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Association of Fc Gamma Receptor 3B Gene Copy Number Variation with Rheumatoid Arthritis Susceptibility. Genes (Basel) 2022; 13:genes13122238. [PMID: 36553504 PMCID: PMC9778311 DOI: 10.3390/genes13122238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Structural variations such as copy number variants (CNVs) have been associated with multiple autoimmune diseases. In this study, we explored the association of the Fc gamma receptor 3B gene (FCGR3B) copy number variation (CNV) with rheumatoid arthritis (RA) susceptibility and related serological traits in the Pakistani population. We also performed a meta-analysis of four published FCGR3B CNV studies along with the current study. A total of 927 subjects (597 RA cases, 330 healthy controls) were recruited from three rheumatology centers in Pakistan. Anti-cyclic citrullinated peptide (anti-CCP) antibodies and rheumatoid factor (RF) were measured in RA patients. FCGR3B copy number was assayed using the TaqMan® CN assay (Hs04211858_cn, Applied Biosystems, Foster City, CA, USA) and the copy number was estimated by using CopyCaller® software (version 2.1; Applied Biosystems, USA). Logistic regression was applied to calculate the odds ratio (OR) of RA risk associated with FCGR3B CNV using sex and age as covariates in R. Meta-analysis on four previously published studies and the current study was performed using the random-effect model. We observed a significant association between FCGR3B copy number < 2 and RA susceptibility (OR = 1.53; 95% CI: 1.05 to 2.22; p = 0.0259) and anti-CCP seropositivity (OR 2.56; 95% CI: 1.34 to 4.89; p = 0.0045). A non-significant association of FCGR3B copy number < 2 was also observed between increased rheumatoid factor (RF) seropositivity (OR = 1.74; 95% CI:0.93 to 3.26; p = 0.0816). Meta-analysis on 13,915 subjects (7005 RA cases and 6907 controls) also showed significant association of copy number < 2 with the increased risk of RA (OR = 1.30; 95% CI: 1.07 to 1.56; p = 0.00671). FCGR3B copy number < 2 is associated with increased RA risk and anti-CCP seropositivity.
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Ji J, Zhang X, Ling Y, Tian J, Wang Y, Luo Y, Zhu R, Zhou Y, Zhu T, Wang L, Zhu H. Hsa_circ_0008301 as a potential biomarker of disease activity for primary Sjogren's syndrome: Increased expression in peripheral blood of patients with primary Sjogren's syndrome. Int Immunopharmacol 2022; 112:109231. [PMID: 36113315 DOI: 10.1016/j.intimp.2022.109231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To explore the expression level, association with disease activity and clinical significance of hsa_circ_0008301 in the peripheral blood of patients with primary Sjögren's syndrome (pSS). METHODS We selected 70 pSS patients hospitalized under the Rheumatology service line at the General Hospital of Ningxia Medical University from September 2018 to June 2021 as the disease group, in which general data and clinical indicators were collected. Fifty-three patients with healthy physical examinations for the same period were selected as the healthy control group, and 32 patients with non-pSS rheumatic diseases were selected as the disease control group. We collected peripheral blood samples and used fluorescence quantitative PCR to detect the expression level of hsa_circ_0008301. In addition, we analyzed the association of the expression level of hsa_circ_0008301 with the clinical characteristics and disease activity of pSS patients. A receiver operating characteristic curve was used to evaluate the diagnosis and the disease activity value of hsa_circ_0008301 in patients with pSS. Meanwhile, we analyzed the differential expression of hsa_circ_0008301 in 24 pSS patients selected from the disease group before and after treatment. RESULTS The relative expression of hsa_circ_0008301 in the peripheral blood of pSS patients was significantly higher than that in the control groups including healthy control group and disease control group. The expression level of hsa_circ_0008301 was high in pSS patients with a course of disease ≥ 10 years, fatigue symptoms, platelets < 100*10^9/L, erythrocyte sedimentation rate ≥ 50 mm/h, immunoglobulin IgG > 16 g/L, complement C3 < 0.9 g/L, ESSDAI score ≥ 5 and positively correlated with the above groups. Furthermore, ROC analysis showed that hsa_circ_0008301 was statistically significant between pSS patients and healthy controls. We selected patients from the disease group before and after treatment and showed that the expression level of hsa_circ_0008301 decreased significantly after treatment, compared with before. The area under the curve (AUC) was 0.825 (95% CI: 0.754 ∼ 0.897; P < 0.0001). The AUC of hsa_circ_0008301 in pSS patients and the disease control group was 0.673 (95% CI: 0.563 ∼ 0.782; P = 0.005), the sensitivity was 40.00%, the specificity was 93.70%, the optimal truncation value was > 0.0420, and the maximum Youden index was 0.337. In addition, ROC analysis revealed that hsa_circ_0008301 was statistically significant between disease-active patients and stable patients. The AUC value was 0.681 (95% CI: 0.553 ∼ 0.809; P = 0.010), the sensitivity was 65.90%, the specificity was 72.40%, the optimal truncation value was > 0.0285, and the maximum Youden index was 0.383. ROC analysis indicated that hsa_circ_0008301 has some value in the diagnosis and disease activity of patients with pSS. Comparison of 24 pSS patients selected from the disease group before and after treatment showed that the expression level of hsa_circ_0008301 decreased significantly after treatment compared with before treatment (Z = - 4.257, P < 0.0001). ROC analysis indicated that hsa_circ_0008301 has some value in the diagnosis and disease activity of patients with pSS. CONCLUSIONS Hsa_circ_0008301 is expressed in higher levels in the peripheral blood of patients with pSS, which is related to the disease activity. It may be involved in the occurrence and development of pSS and may have a potential biomarker for the disease.
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Affiliation(s)
- Jinghui Ji
- Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Xiaoyu Zhang
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, Guangdong, China; Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510000, Guangdong, China
| | - Yitong Ling
- Department of Neurology, Rizhao People's Hospital, Rizhao 276826, Shandong, China
| | - Jinhai Tian
- Biochip Center, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Yi Wang
- Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Yunxia Luo
- Department of Internal medicine 2, Changdu People's Hospital, Changdu 854000, Xizang, China
| | - Rong Zhu
- Department of Rheumatology, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Yan Zhou
- Department of Rheumatology, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China
| | - Tiantian Zhu
- Yinchuan Yiyang Geriatric Hospital, Yinchuan 750004, Ningxia, China
| | - Libin Wang
- Biochip Center, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China.
| | - Hong Zhu
- Department of Rheumatology, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia, China.
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López-Cade I, García-Barberán V, Cabañas Morafraile E, Díaz-Tejeiro C, Saiz-Ladera C, Sanvicente A, Pérez Segura P, Pandiella A, Győrffy B, Ocaña A. Genomic mapping of copy number variations influencing immune response in breast cancer. Front Oncol 2022; 12:975437. [PMID: 36119512 PMCID: PMC9476651 DOI: 10.3389/fonc.2022.975437] [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: 06/22/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Identification of genomic alterations that influence the immune response within the tumor microenvironment is mandatory in order to identify druggable vulnerabilities. In this article, by interrogating public genomic datasets we describe copy number variations (CNV) present in breast cancer (BC) tumors and corresponding subtypes, associated with different immune populations. We identified regulatory T-cells associated with the Basal-like subtype, and type 2 T-helper cells with HER2 positive and the luminal subtype. Using gene set enrichment analysis (GSEA) for the Type 2 T-helper cells, the most relevant processes included the ERBB2 signaling pathway and the Fibroblast Growth Factor Receptor (FGFR) signaling pathway, and for CD8+ T-cells, cellular response to growth hormone stimulus or the JAK-STAT signaling pathway. Amplification of ERBB2, GRB2, GRB7, and FGF receptor genes strongly correlated with the presence of type 2 T helper cells. Finally, only 8 genes were highly upregulated and present in the cellular membrane: MILR1, ACE, DCSTAMP, SLAMF8, CD160, IL2RA, ICAM2, and SLAMF6. In summary, we described immune populations associated with genomic alterations with different BC subtypes. We observed a clear presence of inhibitory cells, like Tregs or Th2 when specific chromosomic regions were amplified in basal-like or HER2 and luminal groups. Our data support further evaluation of specific therapeutic strategies in specific BC subtypes, like those targeting Tregs in the basal-like subtype.
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Affiliation(s)
- Igor López-Cade
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Vanesa García-Barberán
- Molecular Oncology Laboratory, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Esther Cabañas Morafraile
- Center for Biological Research, Margarita Salas Centro de Investigaciones Biologicas (CIB)-Consejo Superior de Investigaciones Cientificas (CSIC), Spanish National Research Council, Madrid, Spain
| | - Cristina Díaz-Tejeiro
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Cristina Saiz-Ladera
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Adrián Sanvicente
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Pedro Pérez Segura
- Medical Oncology Department, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Atanasio Pandiella
- Instituto de Biología Molecular y Celular del Cáncer [IBMCC-Centro de Investigacion del Cancer (CIC)], Instituto de Investigación Biomédica de Salamanca (IBSAL), Consejo Superior de Investigaciones Científicas (CSIC) Salamanca, Salamanca, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- 2Department of Pediatrics, Semmelweis University, Budapest, Hungary
- Termeszettudomanyi Kutatokozpont (TTK) Lendület Cancer Biomarker Research Group, Institute of Enzymology, Budapest, Hungary
| | - Alberto Ocaña
- Experimental Therapeutics Unit, Hospital Clínico San Carlos (HCSC), Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
- Centro de Investigación Biomédica en Red en Oncología (CIBERONC), Madrid, Spain
- Translational Oncology Laboratory, Translational Research Unit, Albacete University Hospital, Albacete, Spain
- Centro Regional de Investigaciones Biomédicas, Castilla-La Mancha University (CRIB-UCLM), Albacete, Spain
- *Correspondence: Alberto Ocaña,
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Song RH, Gao CQ, Zhao J, Zhang JA. An Update Evolving View of Copy Number Variations in Autoimmune Diseases. Front Genet 2022; 12:794348. [PMID: 35126462 PMCID: PMC8810490 DOI: 10.3389/fgene.2021.794348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/06/2021] [Indexed: 02/01/2023] Open
Abstract
Autoimmune diseases (AIDs) usually share possible common mechanisms, i.e., a defect in the immune tolerance exists due to diverse causes from central and peripheral tolerance mechanisms. Some genetic variations including copy number variations (CNVs) are known to link to several AIDs and are of importance in the susceptibility to AIDs and the potential therapeutic responses to medicines. As an important source of genetic variants, DNA CNVs have been shown to be very common in AIDs, implying these AIDs may possess possible common mechanisms. In addition, some CNVs are differently distributed in various diseases in different ethnic populations, suggesting that AIDs may have their own different phenotypes and different genetic and/or environmental backgrounds among diverse populations. Due to the continuous advancement in genotyping technology, such as high-throughput whole-genome sequencing method, more susceptible variants have been found. Moreover, further replication studies should be conducted to confirm the results of studies with different ethnic cohorts and independent populations. In this review, we aim to summarize the most relevant data that emerged in the past few decades on the relationship of CNVs and AIDs and gain some new insights into the issue.
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Chiliński M, Sengupta K, Plewczynski D. From DNA human sequence to the chromatin higher order organisation and its biological meaning: Using biomolecular interaction networks to understand the influence of structural variation on spatial genome organisation and its functional effect. Semin Cell Dev Biol 2021; 121:171-185. [PMID: 34429265 DOI: 10.1016/j.semcdb.2021.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/30/2022]
Abstract
The three-dimensional structure of the human genome has been proven to have a significant functional impact on gene expression. The high-order spatial chromatin is organised first by looping mediated by multiple protein factors, and then it is further formed into larger structures of topologically associated domains (TADs) or chromatin contact domains (CCDs), followed by A/B compartments and finally the chromosomal territories (CTs). The genetic variation observed in human population influences the multi-scale structures, posing a question regarding the functional impact of structural variants reflected by the variability of the genes expression patterns. The current methods of evaluating the functional effect include eQTLs analysis which uses statistical testing of influence of variants on spatially close genes. Rarely, non-coding DNA sequence changes are evaluated by their impact on the biomolecular interaction network (BIN) reflecting the cellular interactome that can be analysed by the classical graph-theoretic algorithms. Therefore, in the second part of the review, we introduce the concept of BIN, i.e. a meta-network model of the complete molecular interactome developed by integrating various biological networks. The BIN meta-network model includes DNA-protein binding by the plethora of protein factors as well as chromatin interactions, therefore allowing connection of genomics with the downstream biomolecular processes present in a cell. As an illustration, we scrutinise the chromatin interactions mediated by the CTCF protein detected in a ChIA-PET experiment in the human lymphoblastoid cell line GM12878. In the corresponding BIN meta-network the DNA spatial proximity is represented as a graph model, combined with the Proteins-Interaction Network (PIN) of human proteome using the Gene Association Network (GAN). Furthermore, we enriched the BIN with the signalling and metabolic pathways and Gene Ontology (GO) terms to assert its functional context. Finally, we mapped the Single Nucleotide Polymorphisms (SNPs) from the GWAS studies and identified the chromatin mutational hot-spots associated with a significant enrichment of SNPs related to autoimmune diseases. Afterwards, we mapped Structural Variants (SVs) from healthy individuals of 1000 Genomes Project and identified an interesting example of the missing protein complex associated with protein Q6GYQ0 due to a deletion on chromosome 14. Such an analysis using the meta-network BIN model is therefore helpful in evaluating the influence of genetic variation on spatial organisation of the genome and its functional effect in a cell.
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Affiliation(s)
- Mateusz Chiliński
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Kaustav Sengupta
- Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Dariusz Plewczynski
- Laboratory of Bioinformatics and Computational Genomics, Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland; Laboratory of Functional and Structural Genomics, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
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Nagelkerke SQ, Schmidt DE, de Haas M, Kuijpers TW. Genetic Variation in Low-To-Medium-Affinity Fcγ Receptors: Functional Consequences, Disease Associations, and Opportunities for Personalized Medicine. Front Immunol 2019; 10:2237. [PMID: 31632391 PMCID: PMC6786274 DOI: 10.3389/fimmu.2019.02237] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/04/2019] [Indexed: 12/23/2022] Open
Abstract
Fc-gamma receptors (FcγR) are the cellular receptors for Immunoglobulin G (IgG). Upon binding of complexed IgG, FcγRs can trigger various cellular immune effector functions, thereby linking the adaptive and innate immune systems. In humans, six classic FcγRs are known: one high-affinity receptor (FcγRI) and five low-to-medium-affinity FcγRs (FcγRIIA, -B and -C, FcγRIIIA and -B). In this review we describe the five genes encoding the low-to-medium -affinity FcγRs (FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B), including well-characterized functionally relevant single nucleotide polymorphisms (SNPs), haplotypes as well as copy number variants (CNVs), which occur in distinct copy number regions across the locus. The evolution of the locus is also discussed. Importantly, we recommend a consistent nomenclature of genetic variants in the FCGR2/3 locus. Next, we focus on the relevance of genetic variation in the FCGR2/3 locus in auto-immune and auto-inflammatory diseases, highlighting pathophysiological insights that are informed by genetic association studies. Finally, we illustrate how specific FcγR variants relate to variation in treatment responses and prognosis amongst autoimmune diseases, cancer and transplant immunology, suggesting novel opportunities for personalized medicine.
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Affiliation(s)
- Sietse Q Nagelkerke
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - David E Schmidt
- Sanquin Research and Landsteiner Laboratory, Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Masja de Haas
- Sanquin Diagnostic Services, Department of Immunohematology Diagnostics, Amsterdam, Netherlands.,Sanquin Research, Center for Clinical Transfusion Research, Leiden, Netherlands.,Jon J. van Rood Center for Clinical Transfusion Science, Leiden University Medical Center, Leiden, Netherlands.,Department of Immunohematology and Blood Transfusion, Leiden University Medical Center, Leiden, Netherlands
| | - Taco W Kuijpers
- Sanquin Research and Landsteiner Laboratory, Department of Blood Cell Research, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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Dahmani CA, Benzaoui A, Amroun H, Zemani-Fodil F, Petit-Teixeira E, Boudjema A. Association study of copy number variants in CCL3L1, FCGR3A and FCGR3B genes with risk of ankylosing spondylitis in a West Algerian population. Int J Immunogenet 2019; 46:437-443. [PMID: 31433132 DOI: 10.1111/iji.12454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/25/2019] [Accepted: 07/27/2019] [Indexed: 12/19/2022]
Abstract
Numerous single nucleotide polymorphisms (SNPs) were explored in the Algerian population to evaluate associated ankylosing spondylitis (AS) genetic risk factors, but no study has identified the impact of copy number variations (CNVs). The aim of the study was to determine whether CNVs of CCL3L1, FCGR3A and FCGR3B genes were also associated with the susceptibility of AS disease in Algerian population. The data set of the current study is composed of 81 patients with AS and 119 healthy controls. All samples were genotyped by digital droplet PCR (ddPCR). Chi-square test and OR calculation were used to evaluate association between CNVs and AS and the risk associated with copy numbers (CN). In results, FCGR3A CN less than two copies (<2) was significantly increased in spondylitis patients (p = .0001, OR = 7.74 [2.32-25.74]). Additionally, FCGR3A CN < 2 copies association was present only in HLA-B27 (-) patients. We have concluded that FCGR3A deletions have an independent effect on AS regarding HLA-B27 status. This is the first study that investigated the CCL3L1 CNVs in relation to AS risk disease. It reveals that CCL3L1 and FCGR3B CNVs may not be involved in susceptibility to AS risk in the Algerian population.
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Affiliation(s)
- Chahinez Amira Dahmani
- Laboratoire de Génétique Moléculaire et Cellulaire/Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | - Ahmed Benzaoui
- Service de Rhumatologie/Centre Hospitalo-universitaire d'Oran (CHUO), Oran, Algeria
| | - Habiba Amroun
- Laboratoire d'Immunogénétique et de Transplantation, Département d'Immunologie, Institut Pasteur d'Algérie à Alger, Oran, Algeria
| | - Faouzia Zemani-Fodil
- Laboratoire de Génétique Moléculaire et Cellulaire/Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf (USTO-MB), Oran, Algeria
| | | | - Abdallah Boudjema
- Laboratoire de Génétique Moléculaire et Cellulaire/Université des Sciences et de la Technologie d'Oran Mohamed Boudiaf (USTO-MB), Oran, Algeria
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Gabur I, Chawla HS, Snowdon RJ, Parkin IAP. Connecting genome structural variation with complex traits in crop plants. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:733-750. [PMID: 30448864 DOI: 10.1007/s00122-018-3233-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 11/07/2018] [Indexed: 05/05/2023]
Abstract
Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.
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Affiliation(s)
- Iulian Gabur
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany.
| | - Isobel A P Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N OX2, Canada
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Pang Y, Guan Y, Jin X, Shen H, Liu L, Jia Q, Meng F, Zhang X. Association of TSHR Gene Copy Number Variation with TSH Abnormalities. Biol Trace Elem Res 2018; 186:85-90. [PMID: 29546542 DOI: 10.1007/s12011-018-1300-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/06/2018] [Indexed: 12/09/2022]
Abstract
Thyroid-stimulating hormone (TSH) is secreted by the pituitary gland and promotes thyroid growth and function, with increased TSH levels typically associated with hypothyroidism. By consulting the literature, we found that the TSHR, PAX8, and PDE4B genes are associated with thyroid function. Recently, copy number variations (CNVs) have been used as genetic markers to investigate inter-individual variation. Therefore, we investigated the relationship between the TSHR, PAX8, and PDE4B gene CNVs and TSH abnormalities, by calculating variations in gene copy number. Four hundred and eighty-one participants, 232 healthy controls and 249 patients with TSH abnormalities, were selected from three distinct areas in China with different iodine statuses. RT-PCR was used to detect CNVs. Urinary iodine concentrations (UIC) were measured by As3+-Ce4+ catalytic spectrophotometry. There was an association between a CNV at the TSHR gene and TSH abnormalities (p = 0.002). The distribution of PAX8 and PDE4B gene CNVs between patients with TSH abnormalities and healthy controls was not significantly different. UIC > 200 μg/l (OR = 1.49, 95% CI = 1.01-2.22) and the TSHR gene (OR = 6.01, 95% CI = 1.96-18.41) were found to be risk factors for TSH abnormalities. PAX8 and PDE4B gene CNVs were not significantly associated with TSH abnormalities. There was no significant interaction between UIC and any of the examined CNVs. In conclusion, the TSHR gene CNV was associated with the development of TSH abnormalities. No significant associations were revealed between urinary iodine levels and candidate gene CNVs.
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Affiliation(s)
- Yi Pang
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfeng Guan
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xing Jin
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China.
| | - Lixiang Liu
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Qingzhen Jia
- Institute for Endemic Disease Prevention and Treatment of Shanxi Province, Linfen, Shanxi, China
| | - Fangang Meng
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoye Zhang
- Key Laboratory of Etiology and Epidemiology, National Health and Family Planning Commission, Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
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Sandhya P, Kurien BT, Danda D, Scofield RH. Update on Pathogenesis of Sjogren's Syndrome. Curr Rheumatol Rev 2018; 13:5-22. [PMID: 27412602 DOI: 10.2174/1573397112666160714164149] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 11/15/2015] [Accepted: 01/01/2016] [Indexed: 01/06/2023]
Abstract
Sjogren's syndrome is a common autoimmune disease that presents with sicca symptoms and extraglandular features. Sjogren's syndrome is presumably as common as RA; yet it is poorly understood, underdiagnosed and undertreated. From the usual identity as an autoimmune exocrinopathy to its most recent designate as an autoimmune epithelitis - the journey of SS is complex. We herein review some of the most important milestones that have shed light on different aspects of pathogenesis of this enigmatic disease. This includes role of salivary gland epithelial cells, and their interaction with cells of the innate and adaptive immune system. Non-immune factors acting in concert or in parallel with immune factors may also be important. The risk genes identified so far have only weak association, nevertheless advances in genetics have enhanced understanding of disease mechanisms. Role of epigenetic and environmental role factors is also being explored. SS has also some unique features such as congenital heart block and high incidence of lymphoma; disease mechanisms accounting for these manifestations are also reviewed.
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11
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Anaya JM, Leon KJ, Rojas M, Rodriguez Y, Pacheco Y, Acosta-Ampudia Y, Monsalve DM, Ramirez-Santana C. Progress towards precision medicine for lupus: the role of genetic biomarkers. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2018. [DOI: 10.1080/23808993.2018.1448266] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Kelly J. Leon
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel Rojas
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Yhojan Rodriguez
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Yovana Pacheco
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Yeny Acosta-Ampudia
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Diana M. Monsalve
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Carolina Ramirez-Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
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12
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Fu R, Mokhtar SS, Phipps ME, Hoh BP, Xu S. A genome-wide characterization of copy number variations in native populations of Peninsular Malaysia. Eur J Hum Genet 2018; 26:886-897. [PMID: 29476164 DOI: 10.1038/s41431-018-0120-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/20/2017] [Accepted: 02/01/2018] [Indexed: 11/09/2022] Open
Abstract
Copy number variations (CNVs) are genomic structural variations that result from the deletion or duplication of large genomic segments. The characterization of CNVs is largely underrepresented, particularly those of indigenous populations, such as the Orang Asli in Peninsular Malaysia. In the present study, we first characterized the genome-wide CNVs of four major native populations from Peninsular Malaysia, including the Malays and three Orang Asli populations; namely, Proto-Malay, Senoi, and Negrito (collectively called PM). We subsequently assessed the distribution of CNVs across the four populations. The resulting global CNV map revealed 3102 CNVs, with an average of more than 100 CNVs per individual. We identified genes harboring CNVs that are highly differentiated between PM and global populations, indicating that these genes are predominantly enriched in immune responses and defense functions, including APOBEC3A_B, beta-defensin genes, and CCL3L1, followed by other biological functions, such as drug and toxin metabolism and responses to radiation, suggesting some attributions between CNV variations and adaptations of the PM groups to the local environmental conditions of tropical rainforests.
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Affiliation(s)
- Ruiqing Fu
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Siti Shuhada Mokhtar
- Institute of Medical Molecular Biotechnology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Selangor, Malaysia
| | - Maude Elvira Phipps
- School of Medicine, Monash University Sunway Campus, Petaling Jaya, Malaysia
| | - Boon-Peng Hoh
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China.,Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, Kuala Lumpur, Malaysia
| | - Shuhua Xu
- Chinese Academy of Sciences (CAS), Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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13
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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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14
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Rahbari R, Zuccherato LW, Tischler G, Chihota B, Ozturk H, Saleem S, Tarazona‐Santos E, Machado LR, Hollox EJ. Understanding the Genomic Structure of Copy-Number Variation of the Low-Affinity Fcγ Receptor Region Allows Confirmation of the Association of FCGR3B Deletion with Rheumatoid Arthritis. Hum Mutat 2017; 38:390-399. [PMID: 27995740 PMCID: PMC5363352 DOI: 10.1002/humu.23159] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 12/14/2016] [Indexed: 11/23/2022]
Abstract
Fcγ receptors are a family of cell-surface receptors that are expressed by a host of different innate and adaptive immune cells, and mediate inflammatory responses by binding the Fc portion of immunoglobulin G. In humans, five low-affinity receptors are encoded by the genes FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B, which are located in an 82.5-kb segmental tandem duplication on chromosome 1q23.3, which shows extensive copy-number variation (CNV). Deletions of FCGR3B have been suggested to increase the risk of inflammatory diseases such as systemic lupus erythematosus and rheumatoid arthritis (RA). In this study, we identify the deletion breakpoints of FCGR3B deletion alleles in the UK population and endogamous native American population, and show that some but not all alleles are likely to be identical-by-descent. We also localize a duplication breakpoint, confirming that the mechanism of CNV generation is nonallelic homologous recombination, and identify several alleles with gene conversion events using fosmid sequencing data. We use information on the structure of the deletion alleles to distinguish FCGR3B deletions from FCGR3A deletions in whole-genome array comparative genomic hybridization (aCGH) data. Reanalysis of published aCGH data using this approach supports association of FCGR3B deletion with increased risk of RA in a large cohort of 1,982 cases and 3,271 controls (odds ratio 1.61, P = 2.9×10-3 ).
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Affiliation(s)
- Raheleh Rahbari
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- Wellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Luciana W Zuccherato
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- Departmento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Belinda Chihota
- School of HealthUniversity of NorthamptonNorthamptonUnited Kingdom
| | - Hasret Ozturk
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
| | - Sara Saleem
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
| | - Eduardo Tarazona‐Santos
- Departmento de Biologia GeralInstituto de Ciências BiológicasUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Lee R Machado
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
- School of HealthUniversity of NorthamptonNorthamptonUnited Kingdom
| | - Edward J Hollox
- Department of GeneticsUniversity of LeicesterLeicesterUnited Kingdom
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15
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Qi Y, Zhou X, Bu D, Hou P, Lv J, Zhang H. Low copy numbers of FCGR3A and FCGR3B associated with Chinese patients with SLE and AASV. Lupus 2017; 26:1383-1389. [PMID: 28355982 DOI: 10.1177/0961203317700485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Low-affinity Fcγ receptors (FcγR) act as key mediators of the pathogenic effects of autoantibodies. In this study, we aimed to determine whether copy number variations (CNVs) in FCGR3A and FCGR3B were associated with systemic lupus nephritis (SLE) and ANCA-associated systemic vasculitis (AASV) in Chinese individuals. A total of 1118 individuals were enrolled, including 415 SLE patients, 139 AASV patients, and 564 healthy controls. FCGR3A and FCGR3B copy numbers (CNs) were determined by both a paralogue ratio test and TaqMan quantitative PCR assay. In the susceptibility associations, a low FCGR3B CN was significantly associated with SLE ( p = 5.01 × 10-3; odds ratio (OR) 1.71; 95% confidence interval (CI) 1.17-2.48) and AASV ( p = 0.04; OR = 1.72; 95% CI 1.02-2.88). A low FCGR3A CN was also significantly associated with SLE ( p = 6.02 × 10-3; OR 2.72; 95% CI 1.30-5.71) and AASV ( p = 0.042; OR 2.64; 95% CI 1.00-6.93). Further subphenotype analysis revealed that low CNs of FCGR3A and FCGR3B were significantly associated with clinical manifestations in SLE and AASV patients. Therefore, in this case-control study, we identified low CNs of FCGR2A and FCGR3B to be common risk factors for SLE and AASV.
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Affiliation(s)
- Y Qi
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - X Zhou
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - D Bu
- 5 Research Central Institute, Peking University First Hospital, Beijing, People's Republic of China
| | - P Hou
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - J Lv
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
| | - H Zhang
- 1 Renal Division, Peking University First Hospital, People's Republic of China.,2 Peking University Institute of Nephrology, People's Republic of China.,3 Key Laboratory of Renal Disease, Ministry of Health of China, People's Republic of China.,4 Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, People's Republic of China
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16
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Qi YY, Zhou XJ, Bu DF, Hou P, Lv JC, Zhang H. Comparison of Multiple Methods for Determination of FCGR3A/B Genomic Copy Numbers in HapMap Asian Populations with Two Public Databases. Front Genet 2016; 7:220. [PMID: 28083015 PMCID: PMC5183586 DOI: 10.3389/fgene.2016.00220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 12/12/2016] [Indexed: 01/23/2023] Open
Abstract
Low FCGR3 copy numbers (CNs) has been associated with susceptibility to several systemic autoimmune diseases. However, inconsistent associations were reported and errors caused by shaky methods were suggested to be the major causes. In large scale case control association studies, robust copy number determination method is thus warranted, which was the main focus of the current study. In the present study, FCGR3 CNs of 90 HapMap Asians were firstly checked using four assays including paralog ratio test combined with restriction enzyme digest variant ratio (PRT-REDVR), real-time quantitative (qPCR) using TaqMan assay, real-time qPCR using SYBR Green dye and short tenden repeat (STR). To improve the comparison precision reproductively, the results were compared with those from recently released sequencing data from 1000 genomes project as well as whole-genome tiling BAC array data. The tendencies of inconsistent samples by these methods were also characterized. Refined in-home TaqMan qPCR assay showed the highest correlation with array-CGH results (r = 0.726, p < 0.001) and the highest concordant rate with 1000 genome sequencing data (FCGR3A 91.76%, FCGR3B 85.88%, and FCGR3 81.18%). For samples with copy number variations, comprehensive analysis of multiple methods was required in order to improve detection accuracy. All these method were prone to detect copy number to be higher than that from direct sequencing. All the four PCR based CN determination methods (qPCR using TaqMan probes or SYBR Green, PRT, STR) were prone to higher estimation errors and thus may lead to artificial associations in large-scale case-control association studies. But different to previous reports, we observed that properly refined TaqMan qPCR assay was not inferior to or even more accurate than PRT when using sequencing data as the reference.
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Affiliation(s)
- Yuan-Yuan Qi
- Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China
| | - Xu-Jie Zhou
- Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China
| | - Ding-Fang Bu
- Research Central Institute, Peking University First Hospital Beijing, China
| | - Ping Hou
- Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China
| | - Ji-Cheng Lv
- Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China
| | - Hong Zhang
- Renal Division, Peking University First HospitalBeijing, China; Peking University Institute of NephrologyBeijing, China; Key Laboratory of Renal Disease, Ministry of Health of ChinaBeijing, China; Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of EducationBeijing, China
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17
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Lee YH, Bae SC, Seo YH, Kim JH, Choi SJ, Ji JD, Song GG. Association between FCGR3B copy number variations and susceptibility to autoimmune diseases: a meta-analysis. Inflamm Res 2015; 64:983-91. [PMID: 26407570 DOI: 10.1007/s00011-015-0882-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 01/24/2023] Open
Abstract
OBJECTIVE This study determined whether FCGR3B copy number variations (CNVs) were associated with susceptibility to autoimmune diseases. METHODS A meta-analysis was conducted to determine the association between FCGR3B CNVs and susceptibility to autoimmune diseases by comparing low FCGR3B CN (<2 to ≥2) and high FCGR3B CN (>2 to ≤2). RESULTS In all, 28 comparative studies from 15 reports involving 12,160 patients and 11,103 controls were included in this meta-analysis. The meta-analysis showed a significant association between low FCGR3B CN and autoimmune diseases (OR=1.496, 95% CI=1.301-1.716, p=1.0×10(-9)). Subgroup analysis according to ethnicity indicated an association between low FCGR3B CN and autoimmune diseases in Caucasians (OR=1.482, 95% CI=1.219-1.801, p=7.7×10(-6)) and Asians (OR=1.498, 95% CI=1.306-1.717, p=1.0×10(-9)). Meta-analysis according to the type of autoimmune disease indicated a significant association of low FCGR3B CN with systemic lupus erythematosus (SLE; OR=1.797, 95% CI=1.562-2.068, p<1.0×10(-9)), primary Sjogren's syndrome (pSS; OR=2.263, 95% CI=1.316-3.892, p=0.003), and Wegener's granulomatosis (WG; OR=1.973, 95% CI=1.178-3.302, p=0.010), but not with rheumatoid arthritis (RA; OR=1.333, 95% CI=0.947-1.877, p=0.099). However, the meta-analysis showed no association between high FCGR3B CN and SLE, RA, pSS, and WG. CONCLUSIONS Thus, the results of this meta-analysis indicated that low FCGR3B CN increased susceptibility to autoimmune diseases, especially SLE, pSS, and WG.
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Affiliation(s)
- Young Ho Lee
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea.
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Ho Seo
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Jae-Hoon Kim
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Sung Jae Choi
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Jong Dae Ji
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
| | - Gwan Gyu Song
- Division of Rheumatology, Department of Internal Medicine, Korea University Anam Hospital, Korea University College of Medicine, 72 Inchon-ro, Seongbuk-gu, Seoul, 136-705, Korea
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Abstract
Hundreds of copy number variants are complex and multi-allelic, in that they have many structural alleles and have rearranged multiple times in the ancestors who contributed chromosomes to current humans. Not only are the relationships of these multi-allelic CNVs (mCNVs) to phenotypes generally unknown, but many mCNVs have not yet been described at the basic levels—alleles, allele frequencies, structural features—that support genetic investigation. To date, most reported disease associations to these variants have been ascertained through candidate gene studies. However, only a few associations have reached the level of acceptance defined by durable replications in many cohorts. This likely stems from longstanding challenges in making precise molecular measurements of the alleles individuals have at these loci. However, approaches for mCNV analysis are improving quickly, and some of the unique characteristics of mCNVs may assist future association studies. Their various structural alleles are likely to have different magnitudes of effect, creating a natural allelic series of growing phenotypic impact and giving investigators a set of natural predictions and testable hypotheses about the extent to which each allele of an mCNV predisposes to a phenotype. Also, mCNVs’ low-to-modest correlation to individual single-nucleotide polymorphisms (SNPs) may make it easier to distinguish between mCNVs and nearby SNPs as the drivers of an association signal, and perhaps, make it possible to preliminarily screen candidate loci, or the entire genome, for the many mCNV–disease relationships that remain to be discovered.
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Yim SH, Jung SH, Chung B, Chung YJ. Clinical implications of copy number variations in autoimmune disorders. Korean J Intern Med 2015; 30:294-304. [PMID: 25995659 PMCID: PMC4438283 DOI: 10.3904/kjim.2015.30.3.294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/30/2015] [Indexed: 11/27/2022] Open
Abstract
Human genetic variation is represented by the genetic differences both within and among populations, and most genetic variants do not cause overt diseases but contribute to disease susceptibility and influence drug response. During the last century, various genetic variants, such as copy number variations (CNVs), have been associated with diverse human disorders. Here, we review studies on the associations between CNVs and autoimmune diseases to gain some insight. First, some CNV loci are commonly implicated in various autoimmune diseases, such as Fcγ receptors in patients with systemic lupus erythemoatosus or idiopathic thrombocytopenic purpura and β-defensin genes in patients with psoriasis or Crohn's disease. This means that when a CNV locus is associated with a particular autoimmune disease, we should examine its potential associations with other diseases. Second, interpopulation or interethnic differences in the effects of CNVs on phenotypes exist, including disease susceptibility, and evidence suggests that CNVs are important to understand susceptibility to and pathogenesis of autoimmune diseases. However, many findings need to be replicated in independent populations and different ethnic groups. The validity and reliability of detecting CNVs will improve quickly as genotyping technology advances, which will support the required replication.
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Affiliation(s)
- Seon-Hee Yim
- Department of Medical Education, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hyun Jung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Boram Chung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yeun-Jun Chung
- Integrated Research Center for Genome Polymorphism, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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20
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Escaramís G, Docampo E, Rabionet R. A decade of structural variants: description, history and methods to detect structural variation. Brief Funct Genomics 2015; 14:305-14. [PMID: 25877305 DOI: 10.1093/bfgp/elv014] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In the past decade, the view on genomic structural variation (SV) has been changed completely. SVs, previously considered rare events, are now recognized as the largest source of interindividual genetic variation affecting more bases than single nucleotide polymorphisms, variable number of tandem repeats and other small genetic variants. They have also been shown to play a role in phenotypic variation and in disease. In this review, the authors will provide an introduction to SV; a short historical perspective on the research of this source of genomic variation; a description of the types of structural variants, and on how they may have arisen; and an overview on methods of detecting structural variants, focusing on the analysis of high-throughput sequencing data.
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21
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Chen JY, Wang CM, Chang SW, Cheng CH, Wu YJJ, Lin JC, Yang B, Ho HH, Wu J. Association of FCGR3A and FCGR3B copy number variations with systemic lupus erythematosus and rheumatoid arthritis in Taiwanese patients. Arthritis Rheumatol 2015; 66:3113-21. [PMID: 25154742 PMCID: PMC4232894 DOI: 10.1002/art.38813] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 07/31/2014] [Indexed: 12/12/2022]
Abstract
Objective To determine whether copy number variations (CNVs) in FCGR3A and FCGR3B are associated with systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) in Taiwanese individuals. Methods FCGR3A and FCGR3B CNV genotypes were determined in 846 patients with SLE, 948 patients with RA, and 1,420 healthy control subjects, using custom TaqMan CNV assays. The FCGR3A and FCGR3B CNV genotypes were compared between healthy control subjects and patients and among patients stratified according to clinical characteristics. Results A low (<2) FCGR3A copy number was significantly associated with SLE (for <2 copies versus 2 copies, P = 5.06 × 10−4, false discovery rate–corrected P [PFDR] = 0.001, odds ratio [OR] 3.26, 95% confidence interval [95% CI] 1.68−6.35) and RA (for <2 copies versus 2 copies, P = 5.83 × 10−4, PFDR = 0.0012, OR 2.82, 95% CI 1.56−5.1). A low FCGR3B copy number was also significantly associated with SLE (for <2 copies versus 2 copies, P = 0.0032, PFDR = 0.0032, OR 1.59, 95% CI 1.17−2.18). Notably, a high (>2) FCGR3A copy number was also associated with SLE (for >2 copies versus 2 copies, P = 0.003, PFDR = 0.0061, OR 1.6, 95% CI 1.17−2.18). Additionally, the FCGR3A low copy number genotype was significantly enriched in subsets of patients with SLE (those with ulcer, arthritis, rash, discoid rash, photosensitivity, nephritis, leukopenia, thrombocytopenia, depressed complement levels, and autoantibody positivity) and patients with RA (those positive for rheumatoid factor) compared with healthy control subjects. The FCGR3B low copy number genotype was also significantly enriched in SLE patients with ulcer, rash, discoid rash, photosensitivity, ascites, nephritis, complement level depression, and anti–double-stranded DNA antibody positivity compared with control subjects. However, FCGR3B CNVs were not associated with RA susceptibility (for <2 copy numbers versus 2 copy numbers, P = 0.3584, OR 1.15, 95% CI 0.85–1.55) and clinical characteristics. Conclusion In Taiwanese individuals, a low FCGR3A copy number is a common risk factor for SLE and RA, while a low FCGR3B copy number confers a risk of SLE but not RA.
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Affiliation(s)
- Ji-Yih Chen
- Chang Gung University College of Medicine, Taiwan, Republic of China
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Nagelkerke SQ, Kuijpers TW. Immunomodulation by IVIg and the Role of Fc-Gamma Receptors: Classic Mechanisms of Action after all? Front Immunol 2015; 5:674. [PMID: 25653650 PMCID: PMC4301001 DOI: 10.3389/fimmu.2014.00674] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 12/15/2014] [Indexed: 11/13/2022] Open
Abstract
Intravenous IgG (IVIg) contains polyclonal immunoglobulin G (IgG) from thousands of donors. It is administered at a low dose at regular intervals as antibody replacement therapy and at a higher dose as immunomodulatory treatment in various auto-immune or auto-inflammatory diseases. The working mechanism of immunomodulation is not well understood. Many different explanations have been given. During the last decade, we have focused on classical antibody binding via the Fc-domain of the IgG molecules to the common IgG receptors, i.e. the Fcγ receptors (FcγRs). Variation in the genes encoding human FcγRs determines function as well as expression among immune cells. As described here, NK cells and myeloid cells, including macrophages, can express different FcγR variants, depending on the individual's genotype, copy number variation (CNV), and promoter polymorphisms. B-cells seem to only express the single inhibitory receptor. Although these inhibitory FcγRIIb receptors are also expressed by monocytes, macrophages, and only rarely by NK cells or neutrophils, their presence is unlikely to explain the immunomodulatory capacity of IVIg, nor does the sialylation of IgG. Direct IVIg effects at the level of the activating FcγRs, including the more recently described FcγRIIc, deserve renewed attention to describe IVIg-related immunomodulation.
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Affiliation(s)
- Sietse Q Nagelkerke
- Department of Blood Cell Research, Sanquin, University of Amsterdam , Amsterdam , Netherlands
| | - Taco W Kuijpers
- Department of Blood Cell Research, Sanquin, University of Amsterdam , Amsterdam , Netherlands ; Department of Pediatric Hematology, Immunology and Infectious Disease, Emma Children's Hospital at the Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
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23
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Phenotypic heterogeneity of Niemann–Pick disease type C in monozygotic twins. J Neurol 2014; 262:642-7. [DOI: 10.1007/s00415-014-7619-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 12/10/2014] [Accepted: 12/12/2014] [Indexed: 01/27/2023]
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24
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Almal SH, Padh H. Frequency distribution of autoimmunity associated FCGR3B gene copy number in Indian population. Int J Immunogenet 2014; 42:26-30. [PMID: 25428402 DOI: 10.1111/iji.12165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/12/2014] [Accepted: 10/23/2014] [Indexed: 11/27/2022]
Abstract
Amongst several human genome variations, copy number variations (CNVs) are considered as an important source of variability contributing to susceptibility to wide range of diseases. Although CNV is scattered for genes throughout the human genome, several of autoimmunity related genes have CN variation and therefore play an important role in susceptibility to autoimmune diseases. The association of the Fc gamma receptor 3B (FCGR3B) gene copy number in autoimmunity is well characterized in various populations studied. The Fc gamma receptor is a low affinity, glycosylphosphatidylinositol-linked receptor for IgG molecule predominantly expressed on human neutrophils. The variable gene copy number of FCGR3B is found to be involved in the impaired clearance of immune complexes, which significantly contribute to the pathogenesis of several autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), type-1 diabetes and others. The FCGR3B copy number ranged from 0 to ≥ 2 copies per diploid genome in other populations, but yet not explored in Indian population. Hence, this study aims to evaluate the variation in the frequency distribution of FCGR3B CNV in Indian population. FCGR3B gene copy number varied significantly when compared to other population of the world. This observation will help us in exploring the potential role of CNV in FCGR3B gene and its association to autoimmune disorders in Indian population.
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Affiliation(s)
- S H Almal
- Department of Cell and Molecular Biology, B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Thaltej, Ahmedabad, Gujarat, India
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Wu Y, Zhang Z, Tao L, Chen G, Liu F, Wang T, Xue F, Chen Y, He L, Zheng J, Liu Y. A high copy number of FCGR3B is associated with psoriasis vulgaris in Han Chinese. Dermatology 2014; 229:70-5. [PMID: 25012234 DOI: 10.1159/000360160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 01/29/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Copy number variations of FCGR3B are associated with several immune related diseases such as systemic lupus erythematosus, rheumatoid arthritis and primary Sjögren's syndrome. Little is known about the association between FCGR3B copy number variants and psoriasis. OBJECTIVE To investigate whether FCGR3B copy number variants are associated with susceptibility to psoriasis vulgaris in the Chinese Han population. METHODS 343 psoriasis vulgaris patients and 574 healthy individuals were recruited as cases and controls. TaqMan® Copy Number Assays were performed to quantify the copy numbers in the FCGR3B locus. CopyCaller v1.0 software and R (version 2.15.3) were used to do the subsequent statistical analysis. RESULTS A significant association between psoriasis vulgaris and a high copy number (>2) of FCGR3B was observed (odds ratio = 1.63, 95% confidence interval 1.09-2.45, p < 0.02). However, the low copy number of FCGR3B was not significantly associated with psoriasis vulgaris. CONCLUSION A high copy number of FCGR3B is associated with psoriasis vulgaris in Han Chinese.
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Affiliation(s)
- Yumei Wu
- Department of Dermatology, Luwan Branch, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, PR China
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26
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Perry RT, Nyaku MK, Aissani B, Shrestha S. Identification of sequence variants in the CCL3 chemokine gene family in the HapMap West African reference population. Hum Immunol 2014; 75:854-8. [PMID: 24952210 DOI: 10.1016/j.humimm.2014.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/05/2014] [Accepted: 06/09/2014] [Indexed: 11/19/2022]
Abstract
Gene copy number variation (CNV) of the CC Chemokine ligand 3-Like-1 (CCL3L1) gene located on chromosome 17q12 has been associated with many diseases, including viral infections and autoimmune diseases. High sequence homology between CCL3L1 and three other related genes within the same cluster, CCL3, CCL3L2, and CCL3L3, make it difficult to determine the copy number of each gene as well as distinguishing variants within each gene versus between genes. We identified a total of 50SNPs, 31 known and 19 novel SNPs, in a subset of West Africa Reference (Yoruba individuals from Ibadan, Nigeria (YRI)) samples from HapMap. One of these previously unidentified variations is a non-synonymous change while several other unreported variations are located near potential regulatory sites. The variations identified in these immune-related genes from this study will shed light in the understanding of both structural and nucleotide polymorphisms that can be used in association studies of diseases in populations.
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Affiliation(s)
- Rodney T Perry
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Mawuli K Nyaku
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Brahim Aissani
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sadeep Shrestha
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL, USA.
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27
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Association between HLA-DQA1 gene copy number polymorphisms and susceptibility to rheumatoid arthritis in Chinese Han population. J Genet 2014; 93:215-8. [DOI: 10.1007/s12041-014-0339-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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28
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Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Seldin MF, Lasalle JM, Gershwin ME. Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front Immunol 2014; 5:128. [PMID: 24734033 PMCID: PMC3975093 DOI: 10.3389/fimmu.2014.00128] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 03/13/2014] [Indexed: 01/12/2023] Open
Abstract
Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.
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Affiliation(s)
- Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
| | - Francesca Cavaciocchi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Ana Lleo
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | | | | | - Simone A Lombardi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria De Santis
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Francesca Meda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria Gabriella Raimondo
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Chiara Crotti
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Marco Folci
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Luca Zammataro
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Nancy Bach
- Mt. Sinai University , New York, NY , USA
| | - Shinji Shimoda
- Clinical Research Center, National Nagasaki Medical Center , Nagasaki , Japan
| | | | - Monica Miozzo
- Department of Pathophysiology and Transplantation, University of Milan , Milan , Italy ; Division of Pathology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Pietro Invernizzi
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | - Mauro Podda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Michelle R Martin
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA; Department of Internal Medicine, University of California at Davis, Davis, CA, USA
| | - Janine M Lasalle
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
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29
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Selmi C, Cavaciocchi F, Lleo A, Cheroni C, De Francesco R, Lombardi SA, De Santis M, Meda F, Raimondo MG, Crotti C, Folci M, Zammataro L, Mayo MJ, Bach N, Shimoda S, Gordon SC, Miozzo M, Invernizzi P, Podda M, Scavelli R, Martin MR, Seldin MF, Lasalle JM, Gershwin ME. Genome-wide analysis of DNA methylation, copy number variation, and gene expression in monozygotic twins discordant for primary biliary cirrhosis. Front Immunol 2014. [PMID: 24734033 PMCID: PMC4132258 DOI: 10.3389/fimmu.2014.00371] [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: 12/17/2022] Open
Abstract
Primary biliary cirrhosis (PBC) is an uncommon autoimmune disease with a homogeneous clinical phenotype that reflects incomplete disease concordance in monozygotic (MZ) twins. We have taken advantage of a unique collection consisting of genomic DNA and mRNA from peripheral blood cells of female MZ twins (n = 3 sets) and sisters of similar age (n = 8 pairs) discordant for disease. We performed a genome-wide study to investigate differences in (i) DNA methylation (using a custom tiled four-plex array containing tiled 50-mers 19,084 randomly chosen methylation sites), (ii) copy number variation (CNV) (with a chip including markers derived from the 1000 Genomes Project, all three HapMap phases, and recently published studies), and/or (iii) gene expression (by whole-genome expression arrays). Based on the results obtained from these three approaches we utilized quantitative PCR to compare the expression of candidate genes. Importantly, our data support consistent differences in discordant twins and siblings for the (i) methylation profiles of 60 gene regions, (ii) CNV of 10 genes, and (iii) the expression of 2 interferon-dependent genes. Quantitative PCR analysis showed that 17 of these genes are differentially expressed in discordant sibling pairs. In conclusion, we report that MZ twins and sisters discordant for PBC manifest particular epigenetic differences and highlight the value of the epigenetic study of twins.
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Affiliation(s)
- Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
| | - Francesca Cavaciocchi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Ana Lleo
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | | | | | - Simone A Lombardi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria De Santis
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy ; BIOMETRA Department, University of Milan , Milan , Italy
| | - Francesca Meda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Maria Gabriella Raimondo
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Chiara Crotti
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Marco Folci
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | - Luca Zammataro
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Nancy Bach
- Mt. Sinai University , New York, NY , USA
| | - Shinji Shimoda
- Clinical Research Center, National Nagasaki Medical Center , Nagasaki , Japan
| | | | - Monica Miozzo
- Department of Pathophysiology and Transplantation, University of Milan , Milan , Italy ; Division of Pathology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico , Milan , Italy
| | - Pietro Invernizzi
- Liver Unit and Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center , Milan , Italy
| | - Mauro Podda
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center , Milan , Italy
| | | | - Michelle R Martin
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - Michael F Seldin
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA; Department of Internal Medicine, University of California at Davis, Davis, CA, USA
| | - Janine M Lasalle
- Genome Center and M.I.N.D. Institute, University of California Davis , Davis, CA , USA
| | - M Eric Gershwin
- Division of Rheumatology, Allergy, and Clinical Immunology, University of California at Davis , Davis, CA , USA
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Yuan J, Zhao D, Wu L, Xu X, Pang Y, Zhang J, Ma Y, Liu J, Wang J. FCGR3Bcopy number loss rather than gain is a risk factor for systemic lupus erythematous and lupus nephritis: a meta-analysis. Int J Rheum Dis 2014; 18:392-7. [PMID: 24673810 DOI: 10.1111/1756-185x.12342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jin Yuan
- Department of Dermatology; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Dongbao Zhao
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Lijun Wu
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Xia Xu
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Yafei Pang
- Department of Rheumatology and Immunology; Changhai Hospital affiliated to Second Military Medical University; Shanghai China
| | - Jun Zhang
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering; School of Life Sciences; Fudan University; Shanghai China
| | - Jie Liu
- Department of Digestive Diseases; Huashan Hospital affiliated to Fudan University; Shanghai China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering; School of Life Sciences; Fudan University; Shanghai China
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Liao WL, Wan L, Wang TY, Chen CC, Tse SS, Lu CH, Tsai FJ. Association of TLR7 and TSHR copy number variation with Graves' disease and Graves' ophthalmopathy in Chinese population in Taiwan. BMC Ophthalmol 2014; 14:15. [PMID: 24517461 PMCID: PMC3929160 DOI: 10.1186/1471-2415-14-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 01/27/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Graves' disease (GD) and Graves' ophthalmopathy (GO) are autoimmune disorders, which might be influenced by genetic factors. Copy number variation (CNV) is an important source of genomic diversity in humans, and influences disease susceptibility. This study investigated the association between CNV in the TSHR and TLR7 genes and the development of GD and GO in a Chinese population in Taiwan. METHODS For this case-control study, sample from 196 healthy controls and 484 GD patients, including 203 patients with GO were studied. CNV was detected by real-time polymerase chain reaction (PCR) using TaqMan™ probes and the relative copy number (CN) was estimated by using the comparative Ct method. RESULTS The differences in the distribution of TSHR CNV in healthy controls and GD patients were statistically significant (p value = 0.01). However, the difference in the distribution of TSHR CNV in the control group and the GO group was not statistically significant (p value = 0.06). For TLR7 CNV, the results were not significantly different when we compared the distribution in healthy controls and GD patients and in healthy controls and GO patients (p values for Fisher's exact test were 0.13 and 0.09, respectively). However, a lower than normal CNV for TLR7 (CNV < 2 for female and CNV < 1 for male) was found to have a protective effect against the development of GD (odds ratio (OR) = 0.24; 95% confidence interval (CI), 0.07-0.75) after adjusting for age and gender. CONCLUSIONS These results suggested that TSHR and TLR7 CNV might be associated with susceptibility to GD.
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Affiliation(s)
| | | | | | | | | | | | - Fuu-Jen Tsai
- Department of Medical Genetics and Medical Research, China Medical University Hospital, No,2 Yuh-Der Road, 404 Taichung City, Taiwan.
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32
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Comment on ‘No association of primary Sjögren’s syndrome with Fcγ receptor gene variants’. Genes Immun 2013; 14:530-1. [DOI: 10.1038/gene.2013.52] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Haldorsen K, Bruland O, Appel S, Bolstad AI. Reply to ‘Comment on No association of primary Sjögren’s syndrome with Fcγ receptor gene variants’. Genes Immun 2013; 14:532. [DOI: 10.1038/gene.2013.51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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34
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Bullich G, Ballarín J, Oliver A, Ayasreh N, Silva I, Santín S, Díaz-Encarnación MM, Torra R, Ars E. HLA-DQA1 and PLA2R1 polymorphisms and risk of idiopathic membranous nephropathy. Clin J Am Soc Nephrol 2013; 9:335-43. [PMID: 24262501 DOI: 10.2215/cjn.05310513] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES Single nucleotide polymorphisms (SNPs) within HLA complex class II HLA-DQ α-chain 1 (HLA-DQA1) and M-type phospholipase A2 receptor (PLA2R1) genes were identified as strong risk factors for idiopathic membranous nephropathy (IMN) development in a recent genome-wide association study. Copy number variants (CNVs) within the Fc gamma receptor III (FCGR3) locus have been associated with several autoimmune diseases, but their role in IMN has not been studied. This study aimed to validate the association of HLA-DQA1 and PLA2R1 risk alleles with IMN in a Spanish cohort, test the putative association of FCGR3A and FCGR3B CNVs with IMN, and assess the use of these genetic factors to predict the clinical outcome of the disease. DESIGN, SETTINGS, PARTICIPANTS, & MEASUREMENTS A Spanish cohort of 89 IMN patients and 286 matched controls without nephropathy was recruited between October of 2009 and July of 2012. Case-control studies for SNPs within HLA-DQA1 (rs2187668) and PLA2R1 (rs4664308) genes and CNVs for FCGR3A and FCGR3B genes were performed. The contribution of these polymorphisms to predict clinical outcome and renal function decline was analyzed. RESULTS This study validated the association of these HLA-DQA1 and PLA2R1 SNPs with IMN in a Spanish cohort and its increased risk when combining both risk genotypes. No significant association was found between FCGR3 CNVs and IMN. These results revealed that HLA-DQA1 and PLA2R1 genotype combination adjusted for baseline proteinuria strongly predicted response to immunosuppressive therapy. HLA-DQA1 genotype adjusted for proteinuria was also linked with renal function decline. CONCLUSION This study confirms that HLA-DQA1 and PLA2R1 genotypes are risk factors for IMN, whereas no association was identified for FCGR3 CNVs. This study provides, for the first time, evidence of the contribution of these HLA-DQA1 and PLA2R1 polymorphisms in predicting IMN response to immunosuppressors and disease progression. Future studies are needed to validate and identify prognostic markers.
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Affiliation(s)
- Gemma Bullich
- Molecular Biology Laboratory and, †Nephrology Department, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Red de Investigación Renal, Instituto de Investigación Carlos III, Barcelona, Spain
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Bendjilali N, Kim H, Weinsheimer S, Guo DE, Kwok PY, Zaroff JG, Sidney S, Lawton MT, McCulloch CE, Koeleman BPC, Klijn CJM, Young WL, Pawlikowska L. A genome-wide investigation of copy number variation in patients with sporadic brain arteriovenous malformation. PLoS One 2013; 8:e71434. [PMID: 24098321 PMCID: PMC3789669 DOI: 10.1371/journal.pone.0071434] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 06/30/2013] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Brain arteriovenous malformations (BAVM) are clusters of abnormal blood vessels, with shunting of blood from the arterial to venous circulation and a high risk of rupture and intracranial hemorrhage. Most BAVMs are sporadic, but also occur in patients with Hereditary Hemorrhagic Telangiectasia, a Mendelian disorder caused by mutations in genes in the transforming growth factor beta (TGFβ) signaling pathway. METHODS To investigate whether copy number variations (CNVs) contribute to risk of sporadic BAVM, we performed a genome-wide association study in 371 sporadic BAVM cases and 563 healthy controls, all Caucasian. Cases and controls were genotyped using the Affymetrix 6.0 array. CNVs were called using the PennCNV and Birdsuite algorithms and analyzed via segment-based and gene-based approaches. Common and rare CNVs were evaluated for association with BAVM. RESULTS A CNV region on 1p36.13, containing the neuroblastoma breakpoint family, member 1 gene (NBPF1), was significantly enriched with duplications in BAVM cases compared to controls (P = 2.2×10(-9)); NBPF1 was also significantly associated with BAVM in gene-based analysis using both PennCNV and Birdsuite. We experimentally validated the 1p36.13 duplication; however, the association did not replicate in an independent cohort of 184 sporadic BAVM cases and 182 controls (OR = 0.81, P = 0.8). Rare CNV analysis did not identify genes significantly associated with BAVM. CONCLUSION We did not identify common CNVs associated with sporadic BAVM that replicated in an independent cohort. Replication in larger cohorts is required to elucidate the possible role of common or rare CNVs in BAVM pathogenesis.
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Affiliation(s)
- Nasrine Bendjilali
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Helen Kim
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Shantel Weinsheimer
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Diana E. Guo
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Jonathan G. Zaroff
- Kaiser Northern California Division of Research, San Francisco, California, United States of America
| | - Stephen Sidney
- Kaiser Northern California Division of Research, San Francisco, California, United States of America
| | - Michael T. Lawton
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
| | - Charles E. McCulloch
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Bobby P. C. Koeleman
- Department of Medical Genetics, University Medical Center, Utrecht, The Netherlands
| | - Catharina J. M. Klijn
- Department of Neurology and Neurosurgery, Rudolf Magnus Institute of Neuroscience, University Medical Center, Utrecht, The Netherlands
| | - William L. Young
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, United States of America
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | - Ludmila Pawlikowska
- Center for Cerebrovascular Research, Department of Anesthesia and Perioperative Care, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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Makowsky R, Wiener HW, Ptacek TS, Silva M, Shendre A, Edberg JC, Portman MA, Shrestha S. FcγR gene copy number in Kawasaki disease and intravenous immunoglobulin treatment response. Pharmacogenet Genomics 2013; 23:455-62. [PMID: 23778324 PMCID: PMC4400828 DOI: 10.1097/fpc.0b013e328363686e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Kawasaki disease (KD), response to intravenous immunoglobulin (IVIG) therapy, and associated coronary artery disease progression have been associated with genetic polymorphisms in Fc gamma receptor (FcγR) genes. However, it is not known whether the existing gene copy number (GCN) variability relates to KD treatment response, susceptibility, or associated sequelae. METHODS The copy number of individuals with KD (n=510) and their family members (n=808) for three variable FcγRs was assessed using pyrosequencing. We performed the transmission disequilibrium test to examine the association of GCN for FcγRs (FcγR2C, FcγR3A, and FcγR3B) with susceptibility and used logistic regression models to determine its association with IVIG treatment outcomes. RESULTS FcγR2C and FcγR3B GCN were significantly associated with KD susceptibility. IVIG response was associated with GCN variations of FcγR3B in Whites and FcγR2C in Hispanics, and gene risk score based on single nucleotide polymorphism and GCN in FcγRs were significantly different between IVIG responders and nonresponders among Whites. We found no significant associations between coronary artery disease and any of the FcγR copy numbers. CONCLUSION GCN of FcγR2C and FcγR3B influences IVIG treatment response and predisposes individuals to KD, providing potential insights into understanding the mechanism of the FcγR gene family in the IVIG pathway.
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Affiliation(s)
- Robert Makowsky
- Department of Biostatistics, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Howard W. Wiener
- Department of Epidemiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Travis S. Ptacek
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Miriam Silva
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington, Seattle, Washington, USA
| | - Aditi Shendre
- Department of Epidemiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jeffrey C. Edberg
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Michael A. Portman
- Department of Pediatrics, Seattle Children's Research Institute, University of Washington, Seattle, Washington, USA
| | - Sadeep Shrestha
- Department of Epidemiology, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama
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Dunstan E, Lester S, Black R, Rischmueller M, Chan H, Hewitt AW, Hill CL. No Association between FC γ R3B Copy Number Variation and Susceptibility to Biopsy-Proven Giant Cell Arteritis. ARTHRITIS 2013; 2013:514914. [PMID: 24027635 PMCID: PMC3762162 DOI: 10.1155/2013/514914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022]
Abstract
Objective. To determine the relationship between FCGR3B gene copy number variation (CNV) and biopsy proven giant cell arteritis (GCA). Methods. FCGR3B CNV was determined in 139 Australian biopsy proven GCA patients and 162 population matched controls, using a duplex qPCR assay and RNase P as the reference gene. Copy number was determined using Copy Caller software (v.1.0, Applied Biosystems, USA). CNV genotypes were classified into 3 groups (<2, 2, 3+) for analysis purposes, and analysis was performed using logistic regression. Results. All GCA patients had a positive temporal artery biopsy, and the most common presenting symptoms were visual disturbance and temporal headache. The mean age of patients at biopsy was 74 years (range 51-94) and 88/139 (63%) were female. The frequency of low (<2) FCGR3B copy number was comparable between GCA patients (9/139 = 6.5%) and controls (10/162 = 6.2%), as was the frequency of high (3+) FCGR3B copy number (15/130 (10.8%) in GCA patients versus 13/162 (8.0%) in controls). Overall there was no evidence that FCGR3B CNV frequencies differed between GCA patients and controls (χ (2) = 0.75, df = 2, P = 0.69). Conclusion. FCGR3B CNV is not associated with GCA; however, replicate studies are required.
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Affiliation(s)
- Emma Dunstan
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- The Health Observatory, Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Sue Lester
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
| | - Rachel Black
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
| | - Maureen Rischmueller
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Helen Chan
- Centre for Eye Research, Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, VIC 3002, Australia
| | - Alex W. Hewitt
- Centre for Eye Research, Royal Victorian Eye and Ear Hospital, University of Melbourne, East Melbourne, VIC 3002, Australia
- Lions Institute, University of Western Australia, Nedlands, WA 6009, Australia
| | - Catherine L. Hill
- Rheumatology Department, The Queen Elizabeth Hospital, Woodville South, SA 5011, Australia
- The Health Observatory, Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
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Nossent JC, Becker-Merok A, Rischmueller M, Lester S. Susceptibility for Lupus Nephritis by Low Copy Number of the FCGR3B Gene Is Linked to Increased Levels of Pathogenic Autoantibodies. Autoimmune Dis 2013; 2013:750814. [PMID: 23864940 PMCID: PMC3705838 DOI: 10.1155/2013/750814] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/03/2013] [Indexed: 12/14/2022] Open
Abstract
Low copy number (CN) of the FCGR3B gene reduces FCGR3B membrane expression on neutrophils and results in clearance of a smaller amount of immune complex. We investigated FCGR3B CN in relation to the clinical phenotype in a Caucasian SLE cohort (n = 107). FCGR3B CN was determined by three different qPCR parameter estimations (Ct-, Cy0, and cpD1) and confirmed by the FCGR2C/FCGR2A paralog ratio test. Clinical and serological data were then analyzed for their association with FCGR3B CN. Low FCGR3B CN (<2) was more frequent in SLE patients than in healthy controls (n = 162) (20% versus 6%, OR 4.15, P = 0.003) and associated with higher disease activity scores (SLEDAI 10.4 versus 6.1, P = 0.03), lupus nephritis (LN) (25 versus 5%, P = 0.03), and increased levels of antibodies against dsDNA (81 versus 37 IU, P = 0.03), C1q (22 versus 6 IU, P = 0.003), and ribosomal P (10 versus 5 IU, P = 0.01). No such associations were seen with antibodies against extractable nuclear antigens or high FCGR3B CN (>2). In multivariate analyses, LN was independently associated with anti-C1q-Ab levels (P = 0.03) and low FCGR3B CN (P = 0.09). We conclude that the susceptibility for LN in patients with low FCGR3B CN is linked to increased levels of pathogenic autoantibodies.
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Affiliation(s)
- Johannes C. Nossent
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
| | - Andrea Becker-Merok
- Department of Rheumatology, Institute of Clinical Medicine, University of Tromsø, 9037 Tromsø, Norway
- Department of Rheumatology, University Hospital Northern Norway, P.O. Box 14, 9038 Tromsø, Norway
| | - Maureen Rischmueller
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
- Division of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Sue Lester
- Department of Rheumatology, Basil Hetzel Institute, The Queen Elizabeth Hospital, Adelaide, SA 5020, Australia
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CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B. PLoS One 2013; 8:e63219. [PMID: 23646200 PMCID: PMC3640002 DOI: 10.1371/journal.pone.0063219] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 04/04/2013] [Indexed: 01/09/2023] Open
Abstract
The extent of contribution from common gene copy number (CN) variants in human disease is currently unresolved. Part of the reason for this is the technical difficulty in directly measuring CN variation (CNV) using molecular methods, and the lack of single nucleotide polymorphisms (SNPs) that can tag complex CNV that has arisen multiple times on different SNP haplotypes. One CNV locus implicated in human disease is FCGR. Here we aimed to use next-generation sequencing (NGS) data from the 1000 Genomes Project to assign CN at FCGR3A and FCGR3B and to comprehensively assess the ability of SNPs to tag specific CN variants. A read-depth algorithm was developed (CNVrd) and validated on a subset of HapMap samples using CN assignments that had previously been determined using molecular and microarray methods. At 7 out of 9 other complex loci there was >90% concordance with microarray data. However, given that some prior knowledge of CN is required, the generalizability of CNVrd is limited and should be applied to other complex CNV loci with caution. Subsequently, CN was assigned et FCGR3B using CNVrd in a total of 952 samples from the 1000 Genomes Project, using three classes and SNPs that correlated with duplication were identified. The best tag SNP was observed in the Mexican-American sample set for duplication at FCGR3B. This SNP (rs117435514, r2 = 0.79) also tagged similar duplication in Chinese and Japanese (r2 = 0.35–0.60), but not in Caucasian or African. No tag SNP for duplication at FCGR3A or deletion at FCGR3B was identified in any population. We conclude that it is possible to tag CNV at the FCGR locus, but CN and SNPs have to be characterized and correlated on a population-specific basis.
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Abstract
The genetic background of primary Sjögren's syndrome (pSS) is partly shared with systemic lupus erythematosus (SLE). Immunoglobulin G Fc receptors are important for clearance of immune complexes. Fcγ receptor variants and gene deletion have been found to confer SLE risk. In this study, four Fcγ receptor single-nucleotide polymorphisms (SNPs) and one copy number variation (CNV) were studied. Swedish and Norwegian pSS patients (N=527) and controls (N=528) were genotyped for the Fcγ receptor gene variant FCGR2A H131R (rs1801274) by the Illumina GoldenGate assay. FCGR3A F158V (rs396991) was analysed in 488 patients and 485 controls, FCGR3B rs447536 was analysed in 471 patients and 467 controls, and FCGR3B rs448740 was analysed in 478 cases and 455 controls, using TaqMan SNP genotyping assays. FCGR3B CNV was analysed in 124 patients and 139 controls using a TaqMan copy number assay. None of the SNPs showed any association with pSS. Also, no FCGR3B CNV association was detected. The lack of association of pSS with Fcγ receptor gene variants indicates that defective immune complex clearance may not be as important in pSS pathogenesis as in SLE, and may point to important differences between SLE and pSS.
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Watson C, Steinberg K, Huddleston J, Warren R, Malig M, Schein J, Willsey AJ, Joy J, Scott J, Graves TA, Wilson R, Holt R, Eichler E, Breden F. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet 2013; 92:530-46. [PMID: 23541343 DOI: 10.1016/j.ajhg.2013.03.004] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/08/2013] [Accepted: 03/06/2013] [Indexed: 01/02/2023] Open
Abstract
The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3-0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested.
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Rullo OJ, Tsao BP. Recent insights into the genetic basis of systemic lupus erythematosus. Ann Rheum Dis 2012; 72 Suppl 2:ii56-61. [PMID: 23253915 DOI: 10.1136/annrheumdis-2012-202351] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Many identified genetic risk factors for systemic lupus erythematosus (SLE) contribute to the function of the immune system, which has expanded our understanding of disease pathogenesis. We outline the genetic variants in recently identified SLE-associated loci, the immunological pathways affected by these gene products and the disease manifestations linked to these loci. Pathways potentially influenced by SLE risk variants include: apoptosis, DNA degradation and clearance of cellular debris; antigen presentation; type I interferon, Toll-like receptor and nuclear factor kappa κB activation; defective clearance of immune complexes containing nuclear antigens; B and T-cell function and signalling; and monocyte and neutrophil function and signalling. These identified SLE susceptibility loci are predominantly common variants that have been confirmed among multiple ancestries, suggesting shared mechanisms in disease aetiology. Ongoing genetic studies continue the investigation of specific functional variants, and their potential consequences on immune dysregulation, enhancing our understanding of links between genotypes and specific disease manifestations. The next generation of sequencing explores the identification of causal rare variants that may contribute robust genetic effects to developing SLE. Novel insights coming from genetic studies of SLE provide the opportunity to elucidate pathogenic mechanisms as well as contribute to the development of innovative therapeutic targets for this complex disease.
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Liu YZ, Li J, Pan R, Shen H, Tian Q, Zhou Y, Liu YJ, Deng HW. Genome-wide copy number variation association analyses for age at menarche. J Clin Endocrinol Metab 2012; 97:E2133-9. [PMID: 22904172 PMCID: PMC3485608 DOI: 10.1210/jc.2012-1145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Menarche is a significant physiological event for women. Age at menarche (AAM) is a heritable trait associated with many common female diseases. The genetic basis and the mechanism for AAM are largely unknown. Copy number variation (CNV) is a common type of genetic variation underlying human complex traits. The importance of CNV to AAM variation is unclear. OBJECTIVE The objective of the study was to identify CNV important to AAM variation. DESIGN We performed the first genome-wide CNV study of AAM in 1654 Caucasian females using Affymetrix human single-nucleotide polymorphism 6.0 array. We also replicated our findings in another Chinese cohort containing 752 women. RESULTS We identified a CNV, variation_38399, in the 2q14.2 region, for association with AAM (P = 1.03 × 10(-3)). The CNV has two variants (one copy and two copy), with a mean AAM of 14.00 yr and 12.90 yr, respectively. Interestingly, in a Chinese sample containing 752 women, this CNV has been replicated both with a marginally significant P = 0.090 and with a same direction of effect (a lower copy number for a later AAM). The CNV is located approximately 75 kb upstream of the diazepam binding inhibitor (DBI), a gene known to regulate estrogen levels, a key factor for menarche. CONCLUSION Our findings for the first time identified a novel CNV and suggested the DBI-mediated endocrinological pathway as a potential mechanism for AAM regulation.
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Affiliation(s)
- Yao-Zhong Liu
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana 70112, USA.
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Olsson LM, Holmdahl R. Copy number variation in autoimmunity--importance hidden in complexity? Eur J Immunol 2012; 42:1969-76. [PMID: 22865047 DOI: 10.1002/eji.201242601] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Copy number variation, namely regions of the genome that can be either deleted or duplicated in a variable way, has emerged as an important source of genetic variance in the human genome. Genes with immunological functions are particularly prone to copy number variation, in part because this is a mechanism to expand the recognition repertoire; however, immunological genes not directly involved in immune recognition are also copy number variable but, despite the link between immunological function and copy number variation, very few copy number variants (CNVs) have been found to be associated with autoimmune diseases, even in recent large genome-wide CNV-association studies. Nonetheless, CNVs in FCGR3B, DEFB4, CCL3L1, C4A/B and NCF1 have been suggested to be associated with autoimmune diseases, although there is conflicting evidence in all cases. The reasons for the lack of definitive data on CNV-autoimmunity associations, as well as the technical challenges for the field are the focus of this review.
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Affiliation(s)
- Lina M Olsson
- Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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NOSSENT JOHANNESC, RISCHMUELLER MAUREEN, LESTER SUE. Low Copy Number of the Fc-γ Receptor 3B Gene FCGR3B Is a Risk Factor for Primary Sjögren’s Syndrome. J Rheumatol 2012; 39:2142-7. [DOI: 10.3899/jrheum.120294] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Objective.Immune complexes play an important role in the pathogenesis of primary Sjögren’s syndrome (pSS). Crosslinking of the neutrophil-specific Fc-γ receptor 3b (FCGR3B) facilitates immune complex clearance, and copy number variation (CNV) of the FCGR3B gene is known to reduce the uptake, and potentially clearance, of circulating immune complexes. Our objective was to determine whether FCGR3B CNV is a risk factor for pSS.Methods.This was a cross-sectional study of patients with established pSS (n = 174) and population-matched controls (n = 162). FCGR3B CNV was determined by a quantitative real-time polymerase chain reaction assay, using genomic DNA as template and Taqman chemistry. Reactions were performed as a duplex, with RNAse P as the reference gene. Clinical and serological data were analyzed for their association with FCGR3B copy number (CN).Results.Low FCGR3B CN (< 2 copies) was a risk factor for pSS in this cohort (p = 0.016), and combined results from this and a previous study yielded an overall OR of 2.3 (95% CI 1.3, 3.9, p = 0.003). Among patients with pSS in our cohort, low FCGR3B CN was not associated with anti-Ro ± La autoantibodies, but was associated with lower rheumatoid factor titers (p = 0.001) and serum IgG levels (p = 0.031).Conclusion.We confirmed that, similarly to other systemic autoimmune diseases, FCGR3B CN is a genetic susceptibility factor for pSS. As in rheumatoid arthritis, the mechanism does not appear to be related to seropositivity for characteristic autoantibodies.
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Cantsilieris S, White SJ. Correlating multiallelic copy number polymorphisms with disease susceptibility. Hum Mutat 2012; 34:1-13. [PMID: 22837109 DOI: 10.1002/humu.22172] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Accepted: 07/13/2012] [Indexed: 01/20/2023]
Abstract
The human genome contains a significant amount of sequence variation, from single nucleotide polymorphisms to large stretches of DNA that may be present in a range of different copies between individuals. Several such regions are variable in >1% of the population (referred to as copy number polymorphisms or CNPs), and many studies have looked for associations between the copy number of genes within multiallelic CNPs and disease susceptibility. Associations have indeed been described for several genes, including the β-defensins (DEFB4, DEFB103, DEFB104), chemokine ligand 3 like 1 (CCL3L1), Fc gamma receptor 3B (FCGR3B), and complement component C4 (C4). However, follow-up replication in independent cohorts has failed to reproduce a number of these associations. It is clear that replicated associations such as those between C4 and systemic lupus erythematosus, and β-defensin and psoriasis, have used robust genotyping methodologies. Technical issues associated with genotyping sequences of high identity may therefore account for failure to replicate other associations. Here, we compare and contrast the most popular approaches that have been used to genotype CNPs, describe how they have been applied in different situations, and discuss potential reasons for the difficulty in reproducibly linking multiallelic CNPs to complex diseases.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Reproduction and Development, Monash Institute of Medical Research, Monash University, Melbourne, Victoria, Australia
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Zhao X, Onteru SK, Piripi S, Thompson KG, Blair HT, Garrick DJ, Rothschild MF. In a shake of a lamb's tail: using genomics to unravel a cause of chondrodysplasia in Texel sheep. Anim Genet 2012; 43 Suppl 1:9-18. [DOI: 10.1111/j.1365-2052.2011.02304.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- X. Zhao
- Department of Animal Science and Center for Integrated Animal Genomics; Iowa State University; Ames; IA; 50011; USA
| | - S. K. Onteru
- Department of Animal Science and Center for Integrated Animal Genomics; Iowa State University; Ames; IA; 50011; USA
| | | | - K. G. Thompson
- Institute of Veterinary, Animal & Biomedical Sciences; Massey University; Palmerston North; 4474; New Zealand
| | - H. T. Blair
- Institute of Veterinary, Animal & Biomedical Sciences; Massey University; Palmerston North; 4474; New Zealand
| | | | - M. F. Rothschild
- Department of Animal Science and Center for Integrated Animal Genomics; Iowa State University; Ames; IA; 50011; USA
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Black R, Lester S, Dunstan E, Shahram F, Nadji A, Bayat N, Saeedfar K, Ziaei N, Hill C, Rischmueller M, Davatchi F. Fc-Gamma Receptor 3B Copy Number Variation Is Not a Risk Factor for Behçet's Disease. Int J Rheumatol 2012; 2012:167096. [PMID: 22701122 PMCID: PMC3369435 DOI: 10.1155/2012/167096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/10/2012] [Indexed: 11/29/2022] Open
Abstract
Behçet's disease (BD) is an immune-mediated systemic vasculitis associated with HLAB51. Other gene associations are likely and may provide further insight into the pathogenesis of this disease. Fc-gamma receptors play an important role in regulating immune function. Copy number variation (CNV) of the Fc-gamma receptor 3B (FCGR3B) gene is associated with other inflammatory conditions and may also play a role in BD. The aim of this study was to determine whether CNV of the FCGR3B gene is associated with BD or its clinical features. FCGR3B copy number was determined for 187 Iranian patients and 178 ethnicity-matched controls using quantitative real-time PCR. The genotype frequencies were comparable in both BD patients and controls. The odds ratio for low copy number (<2CN) was 0.6 (P = 0.16) and the odds ratio for high copy number (>2CN) was 0.75 (P = 0.50). There was no association found between high or low CN of the FCGR3B gene and BD or its clinical features in this Iranian population. We are the first to report this finding which, when looked at in the context of other genetic studies, gives us further insight into the complex pathogenesis of BD.
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Affiliation(s)
- Rachel Black
- Department of Rheumatology, The Queen Elizabeth Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
| | - Sue Lester
- Department of Rheumatology, The Queen Elizabeth Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
| | - Emma Dunstan
- Department of Rheumatology, The Queen Elizabeth Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
| | - Farhad Shahram
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
| | - Abdolhadi Nadji
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
| | - Noushin Bayat
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
- Rheumatology Department, Baqyiatallah University of Medical Sciences, Baghiatallah hospital, Molla Sadra Street, Tehran 14359, Iran
| | - Kayvan Saeedfar
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
- Chronic Respiratory Diseases Research Centre, Shahid Beheshti University of Medical Sciences, Massih Daneshvari Hospital, Shaid Bahonar Street, Tehran 19556, Iran
| | - Naghmeh Ziaei
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
| | - Catherine Hill
- Department of Rheumatology, The Queen Elizabeth Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
- Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maureen Rischmueller
- Department of Rheumatology, The Queen Elizabeth Hospital, 28 Woodville Road, Woodville South, SA, 5011, Australia
- Discipline of Medicine, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Fereydoun Davatchi
- Rheumatology Research Centre, Tehran University of Medical Sciences, Shariati Hospital, Kargar Avenue, Tehran 14114, Iran
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McKinney C, Broen JCA, Vonk MC, Beretta L, Hesselstrand R, Hunzelmann N, Riemekasten G, Scorza R, Simeon CP, Fonollosa V, Carreira PE, Ortego-Centeno N, Gonzalez-Gay MA, Airo P, Coenen M, Martin J, Radstake TRDJ, Merriman TR. Evidence that deletion at FCGR3B is a risk factor for systemic sclerosis. Genes Immun 2012; 13:458-60. [PMID: 22551723 DOI: 10.1038/gene.2012.15] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
There is increasing evidence that gene copy number (CN) variation influences clinical phenotype. The low-affinity Fc receptor 3B (FCGR3B) located in the FCGR gene cluster is a CN polymorphic gene involved in the recruitment of polymorphonuclear neutrophils to sites of inflammation and their activation. Given the genetic overlap between systemic lupus erythematosus and systemic sclerosis (SSc) and the strong evidence for FCGR3B CN in the pathology of SLE, we hypothesised that FCGR3B gene dosage influences susceptibility to SSc. We obtained FCGR3B deletion status in 777 European Caucasian cases and 1000 controls. There was an inverse relationship between FCGR3B CN and disease susceptibility. CN of ≤ 1 was a significant risk factor for SSc (OR=1.55 (1.13-2.14), P=0.007) relative to CN ≥ 2. Although requiring replication, these results suggest that impaired immune complex clearance arising from FCGR3B deficiency contributes to the pathology of SSc, and FCGR3B CN variation is a common risk factor for systemic autoimmunity.
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Affiliation(s)
- C McKinney
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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50
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Cantsilieris S, White SJ, Richardson AJ, Guymer RH, Baird PN. Comprehensive analysis of Copy Number Variation of genes at chromosome 1 and 10 loci associated with late age related macular degeneration. PLoS One 2012; 7:e35255. [PMID: 22558131 PMCID: PMC3338825 DOI: 10.1371/journal.pone.0035255] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 03/14/2012] [Indexed: 11/18/2022] Open
Abstract
Copy Number Variants (CNVs) are now recognized as playing a significant role in complex disease etiology. Age-related macular degeneration (AMD) is the most common cause of irreversible vision loss in the western world. While a number of genes and environmental factors have been associated with both risk and protection in AMD, the role of CNVs has remained largely unexplored. We analyzed the two major AMD risk-associated regions on chromosome 1q32 and 10q26 for CNVs using Multiplex Ligation-dependant Probe Amplification. The analysis targeted nine genes in these two key regions, including the Complement Factor H (CFH) gene, the 5 CFH-related (CFHR) genes representing a known copy number "hotspot", the F13B gene as well as the ARMS2 and HTRA1 genes in 387 cases of late AMD and 327 controls. No copy number variation was detected at the ARMS2 and HTRA1 genes in the chromosome 10 region, nor for the CFH and F13B genes at the chromosome 1 region. However, significant association was identified for the CFHR3-1 deletion in AMD cases (p = 2.38 × 10(-12)) OR = 0.31, CI-0.95 (0.23-0.44), for both neovascular disease (nAMD) (p = 8.3 × 10(-9)) OR = 0.36 CI-0.95 (0.25-0.52) and geographic atrophy (GA) (p = 1.5 × 10(-6)) OR = 0.36 CI-0.95 (0.25-0.52) compared to controls. In addition, a significant association with deletion of CFHR1-4 was identified only in patients who presented with bilateral GA (p = 0.02) (OR = 7.6 CI-0.95 1.38-41.8). This is the first report of a phenotype specific association of a CNV for a major subtype of AMD and potentially allows for pre-diagnostic identification of individuals most likely to proceed to this end stage of disease.
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Affiliation(s)
- Stuart Cantsilieris
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Centre for Reproduction and Development, Monash Institute of Medical Research, Melbourne, Victoria, Australia
| | - Stefan J. White
- Centre for Reproduction and Development, Monash Institute of Medical Research, Melbourne, Victoria, Australia
| | - Andrea J. Richardson
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Robyn H. Guymer
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
| | - Paul N. Baird
- Centre for Eye Research Australia, University of Melbourne, Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
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