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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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Shi X, Qu M, Jin X, Liu L, Meng F, Shen H. Relationship between TSHR, BRAF and PIK3CA gene copy number variations and thyroid nodules. Endocrine 2021; 73:116-124. [PMID: 33428122 DOI: 10.1007/s12020-020-02587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/09/2020] [Indexed: 10/22/2022]
Abstract
PURPOSE This study aims to investigate the relationship between the TSHR, BRAF, and PIK3CA gene copy number variations (CNVs) and thyroid nodules by analyzing gene CNVs, and to explore the interaction between iodine status and the above genes CNVs in the occurrence of thyroid nodules. METHODS Three hundred and ninety-five subjects were selected from 3 regions with different iodine status in Shanxi Province of China, including 192 patients with thyroid nodules and 203 healthy controls. The basic information about subjects had been obtained through a questionnaire. B ultrasound was utilized to check thyroid nodules. Blood and urine samples were harvested to detect the thyroid function and urinary iodine concentration. Real-time quantitative polymerase chains reaction (RT-PCR) served to detect CNVs in DNA from human blood. RESULTS There was an association between TSHR gene CNV and thyroid nodules (χ2 = 8.403, P = 0.004). The prevalence of BRAF and PIK3CA gene CNVs was not statistically significant between the case group and the control group. Differences in the TSHR gene CNV rates for cases of the 3 areas were statistically significant (χ2 = 10.072, P = 0.007). No statistical difference in the prevalence rates of the 3 genes CNVs between diverse characteristics of thyroid nodules was observed. UIC > 300 μg/L (OR = 1.74, 95% CI: 1.02-2.96, P = 0.041) and TSHR gene CNV (OR = 3.53, 95% CI: 1.40-8.92, P = 0.008) were risk factors for thyroid nodules. There was no significant interaction between the UIC and the examined genes CNVs. CONCLUSIONS TSHR gene CNV and high urinary iodine levels can increase the risk of thyroid nodules. But the interactions between the 3 above genes CNVs and iodine nutrition were not found in the occurrence of thyroid nodules.
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Affiliation(s)
- Xiaoli Shi
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Department of Medical Administration, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengying Qu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xing Jin
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
- Department of Epidemiology, School of Public Health, Dalian Medical University, Dalian, China
| | - Lixiang Liu
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Fangang Meng
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Centre for Endemic Disease Control, Chinese Centre for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China.
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Mousavi MJ, Mahmoudi M, Ghotloo S. Escape from X chromosome inactivation and female bias of autoimmune diseases. Mol Med 2020; 26:127. [PMID: 33297945 PMCID: PMC7727198 DOI: 10.1186/s10020-020-00256-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Generally, autoimmune diseases are more prevalent in females than males. Various predisposing factors, including female sex hormones, X chromosome genes, and the microbiome have been implicated in the female bias of autoimmune diseases. During embryogenesis, one of the X chromosomes in the females is transcriptionally inactivated, in a process called X chromosome inactivation (XCI). This equalizes the impact of two X chromosomes in the females. However, some genes escape from XCI, providing a basis for the dual expression dosage of the given gene in the females. In the present review, the contribution of the escape genes to the female bias of autoimmune diseases will be discussed.
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Affiliation(s)
- Mohammad Javad Mousavi
- Department of Hematology, Faculty of Allied Medicine, Bushehr University of Medical Sciences, Bushehr, Iran.,Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Somayeh Ghotloo
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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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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Jin X, Guan Y, Shen H, Pang Y, Liu L, Jia Q, Meng F, Zhang X. Copy Number Variation of Immune-Related Genes and Their Association with Iodine in Adults with Autoimmune Thyroid Diseases. Int J Endocrinol 2018; 2018:1705478. [PMID: 29713342 PMCID: PMC5866896 DOI: 10.1155/2018/1705478] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/31/2018] [Accepted: 02/06/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Autoimmune thyroid diseases (AITD) are complex conditions that are caused by an interaction between genetic susceptibility and environmental triggers. Iodine is already known to be an environmental trigger for AITD, but genes associated with susceptibility need to be further assessed. Therefore, the aims of this study were to assess the association between copy number variations (CNVs) and AITD, to identify genes related with susceptibility to AITD, and to investigate the interaction between iodine status and CNVs in the occurrence of AITD. METHODS Blood samples from 15 patients with AITD and 15 controls were assessed by chromosome microarray to identify candidate genes. The copy number of candidate genes and urinary iodine level was determined in adults from areas of different iodine statuses including 158 patients and 181 controls. RESULTS The immune-related genes, SIRPB1 and TMEM91, were selected as candidate genes. The distribution of SIRPB1 CNV in AITD patients and controls was significantly different and was considered a risk factor for AITD. There was no significant association between urinary iodine level and candidate gene CNVs. CONCLUSION SIRPB1 CNV and an excess of iodine were risk factors for AITD, but an association with the occurrence of AITD was not found.
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Affiliation(s)
- Xing Jin
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunfeng Guan
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Hongmei Shen
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Yi Pang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Lixiang Liu
- 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
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiaoye Zhang
- Center for Endemic Disease Control, Chinese Center for Disease Control and Prevention, Harbin Medical University, Harbin, Heilongjiang, China
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Abstract
BACKGROUND Few previous published papers reported copy number variations of genes could affect the predisposition of Graves' disease (GD). Herein, the aim of this study was to explore the association between copy number variations (CNV) profile and GD. METHODS The preliminary copy number microarray used to screen copy number variant genes was performed in 6 GD patients. Five CNV candidate genes (CFH, CFHR1, KIAA0125, UGT2B15, and UGT2B17) were then validated in an independent set of samples (50 GD patients and 50 matched healthy ones) by the Accucopy assay method. The CNV of the other 2 genes TRY6 and CCL3L1 was investigated in 144 GD patients and 144 healthy volunteers by the definitive genotyping technique using the Taqman quantitative polymerase-chain-reaction (Taqman qPCR). TRY6 gene-associated single nucleotide polymorphism (SNP), rs13230029, was genotyped by the PCR-ligase detection reaction (LDR) in 675 GD patients and 898 healthy controls. RESULTS There were no correlation of the gene copy number (GCN) of CFH, CFHR1, KIAA0125, UGT2B15, and UGT2B17 with GD. In comparison with that of controls, the GCN distribution of TRY6 and CCL3L1 in GD patients did not show significantly differ (P > 0.05). Furthermore, TRY6-related polymorphism (rs13230029) showed no difference between GD patients and controls. No correlation was found between CNV or SNP genotype and clinical phenotypes. Generally, there were no link of the copy numbers of several genes, including CFH, CFHR1, KIAA0125, UGT2B15, UGT2B17, TRY6, and CCL3L1 to GD. CONCLUSION Our results clearly indicated that the copy number variations of multiple genes, namely CFH, CFHR1, KIAA0125, UGT2B15, UGT2B17, TRY6, and CCL3L1, were not associated with the development of GD.
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Lahooti H, Cultrone D, Edirimanne S, Walsh JP, Delbridge L, Cregan P, Champion B, Wall JR. Novel single-nucleotide polymorphisms in the calsequestrin-1 gene are associated with Graves' ophthalmopathy and Hashimoto's thyroiditis. Clin Ophthalmol 2015; 9:1731-40. [PMID: 26445519 PMCID: PMC4590686 DOI: 10.2147/opth.s87972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The eye disorder associated with Graves' disease, called Graves' ophthalmopathy (GO), greatly reduces the quality of life in affected patients. Expression of the calsequestrin (CASQ1) protein in thyroid tissue may be the trigger for the development of eye muscle damage in patients with GO. We determined the prevalence of rs74123279, rs3747673, and rs2275703 single-nucleotide polymorphism (SNPs) in patients with autoimmune thyroid disorders, GO, Graves' hyperthyroidism (GH), or Hashimoto's thyroiditis (HT) and control subjects with no personal or family history of autoimmune thyroid disorders. Furthermore, we measured the concentration of the CASQ1 protein in normal and Graves' thyroid tissue, correlating levels with parameters of the eye signs, CASQ1 antibody levels, and the CASQ1 gene polymorphism rs74123279 and rs2275703. METHODS High-quality genomic DNA was isolated from fresh blood samples, assayed for identification of rs74123279, rs3747673, and rs2275703 SNPs in CASQ1 gene by MassARRAY SNP analysis using iPLEX technology of SEQUENOM. RESULTS DNA samples from 300 patients and 106 control subjects (100 males, 306 females) with GO (n=74), GH (n=130), HT (n=96) and control subjects (n=106) were genotyped for the SNPs rs74123279, rs3747673 (n=405), and rs2275703 (n=407). The SNP rs74123279, rs3747673, and rs2275703 were identified as 1) common homozygous or wild type, 2) heterozygote, and 3) rare homozygous. Minor allele frequency for rs74123279, rs3747763, and rs2275703 were 21%, 40%, and 44%, respectively. Multiple comparisons of genotype frequency for rs74123279, rs3747763, and rs2275703 in the GO, GH, HT, and control groups showed P=0.06, 0.641, and 0.189, respectively. These results were substantiated by multiple comparison of alleles frequency for rs74123279, rs3838216, rs3747763, and rs2275703 in the GO, GH, HT, and control groups showed, P=0.36, 0.008, 0.66, and 0.05, respectively. Pairwise analysis of alleles frequency distribution in patients with GO showed significant probability for rs2275703, P=0.008. CONCLUSION Based on their evolutionary conservation and their significant prevalence, we suggest that CASQ1 gene SNPs rs74123279, rs3838216, and rs2275703 may be considered as genetic markers for GO.
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Affiliation(s)
- Hooshang Lahooti
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
| | - Daniele Cultrone
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
| | - Senarath Edirimanne
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
| | - John P Walsh
- Department of Endocrinology and Diabetes, Sir Charles Gairdner Hospital, Nedlands, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, WA, Australia
| | - Leigh Delbridge
- Department of Surgery, Royal North Shore Hospital, The University of Sydney, St Leonards, NSW, Australia
- Sydney Medical School – Northern Clinical School, The University of Sydney, St Leonards, NSW, Australia
| | - Patrick Cregan
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
| | - Bernard Champion
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
| | - Jack R Wall
- Thyroid Research Laboratory, Sydney Medical School – Nepean Clinical School, The University of Sydney, Kingswood, NSW, Australia
- Nepean Blue Mountains Local Health District, Nepean Hospital, Kingswood, NSW, Australia
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Xiao W, Liu Z, Lin J, Li J, Wu K, Ma Y, Xiong C, Gong Y, Liu Z. Association of Toll-like receptor 7 and 8 gene polymorphisms with Graves' disease in Chinese Cantonese population. ACTA ACUST UNITED AC 2014; 85:29-34. [DOI: 10.1111/tan.12479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/17/2014] [Accepted: 10/26/2014] [Indexed: 12/13/2022]
Affiliation(s)
- WenJuan Xiao
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - ZeLin Liu
- Shenzhen People's Hospital; Shenzhen China
| | - JiangHai Lin
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - JingBo Li
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - KeJing Wu
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - Yun Ma
- Shenzhen People's Hospital; Shenzhen China
| | - ChunJiang Xiong
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - YingXue Gong
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
| | - ZeHuan Liu
- Research Center for Molecular Biology, College of Life Science and Technology; Jinan University; Guangzhou China
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