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Guo S, Jin Y, Zhou J, Zhu Q, Jiang T, Bian Y, Zhang R, Chang C, Xu L, Shen J, Zheng X, Shen Y, Qin Y, Chen J, Tang X, Cheng P, Ding Q, Zhang Y, Liu J, Cheng Q, Guo M, Liu Z, Qiu W, Qian Y, Sun Y, Shen Y, Nie H, Schrodi SJ, He D. MicroRNA Variants and HLA-miRNA Interactions are Novel Rheumatoid Arthritis Susceptibility Factors. Front Genet 2021; 12:747274. [PMID: 34777472 PMCID: PMC8585984 DOI: 10.3389/fgene.2021.747274] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/11/2021] [Indexed: 12/25/2022] Open
Abstract
Genome-wide association studies have identified >100 genetic risk factors for rheumatoid arthritis. However, the reported genetic variants could only explain less than 40% heritability of rheumatoid arthritis. The majority of the heritability is still missing and needs to be identified with more studies with different approaches and populations. In order to identify novel function SNPs to explain missing heritability and reveal novel mechanism pathogenesis of rheumatoid arthritis, 4 HLA SNPs (HLA-DRB1, HLA-DRB9, HLA-DQB1, and TNFAIP3) and 225 common SNPs located in miRNA, which might influence the miRNA target binding or pre-miRNA stability, were genotyped in 1,607 rheumatoid arthritis and 1,580 matched normal individuals. We identified 2 novel SNPs as significantly associated with rheumatoid arthritis including rs1414273 (miR-548ac, OR = 0.84, p = 8.26 × 10-4) and rs2620381 (miR-627, OR = 0.77, p = 2.55 × 10-3). We also identified that rs5997893 (miR-3928) showed significant epistasis effect with rs4947332 (HLA-DRB1, OR = 4.23, p = 0.04) and rs2967897 (miR-5695) with rs7752903 (TNFAIP3, OR = 4.43, p = 0.03). In addition, we found that individuals who carried 8 risk alleles showed 15.38 (95%CI: 4.69-50.49, p < 1.0 × 10-6) times more risk of being affected by RA. Finally, we demonstrated that the targets of the significant miRNAs showed enrichment in immune related genes (p = 2.0 × 10-5) and FDA approved drug target genes (p = 0.014). Overall, 6 novel miRNA SNPs including rs1414273 (miR-548ac, p = 8.26 × 10-4), rs2620381 (miR-627, p = 2.55 × 10-3), rs4285314 (miR-3135b, p = 1.10 × 10-13), rs28477407 (miR-4308, p = 3.44 × 10-5), rs5997893 (miR-3928, p = 5.9 × 10-3) and rs45596840 (miR-4482, p = 6.6 × 10-3) were confirmed to be significantly associated with RA in a Chinese population. Our study suggests that miRNAs might be interesting targets to accelerate understanding of the pathogenesis and drug development for rheumatoid arthritis.
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Affiliation(s)
- Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Yehua Jin
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jieru Zhou
- Department of Health Management, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qi Zhu
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ting Jiang
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yanqin Bian
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Runrun Zhang
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Cen Chang
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lingxia Xu
- Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jie Shen
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Xinchun Zheng
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Shen
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yingying Qin
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jihong Chen
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaorong Tang
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Peng Cheng
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qin Ding
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanyuan Zhang
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jia Liu
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qingqing Cheng
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengru Guo
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhaoyi Liu
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Weifang Qiu
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi Qian
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yang Sun
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yu Shen
- Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Hong Nie
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Steven J Schrodi
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Department of Rheumatology,Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Arthritis Research in Integrative Medicine, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
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Guo S, Zhu Q, Jiang T, Wang R, Shen Y, Zhu X, Wang Y, Bai F, Ding Q, Zhou X, Chen G, He DY. Genome-wide DNA methylation patterns in CD4+ T cells from Chinese Han patients with rheumatoid arthritis. Mod Rheumatol 2016; 27:441-447. [PMID: 27585642 DOI: 10.1080/14397595.2016.1218595] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
INTRODUCTION Rheumatoid arthritis (RA) is an autoimmune disease that causes chronic inflammation of the joints. Recent evidence indicated the epigenetic changes may contribute to the pathogenesis of RA. METHOD To understand the extent and nature of dysregulated DNA methylation in RA CD4T cells, we performed a genome-wide DNA methylation study in CD4 + T cells in 12 RA patients compared to 12 matched normal healthy controls. Cytosine methylation status was quantified with Illumina methylation 450K microarray. RESULT The DNA methylation profiling showed 383 hyper- and 785 hypo-methylated genes in the CD4 + T cells of the RA patients (p < 3.4 × 10-7). Gene ontology analysis indicated transcript alternative splicing and protein modification mediated by DNA methylation might play an important role in the pathogenesis of RA. In addition, the result showed that human leukocyte antigen (HLA) region including HLA-DRB6, HLA-DQA1 and HLA-E was frequently hypomethylated, but HLA-DQB1 hypermethylated in CpG island region and hypomethylated in CpG shelf region in RA patients. Outside the MHC region, HDAC4, NXN, TBCD and TMEM61 were the most hypermethylated genes, while ITIH3, TCN2, PRDM16, SLC1A5 and GALNT9 are the most hypomethylated genes. CONCLUSION Genome-wide DNA methylation profile revealed significant DNA methylation change in CD4 + T cells from patients with RA.
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Affiliation(s)
- Shicheng Guo
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Qi Zhu
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Ting Jiang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Rongsheng Wang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Yi Shen
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Xiao Zhu
- c Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics , Dongguan Scientific Research Center, Guangdong Medical University , Dongguan , China
| | - Yan Wang
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China
| | - Fengmin Bai
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Qin Ding
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
| | - Xiaodong Zhou
- d University of Texas Medical School at Houston , Houston , TX , USA , and
| | - Guangjie Chen
- e Department of Immunology and Microbiology , Shanghai JiaoTong University School of Medicine , Shanghai , China
| | - Dong Yi He
- a Department of Rheumatology , Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine , Shanghai , China.,b Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute , Shanghai , China
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