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Identification of novel genes in Behcet's disease using integrated bioinformatic analysis. Immunol Res 2022; 70:461-468. [PMID: 35364782 PMCID: PMC9273552 DOI: 10.1007/s12026-022-09270-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/22/2022] [Indexed: 12/24/2022]
Abstract
Behcet’s disease (BD) is a chronic vascular inflammatory disease. However, the etiology and molecular mechanisms underlying BD development have not been thoroughly understood. Gene expression data for BD were obtained from the Gene Expression Omnibus database. We used robust rank aggregation (RRA) to identify differentially expressed genes (DEGs) between patients with BD and healthy controls. Gene ontology functional enrichment was used to investigate the potential functions of the DEGs. Protein–protein interaction (PPI) network analysis was performed to identify the hub genes. Receiver operating characteristic analyses were performed to investigate the value of hub genes in the diagnosis of BD. GSE17114 and GSE61399 datasets were included, comprising 32 patients with BD and 26 controls. The RRA integrated analysis identified 44 significant DEGs among the GSE17114 and GSE61399 CD4 + T lymphocytes. Functional enrichment analysis revealed that protein tyrosine/threonine phosphatase activity and immunoglobulin binding were enriched in BD. PPI analysis identified FCGR3B as a hub gene in the CD4 + T lymphocytes of BD patients. Our bioinformatic analysis identified new genetic features, which will enable further understanding of the pathogenesis of BD.
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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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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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Validity and reliability of the Persian version of Behçet's disease quality-of-life (BD-QoL) questionnaire: a cross-cultural adaptation. Rheumatol Int 2014; 35:677-84. [PMID: 25216713 DOI: 10.1007/s00296-014-3128-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 09/03/2014] [Indexed: 10/24/2022]
Abstract
The Leeds Behçet's disease quality-of-life (BD-QoL) questionnaire is a specific and valid measure which is applied in English-speaking patients. We conducted Persian adaptation of BD-QoL questionnaire. Between June and December 2012, 220 Iranian patients fulfilling International Study Group criteria for the diagnosis of BD attending the rheumatology clinics at Tehran University of Medical Sciences were enrolled. Bilingual translators undertook the forward translation and cross-cultural adaptation of the BD-QoL questionnaire. Back-translation was conducted, and this version was sent to the designer of the questionnaire and revised accordingly. SF-36 health survey, Iranian Behçet's disease dynamic activity measure (IBDDAM), and Behçet's Disease Current Activity Form (BDCAF) were other administered measures. The Varimax rotation method with Kaiser normalization defined 5 factors with eigenvalues greater than 1.0. Studied cases were comprised of 118 males (53.6 %) and 102 females (46.4 %). Mean age of the patients was 38.3 ± 11.3 years (range 16-73). The mean BD-QoL score was 10.3 ± 8.8. Test-retest reliability was high, and two time points were significantly correlated (Spearman's correlation coefficient of 0.75-0.84). Cronbach's α coefficient of 0.949 demonstrated the excellent internal consistency. These factors cumulatively explained 58.74 % of total variance. The ratio of first to second eigenvalue was 7.08, which underlined the undimensionality. The results revealed adapted BD-QoL scores had significant correlation with IBDDAM (correlation coefficient = 0.19, P value = 0.005) and BDCAF (correlation coefficient = 0.21, P value = 0.002). Conversely, no significant correlation between BD-QoL and SF-36 results was detected (P value = 0.078). The Persian version of BD-QoL was shown to be unidimensional, highly reliable, and adequate construct validity.
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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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