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Swarnkar G, Semenkovich NP, Arra M, Mims DK, Naqvi SK, Peterson T, Mbalaviele G, Wu CL, Abu-Amer Y. DNA hypomethylation ameliorates erosive inflammatory arthritis by modulating interferon regulatory factor-8. Proc Natl Acad Sci U S A 2024; 121:e2310264121. [PMID: 38319963 PMCID: PMC10873594 DOI: 10.1073/pnas.2310264121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Epigenetic regulation plays a crucial role in the pathogenesis of autoimmune diseases such as inflammatory arthritis. DNA hypomethylating agents, such as decitabine (DAC), have been shown to dampen inflammation and restore immune homeostasis. In the present study, we demonstrate that DAC elicits potent anti-inflammatory effects and attenuates disease symptoms in several animal models of arthritis. Transcriptomic and epigenomic profiling show that DAC-mediated hypomethylation regulates a wide range of cell types in arthritis, altering the differentiation trajectories of anti-inflammatory macrophage populations, regulatory T cells, and tissue-protective synovial fibroblasts (SFs). Mechanistically, DAC-mediated demethylation of intragenic 5'-Cytosine phosphate Guanine-3' (CpG) islands of the transcription factor Irf8 (interferon regulatory factor 8) induced its re-expression and promoted its repressor activity. As a result, DAC restored joint homeostasis by resetting the transcriptomic signature of negative regulators of inflammation in synovial macrophages (MerTK, Trem2, and Cx3cr1), TREGs (Foxp3), and SFs (Pdpn and Fapα). In conclusion, we found that Irf8 is necessary for the inhibitory effect of DAC in murine arthritis and that direct expression of Irf8 is sufficient to significantly mitigate arthritis.
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Affiliation(s)
- Gaurav Swarnkar
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | | | - Manoj Arra
- Department of Emergency Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Dorothy K. Mims
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | - Syeda Kanwal Naqvi
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy Peterson
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
- HealthSpan Technologies, Inc, St. Louis, MO63110
| | - Gabriel Mbalaviele
- Department of Medicine, Washington University School of Medicine, St. Louis, MO63110
| | - Chia-Lung Wu
- Department of Orthopedics and Physical Performance, University of Rochester, Rochester, NY14642
| | - Yousef Abu-Amer
- Department of Orthopedic Surgery, Washington University School of Medicine, St. Louis, MO63110
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO63110
- Shriners Hospital for Children, St. Louis, MO63110
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2
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Jiang P, Wei K, Xu L, Chang C, Zhang R, Zhao J, Jin Y, Xu L, Shi Y, Qian Y, Sun S, Guo S, Wang R, Qin Y, He D. DNA methylation change of HIPK3 in Chinese rheumatoid arthritis and its effect on inflammation. Front Immunol 2023; 13:1087279. [PMID: 36703984 PMCID: PMC9872787 DOI: 10.3389/fimmu.2022.1087279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction Homeodomain-interacting protein kinase 3 (HIPK3) plays an important role in cell proliferation, apoptosis, and inflammation. Over-expression of HIPK3 in immune cells in rheumatoid arthritis (RA) has been reported. In this study, we investigated blood methylation levels and clinical characteristics of RA in a Chinese population. Methods A total of 235 patients with RA, 30 with osteoarthritis (OA), and 30 matched healthy controls were recruited. The methylation status of seven CpGs in the differentially methylated region of HIPK3 (cg05501357) was measured using targeted methylation-sequencing technology. The association between methylation haplotypes and the overall methylation status of HIPK3 with clinical characteristics was assessed using generalized linear regression. Results All seven CpGs showed hypomethylation status in RA blood compared with OA and normal individuals (overall p= 1.143×10-8 and FDR= 2.799×10-7), which is consistent with the previously reported high expression of HIPK3 in RA immune cells. Among all seven CpGs, 33286785 showed the highest predictive power with an area under the curve (AUC) of 0.829; we received a higher AUC=0.864 when we combined HIPK3 with anti-citrullinated protein antibodies (ACPA -) and rheumatoid factor (RF +) in the prediction model, indicating that when a patient's ACPA is negative, HIPK3 can assist RF as a new clinical index for the diagnosis of RA. We also found that HIPK3 methylation levels were negatively correlated with C-reactive protein (CRP; r= -0.16, p= 0.01). Methylation haplotypes were analyzed, and the full methylation haplotype (FMH; r= 0.16, p= 0.01) and full non-methylation haplotype (FNH; r= 0.18, p= 0.0061) were negatively correlated with CRP. Conclusion Circulating blood methylation levels in the protein region of HIPK3 can be utilized as a supportive diagnostic biomarker and CRP level indicator for RA.
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Affiliation(s)
- Ping Jiang
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Kai Wei
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Lingxia Xu
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Cen Chang
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Runrun Zhang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yehua Jin
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Linshuai Xu
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Yiming Shi
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
| | - Yi Qian
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Songtao Sun
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China
| | - Shicheng Guo
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States,Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States
| | - Rongsheng Wang
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,*Correspondence: Rongsheng Wang, ; Dongyi He, ; Yingying Qin,
| | - Yingying Qin
- Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,*Correspondence: Rongsheng Wang, ; Dongyi He, ; Yingying Qin,
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China,Shanghai Guanghua Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, China,Arthritis Institute of Integrated Traditional and Western medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China,*Correspondence: Rongsheng Wang, ; Dongyi He, ; Yingying Qin,
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3
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Hu Q, Zhang X, Sun M, jiang B, Zhang Z, Sun D. Potential epigenetic molecular regulatory networks in ocular neovascularization. Front Genet 2022; 13:970224. [PMID: 36118885 PMCID: PMC9478661 DOI: 10.3389/fgene.2022.970224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/02/2022] [Indexed: 11/23/2022] Open
Abstract
Neovascularization is one of the many manifestations of ocular diseases, including corneal injury and vascular diseases of the retina and choroid. Although anti-VEGF drugs have been used to effectively treat neovascularization, long-term use of anti-angiogenic factors can cause a variety of neurological and developmental side effects. As a result, better drugs to treat ocular neovascularization are urgently required. There is mounting evidence that epigenetic regulation is important in ocular neovascularization. DNA methylation and histone modification, non-coding RNA, and mRNA modification are all examples of epigenetic mechanisms. In order to shed new light on epigenetic therapeutics in ocular neovascularization, this review focuses on recent advances in the epigenetic control of ocular neovascularization as well as discusses these new mechanisms.
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Simple Detection of DNA Methyltransferase with an Integrated Padlock Probe. BIOSENSORS 2022; 12:bios12080569. [PMID: 35892466 PMCID: PMC9332213 DOI: 10.3390/bios12080569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/16/2022]
Abstract
DNA methyltransferases (MTases) can be regarded as biomarkers, as demonstrated by many studies on genetic diseases. Many researchers have developed biosensors to detect the activity of DNA MTases, and nucleic acid amplification, which need other probe assistance, is often used to improve the sensitivity of DNA MTases. However, there is no integrated probe that incorporates substrates and template and primer for detecting DNA MTases activity. Herein, we first designed a padlock probe (PP) to detect DNA MTases, which combines target detection with rolling circle amplification (RCA) without purification or other probe assistance. As the substrate of MTase, the PP was methylated and defended against HpaII, lambda exonuclease, and ExoI cleavage, as well as digestion, by adding MTase and the undestroyed PP started RCA. Thus, the fluorescent signal was capable of being rapidly detected after adding SYBRTM Gold to the RCA products. This method has a detection limit of approximately 0.0404 U/mL, and the linear range was 0.5–110 U/mL for M.SssI. Moreover, complex biological environment assays present prospects for possible application in intricacy environments. In addition, the designed detection system can also screen drugs or inhibitors for MTases.
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Luo JF, Yao YD, Cheng CS, Lio CK, Liu JX, Huang YF, He F, Xie Y, Liu L, Liu ZQ, Zhou H. Sinomenine increases the methylation level at specific GCG site in mPGES-1 promoter to facilitate its specific inhibitory effect on mPGES-1. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194813. [PMID: 35417776 DOI: 10.1016/j.bbagrm.2022.194813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/08/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Prostaglandin E2 (PGE2) in cancer and inflammatory diseases is a key mediator of disease progression. Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used to inhibit the expression of PGE2 by depressing cyclooxygenase (COX) in inflammatory treatments. However, the inhibition to COXs may cause serious side effects. Thus, it is urgent to develop new anti-inflammatory drugs aiming new targets to inhibit PGE2 production. Microsomal prostaglandin E synthase 1 (mPGES-1) catalyzes the final step of PGE2 biosynthesis. Therefore, the selective inhibition of mPGES-1 has become a promising strategy in the treatments of cancer and inflammatory diseases. Our previous studies confirmed that sinomenine (SIN) is a specific mPGES-1 inhibitor. However, the exact mechanism by which SIN inhibits mPGES-1 remains unknown. This study aimed to explain the regulation effect of SIN to mPGES-1 gene expression by its DNA methylation induction effect. We found that the demethylating agent 5-azacytidine (5-AzaC) reversed the inhibitory effect of SIN to mPGES-1. Besides, SIN selectively increased the methylation level of the promoter region in the mPGES-1 gene while the pretreatment of 5-AzaC suppressed this effect. The results also shows that pretreatment with SIN increased the methylation level of specific GCG sites in the promoter region of mPGES-1. This specific methylation site may become a new biomarker for predicting and diagnosing RA and cancer with high expression of mPGES-1. Also, our research provides new ideas and solutions for clinical diagnosis and treatment of diseases related to mPGES-1 and for targeted methylation strategy in drug development.
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Affiliation(s)
- Jin-Fang Luo
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Basic Medical College, Guizhou University of Traditional Chinese Medicine, Guian District, Guiyang, Guizhou, PR China
| | - Yun-Da Yao
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China
| | - Chun-Song Cheng
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant, Lushan Botanical Garden, Chinese Academy of Science, Jiujiang City, Jiangxi Province, PR China
| | - Chon-Kit Lio
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China
| | - Jian-Xin Liu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, Hunan, PR China
| | - Yu-Feng Huang
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China
| | - Fan He
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China
| | - Ying Xie
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China.
| | - Liang Liu
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China.
| | - Zhong-Qiu Liu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China.
| | - Hua Zhou
- Faculty of Chinese Medicine, Macau University of Science and Technology and State Key Laboratory of Quality Research in Chinese Medicine (Macau University of Science and Technology), Taipa, Macao, PR China; Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, Guangdong, PR China; Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, PR China.
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Chang L, Zhou R. Histone methyltransferase EZH2 in proliferation, invasion, and migration of fibroblast-like synoviocytes in rheumatoid arthritis. J Bone Miner Metab 2022; 40:262-274. [PMID: 35083555 DOI: 10.1007/s00774-021-01299-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/27/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) may lead to irreversible joint damage. The role of histone modifications in RA has been emphasized. This study investigated the effect of histone methyltransferase EZH2 on fibroblast-like synoviocytes (FLSs) in RA. MATERIALS AND METHODS Synovial tissues were collected from RA patients and non-RA patients (NC). RA-FLSs and NC-FLSs were isolated and identified using flow cytometry. EZH2 expression in synovial tissues and FLSs was detected using RT-qPCR and Western blot. The proliferation, migration, and invasion of RA-FLSs and NC-FLSs were measured using MTT, EdU, and Transwell assays. The binding of EZH2, H3K27me3, and miR-22-3p was analyzed using ChIP assay. The targeting relationship between miR-22-3p and CYR61 was verified using dual-luciferase assay. miR-22-3p and CYR61 expressions were detected using RT-qPCR. CYR61 and H3K27me3 levels were detected using Western blot. Functional rescue experiments were performed to verify the effect of miR-22-3p or CYR61 on RA-FLSs. RESULTS EZH2 was highly expressed in synovial tissues and FLSs from RA patients. The proliferation, migration, and invasion ability of RA-FLSs was stronger than that of NC-FLSs. Downregulation of EZH2 repressed proliferation, migration, and invasion of RA-FLSs. EZH2 inhibited miR-22-3p expression by binding to the miR-22-3p promoter and increasing H3K27me3 methylation level, and thereby upregulated CYR61 expression. Downregulation of miR-22-3p or overexpression of CYR61 annulled the inhibitory effect of EZH2 silencing on RA-FLS proliferation, migration, and invasion. CONCLUSION EZH2 bound to the miR-22-3p promoter and inhibited miR-22-3p expression by upregulating H3K27me3 level, thereby promoting CYR61 expression and inducing the proliferation, migration, and invasion of RA-FLSs.
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Affiliation(s)
- Lihua Chang
- Department of Rheumatology and Immunology, Shengjing Hospital of China Medical University, Shenyang City, 110000, Liaoning Province, China
| | - Renyi Zhou
- Department of Orthopaedics, The First Hospital of China Medical University, No.155 Nan Jing North Street, Shenyang City, 110001, Liaoning Province, China.
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Stefan-Lifshitz M, Karakose E, Cui L, Ettela A, Yi Z, Zhang W, Tomer Y. Epigenetic modulation of β cells by interferon-α via PNPT1/mir-26a/TET2 triggers autoimmune diabetes. JCI Insight 2019; 4:126663. [PMID: 30721151 DOI: 10.1172/jci.insight.126663] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Type 1 diabetes (T1D) is caused by autoimmune destruction of pancreatic β cells. Mounting evidence supports a central role for β cell alterations in triggering the activation of self-reactive T cells in T1D. However, the early deleterious events that occur in β cells, underpinning islet autoimmunity, are not known. We hypothesized that epigenetic modifications induced in β cells by inflammatory mediators play a key role in initiating the autoimmune response. We analyzed DNA methylation (DNAm) patterns and gene expression in human islets exposed to IFN-α, a cytokine associated with T1D development. We found that IFN-α triggers DNA demethylation and increases expression of genes controlling inflammatory and immune pathways. We then demonstrated that DNA demethylation was caused by upregulation of the exoribonuclease, PNPase old-35 (PNPT1), which caused degradation of miR-26a. This in turn promoted the upregulation of ten-eleven translocation 2 (TET2) enzyme and increased 5-hydroxymethylcytosine levels in human islets and pancreatic β cells. Moreover, we showed that specific IFN-α expression in the β cells of IFNα-INS1CreERT2 transgenic mice led to development of T1D that was preceded by increased islet DNA hydroxymethylation through a PNPT1/TET2-dependent mechanism. Our results suggest a new mechanism through which IFN-α regulates DNAm in β cells, leading to changes in expression of genes in inflammatory and immune pathways that can initiate islet autoimmunity in T1D.
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Affiliation(s)
- Mihaela Stefan-Lifshitz
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Lingguang Cui
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Abora Ettela
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
| | - Zhengzi Yi
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Weijia Zhang
- Department of Medicine Bioinformatics Core, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yaron Tomer
- Division of Endocrinology and the Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, New York, New York, USA
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Shafabakhsh R, Aghadavod E, Ghayour‐Mobarhan M, Ferns G, Asemi Z. Role of histone modification and DNA methylation in signaling pathways involved in diabetic retinopathy. J Cell Physiol 2018; 234:7839-7846. [DOI: 10.1002/jcp.27844] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Rana Shafabakhsh
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Esmat Aghadavod
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
| | - Majid Ghayour‐Mobarhan
- Metabolic Syndrome Research Center School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton UK
| | - Zatollah Asemi
- Research Center for Biochemistry and Nutrition in Metabolic Diseases Kashan University of Medical Sciences Kashan Iran
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CUL4B promotes the pathology of adjuvant-induced arthritis in rats through the canonical Wnt signaling. J Mol Med (Berl) 2018; 96:495-511. [DOI: 10.1007/s00109-018-1635-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 02/07/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
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10
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Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
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11
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Fang G, Zhang QH, Tang Q, Jiang Z, Xing S, Li J, Pang Y. Comprehensive analysis of gene expression and DNA methylation datasets identify valuable biomarkers for rheumatoid arthritis progression. Oncotarget 2017; 9:2977-2983. [PMID: 29423022 PMCID: PMC5790439 DOI: 10.18632/oncotarget.22918] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/03/2017] [Indexed: 11/29/2022] Open
Abstract
Rheumatoid arthritis (RA) represents a common systemic autoimmune disease which lays chronic and persistent pain on patients. The purpose of our study is to identify novel RA-related genes and biological processes/pathways. All the datasets of this study, including gene expression and DNA methylation datasets of RA and OA samples, were obtained from the free available database, i.e. Gene Expression Omnibus (GEO). We firstly identified the differentially expressed genes (DEGs) between RA and OA samples through the limma package of R programming software followed by the functional enrichment analysis in the Database for Annotation, Visualization and Integrated Discovery (DAVID) for the exploring of potential involved biological processes/pathways of DEGs. For DNA methylation datasets, we used the IMA package for their normalization and identification of differential methylation genes (DMGs) in RA compared with OA samples. Comprehensive analysis of DEGs and DMGs was also conducted for the identification of valuable RA-related biomarkers. As a result, we obtained 394 DEGs and 363 DMGs in RA samples with the thresholds of |log2fold change|> 1 and p-value < 0.05, and |delta beta|> 0.2 and p-value < 0.05 respectively. Functional analysis of DEGs obtained immune and inflammation associated biological processes/pathways. Besides, several valuable biomarkers of RA, including BCL11B, CCDC88C, FCRLA and APOL6, were identified through the integrated analysis of gene expression and DNA methylation datasets. Our study should be helpful for the development of novel drugs and therapeutic methods for RA.
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Affiliation(s)
- Gang Fang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Qing Huai Zhang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Qianqian Tang
- Department of Rheumatism, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Zuling Jiang
- Department of Zhuang Medicine, The First Affiliated of Guangxi University of Chinese Medicine, Nanning, China
| | - Shasha Xing
- Department of Rheumatism, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jianying Li
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
| | - Yuzhou Pang
- Laboratory of Zhuang Medicine Prescriptions Basis and Application Research, Guangxi University of Chinese Medicine, Nanning, China
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12
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Zhao J, Fan YC, Chen LY, Gao S, Li F, Wang K. Alteration of methyl-CpG binding domain family in patients with chronic hepatitis B. Clin Res Hepatol Gastroenterol 2017; 41:272-283. [PMID: 28065745 DOI: 10.1016/j.clinre.2016.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/25/2016] [Accepted: 11/30/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Epigenetics contributes to the outcome of chronic hepatitis B virus (HBV) infection. However, the role of methyl-CpG binding domain (MBD) family in the natural history of chronic hepatitis B (CHB) has not been demonstrated. It is aimed to investigate the dynamic expression of MBD family and assess the potential association of MBD family in the progression of CHB. METHODS Quantitative real-time polymerase chain reaction (RT-PCR) was used to determine the mRNA levels of MBD family in peripheral blood mononuclear cells (PBMCs) from 223 patients with CHB as training cohort, 146 patients with CHB as validation cohort [immune-tolerant (IT), immune clearance (IC), non/low-replicative (LR) and HBeAg negative hepatitis (ENH)], and 14 healthy controls (HCs). RESULTS The mRNA levels of MeCP2, MBD1, MBD2 and MBD4 were upregulated in patients with CHB compared with HCs. MBD1 mRNA was highest expressed in IT phase than other phases. The optimal cut-off value for MBD1 mRNA in discriminating IT phase from CHB was 0.0305 in both training and validation cohorts. Both MBD2 and MBD4 mRNA were highest expressed in IC phase than other phases. Moreover, the optimal cut-off values for MBD2 and MBD4 mRNA in discriminating IC phase from CHB were 0.0069 and 0.00099. Furthermore, MBD2 plus MBD4 performed better than MBD2 alone for discriminating IC phase from CHB in training (area under the curve of receiver operating characteristics [AUC] 0.736 vs. 0.671, P=0.0225) and validation cohorts (AUC 0.754 vs. 0.665, P=0.004). MeCP2 mRNA was highest expressed in patients with S3+S4. MeCP2 mRNA has higher AUC than APRI score for predicting S3+S4 and S4 in fibrosis. CONCLUSIONS MBD family is involved in the pathogenesis of CHB and is correlated with disease progression, suggesting the value in evaluating disease severity.
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Affiliation(s)
- Jing Zhao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Long-Yan Chen
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China
| | - Feng Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan 250012, China; Institute of Hepatology, Shandong University, Jinan 250012, China.
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Song YJ, Li G, He JH, Guo Y, Yang L. Bioinformatics-Based Identification of MicroRNA-Regulated and Rheumatoid Arthritis-Associated Genes. PLoS One 2015; 10:e0137551. [PMID: 26359667 PMCID: PMC4567271 DOI: 10.1371/journal.pone.0137551] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 08/19/2015] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) act as epigenetic markers and regulate the expression of their target genes, including those characterized as regulators in autoimmune diseases. Rheumatoid arthritis (RA) is one of the most common autoimmune diseases. The potential roles of miRNA-regulated genes in RA pathogenesis have greatly aroused the interest of clinicians and researchers in recent years. In the current study, RA-related miRNAs records were obtained from PubMed through conditional literature retrieval. After analyzing the selected records, miRNA targeted genes were predicted. We identified 14 RA-associated miRNAs, and their sub-analysis in 5 microarray or RNA sequencing (RNA-seq) datasets was performed. The microarray and RNA-seq data of RA were also downloaded from NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA), analyzed, and annotated. Using a bioinformatics approach, we identified a series of differentially expressed genes (DEGs) by comparing studies on RA and the controls. The RA-related gene expression profile was thus obtained and the expression of miRNA-regulated genes was analyzed. After functional annotation analysis, we found GO molecular function (MF) terms significantly enriched in calcium ion binding (GO: 0005509). Moreover, some novel dysregulated target genes were identified in RA through integrated analysis of miRNA/mRNA expression. The result revealed that the expression of a number of genes, including ROR2, ABI3BP, SMOC2, etc., was not only affected by dysregulated miRNAs, but also altered in RA. Our findings indicate that there is a close association between negatively correlated mRNA/miRNA pairs and RA. These findings may be applied to identify genetic markers for RA diagnosis and treatment in the future.
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Affiliation(s)
- Yi-Jiang Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Guiling Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang Province, China
| | - Jian-Hua He
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Yao Guo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
| | - Li Yang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Bioengineering College, Chongqing University, Chongqing, China
- * E-mail:
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ADAMTS-12: a multifaced metalloproteinase in arthritis and inflammation. Mediators Inflamm 2014; 2014:649718. [PMID: 24876675 PMCID: PMC4020202 DOI: 10.1155/2014/649718] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Revised: 03/28/2014] [Accepted: 04/07/2014] [Indexed: 12/12/2022] Open
Abstract
ADAMTS-12 is a member of a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) family of proteases, which were known to play important roles in various biological and pathological processes, such as development, angiogenesis, inflammation, cancer, arthritis, and atherosclerosis. In this review, we briefly summarize the structural organization of ADAMTS-12; concentrate on the emerging role of ADAMTS-12 in several pathophysiological conditions, including intervertebral disc degeneration, tumorigenesis and angioinhibitory effects, pediatric stroke, gonad differentiation, trophoblast invasion, and genetic linkage to schizophrenia and asthma, with special focus on its role in arthritis and inflammation; and end with the perspective research of ADAMTS-12 and its potential as a promising diagnostic and therapeutic target in various kinds of diseases and conditions.
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