 2017; 7:14998. [PMID: 29118363 PMCID: PMC5678145 DOI: 10.1038/s41598-017-15096-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 10/18/2017] [Indexed: 02/07/2023] Open
Abstract
Mineral oils are extensively used in our daily life, in food, cosmetics, biomedicine, vaccines and in different industrial applications. However, exposure to these mineral oils has been associated with immune adjuvant effects and the development of autoimmune diseases. Here we investigate the structural impacts of the hydrocarbon oil molecules on their adjuvanticity and autoimmunity. First, we showed that hydrocarbon oil molecules with small atomic differences could result in experimental arthritis in DA rats differing in disease severity, incidence, weight change and serum levels of acute phase proteins. Injection of these hydrocarbon oils resulted in the activation, proliferation and elevated expression of Th1 and especially Th17 cytokines by the T cells, which correlate with the arthritogenicity of the T cells. Furthermore, the more arthritogenic hydrocarbon oils resulted in an increased production of autoantibodies against cartilage joint specific, triple-helical type II collagen epitopes. When injected together with ovalbumin, the more arthritogenic hydrocarbon oils resulted in an increased production of αβ T cell-dependent anti-ovalbumin antibodies. This study shows the arthritogenicity of hydrocarbon oils is associated with their adjuvant properties with implications to not only arthritis research but also other diseases and medical applications such as vaccines in which oil adjuvants are involved.
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Affiliation(s)
- Anthony C Y Yau
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Erik Lönnblom
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Jianghong Zhong
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 77, Stockholm, Sweden.
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15
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Typiak M, Rębała K, Haraś A, Skotarczak M, Słomiński JM, Dubaniewicz A. Copy number variation of FCGR genes in etiopathogenesis of sarcoidosis. PLoS One 2017; 12:e0177194. [PMID: 28472129 PMCID: PMC5417662 DOI: 10.1371/journal.pone.0177194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
We have previously revealed that, in contrast to polymorphism of FCGR2B and FCGR3B, polymorphism of FCGR2A, FCGR2C and FCGR3A genes, encoding receptors for Fc fragment of immunoglobulin G (Fcγ receptors), play a role in increased level of circulating immune complexes with occurrence of Mycobacterium tuberculosis heat shock proteins in patients with sarcoidosis. However, this immunocomplexemia might also be caused by decreased clearance by immune cells due to a changed copy number of FCGR genes. Thus, the next step of our study was to evaluate copy number variation of FCGR2A, FCGR2B, FCGR2C, FCGR3A and FCGR3B in this disease. The analysis was carried out by real-time quantitative PCR on 104 patients and 110 healthy volunteers. Despite previously detected variation in allele/genotype frequencies of FCGR in sarcoidosis and its particular stages, there was no copy number variation of the tested genes between sarcoidosis or its stages and healthy control, as well as between stages themselves. A relevant increase in copy number of FCGR2C and FCGR3B in Stage IV of sarcoidosis vs. other stages and controls was detected, but this observation was based on a limited number of Stage IV patients. Hence, polymorphism of FCGR genes seems to be more important than their copy number variation in etiopathogenesis of sarcoidosis in patients from the Polish population.
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Affiliation(s)
- Marlena Typiak
- Department of Pulmonology, Medical University of Gdansk, Gdansk, Poland
| | - Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Agnieszka Haraś
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Monika Skotarczak
- 2nd Department of Radiology, Medical University of Gdansk, Gdansk, Poland
| | | | - Anna Dubaniewicz
- Department of Pulmonology, Medical University of Gdansk, Gdansk, Poland
- * E-mail:
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16
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Li N, Zhang J, Liao D, Yang L, Wang Y, Hou S. Association between C4, C4A, and C4B copy number variations and susceptibility to autoimmune diseases: a meta-analysis. Sci Rep 2017; 7:42628. [PMID: 28205620 PMCID: PMC5311832 DOI: 10.1038/srep42628] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/04/2017] [Indexed: 12/16/2022] Open
Abstract
Although several studies have investigated the association between C4, C4A, and C4B gene copy number variations (CNVs) and susceptibility to autoimmune diseases, the results remain inconsistency for those diseases. Thus, in this study, a comprehensive meta-analysis was conducted to assess the role of C4, C4A, and C4B CNVs in autoimmune diseases in different ethnic groups. A total of 16 case-control studies described in 12 articles (8663 cases and 11099 controls) were included in this study. The pooled analyses showed that a low C4 gene copy number (GCN) (<4) was treated as a significant risk factor (odds ratio [OR] = 1.46, 95% confidence interval [CI] = 1.19–1.78) for autoimmune diseases compared with a higher GCN (>4). The pooled statistical results revealed that low C4 (<4) and low C4A (<2) GCNs could be risk factors for systemic lupus erythematosus (SLE) in Caucasian populations. Additionally, the correlation between C4B CNVs and all type of autoimmune diseases could not be confirmed by the current meta-analysis (OR = 1.07, 95% CI = 0.93–1.24). These data suggest that deficiency or absence of C4 and C4A CNVs may cause susceptibility to SLE.
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Affiliation(s)
- Na Li
- Basic Medical College, Chongqing Medical University, Chongqing, China
| | - Jun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Liao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Lu Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yingxiong Wang
- Basic Medical College, Chongqing Medical University, Chongqing, China.
| | - Shengping Hou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China. .,Chongqing Eye Institute and Chongqing Key Laboratory of Ophthalmology, Chongqing, China.
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17
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Copy-number variation of housekeeping gene rpl13a in rat strains selected for nervous system excitability. Mol Cell Probes 2017; 33:11-15. [PMID: 28192165 DOI: 10.1016/j.mcp.2017.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/07/2017] [Accepted: 02/07/2017] [Indexed: 11/20/2022]
Abstract
We evaluated copy number variation (CNV) for four genes in rat strains differing in nervous system excitability. rpl13a copy number is significantly reduced in hippocampus and bone marrow in rats with a high excitability threshold and stress. The observed phenomenon may be associated with a role for rpl13a in lipid metabolism.
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18
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Zmienko A, Samelak-Czajka A, Kozlowski P, Szymanska M, Figlerowicz M. Arabidopsis thaliana population analysis reveals high plasticity of the genomic region spanning MSH2, AT3G18530 and AT3G18535 genes and provides evidence for NAHR-driven recurrent CNV events occurring in this location. BMC Genomics 2016; 17:893. [PMID: 27825302 PMCID: PMC5101643 DOI: 10.1186/s12864-016-3221-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/27/2016] [Indexed: 12/28/2022] Open
Abstract
Background Intraspecies copy number variations (CNVs), defined as unbalanced structural variations of specific genomic loci, ≥1 kb in size, are present in the genomes of animals and plants. A growing number of examples indicate that CNVs may have functional significance and contribute to phenotypic diversity. In the model plant Arabidopsis thaliana at least several hundred protein-coding genes might display CNV; however, locus-specific genotyping studies in this plant have not been conducted. Results We analyzed the natural CNVs in the region overlapping MSH2 gene that encodes the DNA mismatch repair protein, and AT3G18530 and AT3G18535 genes that encode poorly characterized proteins. By applying multiplex ligation-dependent probe amplification and droplet digital PCR we genotyped those genes in 189 A. thaliana accessions. We found that AT3G18530 and AT3G18535 were duplicated (2–14 times) in 20 and deleted in 101 accessions. MSH2 was duplicated in 12 accessions (up to 12-14 copies) but never deleted. In all but one case, the MSH2 duplications were associated with those of AT3G18530 and AT3G18535. Considering the structure of the CNVs, we distinguished 5 genotypes for this region, determined their frequency and geographical distribution. We defined the CNV breakpoints in 35 accessions with AT3G18530 and AT3G18535 deletions and tandem duplications and showed that they were reciprocal events, resulting from non-allelic homologous recombination between 99 %-identical sequences flanking these genes. The widespread geographical distribution of the deletions supported by the SNP and linkage disequilibrium analyses of the genomic sequence confirmed the recurrent nature of this CNV. Conclusions We characterized in detail for the first time the complex multiallelic CNV in Arabidopsis genome. The region encoding MSH2, AT3G18530 and AT3G18535 genes shows enormous variation of copy numbers among natural ecotypes, being a remarkable example of high Arabidopsis genome plasticity. We provided the molecular insight into the mechanism underlying the recurrent nature of AT3G18530-AT3G18535 duplications/deletions. We also performed the first direct comparison of the two leading experimental methods, suitable for assessing the DNA copy number status. Our comprehensive case study provides foundation information for further analyses of CNV evolution in Arabidopsis and other plants, and their possible use in plant breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3221-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Maja Szymanska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland. .,Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965, Poznan, Poland.
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19
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Jiang W, Johnson C, Simecek N, López-Álvarez MR, Di D, Trowsdale J, Traherne JA. qKAT: a high-throughput qPCR method for KIR gene copy number and haplotype determination. Genome Med 2016; 8:99. [PMID: 27686127 PMCID: PMC5041586 DOI: 10.1186/s13073-016-0358-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/15/2016] [Indexed: 12/15/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs), expressed on natural killer cells and T cells, have considerable biomedical relevance playing significant roles in immunity, pregnancy and transplantation. The KIR locus is one of the most complex and polymorphic regions of the human genome. Extensive sequence homology and copy number variation makes KIRs technically laborious and expensive to type. To aid the investigation of KIRs in human disease we developed a high-throughput, multiplex real-time polymerase chain reaction method to determine gene copy number for each KIR locus. We used reference DNA samples to validate the accuracy and a cohort of 1698 individuals to evaluate capability for precise copy number discrimination. The method provides improved information and identifies KIR haplotype alterations that were not previously visible using other approaches.
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Affiliation(s)
- W Jiang
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - C Johnson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - N Simecek
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - M R López-Álvarez
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - D Di
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - J Trowsdale
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - J A Traherne
- Immunology Division, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
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20
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Budzko L, Marcinkowska-Swojak M, Jackowiak P, Kozlowski P, Figlerowicz M. Copy number variation of genes involved in the hepatitis C virus-human interactome. Sci Rep 2016; 6:31340. [PMID: 27510840 PMCID: PMC4980658 DOI: 10.1038/srep31340] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/18/2016] [Indexed: 02/06/2023] Open
Abstract
Copy number variation (CNV) is a newly discovered form of intra-species genetic polymorphism that is defined as deletions or duplications of genome segments ranging from 1 kbp to several Mbp. CNV accounts for the majority of the genetic variation observed in humans (CNV regions cover more than 10% of the human genome); therefore, it may significantly influence both the phenotype and susceptibility to various diseases. Unfortunately, the impact of CNV on a number of diseases, including hepatitis C virus (HCV) infection, remains largely unexplored. Here, we analyzed 421 human genes encoding proteins that have been shown to interact with HCV proteins or genomic RNA (proteins from the HCV-human interactome). We found that 19 of the 421 candidate genes are located in putative CNV regions. For all of these genes, copy numbers were determined for European, Asiatic and African populations using the multiplex ligation-dependent amplification (MLPA) method. As a result, we identified 4 genes, IGLL1, MLLT4, PDPK1, PPP1R13L, for which the CN-genotype ranged from 1 to 6. All of these genes are involved in host-virus interaction; thus, their polymorphism has a potential impact on the development of HCV infection and/or therapy outcome.
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Affiliation(s)
- Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | | | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
| | - Piotr Kozlowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, Poznan, Poland
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21
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Stangler Herodež Š, Fijavž L, Zagradišnik B, Kokalj Vokač N. Detection of mutations in the CYP21A2 gene: genotype-phenotype correlation in Slovenian couples with conceiving problems. Balkan J Med Genet 2016; 18:25-32. [PMID: 27785393 PMCID: PMC5026265 DOI: 10.1515/bjmg-2015-0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The objective of this study was to compare the CYP 21A2 genetic profiles of couples with unexplained fertility problems (UFP) with genetic profiles of healthy controls (HCs). Furthermore, we analyzed associations between mutations in the CYP21A2 gene and various clinical and laboratory parameters. Allele-specific polymerase chain reaction (PCR) was used in 638 probands with UFP and 200 HCs. Statistic analysis with χ2 was used to study the association of mutations with infertility. The effect of mutations on particular clinical and laboratory parameters was assessed with the analysis of variance (ANOVA) test. With regard to the CYP21A2 gene, 0.6% of probands with UFP and 0.5% of HCs were positive for the c.290-13A/C>G mutation; 0.6% of probands with UFP and 1.5% of HCs were positive for the p.I172N mutation; there were no probands with UFP positive for the p.P30L mutation, whereas 0.5% of HCs were; and 0.2% of probands with UFP and 0.5% of HCs were found to have the p.V281L mutation. We found a significant association between c.290-13A/C>G mutation and the frequency of significant hormone deviations (χ2 = 6.997, p = 0.008). Similar association was also observed between the c.29013A/C>G mutation and the frequency of polycystic ovary syndrome (PCOS) (χ2 = 16.775, p = 0.000). Our findings indicate that no significant difference in the prevalence of CYP 21A2 mutations can be found in probands with UFP when compared with HCs without infertility history. The results also imply the significant association of the c.290-13A/ C>G mutation in the CYP21A2 gene, not only with the frequency of PCOS, but also with the frequency of significant hormone deviations.
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Affiliation(s)
- Š Stangler Herodež
- Laboratory of Medical Genetics, University Clinical Centre Maribor, Maribor, Slovenia
| | - L Fijavž
- Medical Faculty, University of Maribor, Maribor, Slovenia
| | - B Zagradišnik
- Laboratory of Medical Genetics, University Clinical Centre Maribor, Maribor, Slovenia
| | - N Kokalj Vokač
- Laboratory of Medical Genetics, University Clinical Centre Maribor, Maribor, Slovenia; Medical Faculty, University of Maribor, Maribor, Slovenia
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Rodriguez-Nunez I, Wcisel DJ, Litman RT, Litman GW, Yoder JA. The identification of additional zebrafish DICP genes reveals haplotype variation and linkage to MHC class I genes. Immunogenetics 2016; 68:295-312. [PMID: 26801775 DOI: 10.1007/s00251-016-0901-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
Abstract
Bony fish encode multiple multi-gene families of membrane receptors that are comprised of immunoglobulin (Ig) domains and are predicted to function in innate immunity. One of these families, the diverse immunoglobulin (Ig) domain-containing protein (DICP) genes, maps to three chromosomal loci in zebrafish. Most DICPs possess one or two Ig ectodomains and include membrane-bound and secreted forms. Membrane-bound DICPs include putative inhibitory and activating receptors. Recombinant DICP Ig domains bind lipids with varying specificity, a characteristic shared with mammalian CD300 and TREM family members. Numerous DICP transcripts amplified from different lines of zebrafish did not match the zebrafish reference genome sequence suggesting polymorphic and haplotypic variation. The expression of DICPs in three different lines of zebrafish has been characterized employing PCR-based strategies. Certain DICPs exhibit restricted expression in adult tissues whereas others are expressed ubiquitously. Transcripts of a subset of DICPs can be detected during embryonic development suggesting roles in embryonic immunity or other developmental processes. Transcripts representing 11 previously uncharacterized DICP sequences were identified. The assignment of two of these sequences to an unplaced genomic scaffold resulted in the identification of an alternative DICP haplotype that is linked to a MHC class I Z lineage haplotype on zebrafish chromosome 3. The linkage of DICP and MHC class I genes also is observable in the genomes of the related grass carp (Ctenopharyngodon idellus) and common carp (Cyprinus carpio) suggesting that this is a shared character with the last common Cyprinidae ancestor.
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Affiliation(s)
- Ivan Rodriguez-Nunez
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Dustin J Wcisel
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA
| | - Ronda T Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL, 33701, USA
| | - Gary W Litman
- Department of Pediatrics, University of South Florida Morsani College of Medicine, USF/ACH Children's Research Institute, 140 7th Avenue South, St. Petersburg, FL, 33701, USA.,Department of Molecular Genetics, All Children's Hospital Johns Hopkins Medicine, 501 6th Avenue South, St. Petersburg, FL, 33701, USA
| | - Jeffrey A Yoder
- Department of Molecular Biomedical Sciences and Center for Comparative Medicine and Translational Research, North Carolina State University, 1060 William Moore Drive, Raleigh, NC, 27607, USA.
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23
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Hameed AF, Jaradat S, Al-Musawi BM, Sharquie K, Ibrahim MJ, Hayani RK, Norgauer J. Association of Higher Defensin β-4 Genomic Copy Numbers with Behçet's Disease in Iraqi Patients. Sultan Qaboos Univ Med J 2015; 15:e491-5. [PMID: 26629375 DOI: 10.18295/squmj.2015.15.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 06/11/2015] [Accepted: 07/21/2015] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES Behçet's disease (BD) is an immune-mediated small vessel systemic vasculitis. Human β-defensins are antimicrobial peptides associated with many inflammatory diseases and are encoded by the β-defensin family of multiple-copy genes. However, their role in BD necessitates further investigation. The aim of the present study was to investigate the possible association of BD in its various clinical forms with defensin β-4 (DEFB4) genomic copy numbers. METHODS This case-control study was conducted from January to September 2011 and included 50 control subjects and 27 unrelated Iraqi BD patients registered at Baghdad Teaching Hospital, Bagdad, Iraq. Copy numbers of the DEFB4 gene were determined using the comparative cycle threshold method by duplex real-time polymerase chain reaction technology at the Department of Dermatology of Jena University Hospital, Jena, Germany. RESULTS DEFB4 genomic copy numbers were significantly higher in the BD group compared to the control group (P = 0.010). However, no statistically significant association was found between copy numbers and clinical variables within the BD group. CONCLUSION The DEFB4 copy number polymorphism may be associated with BD; however, it is not associated with different clinical manifestations of the disease.
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Affiliation(s)
- Ammar F Hameed
- Departments of Dermatology, College of Medicine, University of Baghdad, Baghdad, Iraq
| | - Sameh Jaradat
- Department of Dermatology, Jena University Hospital, Jena, Germany
| | | | - Khalifa Sharquie
- Departments of Dermatology, College of Medicine, University of Baghdad, Baghdad, Iraq
| | - Mazin J Ibrahim
- Pathology, College of Medicine, University of Baghdad, Baghdad, Iraq
| | - Raafa K Hayani
- Department of Dermatology, Baghdad Teaching Hospital, Baghdad, Iraq
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Allelic and copy-number variations of FcγRs affect granulocyte function and susceptibility for autoimmune blistering diseases. J Autoimmun 2015; 61:36-44. [PMID: 26032265 DOI: 10.1016/j.jaut.2015.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/05/2015] [Accepted: 05/06/2015] [Indexed: 01/03/2023]
Abstract
Low-affinity Fcγ receptors (FcγR) bridge innate and adaptive immune responses. In many autoimmune diseases, these receptors act as key mediators of the pathogenic effects of autoantibodies. Genes encoding FcγR exhibit frequent variations in sequence and gene copy number that influence their functional properties. FcγR variations also affect the susceptibility to systemic autoimmunity, e.g. systemic lupus erythematosus and rheumatoid arthritis. This raises the question whether FcγR variations are also associated with organ-specific autoimmunity, particularly autoantibody-mediated diseases, such as subepidermal autoimmune blistering diseases (AIBD). A multitude of evidence suggests a pathogenic role of neutrophil granulocyte interaction with autoantibodies via FcγR. In a two-stage study, we analyzed whether the FcγR genotype affects neutrophil function and mRNA expression, and consequently, bullous pemphigoid (BP) disease risk. We compared this to findings in pemphigus vulgaris/foliaceus (PV/PF), two Fc-independent AIBDs. Our results indicate that both allele and copy number variation of FcγR genes affect FcγR mRNA expression and reactive oxygen species (ROS) release by granulocytes. Susceptibility of BP was associated with FcγR genotypes that led to a decreased ROS release by neutrophils, indicating an unexpected protective role for these cells. BP and PV/PF differed substantially regarding the FcγR genotype association patterns, pointing towards different disease etiologies.
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25
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Hardy-Weinberg equilibrium revisited for inferences on genotypes featuring allele and copy-number variations. Sci Rep 2015; 5:9066. [PMID: 25765626 PMCID: PMC4357990 DOI: 10.1038/srep09066] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/11/2015] [Indexed: 12/22/2022] Open
Abstract
Copy number variations represent a substantial source of genetic variation and are associated with a plethora of physiological and pathophysiological conditions. Joint copy number and allelic variations (CNAVs) are difficult to analyze and require new strategies to unravel the properties of genotype distributions. We developed a Bayesian hidden Markov model (HMM) approach that allows dissecting intrinsic properties and metastructures of the distribution of CNAVs within populations, in particular haplotype phases of genes with varying copy numbers. As a key feature, this approach incorporates an extension of the Hardy-Weinberg equilibrium, allowing both a comprehensive and parsimonious model design. We demonstrate the quality of performance and applicability of the HMM approach with a real data set describing the Fcγ receptor (FcγR) gene region. Our concept, using a dynamic process to analyze a static distribution, establishes the basis for a novel understanding of complex genomic data sets.
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Cooper NJ, Shtir CJ, Smyth DJ, Guo H, Swafford AD, Zanda M, Hurles ME, Walker NM, Plagnol V, Cooper JD, Howson JMM, Burren OS, Onengut-Gumuscu S, Rich SS, Todd JA. Detection and correction of artefacts in estimation of rare copy number variants and analysis of rare deletions in type 1 diabetes. Hum Mol Genet 2014; 24:1774-90. [PMID: 25424174 PMCID: PMC4381751 DOI: 10.1093/hmg/ddu581] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Copy number variants (CNVs) have been proposed as a possible source of ‘missing heritability’ in complex human diseases. Two studies of type 1 diabetes (T1D) found null associations with common copy number polymorphisms, but CNVs of low frequency and high penetrance could still play a role. We used the Log-R-ratio intensity data from a dense single nucleotide polymorphism (SNP) array, ImmunoChip, to detect rare CNV deletions (rDELs) and duplications (rDUPs) in 6808 T1D cases, 9954 controls and 2206 families with T1D-affected offspring. Initial analyses detected CNV associations. However, these were shown to be false-positive findings, failing replication with polymerase chain reaction. We developed a pipeline of quality control (QC) tests that were calibrated using systematic testing of sensitivity and specificity. The case–control odds ratios (OR) of CNV burden on T1D risk resulting from this QC pipeline converged on unity, suggesting no global frequency difference in rDELs or rDUPs. There was evidence that deletions could impact T1D risk for a small minority of cases, with enrichment for rDELs longer than 400 kb (OR = 1.57, P = 0.005). There were also 18 de novo rDELs detected in affected offspring but none for unaffected siblings (P = 0.03). No specific CNV regions showed robust evidence for association with T1D, although frequencies were lower than expected (most less than 0.1%), substantially reducing statistical power, which was examined in detail. We present an R-package, plumbCNV, which provides an automated approach for QC and detection of rare CNVs that can facilitate equivalent analyses of large-scale SNP array datasets.
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Affiliation(s)
- Nicholas J Cooper
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Corina J Shtir
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Deborah J Smyth
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Hui Guo
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Austin D Swafford
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Manuela Zanda
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, University College London, Darwin Building, London WC1E 6BT, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Neil M Walker
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Vincent Plagnol
- University College London, Darwin Building, London WC1E 6BT, UK
| | - Jason D Cooper
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Joanna M M Howson
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK, Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Worts Causeway, Cambridge CB1 8RN, UK
| | - Oliver S Burren
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics, West Complex, University of Virginia, Charlottesville, VA 22908, USA
| | - Stephen S Rich
- Center for Public Health Genomics, West Complex, University of Virginia, Charlottesville, VA 22908, USA
| | - John A Todd
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, NIHR Cambridge Biomedical Research Centre, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK,
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Singh N, Traisak P, Martin KA, Kaplan MJ, Cohen PL, Denny MF. Genomic alterations in abnormal neutrophils isolated from adult patients with systemic lupus erythematosus. Arthritis Res Ther 2014; 16:R165. [PMID: 25107306 PMCID: PMC4262380 DOI: 10.1186/ar4681] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 07/18/2014] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION Patients with systemic lupus erythematosus (SLE) have an abnormal population of neutrophils, called low-density granulocytes (LDGs), that express the surface markers of mature neutrophils, yet their nuclear morphology resembles an immature cell. Because a similar discrepancy in maturation status is observed in myelodysplasias, and disruption of neutrophil development is frequently associated with genomic alterations, genomic DNA isolated from autologous pairs of LDGs and normal-density neutrophils was compared for genomic changes. METHODS Alterations in copy number and losses of heterozygosity (LOH) were detected by cytogenetic microarray analysis. Microsatellite instability (MSI) was detected by capillary gel electrophoresis of fluorescently labeled PCR products. RESULTS Control neutrophils and normal-density SLE neutrophils had similar levels of copy number variations, while the autologous SLE LDGs had an over twofold greater number of copy number alterations per genome. The additional copy number alterations found in LDGs were prevalent in six of the thirteen SLE patients, and occurred preferentially on chromosome 19, 17, 8, and X. These same SLE patients also displayed an increase in LOH. Several SLE patients had a common LOH on chromosome 5q that includes several cytokine genes and a DNA repair enzyme. In addition, three SLE patients displayed MSI. Two patients displayed MSI in greater than one marker, and one patient had MSI and increased copy number alterations. No correlations between genomic instability and immunosuppressive drugs, disease activity or disease manifestations were apparent. CONCLUSIONS The increased level of copy number alterations and LOH in the LDG samples relative to autologous normal-density SLE neutrophils suggests somatic alterations that are consistent with DNA strand break repair, while MSI suggests a replication error-prone status. Thus, the LDGs isolated have elevated levels of somatic alterations that are consistent with genetic damage or genomic instability. This suggests that the LDGs in adult SLE patients are derived from cell progenitors that are distinct from the autologous normal-density neutrophils, and may reflect a role for genomic instability in the disease.
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Affiliation(s)
- Namrata Singh
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
| | - Pamela Traisak
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
| | - Kayla A Martin
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
| | - Mariana J Kaplan
- />Systemic Autoimmunity Branch, Intramural Research Program, NIAMS/NIH, 10 Center Drive, Bethesda, MD 20892 USA
| | - Philip L Cohen
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
- />Temple Autoimmunity Center, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
| | - Michael F Denny
- />Section of Rheumatology, Temple University, 3322 North Broad Street, Philadelphia, PA 19140 USA
- />Department of Microbiology and Immunology, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
- />Temple Autoimmunity Center, Temple University, 3500 North Broad Street, Philadelphia, PA 19140 USA
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28
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Human gene copy number variation and infectious disease. Hum Genet 2014; 133:1217-33. [PMID: 25110110 DOI: 10.1007/s00439-014-1457-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 05/20/2014] [Indexed: 01/05/2023]
Abstract
Variability in the susceptibility to infectious disease and its clinical manifestation can be determined by variation in the environment and by genetic variation in the pathogen and the host. Despite several successes based on candidate gene studies, defining the host variation affecting infectious disease has not been as successful as for other multifactorial diseases. Both single nucleotide variation and copy number variation (CNV) of the host contribute to the host's susceptibility to infectious disease. In this review we focus on CNV, particularly on complex multiallelic CNV that is often not well characterised either directly by hybridisation methods or indirectly by analysis of genotypes and flanking single nucleotide variants. We summarise the well-known examples, such as α-globin deletion and susceptibility to severe malaria, as well as more recent controversies, such as the extensive CNV of the chemokine gene CCL3L1 and HIV infection. We discuss the potential biological mechanisms that could underly any genetic association and reflect on the extensive complexity and functional variation generated by a combination of CNV and sequence variation, as illustrated by the Fc gamma receptor genes FCGR3A, FCGR3B and FCGR2C. We also highlight some understudied areas that might prove fruitful areas for further research.
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29
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Marcinkowska-Swojak M, Klonowska K, Figlerowicz M, Kozlowski P. An MLPA-based approach for high-resolution genotyping of disease-related multi-allelic CNVs. Gene 2014; 546:257-62. [PMID: 24942243 DOI: 10.1016/j.gene.2014.05.072] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 05/31/2014] [Indexed: 12/24/2022]
Abstract
Copy number variation has recently been recognized as an important type of genetic variation that modifies human phenotypes. Copy number variants (CNVs) are being increasingly associated with various human phenotypes and diseases. However, the lack of an appropriate method that allows fast, inexpensive and, most importantly, accurate CNVs genotyping significantly hampers CNV analysis. This limitation especially affects the analysis of multi-allelic CNVs that frequently modify various phenotypes. Recently, we developed a multiplex ligation-dependent probe amplification (MLPA)-based strategy for multiplex copy number genotyping and the validation of candidate CNV-miRNAs. Here we present the adaptation and optimization of this recently developed method for high-resolution genotyping of individual disease-related multi-allelic CNVs. We developed appropriate assays for three well-known and extensively studied CNVs: CNV-CCL3L1, CNV-DEFB, and CNV-UGT2B17, which have been associated with various human phenotypes including inflammation-related and infectious diseases. With the use of these assays we identified several general factors that allow to increase the resolution of the copy number genotyping. Performed experiments confirmed the high reproducibility and accuracy of the obtained genotyping results. The reliability of the results and relatively low per-genotype cost makes this strategy an attractive method for large-scale experiments such as genotype-phenotype association studies.
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Affiliation(s)
- Malgorzata Marcinkowska-Swojak
- European Centre of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Katarzyna Klonowska
- European Centre of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
| | - Marek Figlerowicz
- European Centre of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Poznan University of Technology, Pl. Marii Sklodowskiej-Curie 5, 60-965 Poznan, Poland.
| | - Piotr Kozlowski
- European Centre of Bioinformatics and Genomics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Poznan University of Technology, Pl. Marii Sklodowskiej-Curie 5, 60-965 Poznan, Poland.
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30
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Singer J, Jensen‐Jarolim E. IgE-based immunotherapy of cancer: challenges and chances. Allergy 2014; 69:137-49. [PMID: 24117861 PMCID: PMC4022995 DOI: 10.1111/all.12276] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2013] [Indexed: 12/16/2022]
Abstract
Passive immunotherapy with monoclonal antibodies is an indispensable cornerstone of clinical oncology. Notably, all FDA-approved antibodies comprise the IgG class, although numerous research articles proposed monoclonal antibodies of the IgM, IgG, IgA and IgE classes directed specifically against tumor-associated antigens. In particular, for the IgE isotype class, several recent studies could demonstrate high tumoricidic efficacy. Therefore, this review specifically highlights the latest developments toward IgE-based immunotherapy of cancer. Possible mechanisms and safety aspects of IgE-mediated tumor cell death are discussed with special focus on the attracted immune cells. An outlook is given on how especially comparative oncology could contribute to further developments. Humans and dogs have a highly comparable IgE biology, suggesting that translational AllergoOncology studies in patients with canine cancer could have predictive value for the potential of IgE-based anticancer immunotherapy in human clinical oncology.
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Affiliation(s)
- J. Singer
- Comparative Immunology and Oncology Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
| | - E. Jensen‐Jarolim
- Comparative Immunology and Oncology Institute of Pathophysiology and Allergy Research Medical University of Vienna Vienna Austria
- Comparative Medicine Messerli Research Institute of the University of Veterinary Medicine Vienna Medical University Vienna and University Vienna Vienna Austria
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31
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Sisay S, Pryce G, Jackson SJ, Tanner C, Ross RA, Michael GJ, Selwood DL, Giovannoni G, Baker D. Genetic background can result in a marked or minimal effect of gene knockout (GPR55 and CB2 receptor) in experimental autoimmune encephalomyelitis models of multiple sclerosis. PLoS One 2013; 8:e76907. [PMID: 24130809 PMCID: PMC3793915 DOI: 10.1371/journal.pone.0076907] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 08/26/2013] [Indexed: 12/20/2022] Open
Abstract
Endocannabinoids and some phytocannabinoids bind to CB1 and CB2 cannabinoid receptors, transient receptor potential vanilloid one (TRPV1) receptor and the orphan G protein receptor fifty-five (GPR55). Studies using C57BL/10 and C57BL/6 (Cnr2tm1Zim) CB2 cannabinoid receptor knockout mice have demonstrated an immune-augmenting effect in experimental autoimmune encephalomyelitis (EAE) models of multiple sclerosis. However, other EAE studies in Biozzi ABH mice often failed to show any treatment effect of either CB2 receptor agonism or antagonism on inhibition of T cell autoimmunity. The influence of genetic background on the induction of EAE in endocannabinoid system-related gene knockout mice was examined. It was found that C57BL/6.GPR55 knockout mice developed less severe disease, notably in female mice, following active induction with myelin oligodendrocyte glycoprotein 35-55 peptide. In contrast C57BL/6.CB2 (Cnr2Dgen) receptor knockout mice developed augmented severity of disease consistent with the genetically and pharmacologically-distinct, Cnr2tm1Zim mice. However, when the knockout gene was bred into the ABH mouse background and EAE induced with spinal cord autoantigens the immune-enhancing effect of CB2 receptor deletion was lost. Likewise CB1 receptor and transient receptor potential vanilloid one knockout mice on the ABH background demonstrated no alteration in immune-susceptibility, in terms of disease incidence and severity of EAE, in contrast to that reported in some C57BL/6 mouse studies. Furthermore the immune-modulating influence of GPR55 was marginal on the ABH mouse background. Whilst sedative doses of tetrahydrocannabinol could induce immunosuppression, this was associated with a CB1 receptor rather than a CB2 receptor-mediated effect. These data support the fact that non-psychoactive doses of medicinal cannabis have a marginal influence on the immune response in MS. Importantly, it adds a note of caution for the translational value of some transgenic/gene knockout and other studies on low-EAE susceptibility backgrounds with inconsistent disease course and susceptibility.
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MESH Headings
- Animals
- Disease Models, Animal
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Female
- Gene Deletion
- Gene Knockout Techniques
- Immunomodulation/genetics
- Male
- Mice
- Multiple Sclerosis/genetics
- Multiple Sclerosis/immunology
- Phenotype
- Receptor, Cannabinoid, CB2/deficiency
- Receptor, Cannabinoid, CB2/genetics
- Receptors, Cannabinoid/deficiency
- Receptors, Cannabinoid/genetics
- Species Specificity
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Affiliation(s)
- Sofia Sisay
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gareth Pryce
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Samuel J. Jackson
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Carolyn Tanner
- School of Medical Science, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
| | - Ruth A. Ross
- School of Medical Science, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, United Kingdom
- Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Gregory J. Michael
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David L. Selwood
- Biological and Medical Chemistry, the Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Gavin Giovannoni
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - David Baker
- Neuroimmunology, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
- * E-mail:
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