1
|
Chen S, Ye J, Lin Y, Chen W, Huang S, Yang Q, Qian H, Gao S, Hua C. Crucial Roles of RSAD2/viperin in Immunomodulation, Mitochondrial Metabolism and Autoimmune Diseases. Inflammation 2024:10.1007/s10753-024-02076-5. [PMID: 38909344 DOI: 10.1007/s10753-024-02076-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/22/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Autoimmune diseases are typically characterized by aberrant activation of immune system that leads to excessive inflammatory reactions and tissue damage. Nevertheless, precise targeted and efficient therapies are limited. Thus, studies into novel therapeutic targets for the management of autoimmune diseases are urgently needed. Radical S-adenosyl methionine domain-containing 2 (RSAD2) is an interferon-stimulated gene (ISG) renowned for the antiviral properties of the protein it encodes, named viperin. An increasing number of studies have underscored the new roles of RSAD2/viperin in immunomodulation and mitochondrial metabolism. Previous studies have shown that there is a complex interplay between RSAD2/vipeirn and mitochondria and that binding of the iron-sulfur (Fe-S) cluster is necessary for the involvement of viperin in mitochondrial metabolism. Viperin influences the proliferation and development of immune cells as well as inflammation via different signaling pathways. However, the function of RSAD2/viperin varies in different studies and a comprehensive overview of this emerging theme is lacking. This review will describe the characteristics of RSAD2/viperin, decipher its function in immunometabolic processes, and clarify the crosstalk between RSAD2/viperin and mitochondria. Furthermore, we emphasize the crucial roles of RSAD2 in autoimmune diseases and its potential application value.
Collapse
Affiliation(s)
- Siyan Chen
- School of Ophthalmology and Optometry, School of Biomedical Engineering, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Jiani Ye
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Yinfang Lin
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Wenxiu Chen
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Shenghao Huang
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Qianru Yang
- School of the 1st Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Hengrong Qian
- School of the 2nd Clinical Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China
| | - Sheng Gao
- Laboratory Animal Center, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China.
| | - Chunyan Hua
- School of Basic Medical Sciences, Wenzhou Medical University, Zhejiang Province, Wenzhou, 325035, China.
| |
Collapse
|
2
|
Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
Collapse
Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| |
Collapse
|
3
|
Abel TR, Kosarek NN, Parvizi R, Jarnagin H, Torres GM, Bhandari R, Huang M, Toledo DM, Smith A, Popovich D, Mariani MP, Yang H, Wood T, Garlick J, Pioli PA, Whitfield ML. Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586316. [PMID: 38585776 PMCID: PMC10996484 DOI: 10.1101/2024.03.22.586316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Systemic sclerosis (SSc) is an autoimmune disease characterized by skin fibrosis, internal organ involvement and vascular dropout. We previously developed and phenotypically characterized an in vitro 3D skin-like tissue model of SSc, and now analyze the transcriptomic (scRNA-seq) and epigenetic (scATAC-seq) characteristics of this model at single-cell resolution. SSc 3D skin-like tissues were fabricated using autologous fibroblasts, macrophages, and plasma from SSc patients or healthy control (HC) donors. SSc tissues displayed increased dermal thickness and contractility, as well as increased α-SMA staining. Single-cell transcriptomic and epigenomic analyses identified keratinocytes, macrophages, and five populations of fibroblasts (labeled FB1 - 5). Notably, FB1 APOE-expressing fibroblasts were 12-fold enriched in SSc tissues and were characterized by high EGR1 motif accessibility. Pseudotime analysis suggests that FB1 fibroblasts differentiate from a TGF-β1-responsive fibroblast population and ligand-receptor analysis indicates that the FB1 fibroblasts are active in macrophage crosstalk via soluble ligands including FGF2 and APP. These findings provide characterization of the 3D skin-like model at single cell resolution and establish that it recapitulates subsets of fibroblasts and macrophage phenotypes observed in skin biopsies.
Collapse
|
4
|
Liakouli V, Ciancio A, Del Galdo F, Giacomelli R, Ciccia F. Systemic sclerosis interstitial lung disease: unmet needs and potential solutions. Nat Rev Rheumatol 2024; 20:21-32. [PMID: 37923862 DOI: 10.1038/s41584-023-01044-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2023] [Indexed: 11/06/2023]
Abstract
Systemic sclerosis (SSc), or scleroderma, is a rare, complex, systemic autoimmune disease of unknown aetiology, characterized by high morbidity and mortality often resulting from cardiopulmonary complications such as interstitial lung disease and pulmonary arterial hypertension. Despite substantial progress in unravelling the pathways involved in the pathogenesis of SSc and the increasing number of therapeutic targets tested in clinical trials, there is still no cure for this disease, although several proposed treatments might limit the involvement of specific organs, thereby slowing the natural history of the disease. A specific focus of recent research has been to address the plethora of unmet needs regarding the global management of SSc-related interstitial lung disease, including its pathogenesis, early diagnosis, risk stratification of patients, appropriate treatment regimens and monitoring of treatment response, as well as the definition of progression and predictors of progression and mortality. More refined stratification of patients on the basis of clinical features, molecular signatures, identification of subpopulations with distinct clinical trajectories and implementation of outcome measures for future clinical trials could also improve therapeutic management strategies, helping to avoid poor outcomes related to lung involvement.
Collapse
Affiliation(s)
- Vasiliki Liakouli
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
| | - Antonio Ciancio
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Francesco Del Galdo
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, Faculty of Medicine and Health, University of Leeds, Leeds, UK
- Scleroderma Programme, NIHR Biomedical Research Centre, Leeds Teaching Hospital Trusts, Leeds, UK
| | - Roberto Giacomelli
- Rheumatology and Immunology Unit, Department of Medicine, University of Rome Campus Biomedico, Rome, Italy
| | - Francesco Ciccia
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| |
Collapse
|
5
|
Zhu H, Zheng J, Zhou Y, Wu T, Zhu T. PRMT5 participates in B cell overactivation in patients with primary Sjogren's syndrome (pSS) through RSAD2-mediated NF-κB signaling. Immun Inflamm Dis 2023; 11:e1102. [PMID: 38156384 PMCID: PMC10716722 DOI: 10.1002/iid3.1102] [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: 07/03/2023] [Revised: 10/27/2023] [Accepted: 11/16/2023] [Indexed: 12/30/2023] Open
Abstract
OBJECTIVE There are new evidences that protein arginine methyltransferase 5 (PRMT5) is widely involved in the progression of various diseases, but its effect is unclear on Primary Sjogren's syndrome (pSS). The main purpose of this study is to explore the regulatory effect of PRMT5 on pSS and its potential mechanisms. METHODS CD40L treated CD19 + B cells to construct a cell model of pSS. CCK-8 assay and Annexin V-FITC/PI kits were used to measure cell proliferation and apoptosis. ELISA assay was used to determine the contents of IL-6 and TNF-α in CD19 + B cells. And commercial kits were used to detect the levels of immunoglobins (IgG, IgM, and IgA) in CD40L-treated CD19 + B cells. And successfully constructed a pSS mouse model. RESULTS The results revealed an increase in the expression of PRMT5 in CD19 + B cells from patients with pSS. After CD40L treatment, the knockdown of PRMT5 prominently decreased cell viability, the production level of immunoglobulins (IgG, IgM, and IgA), and the content of IL-10, increased the content of IL-6 and IL-8, and promoted the apoptosis of pSS CD19 + B cells. Mechanistically, PRMT5 negatively regulated the RSAD2 and nuclear factor kappa-B (NF-κB) signaling pathway. Furthermore, overexpression of RSAD2 and p65 significantly rescued the effect of PRMT5 knockdown on proliferation, immunoglobin production and secreting cytokines in CD40L-treated CD19 + B cells. More importantly, inhibition of PRMT5 significantly inhibited the symptoms of pSS mice. CONCLUSIONS Low-expression of PRMT5 through inactivation of RSAD2/NF-κB signalling pathway alleviates the hyperactivity of B cells, which may provide theoretical basis and potential therapeutic targets for clinical treatment of pSS.
Collapse
Affiliation(s)
- Hong Zhu
- Department of RheumatologyGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Jian Zheng
- Department of RheumatologyGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Yan Zhou
- Department of RheumatologyGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Tong Wu
- Department of RheumatologyGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| | - Tiantian Zhu
- Department of RheumatologyGeneral Hospital of Ningxia Medical UniversityYinchuanChina
| |
Collapse
|
6
|
Filipowicz G, Wajda A, Stypińska B, Kmiołek T, Felis-Giemza A, Stańczyk S, Czuszyńska Z, Walczyk M, Olesińska M, Paradowska-Gorycka A. Mixed Connective Tissue Disease as Different Entity: Global Methylation Aspect. Int J Mol Sci 2023; 24:15495. [PMID: 37895173 PMCID: PMC10607312 DOI: 10.3390/ijms242015495] [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: 08/18/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Mixed connective tissue disease (MCTD) is a very rare disorder that belongs in the rare and clinically multifactorial groups of diseases. The pathogenesis of MCTD is still unclear. The best understood epigenetic alteration is DNA methylation whose role is to regulate gene expression. In the literature, there are ever-increasing assumptions that DNA methylation can be one of the possible reasons for the development of Autoimmune Connective Tissue Diseases (ACTDs) such as systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). The aim of this study was to define the global DNA methylation changes between MCTD and other ACTDs patients in whole blood samples. The study included 54 MCTD patients, 43 SSc patients, 45 SLE patients, and 43 healthy donors (HC). The global DNA methylation level was measured by ELISA. Although the global DNA methylation was not significantly different between MCTD and control, we observed that hypomethylation distinguishes the MCTD patients from the SSc and SLE patients. The present analysis revealed a statistically significant difference of global methylation between SLE and MCTD (p < 0.001), SLE and HC (p = 0.008), SSc and MCTD (p ≤ 0.001), and SSc and HC (p < 0.001), but neither between MCTD and HC (p = 0.09) nor SSc and SLE (p = 0.08). The highest % of global methylation (median, IQR) has been observed in the group of patients with SLE [0.73 (0.43, 1.22] and SSc [0,91 (0.59, 1.50)], whereas in the MCTD [0.29 (0.20, 0.54)], patients and healthy subjects [0.51 (0.24, 0.70)] were comparable. In addition, our study provided evidence of different levels of global DNA methylation between the SSc subtypes (p = 0.01). Our study showed that patients with limited SSc had a significantly higher global methylation level when compared to diffuse SSc. Our data has shown that the level of global DNA methylation may not be a good diagnostic marker to distinguish MCTD from other ACTDs. Our research provides the groundwork for a more detailed examination of the significance of global DNA methylation as a distinguishing factor in patients with MCTD compared to other ACTDs patients.
Collapse
Affiliation(s)
- Gabriela Filipowicz
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Barbara Stypińska
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Tomasz Kmiołek
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| | - Anna Felis-Giemza
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Sandra Stańczyk
- Biologic Therapy Center, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland (S.S.)
| | - Zenobia Czuszyńska
- Department of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdansk, Smulochowskiego 17, 80-214 Gdansk, Poland
| | - Marcela Walczyk
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Marzena Olesińska
- Department of Connective Tissue Diseases, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, Spartanska 1, 02-637 Warsaw, Poland; (G.F.)
| |
Collapse
|
7
|
Xu S, Zhu C, Jiang J, Cheng H, Wang P, Hong J, Yang S, Li Z, Wang X. Non-invasive diagnosis of primary Sjögren's syndrome using ultrasonography and transcriptome biomarkers. Clin Immunol 2023; 255:109739. [PMID: 37586671 DOI: 10.1016/j.clim.2023.109739] [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: 05/06/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Diagnosing primary Sjögren's syndrome (pSS) is difficult due to clinical heterogeneity and the absence of non-invasive specific biomarkers. To develop non-invasive pSS diagnosis methods that integrate classic clinical indexes, major salivary gland ultrasonography (SGUS), and gene expression profiles shared by labial gland and peripheral blood, we conducted a study on a cohort of 358 subjects. We identified differentially expressed genes (DEGs) in glands and blood that were enriched in defense response to virus and type I interferon production pathways. Four upregulated DEGs common in glands and blood were identified as hub genes based on the protein-protein interaction networks. A random forest model was trained using features, including SGUS, anti-SSA/Ro60, keratoconjunctivitis sicca tests, and gene expression levels of MX1 and RSAD2. The model achieved comparable pSS diagnosis accuracy to the golden standard method based on labial gland biopsy. Our findings implicate this novel model as a promising diagnosis technique of pSS.
Collapse
Affiliation(s)
- Shihao Xu
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
| | - Chengwei Zhu
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jiachun Jiang
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Hui Cheng
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Ping Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Jingwei Hong
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Shiping Yang
- Department of Ultrasonography, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China.
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200001, China.
| |
Collapse
|
8
|
Li K, Shi W, Song Y, Qin L, Zang C, Mei T, Li A, Song Q, Zhang Y. Reprogramming of lipid metabolism in hepatocellular carcinoma resulting in downregulation of phosphatidylcholines used as potential markers for diagnosis and prediction. Expert Rev Mol Diagn 2023; 23:1015-1026. [PMID: 37672012 DOI: 10.1080/14737159.2023.2254884] [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: 07/07/2023] [Accepted: 08/28/2023] [Indexed: 09/07/2023]
Abstract
BACKGROUND Aberrant methylation and metabolic perturbations may deepen our understanding of hepatocarcinogenesis and help identify novel biomarkers for diagnosing hepatocellular carcinoma (HCC). We aimed to develop an HCC model based on a multi-omics. RESEARCH DESIGN AND METHODS Four hundred patient samples (200 with HCC and 200 with hepatitis B virus-related liver disease (HBVLD)) were subjected to liquid chromatography-mass spectrometry and multiplex bisulfite sequencing. Integrative analysis of clinical data, CpG data, and metabolome for the 20 complete imputation datasets within a for-loopwas used to identify biomarker. RESULTS Totally, 1,140 metabolites were annotated, of which 125 were differentially expressed. Lipid metabolism reprogramming in HCC, resulting in phosphatidylcholines (PC) significantly downregulated, partly due to the altered mitochondrial beta-oxidation of fatty acids with diverse chain lengths. Age, sex, serum-fetoprotein levels, cg05166871,cg14171514, cg18772205, PC (O-16:0/20:3(8Z, 11Z, 14Z)), and PC (16:1(9Z)/P-18:0) were used to develop the HCC model. The model presented a good diagnostic and an acceptable predictive performance. The cumulative incidence of HCC in low- and high-risk groups of HBVLD patients were 1.19% and 21.40%, respectively (p = 0.0039). CONCLUSIONS PCs serve as potential plasma biomarkers and help identify patients with HBVLD at risk of HCC who should be screened for early diagnosis and intervention.
Collapse
Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Wanting Shi
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yi Song
- Institute of Clinical Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lin Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Chaoran Zang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
- Hepatobiliary Pancreatic Center Department, Beijing Tsinghua Changgung Hospital Affiliated to Tsinghua University, Beijing, China
| | - Tingting Mei
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Qingkun Song
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
9
|
Yu JCY, Zeng Y, Zhao K, Lu T, Oros Klein K, Colmegna I, Lora M, Bhatnagar SR, Leask A, Greenwood CMT, Hudson M. Novel insights into systemic sclerosis using a sensitive computational method to analyze whole-genome bisulfite sequencing data. Clin Epigenetics 2023; 15:96. [PMID: 37270501 DOI: 10.1186/s13148-023-01513-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/28/2023] [Indexed: 06/05/2023] Open
Abstract
BACKGROUND Abnormal DNA methylation is thought to contribute to the onset and progression of systemic sclerosis. Currently, the most comprehensive assay for profiling DNA methylation is whole-genome bisulfite sequencing (WGBS), but its precision depends on read depth and it may be subject to sequencing errors. SOMNiBUS, a method for regional analysis, attempts to overcome some of these limitations. Using SOMNiBUS, we re-analyzed WGBS data previously analyzed using bumphunter, an approach that initially fits single CpG associations, to contrast DNA methylation estimates by both methods. METHODS Purified CD4+ T lymphocytes of 9 SSc and 4 control females were sequenced using WGBS. We separated the resulting sequencing data into regions with dense CpG data, and differentially methylated regions (DMRs) were inferred with the SOMNiBUS region-level test, adjusted for age. Pathway enrichment analysis was performed with ingenuity pathway analysis (IPA). We compared the results obtained by SOMNiBUS and bumphunter. RESULTS Of 8268 CpG regions of ≥ 60 CpGs eligible for analysis with SOMNiBUS, we identified 131 DMRs and 125 differentially methylated genes (DMGs; p-values less than Bonferroni-corrected threshold of 6.05-06 controlling family-wise error rate at 0.05; 1.6% of the regions). In comparison, bumphunter identified 821,929 CpG regions, 599 DMRs (of which none had ≥ 60 CpGs) and 340 DMGs (q-value of 0.05; 0.04% of all regions). The top ranked gene identified by SOMNiBUS was FLT4, a lymphangiogenic orchestrator, and the top ranked gene on chromosome X was CHST7, known to catalyze the sulfation of glycosaminoglycans in the extracellular matrix. The top networks identified by IPA included connective tissue disorders. CONCLUSIONS SOMNiBUS is a complementary method of analyzing WGBS data that enhances biological insights into SSc and provides novel avenues of investigation into its pathogenesis.
Collapse
Affiliation(s)
- Jeffrey C Y Yu
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Yixiao Zeng
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Kaiqiong Zhao
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Tianyuan Lu
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
| | - Kathleen Oros Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada
| | - Inés Colmegna
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
- Research Institute of the McGill University Health Center, Montreal, Canada
| | - Maximilien Lora
- Research Institute of the McGill University Health Center, Montreal, Canada
| | | | | | - Celia M T Greenwood
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada
| | - Marie Hudson
- McGill University, 845 Sherbrooke St W, Montreal, H3A 0G4, Canada.
- Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Sainte Catherine, Montreal, H3T 1E2, Canada.
| |
Collapse
|
10
|
Allen PC, Smith S, Wilson RC, Wirth JR, Wilson NH, Baker Frost D, Flume J, Gilkeson GS, Cunningham MA, Langefeld CD, Absher DM, Ramos PS. Distinct genome-wide DNA methylation and gene expression signatures in classical monocytes from African American patients with systemic sclerosis. Clin Epigenetics 2023; 15:25. [PMID: 36803404 PMCID: PMC9938585 DOI: 10.1186/s13148-023-01445-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a multisystem autoimmune disorder that has an unclear etiology and disproportionately affects women and African Americans. Despite this, African Americans are dramatically underrepresented in SSc research. Additionally, monocytes show heightened activation in SSc and in African Americans relative to European Americans. In this study, we sought to investigate DNA methylation and gene expression patterns in classical monocytes in a health disparity population. METHODS Classical monocytes (CD14+ + CD16-) were FACS-isolated from 34 self-reported African American women. Samples from 12 SSc patients and 12 healthy controls were hybridized on MethylationEPIC BeadChip array, while RNA-seq was performed on 16 SSc patients and 18 healthy controls. Analyses were computed to identify differentially methylated CpGs (DMCs), differentially expressed genes (DEGs), and CpGs associated with changes in gene expression (eQTM analysis). RESULTS We observed modest DNA methylation and gene expression differences between cases and controls. The genes harboring the top DMCs, the top DEGs, as well as the top eQTM loci were enriched for metabolic processes. Genes involved in immune processes and pathways showed a weak upregulation in the transcriptomic analysis. While many genes were newly identified, several other have been previously reported as differentially methylated or expressed in different blood cells from patients with SSc, supporting for their potential dysregulation in SSc. CONCLUSIONS While contrasting with results found in other blood cell types in largely European-descent groups, the results of this study support that variation in DNA methylation and gene expression exists among different cell types and individuals of different genetic, clinical, social, and environmental backgrounds. This finding supports the importance of including diverse, well-characterized patients to understand the different roles of DNA methylation and gene expression variability in the dysregulation of classical monocytes in diverse populations, which might help explaining the health disparities.
Collapse
Affiliation(s)
- Peter C Allen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah Smith
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jena R Wirth
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Nathan H Wilson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - DeAnna Baker Frost
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Jonathan Flume
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Gary S Gilkeson
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Melissa A Cunningham
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Precision Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Paula S Ramos
- Department of Medicine, Medical University of South Carolina, Charleston, SC, USA.
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA.
| |
Collapse
|
11
|
Hui L, Ziyue Z, Chao L, Bin Y, Aoyu L, Haijing W. Epigenetic Regulations in Autoimmunity and Cancer: from Basic Science to Translational Medicine. Eur J Immunol 2023; 53:e2048980. [PMID: 36647268 DOI: 10.1002/eji.202048980] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/25/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
Epigenetics, as a discipline that aims to explain the differential expression of phenotypes arising from the same gene sequence and the heritability of epigenetic expression, has received much attention in medicine. Epigenetic mechanisms are constantly being discovered, including DNA methylation, histone modifications, noncoding RNAs and m6A. The immune system mainly achieves an immune response through the differentiation and functional expression of immune cells, in which epigenetic modification will have an important impact. Because of immune infiltration in the tumor microenvironment, immunotherapy has become a research hotspot in tumor therapy. Epigenetics plays an important role in autoimmune diseases and cancers through immunology. An increasing number of drugs targeting epigenetic mechanisms, such as DNA methyltransferase inhibitors, histone deacetylase inhibitors, and drug combinations, are being evaluated in clinical trials for the treatment of various cancers (including leukemia and osteosarcoma) and autoimmune diseases (systemic lupus erythematosus, rheumatoid arthritis, systemic sclerosis). This review summarizes the progress of epigenetic regulation for cancers and autoimmune diseases to date, shedding light on potential therapeutic strategies.
Collapse
Affiliation(s)
- Li Hui
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Zhao Ziyue
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Liu Chao
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Yu Bin
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Li Aoyu
- Department of Orthopedics, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Wu Haijing
- Hunan Key Laboratory of Medical Epigenetics, Department of Dermatology, Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| |
Collapse
|
12
|
Hong X, Miao K, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Yu M, Wang H, Wu X, Liu Y, Gao W, Li L. Association Between DNA Methylation and Blood Pressure: A 5-Year Longitudinal Twin Study. Hypertension 2023; 80:169-181. [PMID: 36345830 DOI: 10.1161/hypertensionaha.122.19953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Previous EWASs (Epigenome-Wide Association Studies) have reported hundreds of blood pressure (BP) associated 5'-cytosine-phosphate-guanine-3' (CpG) sites. However, their results were inconsistent. Longitudinal observations on the temporal relationship between DNA methylation and BP are lacking. METHODS A candidate CpG site association study for BP was conducted on 1072 twins in the Chinese National Twin Registry. PubMed and EMBASE were searched for candidate CpG sites. Cross-lagged models were used to assess the temporal relationship between BP and DNA methylation in 308 twins who completed 2 surveys in 2013 and 2018. Then, the significant cross-lagged associations were validated by adopting the Inference About Causation From Examination of Familial Confounding approach. Finally, to evaluate the cumulative effects of DNA methylation on the progression of hypertension, we established methylation risk scores based on BP-associated CpG sites and performed Markov multistate models. RESULTS 16 and 20 CpG sites were validated to be associated with systolic BP and diastolic BP, respectively. In the cross-lagged analysis, we detected that methylation of 2 CpG sites could predict subsequent systolic BP, and systolic BP predicted methylation at another 3 CpG sites. For diastolic BP, methylation at 3 CpG sites had significant cross-lagged effects for predicting diastolic BP levels, while the prediction from the opposite direction was observed at one site. Among these, 3 associations were validated in the Inference About Causation From Examination of Familial Confounding analysis. Using the Markov multistate model, we observed that methylation risk scores were associated with the development of hypertension. CONCLUSIONS Our findings suggest the significance of DNA methylation in the development of hypertension.
Collapse
Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Ke Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, China (Z.P.)
| | - Min Yu
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China (M.Y.)
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China (H.W.)
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China (X.W.)
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China (Y.L.)
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, China (X.H., K.M., W.C., J.L., C.Y., T.H., D.S., C.L., Y.P., W.G., L.L.)
| |
Collapse
|
13
|
Epigenetic regulation of B cells and its role in autoimmune pathogenesis. Cell Mol Immunol 2022; 19:1215-1234. [PMID: 36220996 PMCID: PMC9622816 DOI: 10.1038/s41423-022-00933-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/19/2022] [Indexed: 11/05/2022] Open
Abstract
B cells play a pivotal role in the pathogenesis of autoimmune diseases. Although previous studies have shown many genetic polymorphisms associated with B-cell activation in patients with various autoimmune disorders, progress in epigenetic research has revealed new mechanisms leading to B-cell hyperactivation. Epigenetic mechanisms, including those involving histone modifications, DNA methylation, and noncoding RNAs, regulate B-cell responses, and their dysregulation can contribute to the pathogenesis of autoimmune diseases. Patients with autoimmune diseases show epigenetic alterations that lead to the initiation and perpetuation of autoimmune inflammation. Moreover, many clinical and animal model studies have shown the promising potential of epigenetic therapies for patients. In this review, we present an up-to-date overview of epigenetic mechanisms with a focus on their roles in regulating functional B-cell subsets. Furthermore, we discuss epigenetic dysregulation in B cells and highlight its contribution to the development of autoimmune diseases. Based on clinical and preclinical evidence, we discuss novel epigenetic biomarkers and therapies for patients with autoimmune disorders.
Collapse
|
14
|
de la Calle-Fabregat C, Rodríguez-Ubreva J, Cañete JD, Ballestar E. Designing Studies for Epigenetic Biomarker Development in Autoimmune Rheumatic Diseases. RHEUMATOLOGY AND IMMUNOLOGY RESEARCH 2022; 3:103-110. [PMID: 36788968 PMCID: PMC9895872 DOI: 10.2478/rir-2022-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/13/2022] [Indexed: 02/16/2023]
Abstract
In just a few years, the number of epigenetic studies in autoimmune rheumatic and inflammatory diseases has greatly increased. This is in part due to the need of identifying additional determinants to genetics to explain the pathogenesis and development of these disorders. In this regard, epigenetics provides potential mechanisms that determine gene function, are linked to environmental factors, and could explain a wide range of phenotypic variability among patients with these diseases. Despite the high interest and number of studies describing epigenetic alterations under these conditions and exploring their relationship to various clinical aspects, few of the proposed biomarkers have yet reached clinical practice. The potential of epigenetic markers is high, as these alterations link measurable features with a number of biological traits. In the present article, we present published studies in the field, discuss some frequent limitations in the existing research, and propose a number of considerations that should be taken into account by those starting new projects in the field, with an aim to generate biomarkers that could make it into the clinics.
Collapse
Affiliation(s)
- Carlos de la Calle-Fabregat
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916Badalona, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916Badalona, Barcelona, Spain
| | - Juan D. Cañete
- Rheumatology Department, Arthritis Unit, Hospital Clinic and IDIBAPS, 08036Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916Badalona, Barcelona, Spain
- Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai200241, China
| |
Collapse
|
15
|
Guo L, Wang W, Song W, Cao H, Tian H, Wang Z, Ren J, Ning F, Zhang D, Duan H. Genome-wide DNA methylation analysis of middle-aged and elderly monozygotic twins with age-related hearing loss in Qingdao, China. Gene 2022; 849:146918. [PMID: 36179964 DOI: 10.1016/j.gene.2022.146918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To explore the differences in DNA methylation associated with age-related hearing loss in a study of 57 twin pairs from China. DESIGN Monozygotic twins were identified through the Qingdao Twin Registration system. The median age of participants was >50 years. Their hearing thresholds were measured using a multilevel pure-tone audiometry assessment. The pure-tone audiometry was calculated at low frequencies (0.5, 1.0, and 2.0 kHz), speech frequencies (0.5, 1.0, 2.0, and 4.0kHz), and high frequencies (4.0 and 8 kHz). The CpG sites were tested using a linear mixed-effects model, and the function of the cis-regulatory regions and ontological enrichments were predicted using the online Genomic Regions Enrichment of Annotations Tool. The differentially methylated regions were identified using a comb-p python library approach. RESULTS In each of the PTA categories (low-, speech-, high-frequency), age-related hearing loss was detected in 25.9%, 19.3%, and 52.8% of participants. In the low-, speech- and high-frequency categories we identified 18, 42, and 12 individual CpG sites and 6, 11, and 6 differentially methylated regions. The CpG site located near DUSP4 had the strongest association with low- and speech-frequency, while the strongest association with high-frequency was near C21orf58. We identified associations of ALG10 with high-frequency hearing, C3 and LCK with low- and speech-frequency hearing, and GBX2 with low-frequency hearing. Top pathways that may be related to hearing, such as the Notch signaling pathway, were also identified. CONCLUSION Our study is the first of its kind to identify these genes and their associated with DNA methylation may play essential roles in the hearing process. The results of our epigenome-wide association study on twins clarify the complex mechanisms underlying age-related hearing loss.
Collapse
Affiliation(s)
- Longzi Guo
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Wanxue Song
- Qingdao Maternal and Child Health and Family Planning Service Center, Qingdao, China
| | - Hainan Cao
- Department of Otorhinolaryngology, Qingdao Municipal Hospital, Qingdao, China
| | - Huimin Tian
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Zhaoguo Wang
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Jifeng Ren
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Feng Ning
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, Qingdao, China
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, China.
| |
Collapse
|
16
|
Yu J, Tang R, Ding K. Epigenetic Modifications in the Pathogenesis of Systemic Sclerosis. Int J Gen Med 2022; 15:3155-3166. [PMID: 35342304 PMCID: PMC8942200 DOI: 10.2147/ijgm.s356877] [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: 01/03/2022] [Accepted: 03/04/2022] [Indexed: 11/23/2022] Open
Abstract
Systemic sclerosis is a rare chronic autoimmune disease, which mainly manifests as immune disorders, vascular damage, and progressive fibrosis. The etiology of SSc is complex and involves multiple factors. Both genetic and environmental factors are involved in its pathogenesis. As one of the molecular mechanisms of environmental factors, epigenetic regulation plays an important role in the occurrence and development of systemic sclerosis, which involves DNA methylation, histone modification and non-coding RNA regulation. This review summarizes research advances in epigenetics, including exosomes, lncRNA, and mentions possible biomarkers and therapeutic targets among them.
Collapse
Affiliation(s)
- Jiangfan Yu
- Department of Dermatology, Second Xiangya Hospital of Central South University, Changsha, 410011, People’s Republic of China
| | - Rui Tang
- Department of Rheumatology and Immunology, Second Xiangya Hospital of Central South University, Changsha, 410011, People’s Republic of China
| | - Ke Ding
- Department of Urology, Xiangya Hospital of Central South University, Changsha, 410008, People’s Republic of China
- Correspondence: Ke Ding, Department of Urology, Xiangya Hospital of Central South University, Changsha, 410008, People’s Republic of China, Email
| |
Collapse
|
17
|
Vecellio M, Paraboschi EM, Ceribelli A, Isailovic N, Motta F, Cardamone G, Robusto M, Asselta R, Brescianini S, Sacrini F, Costanzo A, De Santis M, Stazi MA, Duga S, Selmi C. DNA Methylation Signature in Monozygotic Twins Discordant for Psoriatic Disease. Front Cell Dev Biol 2021; 9:778677. [PMID: 34901024 PMCID: PMC8653905 DOI: 10.3389/fcell.2021.778677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/05/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Psoriatic disease is a multifactorial inflammatory condition spanning from skin and nail psoriasis (Pso) to spine and joint involvement characterizing psoriatic arthritis (PsA). Monozygotic twins provide a model to investigate genetic, early life environmental exposure and stochastic influences to complex diseases, mainly mediated by epigenetics. Methods: We performed a genome-wide DNA methylation study on whole blood of monozygotic twins from 7 pairs discordant for Pso/PsA using the Infinium Methylation EPIC array (Illumina). MeDiP—qPCR was used to confirm specific signals. Data were replicated in an independent cohort of seven patients with Pso/PsA and 3 healthy controls. Transcriptomic profiling was performed by RNAsequence on the same 7 monozygotic twin pairs. Results: We identified 2,564 differentially methylated positions between psoriatic disease and controls, corresponding to 1,703 genes, 59% within gene bodies. There were 19 regions with at least two DMPs within 1 kb of distance and significant within-pair Δβ-values (p < 0.005), among them SNX25, BRG1 and SMAD3 genes, all involved in TGF-β signaling pathway, were identified. Co-expression analyses on transcriptome data identified IL-6/JAK/STAT3 and TNF-α pathways as important signaling axes involved in the disease, and they also suggested an altered glucose metabolism in patients’ immune cells, characteristic of pro-inflammatory T lymphocytes. Conclusion: The study suggests the presence of an epigenetic signature in affected individuals, pointing to genes involved in immunological and inflammatory responses. This result is also supported by transcriptome data, that altogether suggest a higher activation state of the immune system, that could promote the disease status.
Collapse
Affiliation(s)
- Matteo Vecellio
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy.,Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Angela Ceribelli
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| | - Natasa Isailovic
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy
| | - Francesca Motta
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Michela Robusto
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Sonia Brescianini
- Italian Twin Registry, Centre for Behavioural Sciences and Mental Health, Italian National Institute of Health, Rome, Italy
| | - Francesco Sacrini
- Dermatology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy
| | - Antonio Costanzo
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,Dermatology, Humanitas Clinical and Research Center-IRCCS, Rozzano, Italy
| | - Maria De Santis
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| | - Maria Antonietta Stazi
- Italian Twin Registry, Centre for Behavioural Sciences and Mental Health, Italian National Institute of Health, Rome, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Rozzano, Italy.,IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Research Hospital IRCCS, Rozzano, Italy.,Department of Biomedical Sciences, Humanitas University, Rozzano, Italy
| |
Collapse
|
18
|
Coit P, Schollaert KL, Mirizio EM, Torok KS, Sawalha AH. DNA methylation patterns in juvenile systemic sclerosis and localized scleroderma. Clin Immunol 2021; 228:108756. [PMID: 33992755 DOI: 10.1016/j.clim.2021.108756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/16/2022]
Abstract
Scleroderma refers to a group of chronic fibrotic immune-mediated diseases of unknown etiology. Characterizing epigenetic changes in childhood-onset scleroderma, systemic sclerosis or localized scleroderma, has not been previously performed. The aim of this study was to assess DNA methylation differences and similarities between juvenile systemic sclerosis (jSSc) and juvenile localized scleroderma (jLS) compared to matched healthy controls. Genome-wide DNA methylation changes in peripheral blood mononuclear cell samples were assessed using the MethylationEPIC array followed by bioinformatic analysis and limited functional assessment. We identified a total of 105 and 144 differentially methylated sites compared to healthy controls in jSSc and jLS, respectively. The majority of differentially methylated sites and genes represented were unique to either jSSc or jLS suggesting a different underlying epigenetic pattern in both diseases. Among shared differentially methylated genes, methylation levels in a CpG site in FGFR2 can distinguish between LS and healthy PBMCs with a high accuracy. Canonical pathway analysis revealed that inflammatory pathways were enriched in genes differentially methylated in jSSc, including STAT3, NF-κB, and IL-15 pathways. In contrast, the HIPPO signaling pathway was enriched in jLS. Our data also suggest a potential role for NOTCH3 in both jSSc and jLS, and revealed a number of transcription factors unique to each of the two diseases. In summary, our data revealed important insights into jSSc and jLS and suggest a potentially novel epigenetic diagnostic biomarker for LS.
Collapse
Affiliation(s)
- Patrick Coit
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA; Graduate Program in Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Kaila L Schollaert
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emily M Mirizio
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kathryn S Torok
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA; Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh Systemic Sclerosis Center of Research Translation, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, USA; Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
| |
Collapse
|
19
|
Knockdown of RSAD2 attenuates B cell hyperactivity in patients with primary Sjögren's syndrome (pSS) via suppressing NF-κb signaling pathway. Mol Cell Biochem 2021; 476:2029-2037. [PMID: 33512636 DOI: 10.1007/s11010-021-04070-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/12/2021] [Indexed: 01/25/2023]
Abstract
Primary Sjögren's syndrome (pSS) is a chronic autoimmune disease that is mainly characterized as abnormal activation of B cells. It is reported that radical s-adenosyl methionine domain-containing 2 (RSAD2) is overexpressed in CD19+ B cells of pSS patients, but its role in pSS B cells remains unknown. Herein, RSAD2 expression was upregulated in CD19+ B cells of pSS patients and positively correlated with the expression of interleukin-10 (IL-10) in serum. After CD40L stimulation, knockdown of RSAD2 significantly attenuated cell viability, the production levels of immunoglobins and the expression of IL-10, while promoted cell apoptosis of pSS CD19+ B cells. Mechanistically, knockdown of RSAD2 negatively regulated nuclear factor kappa-b (NF-κb) signaling pathway. In addition, overexpression of p65 prominently alleviated the inhibitory effect of RSAD2 knockdown on proliferation, immunoglobin production and IL-10 expression in CD40L-induced CD19+ B cells. Our study indicated that silencing RSAD2 attenuated pSS B cell hyperactivity via suppressing NF-κb signaling pathway, which might provide a potential therapeutic target for pSS treatment.
Collapse
|
20
|
Baker Frost D, da Silveira W, Hazard ES, Atanelishvili I, Wilson RC, Flume J, Day KL, Oates JC, Bogatkevich GS, Feghali-Bostwick C, Hardiman G, Ramos PS. Differential DNA Methylation Landscape in Skin Fibroblasts from African Americans with Systemic Sclerosis. Genes (Basel) 2021; 12:129. [PMID: 33498390 PMCID: PMC7909410 DOI: 10.3390/genes12020129] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/20/2023] Open
Abstract
The etiology and reasons underlying the ethnic disparities in systemic sclerosis (SSc) remain unknown. African Americans are disproportionally affected by SSc and yet are underrepresented in research. The aim of this study was to comprehensively investigate the association of DNA methylation levels with SSc in dermal fibroblasts from patients of African ancestry. Reduced representation bisulfite sequencing (RRBS) was performed on primary dermal fibroblasts from 15 SSc patients and 15 controls of African ancestry, and over 3.8 million CpG sites were tested for differential methylation patterns between cases and controls. The dermal fibroblasts from African American patients exhibited widespread reduced DNA methylation. Differentially methylated CpG sites were most enriched in introns and intergenic regions while depleted in 5' UTR, promoters, and CpG islands. Seventeen genes and eleven promoters showed significant differential methylation, mostly in non-coding RNA genes and pseudogenes. Gene set enrichment analysis (GSEA) and gene ontology (GO) analyses revealed an enrichment of pathways related to interferon signaling and mesenchymal differentiation. The hypomethylation of DLX5 and TMEM140 was accompanied by these genes' overexpression in patients but underexpression for lncRNA MGC12916. These data show that differential methylation occurs in dermal fibroblasts from African American patients with SSc and identifies novel coding and non-coding genes.
Collapse
Affiliation(s)
- DeAnna Baker Frost
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Willian da Silveira
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - E. Starr Hazard
- Computational Biology Resource Center, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Ilia Atanelishvili
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Robert C. Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Jonathan Flume
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | | | - James C. Oates
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Rheumatology Section, Ralph H. Johnson VA Medical Center, Charleston, SC 29425, USA
| | - Galina S. Bogatkevich
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Carol Feghali-Bostwick
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
| | - Gary Hardiman
- Institute for Global Food Security, School of Biological Sciences, Queens University Belfast, Belfast BT9 5DL, UK; (W.d.S.); (G.H.)
| | - Paula S. Ramos
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC 29425, USA; (D.B.F.); (I.A.); (J.F.); (J.C.O.); (G.S.B.); (C.F.-B.)
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC 29425, USA
| |
Collapse
|
21
|
Nguyen XX, Nishimoto T, Takihara T, Mlakar L, Bradshaw AD, Feghali-Bostwick C. Lysyl oxidase directly contributes to extracellular matrix production and fibrosis in systemic sclerosis. Am J Physiol Lung Cell Mol Physiol 2020; 320:L29-L40. [PMID: 33026236 DOI: 10.1152/ajplung.00173.2020] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pulmonary fibrosis is one of the important causes of morbidity and mortality in fibroproliferative disorders such as systemic sclerosis (SSc) and idiopathic pulmonary fibrosis (IPF). Lysyl oxidase (LOX) is a copper-dependent amine oxidase whose primary function is the covalent crosslinking of collagens in the extracellular matrix (ECM). We investigated the role of LOX in the pathophysiology of SSc. LOX mRNA and protein levels were increased in lung fibroblasts of SSc patients compared with healthy controls and IPF patients. In vivo, bleomycin induced LOX mRNA expression in lung tissues, and LOX activity increased in the circulation of mice with pulmonary fibrosis, suggesting that circulating LOX parallels levels in lung tissues. Circulating levels of LOX were reduced upon amelioration of fibrosis with an antifibrotic peptide. LOX induced ECM production at the transcriptional level in lung fibroblasts, human lungs, and human skin maintained in organ culture. In vivo, LOX synergistically exacerbated fibrosis in bleomycin-treated mice. Further, LOX increased the production of interleukin (IL)-6, and the increase was mediated by LOX-induced c-Fos expression, the nuclear localization of c-Fos, and its engagement with the IL-6 promoter region. Our findings demonstrate that LOX expression and activity correlate with fibrosis in vitro, ex vivo, and in vivo. LOX induced ECM production via upregulation of IL-6 and nuclear localization of c-Fos. Thus, LOX has a direct pathogenic role in SSc-associated fibrosis that is independent of its crosslinking function. Our findings also suggest that measuring circulating LOX levels and activity can be used for monitoring response to antifibrotic therapy.
Collapse
Affiliation(s)
- Xinh-Xinh Nguyen
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Tetsuya Nishimoto
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Takahisa Takihara
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Kanagawa, Japan
| | - Logan Mlakar
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Amy D Bradshaw
- Division of Cardiology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Carol Feghali-Bostwick
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina
| |
Collapse
|
22
|
Ballestar E, Sawalha AH, Lu Q. Clinical value of DNA methylation markers in autoimmune rheumatic diseases. Nat Rev Rheumatol 2020; 16:514-524. [PMID: 32759997 DOI: 10.1038/s41584-020-0470-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
Abstract
Methylation of cytosine residues in DNA, the best studied epigenetic modification, is associated with gene transcription and nuclear organization, and ultimately the function of a cell. DNA methylation can be influenced by various factors, including changes in neighbouring genomic sites such as those induced by transcription factor binding. The DNA methylation profiles in relevant cell types are altered in most human diseases compared with the healthy state. Given the physical stability of DNA and methylated DNA compared with other epigenetic modifications, DNA methylation is an ideal marker for clinical purposes. However, few DNA methylation-based markers have made it into clinical practice, with the notable exception of some markers used in the field of oncology. Autoimmune rheumatic diseases are genetically complex entities that can vary widely in terms of prognosis, subtypes, progression and treatment responses. Increasing reports showing strong links between DNA methylation profiles and different clinical outcomes and other clinical aspects in autoimmune rheumatic diseases reinforce the usefulness of DNA methylation profiles as novel clinical markers. In this Review, we provide an updated discussion on DNA methylation alterations in autoimmune rheumatic diseases and the advantages and disadvantages of using these markers in clinical practice.
Collapse
Affiliation(s)
- Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Badalona, Barcelona, Spain.
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics; Division of Rheumatology and Clinical Immunology, Department of Medicine, Lupus Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| |
Collapse
|
23
|
Doskaliuk B, Zaiats L, Yatsyshyn R, Gerych P, Cherniuk N, Zimba O. Pulmonary involvement in systemic sclerosis: exploring cellular, genetic and epigenetic mechanisms. Rheumatol Int 2020; 40:1555-1569. [PMID: 32715342 DOI: 10.1007/s00296-020-04658-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022]
Abstract
Systemic sclerosis (SSc) is a chronic progressive autoimmune disease characterized by immune inflammation, vasculopathy, and fibrosis. There are still numerous uncertainties in the understanding of disease initiation and progression. Pulmonary involvement in SSc, and particularly pulmonary fibrosis, is critical for all organ systems affections in this disease. This review is aimed to describe and analyze new findings in the pathophysiology of SSc-associated pulmonary involvement and to explore perspective diagnostic and therapeutic strategies. A myriad of cellular interactions is explored in the dynamics of progressive interstitial lung disease (ILD) and pulmonary hypertension (PH) in SSc. The role of exosomes, microvesicles, and apoptotic bodies is examined and the impact of micro and long non-coding RNAs, DNA methylation, and histone modification in SSc is discussed.
Collapse
Affiliation(s)
- Bohdana Doskaliuk
- Academician Ye. M. Neiko Department of Internal Medicine #1, Clinical Immunology and Allergology, Ivano-Frankivsk National Medical University, Ivano-Frankivsk, Ukraine. .,Department of Pathophysiology, Ivano-Frankivsk National Medical University, Halytska Str. 2, Ivano-Frankivsk, 76000, Ukraine.
| | - Liubomyr Zaiats
- Department of Pathophysiology, Ivano-Frankivsk National Medical University, Halytska Str. 2, Ivano-Frankivsk, 76000, Ukraine
| | - Roman Yatsyshyn
- Academician Ye. M. Neiko Department of Internal Medicine #1, Clinical Immunology and Allergology, Ivano-Frankivsk National Medical University, Ivano-Frankivsk, Ukraine
| | - Petro Gerych
- Academician Ye. M. Neiko Department of Internal Medicine #1, Clinical Immunology and Allergology, Ivano-Frankivsk National Medical University, Ivano-Frankivsk, Ukraine
| | - Nataliia Cherniuk
- Academician Ye. M. Neiko Department of Internal Medicine #1, Clinical Immunology and Allergology, Ivano-Frankivsk National Medical University, Ivano-Frankivsk, Ukraine
| | - Olena Zimba
- Department of Internal Medicine #2, Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| |
Collapse
|
24
|
Zheng JN, Li Y, Yan YM, Shi H, Zou TT, Shao WQ, Wang Q. Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension. Front Genet 2020; 11:816. [PMID: 32793290 PMCID: PMC7393672 DOI: 10.3389/fgene.2020.00816] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/07/2020] [Indexed: 12/27/2022] Open
Abstract
Systemic sclerosis-associated with pulmonary arterial hypertension (SSc-PAH) is still a major cause of SSc related deaths. Early diagnosis and prompt treatment are crucial to reduce the mortality of patients with SSc-PAH. To screen the candidate biomarkers and potential therapeutic targets for SSc-PAH, we analyzed the data set (GSE33463 and GSE19617) for confirming key genes in peripheral blood mononuclear cells from SSc-PAH patients. A total of 105 SSc patients from gene expression omnibus (GEO) were included as discovery cohort (n = 69) and duplication cohort (n = 36) for screening hub genes by weighted gene co-expression network analysis (WGCNA). Furthermore, an independent validation cohort (n = 40), including healthy controls, SSc and SSc-PAH patients, was used for further validation by quantitative real-time polymerase chain reaction. The results showed that four key genes, including IFIT2, IFIT3, RSAD2, and PARP14, may serve as potential biomarkers in SSc-PAH. Also, they could be independent risk factors for SSc-PAH. In conclusion, the four key genes can be expected to become the potential therapeutic targets and early biomarkers for accurate therapy and diagnosis of SSc-PAH in the future, which also provides promising insights into the pathogenesis of SSc-PAH at the molecular level.
Collapse
Affiliation(s)
- Ji-Na Zheng
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Li
- Department of Stomatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yue-Mei Yan
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hui Shi
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tian-Tian Zou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China.,Cancer Metastasis Institute, Fudan University, Shanghai, China
| | - Wen-Qi Shao
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiang Wang
- Department of Dermatology, Zhongshan Hospital, Fudan University, Shanghai, China
| |
Collapse
|
25
|
Li K, Qin L, Jiang S, Li A, Zhang C, Liu G, Sun J, Sun H, Zhao Y, Li N, Zhang Y. The signature of HBV-related liver disease in peripheral blood mononuclear cell DNA methylation. Clin Epigenetics 2020; 12:81. [PMID: 32513305 PMCID: PMC7278209 DOI: 10.1186/s13148-020-00847-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
Background Hepatitis B virus (HBV)-related liver disease induces liver damage by hepatic immune and inflammatory response. The association between aberrant peripheral blood mononuclear cell (PBMC) DNA methylation and progression of liver disease and fibrosis remains unclear. Results Here we applied Infinium 450 K BeadChip investigating PBMC genome-wide methylation profiling of 48 HBV-related liver disease patients including 24 chronic hepatitis B (CHB), 14 compensated liver cirrhosis (LC), and 10 decompensated liver cirrhosis (DLC). In total, there were 7888 differentially methylated CpG sites (36.06% hypermethylation, 63.94% hypomethylation) correlate with liver disease progression. LC was difficult to be diagnosed, intermediating between CHB and DLC. We used least absolute shrinkage and selection operator (LASSO)-logistic regression method to perform a LC predictive model. The predicted probability (P) of having LC was estimated by the combined model: P = 1/(1 − e−x), where X = 11.52 − 2.82 × (if AST within the normal range − 0.19 × (percent methylation of cg05650055) − 0.21 × (percent methylation of cg17149911 ). Pyrosequencing validation and confusion matrix analysis was used for internal testing, area under receiver operating characteristic curve (AUROC) of model was 0.917 (95% CI, 0.80–0.977). On the fibrosis progress, there were 1705 genes in LC compared with CHB, whose differentially methylated CpG sites loading within the “promoter” regions (including TSS1500, TSS200, 5′UTR, and the 1st exon of genes) subject into the enrichment analysis using Ingenuity Pathway Analysis (IPA). There were 113 enriched immune-related pathways indicated that HBV-related liver fibrosis progression caused epigenetic reprogramming of the immune and inflammatory response. Conclusions These data support idea that development of HBV-related chronic liver disease is linked with robust and broad alteration of methylation in peripheral immune system. CpG methylation sites serve as relevant biomarker candidates to monitor and diagnose LC, providing new insight into the immune mechanisms understanding the progression of HBV-related liver fibrosis and cirrhosis.
Collapse
Affiliation(s)
- Kang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Ling Qin
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.,Schools of Basic Medical Science, Capital Medical University, Beijing, China
| | | | - Ang Li
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Chi Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Guihai Liu
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.,University of Oxford, Oxford, UK
| | - Jianping Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Huanqing Sun
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China
| | - Yan Zhao
- Clinical Laboratory Center, Beijing You'An hospital, Capital Medical University, Beijing, China
| | - Ning Li
- Departments of Hepatobiliary Surgery, Beijing You'An Hospital, Capital Medical University, Beijing, China.
| | - Yonghong Zhang
- Biomedical Information Center, Beijing You'An Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
26
|
Abstract
Twin registries have developed as a valuable resource for the study of many aspects of disease and society over the years in many different countries. A number of these registries include large numbers of twins with data collected at varying information levels for twin cohorts over the past several decades. More recent expansion of twin datasets has allowed for the collection of genetic data, together with many other levels of 'omic' information along with multiple demographic, physiological, health outcomes and other measures typically used in epidemiologic research. Other twin data sources outside these registries reflect research interests in particular aspects of disease or specific phenotypic assessment. Twin registries have the potential to play a key role in many aspects of the artificial intelligence/machine learning-driven projects of the future and will continue to keep adapting to the changing research landscape.
Collapse
|
27
|
Abstract
PURPOSE OF REVIEW Macrophages play key roles in tissue homeostasis and immune surveillance, mobilizing immune activation in response to microbial invasion and promoting wound healing to repair damaged tissue. However, failure to resolve macrophage activation can lead to chronic inflammation and fibrosis, and ultimately to pathology. Activated macrophages have been implicated in the pathogenesis of systemic sclerosis (SSc), although the triggers that induce immune activation in SSc and the signaling pathways that underlie aberrant macrophage activation remain unknown. RECENT FINDINGS Macrophages are implicated in fibrotic activation in SSc. Targeted therapeutic interventions directed against SSc macrophages may ameliorate inflammation and fibrosis. While current studies have begun to elucidate the role of macrophages in disease initiation and progression, further work is needed to address macrophage subset heterogeneity within and among SSc end-target tissues to determine the disparate functions mediated by these subsets and to identify additional targets for therapeutic intervention.
Collapse
|