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Jin J, Yang YR, Gong Q, Wang JN, Ni WJ, Wen JG, Meng XM. Role of epigenetically regulated inflammation in renal diseases. Semin Cell Dev Biol 2024; 154:295-304. [PMID: 36328897 DOI: 10.1016/j.semcdb.2022.10.005] [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: 07/15/2022] [Revised: 10/01/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
In recent decades, renal disease research has witnessed remarkable advances. Experimental evidence in this field has highlighted the role of inflammation in kidney disease. Epigenetic dynamics and immunometabolic reprogramming underlie the alterations in cellular responses to intrinsic and extrinsic stimuli; these factors determine cell identity and cell fate decisions and represent current research hotspots. This review focuses on recent findings and emerging concepts in epigenetics and inflammatory regulation and their effect on renal diseases. This review aims to summarize the role and mechanisms of different epigenetic modifications in renal inflammation and injury and provide new avenues for future research on inflammation-related renal disease and drug development.
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Affiliation(s)
- Juan Jin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China; School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Ya-Ru Yang
- Department of Clinical Pharmacology, Second Hospital of Anhui Medical University, Hefei, China
| | - Qian Gong
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Jia-Nan Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Wei-Jian Ni
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China
| | - Jia-Gen Wen
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China.
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, The Key Laboratory of Anti-Inflammatory of Immune Medicines, Ministry of Education, Hefei 230032, China.
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2
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Araki Y, Mimura T. Epigenetic Dysregulation in the Pathogenesis of Systemic Lupus Erythematosus. Int J Mol Sci 2024; 25:1019. [PMID: 38256093 PMCID: PMC10816225 DOI: 10.3390/ijms25021019] [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: 11/07/2023] [Revised: 01/05/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Systemic lupus erythematosus (SLE) is a multisystem autoimmune disease in which immune disorders lead to autoreactive immune responses and cause inflammation and tissue damage. Genetic and environmental factors have been shown to trigger SLE. Recent evidence has also demonstrated that epigenetic factors contribute to the pathogenesis of SLE. Epigenetic mechanisms play an important role in modulating the chromatin structure and regulating gene transcription. Dysregulated epigenetic changes can alter gene expression and impair cellular functions in immune cells, resulting in autoreactive immune responses. Therefore, elucidating the dysregulated epigenetic mechanisms in the immune system is crucial for understanding the pathogenesis of SLE. In this paper, we review the important roles of epigenetic disorders in the pathogenesis of SLE.
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Affiliation(s)
- Yasuto Araki
- Department of Rheumatology and Applied Immunology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan;
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3
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Zhou HY, Luo Q, Sui H, Du XN, Zhao YJ, Liu L, Guan Q, Zhou Y, Wen QS, Shi Y, Sun Y, Lin HL, Wang DP. Recent advances in the involvement of epigenetics in the pathogenesis of systemic lupus erythematosus. Clin Immunol 2024; 258:109857. [PMID: 38043757 DOI: 10.1016/j.clim.2023.109857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/27/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Systemic lupus erythematosus (SLE) is a typical systemic autoimmune disease that manifests as skin rash, arthritis, lymphadenopathy, and multiple organ lesions. Epigenetics, including DNA methylation, histone modification, and non-coding RNA regulation, mainly affect the function and characteristics of cells through the regulation of gene transcription or translation. Increasing evidence indicates that there are a variety of complex epigenetic effects in patients with SLE, which interfere with the differentiation and function of T, and B lymphocytes, monocytes, and neutrophils, and enhance the expression of SLE-associated pathogenic genes. This paper summarizes our currently knowledge regarding pathogenesis of SLE, and introduces current advances in the epigenetic regulation of SLE from three aspects: immune function, inflammatory response, and lupus complications. We propose that epigenetic changes could be used as potential biomarkers and therapeutic targets of SLE.
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Affiliation(s)
- Hong-Yan Zhou
- First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qi Luo
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hua Sui
- Integrated TCM and Western Medicine Collage of Dalian Medical University, Dalian, China
| | - Xiang-Ning Du
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yang-Jianing Zhao
- Integrated TCM and Western Medicine Collage of Dalian Medical University, Dalian, China
| | - Lu Liu
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qing Guan
- Integrated TCM and Western Medicine Collage of Dalian Medical University, Dalian, China
| | - Yue Zhou
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Qing-Si Wen
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yan Shi
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yu Sun
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Hong-Li Lin
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China.
| | - Da-Peng Wang
- Nephrology Department of First Affiliated Hospital of Dalian Medical University, Dalian, China.
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4
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Wang J, Hua G, Cai G, Ma Y, Yang X, Zhang L, Li R, Liu J, Ma Q, Wu K, Zhao Y, Deng X. Genome-wide DNA methylation and transcriptome analyses reveal the key gene for wool type variation in sheep. J Anim Sci Biotechnol 2023; 14:88. [PMID: 37420295 DOI: 10.1186/s40104-023-00893-6] [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: 02/03/2023] [Accepted: 05/07/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wool fibers are valuable materials for textile industry. Typical wool fibers are divided into medullated and non-medullated types, with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles. The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding. The fine wool sheep have a non-medullated coat. However, the critical period determining the type of wool follicles is the embryonic stage, which limits the phenotypic observation and variant contrast, making both selection and studies of wool type variation fairly difficult. RESULTS During the breeding of a modern fine (MF) wool sheep population with multiple-ovulation and embryo transfer technique, we serendipitously discovered lambs with ancestral-like coarse (ALC) wool. Whole-genome resequencing confirmed ALC wool lambs as a variant type from the MF wool population. We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals, and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs. Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes. An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former. Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles. CONCLUSION In this study, we conducted genome-wide differential methylation site association analysis on differential wool type trait, and located the only CpG locus that strongly associated with primary wool follicle development. Combined with transcriptome analysis, SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin. The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.
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Affiliation(s)
- Jiankui Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Guoying Hua
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Ganxian Cai
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yuhao Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xue Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Letian Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qing Ma
- Animal Science Institute of Ningxia Agriculture and Forestry Academy, Yinchuan, 750002, China
| | - Keliang Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xuemei Deng
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
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5
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Blanco LP, Kaplan MJ. Metabolic alterations of the immune system in the pathogenesis of autoimmune diseases. PLoS Biol 2023; 21:e3002084. [PMID: 37098006 PMCID: PMC10128981 DOI: 10.1371/journal.pbio.3002084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Systemic autoimmune diseases are characteristically associated with aberrant autoreactive innate and adaptive immune responses that lead to tissue damage and increased morbidity and mortality. Autoimmunity has been linked to alterations in the metabolic functions of immune cells (immunometabolism) and, more specifically, to mitochondrial dysfunction. Much has been written about immunometabolism in autoimmunity in general, so this Essay focuses on recent research into the role of mitochondrial dysfunction in the dysregulation of innate and adaptive immunity that is characteristic of systemic autoimmune diseases such as systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA). Enhancing the understanding of mitochondrial dysregulation in autoimmunity will hopefully contribute to accelerating the development of immunomodulatory treatments for these challenging diseases.
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Affiliation(s)
- Luz P Blanco
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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Joustra V, Hageman IL, Satsangi J, Adams A, Ventham NT, de Jonge WJ, Henneman P, D’Haens GR, Li Yim AYF. Systematic Review and Meta-analysis of Peripheral Blood DNA Methylation Studies in Inflammatory Bowel Disease. J Crohns Colitis 2023; 17:185-198. [PMID: 35998097 PMCID: PMC10024549 DOI: 10.1093/ecco-jcc/jjac119] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Over the past decade, the DNA methylome has been increasingly studied in peripheral blood of inflammatory bowel disease [IBD] patients. However, a comprehensive summary and meta-analysis of peripheral blood leukocyte [PBL] DNA methylation studies has thus far not been conducted. Here, we systematically reviewed all available literature up to February 2022 and summarized the observations by means of meta-analysis. METHODS We conducted a systematic search and critical appraisal of IBD-associated DNA methylation studies in PBL using the biomarker-based cross-sectional studies [BIOCROSS] tool. Subsequently, we performed meta-analyses on the summary statistics obtained from epigenome-wide association studies [EWAS] that included patients with Crohn's disease [CD], ulcerative colitis [UC] and/or healthy controls [HC]. RESULTS Altogether, we included 15 studies for systematic review. Critical appraisal revealed large methodological and outcome heterogeneity between studies. Summary statistics were obtained from four studies based on a cumulative 552 samples [177 CD, 132 UC and 243 HC]. Consistent differential methylation was identified for 256 differentially methylated probes [DMPs; Bonferroni-adjusted p ≤ 0.05] when comparing CD with HC and 103 when comparing UC with HC. Comparing IBD [CD + UC] with HC resulted in 224 DMPs. Importantly, several of the previously identified DMPs, such as VMP1/TMEM49/MIR21 and RPS6KA2, were consistently differentially methylated across all studies. CONCLUSION Methodological homogenization of IBD epigenetic studies is needed to allow for easier aggregation and independent validation. Nonetheless, we were able to confirm previous observations. Our results can serve as the basis for future IBD epigenetic biomarker research in PBL.
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Affiliation(s)
| | | | - Jack Satsangi
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Alex Adams
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - Wouter J de Jonge
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
- Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands
| | - Peter Henneman
- Amsterdam UMC location University of Amsterdam, Department of Human Genetics, Genome Diagnostics Laboratory, Amsterdam, Netherlands
- Amsterdam Reproduction & Development, Amsterdam, Netherlands
| | - Geert R D’Haens
- Amsterdam UMC location University of Amsterdam, Department of Gastroenterology and Hepatology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Corresponding author: Andrew Y. F. Li Yim, Amsterdam UMC location University of Amsterdam, Tytgat Institute for Liver and Intestinal Research, Amsterdam, Netherlands.
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7
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Ehtesham N, Habibi Kavashkohie MR, Mazhari SA, Azhdari S, Ranjbar H, Mosallaei M, Hazrati E, Behroozi J. DNA methylation alterations in systemic lupus erythematosus: A systematic review of case-control studies. Lupus 2023; 32:363-379. [PMID: 36573333 DOI: 10.1177/09612033221148099] [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: 12/28/2022]
Abstract
BACKGROUND Traditionally, the diagnosis and monitoring of disease activity in systemic lupus erythematosus (SLE) are contingent upon clinical manifestations and serological markers. However, researchers are struggling to find biomarkers with higher sensitivity and specificity. DNA methylation has been the most studied epigenetic feature in SLE. So, in this study, we performed a systematic review of studies about DNA methylation alterations in SLE patients compared to healthy controls. METHODS By searching PubMed, Scopus, and Google Scholar up to July 2022, all case-control studies in which DNA methylation of specific genes was assessed by a non-high-throughput technique and passed the quality of bias assessment were included. RESULTS In total, 44 eligible studies underwent a data extraction process. In all, 3471 SLE patients and 1028 healthy individuals were included. Among the studies that reported the patients' gender (n = 2853), 89.41% were female and 10.59% were male. Forty studies have been conducted on adult patients. The number of works on fractionated and unfractionated blood cells was almost equal. In this regard, 22 studies were conducted on whole blood or peripheral blood mononuclear cells and two studies on unfractionated white blood cells. Sorted blood cells were biological sources in 20 studies. The most investigated gene was IFI44L. Sensitivity, specificity, and diagnostic power of methylation levels were only reported for IFI44L in five studies. The most employed methylation profiling method was bisulfite sequencing polymerase chain reaction. The correlation between methylation patterns and clinical parameters was explored in 22 studies, which of them 16 publications displayed a remarkable association between DNA methylation status and clinical indices. CONCLUSIONS The methylation status of some genes especially IFI44L, FOXP3, and MX1 has been suggested as promising SLE biomarkers. However, given the conflicting findings between studies because of potential confounders such as different sample types, methylation profiling methods, and ethnicity as well as shared DNA methylation patterns of SLE and other autoimmune diseases, DNA methylation biomarkers are currently not reliable diagnostic biomarkers and do not represent surrogate markers of SLE disease activity. Future investigations on a larger scale with the discarding of limitations of previous studies would probably lead to a consensus.
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Affiliation(s)
- Naeim Ehtesham
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, 162996AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, 48533University of Social Welfare and Rehabilitation Science, Tehran, Iran
| | | | - Seyed Amirhossein Mazhari
- Department of Medical Biology and Genetics, 217747Azerbaijan Medical University (AMU), Baku, Azerbaijan
| | - Sara Azhdari
- Department of Anatomy and Embryology, School of Medicine, 394237Bam University of Medical Sciences, Bam, Iran
| | - Hamta Ranjbar
- Student Research Committee, 48463Kerman University of Medical Sciences, Kerman, Iran
| | - Meysam Mosallaei
- Student Research Committee, 48533University of Social Welfare and Rehabilitation Science, Tehran, Iran.,Department of Genetics and Molecular Biology, School of Medicine, 48455Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ebrahim Hazrati
- Department of Anesthesiology and Intensive Care, Medical Faculty, 162996AJA University of Medical Sciences, Tehran, Iran
| | - Javad Behroozi
- Department of Genetics and Advanced Medical Technology, Faculty of Medicine, 162996AJA University of Medical Sciences, Tehran, Iran.,Research Center for Cancer Screening and Epidemiology, 162996AJA University of Medical Sciences, Tehran, Iran
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Burska A, Rodríguez-Carrio J, Biesen R, Dik WA, Eloranta ML, Cavalli G, Visser M, Boumpas DT, Bertsias G, Wahren-Herlenius M, Rehwinkel J, Frémond ML, Crow MK, Ronnblom L, Conaghan PG, Versnel M, Vital E. Type I interferon pathway assays in studies of rheumatic and musculoskeletal diseases: a systematic literature review informing EULAR points to consider. RMD Open 2023; 9:e002876. [PMID: 36863752 PMCID: PMC9990675 DOI: 10.1136/rmdopen-2022-002876] [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: 11/18/2022] [Accepted: 02/08/2023] [Indexed: 03/04/2023] Open
Abstract
OBJECTIVES To systematically review the literature for assay methods that aim to evaluate type I interferon (IFN-I) pathway activation and to harmonise-related terminology. METHODS Three databases were searched for reports of IFN-I and rheumatic musculoskeletal diseases. Information about the performance metrics of assays measuring IFN-I and measures of truth were extracted and summarised. A EULAR task force panel assessed feasibility and developed consensus terminology. RESULTS Of 10 037 abstracts, 276 fulfilled eligibility criteria for data extraction. Some reported more than one technique to measure IFN-I pathway activation. Hence, 276 papers generated data on 412 methods. IFN-I pathway activation was measured using: qPCR (n=121), immunoassays (n=101), microarray (n=69), reporter cell assay (n=38), DNA methylation (n=14), flow cytometry (n=14), cytopathic effect assay (n=11), RNA sequencing (n=9), plaque reduction assay (n=8), Nanostring (n=5), bisulphite sequencing (n=3). Principles of each assay are summarised for content validity. Concurrent validity (correlation with other IFN assays) was presented for n=150/412 assays. Reliability data were variable and provided for 13 assays. Gene expression and immunoassays were considered most feasible. Consensus terminology to define different aspects of IFN-I research and practice was produced. CONCLUSIONS Diverse methods have been reported as IFN-I assays and these differ in what elements or aspects of IFN-I pathway activation they measure and how. No 'gold standard' represents the entirety of the IFN pathway, some may not be specific for IFN-I. Data on reliability or comparing assays were limited, and feasibility is a challenge for many assays. Consensus terminology should improve consistency of reporting.
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Affiliation(s)
- Agata Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Javier Rodríguez-Carrio
- University of Oviedo, Area of Immunology, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Robert Biesen
- Charité University Medicine Berlin, Department of Rheumatology, Berlin, Germany
| | - Willem A Dik
- Erasmus MC, University Medical Center Rotterdam, Laboratory Medical Immunology, Department of Immunology, Rotterdam, Netherlands Immunology, Rotterdam, The Netherlands
| | - Maija-Leena Eloranta
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - Giulio Cavalli
- Unit of Immunology, Rheumatology, Allergy and Rare Diseases, Vita-Salute San Raffaele University, Milan, Italy
- EULAR, PARE Patient Research Partners, Amsterdam, Netherlands
| | - Marianne Visser
- University of Crete, Medical School, Department of Internal Medicine, Heraklion, Greece
| | - Dimitrios T Boumpas
- University of Crete, Medical School, Department of Rheumatology-Clinical Immunology, Heraklion, Greece
| | - George Bertsias
- University of Crete, Medical School, Department of Rheumatology-Clinical Immunology, Heraklion, Greece
| | - Marie Wahren-Herlenius
- Karolinska Institutet, Division of Rheumatology, Stockholm, Sweden
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Norway
| | - Jan Rehwinkel
- Medical Research Council Human Immunology Unit, Medical Research Council Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, UK
| | - Marie-Louise Frémond
- Université de Paris Cité, Hôpital Necker-Enfants Malades, Immuno-Hématologie et Rhumatologie pédiatriques, Paris, France
| | - Mary K Crow
- Hospital for Special Surgery, Weill Cornell Medical College, Mary Kirkland Center for Lupus Research, New York, USA
| | - Lars Ronnblom
- Uppsala University, Department of Medical Sciences, Rheumatology, Uppsala, Sweden
| | - P G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
| | - Marjan Versnel
- Erasmus MC, Department of Immunology, Rotterdam, The Netherlands
| | - Ed Vital
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds & NIHR Leeds Biomedical Research Centre, Leeds, UK
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9
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Wang F, Miao HB, Pei ZH, Chen Z. Serological, fragmentomic, and epigenetic characteristics of cell-free DNA in patients with lupus nephritis. Front Immunol 2022; 13:1001690. [PMID: 36578480 PMCID: PMC9791112 DOI: 10.3389/fimmu.2022.1001690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
Objectives The biological characteristics of plasma circulating cell-free DNA (cfDNA) are related to the pathogenesis of lupus nephritis (LN). The aim of this study was to explore the biological characteristics of cfDNA in patients with LN in terms of serology, fragment omics, and epigenetics, and to discuss the possibility of liquid biopsy for cfDNA as an alternative to conventional tissue biopsy. Methods cfDNA was extracted from plasma samples of 127 patients with systemic lupus erythematosus (64 with LN, 63 without LN). The cfDNA concentration was determined using the Qubit method. Next-generation sequencing cfDNA methylation profiling was performed for three LN patients and six non-LN patients. The methylation panel was designed based on data from The Cancer Genome Atlas cohort. The fragmentation index, motif score, and DELFI score were calculated to explore the fragmentation profile of cfDNA in patients with LN. Statistical and machine learning methods were used to select features to calculate the methylation scores of the samples. Results Patients with LN had significantly lower cfDNA concentrations (P = 0.0347) than those without LN. This may be associated with the presence of anti-double-stranded DNA antibodies (r = -0.4189; P = 0.0296). The mean DELFI score (proportion of short fragments of cfDNA) in patients with LN was significantly higher than that in patients without LN (P = 0.0238). Based on the pan-cancer data, 73, 66, 8, and 10 features were selected and used to calculate the methylation scores. The mean methylation scores of these features in patients with LN differed significantly from those in patients without LN (P = 0.0238). Conclusions The specificity of cfDNA in patients with LN was identified using serological, fragmentomic, and epigenetic analyses. The findings may have implications for the development of new molecular markers of LN.
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Affiliation(s)
- Fang Wang
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China,Department of Immunology, Foresea Life Insurance Guangxi Hospital, Nanning, Guangxi, China
| | - Hai-bing Miao
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China
| | - Zhi-hua Pei
- Hubei Provincial Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhen Chen
- Department of Rheumatology and Immunology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, Fujian, China,*Correspondence: Zhen Chen,
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10
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Wang L, Yang Z, Yu H, Lin W, Wu R, Yang H, Yang K. Predicting diagnostic gene expression profiles associated with immune infiltration in patients with lupus nephritis. Front Immunol 2022; 13:839197. [PMID: 36532018 PMCID: PMC9755505 DOI: 10.3389/fimmu.2022.839197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 11/09/2022] [Indexed: 12/03/2022] Open
Abstract
Objective To identify potential diagnostic markers of lupus nephritis (LN) based on bioinformatics and machine learning and to explore the significance of immune cell infiltration in this pathology. Methods Seven LN gene expression datasets were downloaded from the GEO database, and the larger sample size was used as the training group to obtain differential genes (DEGs) between LN and healthy controls, and to perform gene function, disease ontology (DO), and gene set enrichment analyses (GSEA). Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), were applied to identify candidate biomarkers. The diagnostic value of LN diagnostic gene biomarkers was further evaluated in the area under the ROC curve observed in the validation dataset. CIBERSORT was used to analyze 22 immune cell fractions from LN patients and to analyze their correlation with diagnostic markers. Results Thirty and twenty-one DEGs were screened in kidney tissue and peripheral blood, respectively. Both of which covered macrophages and interferons. The disease enrichment analysis of DEGs in kidney tissues showed that they were mainly involved in immune and renal diseases, and in peripheral blood it was mainly enriched in cardiovascular system, bone marrow, and oral cavity. The machine learning algorithm combined with external dataset validation revealed that C1QA(AUC = 0.741), C1QB(AUC = 0.758), MX1(AUC = 0.865), RORC(AUC = 0.911), CD177(AUC = 0.855), DEFA4(AUC= 0.843)and HERC5(AUC = 0.880) had high diagnostic value and could be used as diagnostic biomarkers of LN. Compared to controls, pathways such as cell adhesion molecule cam, and systemic lupus erythematosus were activated in kidney tissues; cell cycle, cytoplasmic DNA sensing pathways, NOD-like receptor signaling pathways, proteasome, and RIG-1-like receptors were activated in peripheral blood. Immune cell infiltration analysis showed that diagnostic markers in kidney tissue were associated with T cells CD8 and Dendritic cells resting, and in blood were associated with T cells CD4 memory resting, suggesting that CD4 T cells, CD8 T cells and dendritic cells are closely related to the development and progression of LN. Conclusion C1QA, C1QB, MX1, RORC, CD177, DEFA4 and HERC5 could be used as new candidate molecular markers for LN. It may provide new insights into the diagnosis and molecular treatment of LN in the future.
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Affiliation(s)
- Lin Wang
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhihua Yang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hangxing Yu
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Wei Lin
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ruoxi Wu
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongtao Yang
- Nephrology Department, First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Kang Yang
- Nephrology Department, The First Affiliated Hospital of Henan University of Chinese Medicine, Henan, China
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11
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Sung WY, Lin YZ, Hwang DY, Lin CH, Li RN, Tseng CC, Wu CC, Ou TT, Yen JH. Methylation of TET2 Promoter Is Associated with Global Hypomethylation and Hypohydroxymethylation in Peripheral Blood Mononuclear Cells of Systemic Lupus Erythematosus Patients. Diagnostics (Basel) 2022; 12:diagnostics12123006. [PMID: 36553013 PMCID: PMC9776498 DOI: 10.3390/diagnostics12123006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022] Open
Abstract
(1) Background: It is widely accepted that aberrant methylation patterns contribute to the development of systemic lupus erythematosus (SLE). Ten-eleven translocation (TET) methylcytosine dioxygenase is an essential enzyme of which there are three members, TET1, 2, and 3, involved in hydroxymethylation, a newly uncovered mechanism of active DNA methylation. The epigenomes of gene transcription are regulated by 5-hydroxymethylcytocine (5-hmC) and TETs, leading to dysregulation of the immune system in SLE. The purpose of this study was to investigate the global hydroxymethylation status in SLE peripheral blood mononuclear cells (PBMCs) and to explore the role of TETs in changing the patterns of methylation. (2) Methods: We collected PBMCs from 101 SLE patients and 100 healthy donors. TaqMan real-time polymerase chain-reaction assay was performed for the detection of 5-methylcytosine (5-mC), 5-hmC, and TET2 mRNA expression and single-nucleotide polymorphism genotyping. The methylation rates in different CpG sites of TET2 promoters were examined using next-generation sequencing-based deep bisulfite sequencing. Putative transcription factors were investigated using the UCSC Genome Browser on the Human Dec. 2013 (GRCh38/hg38) Assembly. (3) Results: 5-mC and 5-hmC were both decreased in SLE. The mRNA expression level of TET2 was notably high and found to be correlated with the levels of immunologic biomarkers that are indicative of SLE disease activity. The analysis of methylation rates in the TET2 promoter revealed that SLE patients had significantly higher and lower rates of methylation in TET2 105146072-154 and TET2 105146218-331, respectively. (4) Conclusions: TET2 may play an important role in 5-mC/5-hmC dynamics in the PBMCs of SLE patients. The epigenetic modification of TET2 promoters could contribute to the pathogenesis of SLE and the intensity of the immunologic reaction.
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Affiliation(s)
- Wan-Yu Sung
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Correspondence: (W.-Y.S.); (J.-H.Y.)
| | - Yuan-Zhao Lin
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Daw-Yang Hwang
- National Institute of Cancer Research, National Health Research Institutes, Tainan 350401, Taiwan
- Division of Nephrology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Chia-Hui Lin
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Ruei-Nian Li
- Department of Biomedical Science and Environmental Biology, College of Life Science, Kaohsiung Medical University, Kaohsiung 80756, Taiwan
| | - Chia-Chun Tseng
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Cheng-Chin Wu
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Tsan-Teng Ou
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
| | - Jeng-Hsien Yen
- Division of Rheumatology, Department of Internal medicine, Kaohsiung Medical University Hospital, Kaohsiung 80756, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- College of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan
- Institute of Medical Science and Technology, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
- Correspondence: (W.-Y.S.); (J.-H.Y.)
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12
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Coit P, Roopnarinesingh X, Ortiz-Fernández L, McKinnon-Maksimowicz K, Lewis EE, Merrill JT, McCune WJ, Wren JD, Sawalha AH. Hypomethylation of miR-17-92 cluster in lupus T cells and no significant role for genetic factors in the lupus-associated DNA methylation signature. Ann Rheum Dis 2022; 81:1428-1437. [PMID: 35710306 PMCID: PMC10259175 DOI: 10.1136/annrheumdis-2022-222656] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/07/2022] [Indexed: 11/04/2022]
Abstract
OBJECTIVES Lupus T cells demonstrate aberrant DNA methylation patterns dominated by hypomethylation of interferon-regulated genes. The objective of this study was to identify additional lupus-associated DNA methylation changes and determine the genetic contribution to epigenetic changes characteristic of lupus. METHODS Genome-wide DNA methylation was assessed in naïve CD4+ T cells from 74 patients with lupus and 74 age-matched, sex-matched and race-matched healthy controls. We applied a trend deviation analysis approach, comparing methylation data in our cohort with over 16 500 samples. Methylation quantitative trait loci (meQTL) analysis was performed by integrating methylation profiles with genome-wide genotyping data. RESULTS In addition to the previously reported epigenetic signature in interferon-regulated genes, we observed hypomethylation in the promoter region of the miR-17-92 cluster in patients with lupus. Members of this microRNA cluster play an important role in regulating T cell proliferation and differentiation. Expression of two microRNAs in this cluster, miR-19b1 and miR-18a, showed a significant positive correlation with lupus disease activity. Among miR-18a target genes, TNFAIP3, which encodes a negative regulator of nuclear factor kappa B, was downregulated in lupus CD4+ T cells. MeQTL identified in lupus patients showed overlap with genetic risk loci for lupus, including CFB and IRF7. The lupus risk allele in IRF7 (rs1131665) was associated with significant IRF7 hypomethylation. However, <1% of differentially methylated CpG sites in patients with lupus were associated with an meQTL, suggesting minimal genetic contribution to lupus-associated epigenotypes. CONCLUSION The lupus defining epigenetic signature, characterised by robust hypomethylation of interferon-regulated genes, does not appear to be determined by genetic factors. Hypomethylation of the miR-17-92 cluster that plays an important role in T cell activation is a novel epigenetic locus for lupus.
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Affiliation(s)
- Patrick Coit
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Graduate Program in Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Xiavan Roopnarinesingh
- Graduate Program, Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Lourdes Ortiz-Fernández
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Emily E Lewis
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Joan T Merrill
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - W Joseph McCune
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan D Wren
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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13
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Xu N, Liu J, Li X. Lupus nephritis: The regulatory interplay between epigenetic and MicroRNAs. Front Physiol 2022; 13:925416. [PMID: 36187762 PMCID: PMC9523357 DOI: 10.3389/fphys.2022.925416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, small, non-coding RNA molecules that act as epigenetic modifiers to regulate the protein levels of target messenger RNAs without altering their genetic sequences. The highly complex role of miRNAs in the epigenetics of lupus nephritis (LN) is increasingly being recognized. DNA methylation and histone modifications are focal points of epigenetic research. miRNAs play a critical role in renal development and physiology, and dysregulation may result in abnormal renal cell proliferation, inflammation, and fibrosis of the kidneys in LN. However, epigenetic and miRNA-mediated regulation are not mutually exclusive. Further research has established a link between miRNA expression and epigenetic regulation in various disorders, including LN. This review summarizes the most recent evidence regarding the interaction between miRNAs and epigenetics in LN and highlights potential therapeutic and diagnostic targets.
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Affiliation(s)
- Ning Xu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Liu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiangling Li
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, China
- *Correspondence: Xiangling Li,
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14
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Mei X, Jin H, Zhao M, Lu Q. Association of Immune-Related Genetic and Epigenetic Alterations with Lupus Nephritis. KIDNEY DISEASES (BASEL, SWITZERLAND) 2022; 8:286-296. [PMID: 36157263 PMCID: PMC9386430 DOI: 10.1159/000524937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The familial clustering phenomenon together with environmental influences indicates the presence of a genetic and epigenetic predisposition to systematic lupus erythematosus (SLE). Interestingly, regarding lupus nephritis (LN), the worst complication of SLE, mortality, and morbidity were not consistent with SLE in relation to sexuality and ethnicity. SUMMARY Genetic and epigenetic alterations in LN include genes and noncoding RNAs that are involved in antigen-presenting, complements, immune cell infiltration, interferon pathways, and so on. Once genetic or epigenetic change occurs alone or simultaneously, they will promote the formation of immune complexes with autoantibodies that target various autoantigens, which results in inflammatory cytokines and autoreactive immune cells colonizing renal tissues and contributing to LN. KEY MESSAGES Making additional checks for immunopathology-related heredity and epigenetic factors may lead to a more holistic perspective of LN.
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Affiliation(s)
- Xiaole Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Hui Jin
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Qianjin Lu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Key Laboratory of Basic and Translational Research on Immunological Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
- Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
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15
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Shepherd R, Bretherton I, Pang K, Mansell T, Czajko A, Kim B, Vlahos A, Zajac JD, Saffery R, Cheung A, Novakovic B. Gender-affirming hormone therapy induces specific DNA methylation changes in blood. Clin Epigenetics 2022; 14:24. [PMID: 35177097 PMCID: PMC8851870 DOI: 10.1186/s13148-022-01236-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation is an epigenetic mark that is influenced by underlying genetic profile, environment, and ageing. In addition to X-linked DNA methylation, sex-specific methylation patterns are widespread across autosomal chromosomes and can be present from birth or arise over time. In individuals where gender identity and sex assigned at birth are markedly incongruent, as in the case of transgender people, feminization or masculinization may be sought through gender-affirming hormone therapy (GAHT). GAHT is a cornerstone of transgender care, yet no studies to date have investigated its effect on genome-wide methylation. We profiled genome-wide DNA methylation in blood of transgender women (n = 13) and transgender men (n = 13) before and during GAHT (6 months and 12 months into feminizing or masculinizing hormone therapy). Results We identified several thousand differentially methylated CpG sites (DMPs) (Δβ ≥ 0.02, unadjusted p value < 0.05) and several differentially methylated regions (DMRs) in both people undergoing feminizing and masculinizing GAHT, the vast majority of which were progressive changes over time. X chromosome and sex-specific autosomal DNA methylation patterns established in early development are largely refractory to change in association with GAHT, with only 3% affected (Δβ ≥ 0.02, unadjusted p value < 0.05). The small number of sex-specific DMPs that were affected by GAHT were those that become sex-specific during the lifetime, known as sex-and-age DMPs, including DMRs in PRR4 and VMP1 genes. The GAHT-induced changes at these sex-associated probes consistently demonstrated a shift towards the methylation signature of the GAHT-naïve opposite sex, and we observed enrichment of previously reported adolescence-associated methylation changes. Conclusion We provide evidence for GAHT inducing a unique blood methylation signature in transgender people. This study advances our understanding of the complex interplay between sex hormones, sex chromosomes, and DNA methylation in the context of immunity. We highlight the need to broaden the field of ‘sex-specific’ immunity beyond cisgender males and cisgender females, as transgender people on GAHT exhibit a unique molecular profile. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01236-4.
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Affiliation(s)
- Rebecca Shepherd
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Ingrid Bretherton
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Ken Pang
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Adolescent Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Toby Mansell
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Czajko
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Bowon Kim
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Amanda Vlahos
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jeffrey D Zajac
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Richard Saffery
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Ada Cheung
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Boris Novakovic
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
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16
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Jin J, Chen H, Meng XM. Editorial: Epigenetic Regulation in Renal Development, Physiology and Disease. Front Physiol 2022; 12:818190. [PMID: 35069267 PMCID: PMC8766424 DOI: 10.3389/fphys.2021.818190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/10/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Juan Jin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China.,School of Basic Medicine, Anhui Medical University, Hefei, China
| | - Haiyong Chen
- Li Ka Shing Faculty of Medicine, School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xiao-Ming Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui, The Key Laboratory of Anti-inflammatory of Immune Medicines, Ministry of Education, School of Pharmacy, Anhui Institute of Innovative Drugs, Anhui Medical University, Hefei, China
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17
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Ferreté-Bonastre AG, Cortés-Hernández J, Ballestar E. What can we learn from DNA methylation studies in lupus? Clin Immunol 2022; 234:108920. [PMID: 34973429 DOI: 10.1016/j.clim.2021.108920] [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: 11/03/2021] [Revised: 12/23/2021] [Accepted: 12/26/2021] [Indexed: 11/17/2022]
Abstract
During the past twenty years, a wide range of studies have established the existence of epigenetic alterations, particularly DNA methylation changes, in lupus. Epigenetic changes might have different contributions in children-onset versus adult-onset lupus. DNA methylation alterations have been identified and characterized in relation to disease activity and damage, different lupus subtypes and responses to drugs. However, to date there has been no practical application of these findings in the clinical milieu. In this article, we provide a review of key studies showing the relationship between DNA methylation and the many clinical aspects related to lupus. We also propose several options, in relation to the range of methodological developments and experimental design, that could optimize these findings and make them amenable for use in clinical practice.
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Affiliation(s)
| | | | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916 Badalona, Barcelona, Spain; Epigenetics in Inflammatory and Metabolic Diseases Laboratory, Health Science Center (HSC), East China Normal University (ECNU), Shanghai, 200241, China.
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18
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Fava A, Rao DA. Cellular and molecular heterogeneity in systemic lupus erythematosus. Semin Immunol 2021; 58:101653. [PMID: 36184357 DOI: 10.1016/j.smim.2022.101653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/15/2021] [Accepted: 11/15/2021] [Indexed: 12/14/2022]
Affiliation(s)
- Andrea Fava
- Division of Rheumatology, Johns Hopkins University, Baltimore, MD, USA.
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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19
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Marion MC, Ramos PS, Bachali P, Labonte AC, Zimmerman KD, Ainsworth HC, Heuer SE, Robl RD, Catalina MD, Kelly JA, Howard TD, Lipsky PE, Grammer AC, Langefeld CD. Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting. Genes (Basel) 2021; 12:genes12121898. [PMID: 34946847 PMCID: PMC8701117 DOI: 10.3390/genes12121898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.
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Affiliation(s)
- Miranda C. Marion
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Paula S. Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Prathyusha Bachali
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Adam C. Labonte
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Hannah C. Ainsworth
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Sarah E. Heuer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
- The Jackson Laboratory, Tufts Graduate School of Biomedical Sciences, Bar Harbor, ME 04609, USA
| | - Robert D. Robl
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Michelle D. Catalina
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Amrie C. Grammer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
- Correspondence:
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20
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Balci MA, Atli E, GüRKAN H. Investigation of Genes Associated With Atherosclerosis in Patients With Systemic Lupus Erythematosus. Arch Rheumatol 2021; 36:287-295. [PMID: 34527935 PMCID: PMC8418757 DOI: 10.46497/archrheumatol.2021.8024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/04/2020] [Indexed: 12/18/2022] Open
Abstract
Objectives
In this study, we aimed to identify patients with systemic lupus erythematosus (SLE) who are genetically at risk for developing atherosclerosis. Patients and methods
Between November 2014 and May 2016, a total of 38 patients with SLE (36 females, 2 males; mean age: 37.6 years; range, 18 to 71 years) and 32 healthy females (mean age: 31.5 years; range, 19 to 54 years) were included in the study. Carotid intima-media thickness (CIMT) was measured using high-resolution B-mode ultrasonography. SurePrint G3 Human Gene Expression 8x60K Microarray kit was used in our study. Genes showing differences in expression between the groups were identified by using GeneSpring GX 10.0 program. Pathway analyses of gene expressions were performed using Ingenuity Pathways Analysis (IPA). Gene ontology analyses were performed using the Protein Analysis Through Evolutionary Relationships (PANTHER). Results
Clinical findings of SLE patients were mainly photosensitivity (71.1%), arthritis (63.2%), lupus nephritis (55.3%), thrombocytopenia (26.3%), and autoimmune hemolytic anemia (21.1%). A total of 155 genes showing expression level difference were detected between SLE patients and healthy controls. In molecular network analysis, 28.2% of all genes were found to be directly or indirectly associated with atherosclerosis and cardiovascular disease. Conclusion In SLE patients, many genes are expressed differently from healthy individuals. Expression of these genes is important in the pathogenesis of SLE. Genes identified differently in gene expression analysis can help us to identify SLE patients at risk for atherosclerosis in the Turkish population.
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Affiliation(s)
- Mehmet Ali Balci
- Rheumatology Clinic, Gazi Yaşargil Training and Research Hospital, Diyarbakır, Turkey
| | - Engin Atli
- Department of Medical Genetics, Trakya University, Faculty of Medicine, Edirne, Turkey
| | - Hakan GüRKAN
- Department of Medical Genetics, Trakya University, Faculty of Medicine, Edirne, Turkey
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21
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Xie S, Zeng Q, Ouyang S, Liang Y, Xiao C. Bioinformatics analysis of epigenetic and SNP-related molecular markers in systemic lupus erythematosus. Am J Transl Res 2021; 13:6312-6329. [PMID: 34306371 PMCID: PMC8290799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/23/2021] [Indexed: 06/13/2023]
Abstract
We analyzed gene expression in peripheral blood mononuclear cells (PBMCs) from patients with systemic lupus erythematosus (SLE) using public databases. The goal was to identify lupus biomarkers by determining whether differentially expressed genes are mediated by methylation, miRNA, or SNP. Two cDNA microarrays were subjected to integration analysis, and we calculated the mutually differentially expressed genes (|log2fold change (FC)| > 1, P < 0.05). These genes were analyzed using gene otology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein-protein interaction (PPI) networks. The differences in methylation sites for two methylation chips were calculated and the differentially methylated sites were annotated. These genes were compared to the differentially expressed genes. We obtained 135 differentially expressed microRNAs from the microRNA-chip results using PBMCs from SLE and healthy individuals. Predictive microRNA target genes were identified using GO, KEGG pathways, and PPI networks. The target genes identified were compared to the differentially expressed genes. We downloaded Chinese SLE genome-wide association study data from SLE-related literature, analyzed the loci with a P value < 0.05, and used annotated SLE-associated SNPs. We selected the genes corresponding to an SNP located on an exon and determined the intersection with the differentially expressed genes. We found 18 differentially expressed genes in both cDNA microarrays. The methylation chips had 50 corresponding methylation sites. On the basis of these results, we identified two genes, IFI44 and IFI44L. We further identified 135 differentially expressed microRNAs predicted to affect 5766 target genes. Two identified genes were in common with the differentially expressed genes. Finally, SNP annotated genes and cDNA chip genes overlap with identified MX1. Therefore, we used existing data to analyze the causes of differential gene expression in SLE, introducing new methods for determining biomarkers and therapeutic targets.
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Affiliation(s)
- Shuoshan Xie
- Nephrology Department and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal UniversityChangsha, PR China
- Changsha Clinical Research Center for Kidney DiseaseChangsha, PR China
- Hunan Clinical Research Center for Chronic Kidney DiseaseChangsha, PR China
| | - Qinghua Zeng
- Nephrology Department and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal UniversityChangsha, PR China
- Changsha Clinical Research Center for Kidney DiseaseChangsha, PR China
- Hunan Clinical Research Center for Chronic Kidney DiseaseChangsha, PR China
| | - Shaxi Ouyang
- Nephrology Department and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal UniversityChangsha, PR China
- Changsha Clinical Research Center for Kidney DiseaseChangsha, PR China
- Hunan Clinical Research Center for Chronic Kidney DiseaseChangsha, PR China
| | - Yumei Liang
- Nephrology Department and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal UniversityChangsha, PR China
- Changsha Clinical Research Center for Kidney DiseaseChangsha, PR China
- Hunan Clinical Research Center for Chronic Kidney DiseaseChangsha, PR China
| | - Changjuan Xiao
- Nephrology Department and Laboratory of Kidney Disease, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal UniversityChangsha, PR China
- Changsha Clinical Research Center for Kidney DiseaseChangsha, PR China
- Hunan Clinical Research Center for Chronic Kidney DiseaseChangsha, PR China
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22
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Chen XJ, Zhang H, Yang F, Liu Y, Chen G. DNA Methylation Sustains "Inflamed" Memory of Peripheral Immune Cells Aggravating Kidney Inflammatory Response in Chronic Kidney Disease. Front Physiol 2021; 12:637480. [PMID: 33737884 PMCID: PMC7962671 DOI: 10.3389/fphys.2021.637480] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/04/2021] [Indexed: 01/19/2023] Open
Abstract
The incidence of chronic kidney disease (CKD) has rapidly increased in the past decades. A progressive loss of kidney function characterizes a part of CKD even with intensive supportive treatment. Irrespective of its etiology, CKD progression is generally accompanied with the development of chronic kidney inflammation that is pathologically featured by the low-grade but chronic activation of recruited immune cells. Cumulative evidence support that aberrant DNA methylation pattern of diverse peripheral immune cells, including T cells and monocytes, is closely associated with CKD development in many chronic disease settings. The change of DNA methylation profile can sustain for a long time and affect the future genes expression in the circulating immune cells even after they migrate from the circulation into the involved kidney. It is of clinical interest to reveal the underlying mechanism of how altered DNA methylation regulates the intensity and the time length of the inflammatory response in the recruited effector cells. We and others recently demonstrated that altered DNA methylation occurs in peripheral immune cells and profoundly contributes to CKD development in systemic chronic diseases, such as diabetes and hypertension. This review will summarize the current findings about the influence of aberrant DNA methylation on circulating immune cells and how it potentially determines the outcome of CKD.
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Affiliation(s)
- Xiao-Jun Chen
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Hong Zhang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Fei Yang
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Yu Liu
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
| | - Guochun Chen
- Department of Nephrology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, China
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Abstract
PURPOSE OF REVIEW The management of lupus nephritis remains unsatisfactory due to insufficiently effective treatment regimens and the dearth of reliable predictors of disease onset or progression to guide individualized therapeutic decisions. This review summarizes new findings related to lupus nephritis over the last 18 months and discusses clinical needs that should be considered to advance trials of mechanism-based therapeutic strategies. RECENT FINDINGS Collaborative teams are addressing how to improve disease definitions and are developing predictive models for disease onset, disease response and risk of flare in individual patients. More attention is being paid to clinical trial design. Advanced technologic approaches are allowing the analysis of small amounts of human tissue and urine in unprecedented detail so as to discover new pathogenic mechanisms and identify disease biomarkers. Novel therapies continue to be tested in disease models and include new strategies to protect renal tissue from cell damage and fibrosis. SUMMARY The collaborative efforts of patients, clinical and translational researchers, the pharmaceutical industry and funding sources are needed to advance therapies for lupus nephritis. Specialized clinical centers can then deliver optimal and more personalized patient care that will improve patient outcomes.
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24
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Key J, Maletzko A, Kohli A, Gispert S, Torres-Odio S, Wittig I, Heidler J, Bárcena C, López-Otín C, Lei Y, West AP, Münch C, Auburger G. Loss of mitochondrial ClpP, Lonp1, and Tfam triggers transcriptional induction of Rnf213, a susceptibility factor for moyamoya disease. Neurogenetics 2020; 21:187-203. [PMID: 32342250 PMCID: PMC7283203 DOI: 10.1007/s10048-020-00609-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/28/2020] [Indexed: 02/08/2023]
Abstract
Human RNF213, which encodes the protein mysterin, is a known susceptibility gene for moyamoya disease (MMD), a cerebrovascular condition with occlusive lesions and compensatory angiogenesis. Mysterin mutations, together with exposure to environmental trigger factors, lead to an elevated stroke risk since childhood. Mysterin is induced during cell stress, to function as cytosolic AAA+ ATPase and ubiquitylation enzyme. Little knowledge exists, in which context mysterin is needed. Here, we found that genetic ablation of several mitochondrial matrix factors, such as the peptidase ClpP, the transcription factor Tfam, as well as the peptidase and AAA+ ATPase Lonp1, potently induces Rnf213 transcript expression in various organs, in parallel with other components of the innate immune system. Mostly in mouse fibroblasts and human endothelial cells, the Rnf213 levels showed prominent upregulation upon Poly(I:C)-triggered TLR3-mediated responses to dsRNA toxicity, as well as upon interferon gamma treatment. Only partial suppression of Rnf213 induction was achieved by C16 as an antagonist of PKR (dsRNA-dependent protein kinase). Since dysfunctional mitochondria were recently reported to release immune-stimulatory dsRNA into the cytosol, our results suggest that mysterin becomes relevant when mitochondrial dysfunction or infections have triggered RNA-dependent inflammation. Thus, MMD has similarities with vasculopathies that involve altered nucleotide processing, such as Aicardi-Goutières syndrome or systemic lupus erythematosus. Furthermore, in MMD, the low penetrance of RNF213 mutations might be modified by dysfunctions in mitochondria or the TLR3 pathway.
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Affiliation(s)
- Jana Key
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Faculty of Biosciences, Goethe-University, Frankfurt am Main, Germany
| | - Antonia Maletzko
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Aneesha Kohli
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Institute of Biochemistry II, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Suzana Gispert
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Sylvia Torres-Odio
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.,Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX, USA
| | - Ilka Wittig
- Functional Proteomics Group, Goethe-University Hospital, 60590, Frankfurt am Main, Germany
| | - Juliana Heidler
- Functional Proteomics Group, Goethe-University Hospital, 60590, Frankfurt am Main, Germany
| | - Clea Bárcena
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Yuanjiu Lei
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX, USA
| | - A Phillip West
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX, USA
| | - Christian Münch
- Institute of Biochemistry II, Goethe University Medical School, 60590, Frankfurt am Main, Germany
| | - Georg Auburger
- Experimental Neurology, Goethe University Medical School, 60590, Frankfurt am Main, Germany.
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25
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Song W, Tang D, Chen D, Zheng F, Huang S, Xu Y, Yu H, He J, Hong X, Yin L, Liu D, Dai W, Dai Y. Advances in applying of multi-omics approaches in the research of systemic lupus erythematosus. Int Rev Immunol 2020; 39:163-173. [PMID: 32138562 DOI: 10.1080/08830185.2020.1736058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Wencong Song
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Donge Tang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Deheng Chen
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Shaoying Huang
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Yong Xu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Haiyan Yu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Jingquan He
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, USA
| | - Yong Dai
- Department of Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital Southern University of Science and Technology, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
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26
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Abstract
Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and organisms. The coordination of individual immune cells is essential for the generation of effective immune responses to pathogens while immune tolerance is maintained to protect the host. In rheumatic diseases, when immune responses are dysregulated, pathologically important cells might represent only a small fraction of the immune system. Interrogation of the contributions of individual immune cells to pathogenesis and disease progression should therefore reveal important insights into the complicated aetiology of rheumatic diseases. Technological advances are enabling the high-dimensional dissection of single cells at multiple omics levels, which could facilitate the identification of dysregulated molecular mechanisms in patients with rheumatic diseases and the discovery of new therapeutic targets and biomarkers. The single-cell technologies that have been developed over the past decade and the experimental platforms that enable multi-omics integrative analyses have already made inroads into immunology-related fields of study and have potential for use in rheumatology. Layers of omics data derived from single cells are likely to fundamentally change our understanding of the molecular pathways that underpin the pathogenesis of rheumatic diseases.
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27
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Breitbach ME, Ramaker RC, Roberts K, Kimberly RP, Absher D. Population-Specific Patterns of Epigenetic Defects in the B Cell Lineage in Patients With Systemic Lupus Erythematosus. Arthritis Rheumatol 2019; 72:282-291. [PMID: 31430064 DOI: 10.1002/art.41083] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine the stage of B cell development at which a systemic lupus erythematosus (SLE)-associated DNA methylation signature originates in African American (AA) and European American (EA) subjects, and to assess whether epigenetic defects in B cell development patterns could be predictive of SLE status in individual and mixed immune cell populations. METHODS B cells from AA patients (n = 31) and EA patients (n = 49) with or without SLE were sorted using fluorescence-activated cell sorting into 5 B cell subsets. DNA methylation, measured at ~460,000 CpG sites, was interrogated in each subset. Enrichment analysis of transcription factor interaction at SLE-associated methylation sites was performed. A random forests algorithm was used to identify an epigenetic signature of SLE in the B cell subsets, which was then validated in an independent cohort of AA and EA patients and healthy controls. RESULTS Regression analysis across all B cell stages resulted in identification of 60 CpGs that reached genome-wide significance for SLE-associated methylation differences (P ≤ 1.07 × 10-7 ). Interrogation of ethnicity-specific CpGs associated with SLE revealed a hypomethylated pattern that was enriched for interferon (IFN)-regulated genes and binding of EBF1 in AA patients (each P < 0.001). AA patients with SLE could be distinguished from healthy controls when the predictive model developed with the transitional B cell subset was applied to other B cell subsets (mean receiver operating characteristic [ROC] area under the curve [AUC] 0.98), and when applied to CD19+ pan-B cells (mean ROC AUC 0.95) and CD4+ pan-T cells (mean ROC AUC 0.97) from the independent validation cohort. CONCLUSION These results indicate that SLE-specific methylation patterns are ethnicity dependent. A pattern of epigenetic changes near IFN-regulated genes early in B cell development is a hallmark of SLE in AA female subjects. EBF1 binding sites are highly enriched for significant methylation changes, implying that this may be a potential regulator of SLE-associated epigenetic changes.
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Affiliation(s)
- Megan E Breitbach
- University of Alabama at Huntsville and HudsonAlpha Institute for Biotechnology
| | - Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, and University of Alabama at Birmingham
| | - Kevin Roberts
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
| | | | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
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28
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Cao H, Li D, Lu H, Sun J, Li H. Uncovering potential lncRNAs and nearby mRNAs in systemic lupus erythematosus from the Gene Expression Omnibus dataset. Epigenomics 2019; 11:1795-1809. [PMID: 31755746 DOI: 10.2217/epi-2019-0145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: The aim of this study was to find potential differentially expressed long noncoding RNAs (lncRNAs) and mRNAs in systemic lupus erythematosus. Materials & methods: Differentially expressed lncRNAs and mRNAs were obtained in the Gene Expression Omnibus dataset. Functional annotation of differentially expressed mRNAs was performed, followed by protein-protein interaction network analysis. Then, the interaction network of lncRNA-nearby targeted mRNA was built. Results: Several interaction pairs of lncRNA-nearby targeted mRNA including NRIR-RSAD2, RP11-153M7.5-TLR2, RP4-758J18.2-CCNL2, RP11-69E11.4-PABPC4 and RP11-496I9.1-IRF7/HRAS/PHRF1 were identified. Measles and MAPK were significantly enriched signaling pathways of differentially expressed mRNAs. Conclusion: Our study identified several differentially expressed lncRNAs and mRNAs. And their interactions may play a crucial role in the process of systemic lupus erythematosus.
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Affiliation(s)
- Haiyu Cao
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Dong Li
- Department of Dermatology & Sexology, Tongji Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, Hubei 430030, PR China
| | - Huixiu Lu
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Jing Sun
- Department of Dermatology, The First Hospital of Shijiazhuang, Shijiazhuang, Hebei 050000, PR China
| | - Haibin Li
- Department of Medicine, The Third Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, PR China
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29
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Tsai MH, Lin CH, Tsai KW, Lin MH, Ho CJ, Lu YT, Weng KP, Lin Y, Lin PH, Li SC. S100A6 Promotes B Lymphocyte Penetration Through the Blood-Brain Barrier in Autoimmune Encephalitis. Front Genet 2019; 10:1188. [PMID: 31850060 PMCID: PMC6901080 DOI: 10.3389/fgene.2019.01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/28/2019] [Indexed: 12/12/2022] Open
Abstract
Autoimmune encephalitis (AE) is a severe neurological disease. The brain of the AE patient is attacked by a dysregulated immune system, which is caused by the excessive production of autoantibodies against neuronal receptors and synaptic proteins. AE is also characterized by the uncontrolled B lymphocyte infiltration through the blood–brain barrier (BBB) layer, and the investigation of the underlying mechanism involved in this infiltration may facilitate the discovery of novel therapies for AE. However, few AE-related studies have focused on this issue. In this study, we aimed to identify the factors involved in B lymphocyte infiltration in AE. For this purpose, we first enrolled four healthy control and five AE subjects, collecting their serum and/or total white blood cell samples. The white blood cell samples were further used for collecting RNA and DNA. Then, we simulated the in vivo B lymphocyte infiltration with an in vitro leukocyte transendothelial migration model. It turned out that AE serum treatment significantly and specifically promoted B cells to penetrate the BBB endothelial layer without affecting neutrophils. Next, through genome-wide DNA methylation assays on bisulfite-conversion DNA samples, we identified S100A6 and S100A11 as potential hypo-methylated disease genes in the AE samples. Further qPCR assays demonstrated their upregulation in AE samples, reflecting the negative correlations between gene expression and DNA methylation. Finally, recombinant S100A6 protein treatment significantly increased B lymphocyte infiltration through the BBB endothelial layer, which partially recapitulated the effect of AE serum. In summary, by using an in vitro leukocyte transendothelial migration model, we confirmed that S100A6 promoted B lymphocyte to penetrate the BBB endothelial layer, which is similar to the in vivo clinical manifestations of AE. Therefore, further studies on how the S100A6 protein facilitates B lymphocyte infiltration and on whether other factors in serum also contribute to this phenomenon are likely to improve our understanding of AE and hopefully to reveal novel therapeutic targets for this emerging treatable neurological disorder.
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Affiliation(s)
- Meng-Han Tsai
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chih-Hsiang Lin
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Wang Tsai
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Ming-Hong Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chen-Jui Ho
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yan-Ting Lu
- Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Ken-Pen Weng
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan.,Department of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Nursing, Shu-Zen Junior College of Medicine and Management, Kaohsiung, Taiwan
| | - Yuyu Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pei-Hsien Lin
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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30
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Sawalha AH. BCL-6 and EZH2 cooperate to epigenetically repress anti-inflammatory miR-142-3p/5p in lupus CD4+T cells. Cell Mol Immunol 2019; 18:504-505. [PMID: 31511638 DOI: 10.1038/s41423-019-0288-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 11/09/2022] Open
Affiliation(s)
- 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.
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31
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Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA. A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus. Nat Commun 2019; 10:3902. [PMID: 31467281 PMCID: PMC6715644 DOI: 10.1038/s41467-019-11845-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/13/2019] [Indexed: 01/05/2023] Open
Abstract
Systemic lupus erythematous (SLE) is a heterogeneous autoimmune disease in which outcomes vary among different racial groups. Here, we aim to identify SLE subgroups within a multiethnic cohort using an unsupervised clustering approach based on the American College of Rheumatology (ACR) classification criteria. We identify three patient clusters that vary according to disease severity. Methylation association analysis identifies a set of 256 differentially methylated CpGs across clusters, including 101 CpGs in genes in the Type I Interferon pathway, and we validate these associations in an external cohort. A cis-methylation quantitative trait loci analysis identifies 744 significant CpG-SNP pairs. The methylation signature is enriched for ethnic-associated CpGs suggesting that genetic and non-genetic factors may drive outcomes and ethnic-associated methylation differences. Our computational approach highlights molecular differences associated with clusters rather than single outcome measures. This work demonstrates the utility of applying integrative methods to address clinical heterogeneity in multifactorial multi-ethnic disease settings.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ishan Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joanne Nititham
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Milena Gianfrancesco
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manish Paranjpe
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Shan Andrews
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Sharon A Chung
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Laura Trupin
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Patricia Katz
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Maria Dall'Era
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jinoos Yazdany
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
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Donlin LT, Park SH, Giannopoulou E, Ivovic A, Park-Min KH, Siegel RM, Ivashkiv LB. Insights into rheumatic diseases from next-generation sequencing. Nat Rev Rheumatol 2019; 15:327-339. [PMID: 31000790 PMCID: PMC6673602 DOI: 10.1038/s41584-019-0217-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Rheumatic diseases have complex aetiologies that are not fully understood, which makes the study of pathogenic mechanisms in these diseases a challenge for researchers. Next-generation sequencing (NGS) and related omics technologies, such as transcriptomics, epigenomics and genomics, provide an unprecedented genome-wide view of gene expression, environmentally responsive epigenetic changes and genetic variation. The integrated application of NGS technologies to samples from carefully phenotyped clinical cohorts of patients has the potential to solve remaining mysteries in the pathogenesis of several rheumatic diseases, to identify new therapeutic targets and to underpin a precision medicine approach to the diagnosis and treatment of rheumatic diseases. This Review provides an overview of the NGS technologies available, showcases important advances in rheumatic disease research already powered by these technologies and highlights NGS approaches that hold particular promise for generating new insights and advancing the field.
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Affiliation(s)
- Laura T Donlin
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sung-Ho Park
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Eugenia Giannopoulou
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Biological Sciences Department, New York City College of Technology, City University of New York, New York, NY, USA
| | - Aleksandra Ivovic
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kyung-Hyun Park-Min
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Richard M Siegel
- Immunoregulation Section, Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lionel B Ivashkiv
- Arthritis and Tissue Degeneration Program, Hospital for Special Surgery, New York, NY, USA.
- David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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Yeung KS, Lee TL, Mok MY, Mak CCY, Yang W, Chong PCY, Lee PPW, Ho MHK, Choufani S, Lau CS, Lau YL, Weksberg R, Chung BHY. Cell lineage-specific genome-wide DNA methylation analysis of patients with paediatric-onset systemic lupus erythematosus. Epigenetics 2019; 14:341-351. [PMID: 30806140 DOI: 10.1080/15592294.2019.1585176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Patients with paediatric-onset systemic lupus erythematosus (SLE) often present with more severe clinical courses than adult-onset patients. Although genome-wide DNA methylation (DNAm) profiling has been performed in adult-onset SLE patients, parallel data on paediatric-onset SLE are not available. Therefore, we undertook a genome-wide DNAm study in paediatric-onset SLE patients across multiple blood cell lineages. The DNAm profiles of four purified immune cell lineages (CD4 + T cells, CD8 + T cells, B cells and neutrophils) and whole blood were compared in 16 Chinese patients with paediatric-onset SLE and 13 healthy controls using the Illumina HumanMethylationEPIC BeadChip. Comparison of DNAm in whole blood and within each independent cell lineage identified a consistent pattern of loss of DNAm at 21 CpG sites overlapping 15 genes, which represented a robust, disease-specific DNAm signature for paediatric-onset SLE in our cohort. In addition, cell lineage-specific changes, involving both loss and gain of DNAm, were observed in both novel genes and genes with well-described roles in SLE pathogenesis. This study also highlights the importance of studying DNAm changes in different immune cell lineages rather than only whole blood, since cell type-specific DNAm changes facilitated the elucidation of the cell type-specific molecular pathophysiology of SLE.
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Affiliation(s)
- Kit San Yeung
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Tsz Leung Lee
- b The Hong Kong Children's Hospital , Hong Kong , China
| | - Mo Yin Mok
- c Department of Biomedical Sciences , The City University of Hong Kong , Hong Kong , China
| | - Christopher Chun Yu Mak
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Wanling Yang
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Patrick Chun Yin Chong
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Pamela Pui Wah Lee
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Marco Hok Kung Ho
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Sanaa Choufani
- d Genetics and Genome Biology Program , The Hospital for Sick Children , Toronto , Ontario , Canada
| | - Chak Sing Lau
- e Department of Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Yu Lung Lau
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
| | - Rosanna Weksberg
- d Genetics and Genome Biology Program , The Hospital for Sick Children , Toronto , Ontario , Canada.,f Division of Clinical and Metabolic Genetics , The Hospital for Sick Children , Toronto , Ontario , Canada.,g Institute of Medical Science and Department of Pediatrics , University of Toronto , Toronto , Ontario , Canada
| | - Brian Hon Yin Chung
- a Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine , The University of Hong Kong , Hong Kong , China
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Gerussi A, Cristoferi L, Carbone M, Asselta R, Invernizzi P. The immunobiology of female predominance in primary biliary cholangitis. J Autoimmun 2018; 95:124-132. [DOI: 10.1016/j.jaut.2018.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Accepted: 10/17/2018] [Indexed: 12/21/2022]
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Nash AJ, Mandaviya PR, Dib MJ, Uitterlinden AG, van Meurs J, Heil SG, Andrew T, Ahmadi KR. Interaction between plasma homocysteine and the MTHFR c.677C > T polymorphism is associated with site-specific changes in DNA methylation in humans. FASEB J 2018; 33:833-843. [PMID: 30080444 DOI: 10.1096/fj.201800400r] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
One-carbon metabolism provides a direct link among dietary folate/vitamin B12 exposure, the activity of the enzyme methylenetetrahydrofolate reductase (MTHFR), and epigenetic regulation of the genome via DNA methylation. Previously, it has been shown that the common c.677C > T polymorphism in MTHFR influences global DNA methylation status through a direct interaction with folate status and (indirectly) with total homocysteine (tHcy) levels. To build on that and other more recent observations that have further highlighted associations among MTHFR c.677C > T, tHcy, and aberrations in DNA methylation, we investigated whether the interaction between mildly elevated plasma tHcy and the c.677C > T polymorphism is associated with site-specific changes in DNA methylation in humans. We used data on plasma tHcy levels, c.677C > T polymorphism, and site-specific DNA methylation levels for a total of 915 white women and 335 men from the TwinsUK registry ( n = 610) and the Rotterdam study ( n = 670). We performed methylome-wide association analyses in each cohort to model the interaction between levels of tHcy and c.677C > T genotypes on DNA methylation β values. Our meta-analysis identified 13 probes significantly associated with rs1801133 × tHcy levels [false-discovery rate (FDR) < 0.05]. The most significant associations were with a cluster of probes at the AGTRAP-MTHFR-NPPA/B gene locus on chromosome 1 (FDR = 1.3E-04), with additional probes on chromosomes 2, 3, 4, 7, 12, 16, and 19. Our top 2 hits on chromosome 1 were functionally associated with variability in expression of the TNF receptor superfamily member 8 ( TNFRSF8) gene/locus on that chromosome. This is the first study, to our knowledge, to provide a direct link between perturbations in 1-carbon metabolism, through an interaction of tHcy and the activity of MTHFR enzyme on epigenetic regulation of the genome via DNA methylation.-Nash, A. J., Mandaviya, P. R., Dib, M.-J., Uitterlinden, A. G., van Meurs, J., Heil, S. G., Andrew, T., Ahmadi, K. R. Interaction between plasma homocysteine and the MTHFR c.677C>T polymorphism is associated with site-specific changes in DNA methylation in humans.
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Affiliation(s)
- Alexander J Nash
- Institute of Clinical Sciences and Medical Research Council (MRC) London Institute of Medical Sciences, Imperial College, London, United Kingdom
| | - Pooja R Mandaviya
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marie-Joe Dib
- Department of Genomics of Common Disease, Imperial College, London, United Kingdom; and
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sandra G Heil
- Department of Clinical Chemistry, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Toby Andrew
- Department of Genomics of Common Disease, Imperial College, London, United Kingdom; and
| | - Kourosh R Ahmadi
- Department of Nutritional Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
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Lanata CM, Chung SA, Criswell LA. DNA methylation 101: what is important to know about DNA methylation and its role in SLE risk and disease heterogeneity. Lupus Sci Med 2018; 5:e000285. [PMID: 30094041 PMCID: PMC6069928 DOI: 10.1136/lupus-2018-000285] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/25/2018] [Indexed: 12/20/2022]
Abstract
SLE is a complex autoimmune disease that results from the interplay of genetics, epigenetics and environmental exposures. DNA methylation is an epigenetic mechanism that regulates gene expression and tissue differentiation. Among all the epigenetic modifications, DNA methylation perturbations have been the most widely studied in SLE. It mediates processes relevant to SLE, including lymphocyte development, X-chromosome inactivation and the suppression of endogenous retroviruses. The establishment of most DNA methylation marks occurs in utero; however, a small percentage of epigenetic marks are dynamic and can change throughout a person’s lifetime and in relation to exposures. In this review, we discuss the current understanding of the biology of DNA methylation and its regulators, the measurement and interpretation of methylation marks, the effects of genetics on DNA methylation and the role of environmental exposures with relevance to SLE. We also summarise research findings associated with SLE disease risk and heterogeneity. The robust finding of hypomethylation of interferon-responsive genes in patients with SLE and new associations beyond interferon-responsive genes such as cell-specific methylation abnormalities are described. We also discuss methylation changes associated with lupus nephritis, autoantibody status and disease activity. Lastly, we explore future research directions, emphasising the need for longitudinal studies, cell tissue and context-specific profiling, as well as integrative approaches. With new technologies, DNA methylation perturbations could be targeted and edited, offering novel therapeutic approaches.
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Affiliation(s)
- Cristina M Lanata
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sharon A Chung
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Lindsey A Criswell
- Russell/Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, California, USA
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37
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Carnero-Montoro E, Alarcón-Riquelme ME. Epigenome-wide association studies for systemic autoimmune diseases: The road behind and the road ahead. Clin Immunol 2018; 196:21-33. [PMID: 29605707 DOI: 10.1016/j.clim.2018.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]
Abstract
Epigenetics is known to be an important mechanism in the pathogenesis of autoimmune diseases. Epigenetic variations can act as integrators of environmental and genetic exposures and propagate activated states in immune cells. Studying epigenetic alterations by means of genome-wide approaches promises to unravel novel molecular mechanisms related to disease etiology, disease progression, clinical manifestations and treatment responses. This paper reviews what we have learned in the last five years from epigenome-wide studies for three systemic autoimmune diseases, namely systemic lupus erythematosus, primary Sjögren's syndrome, and rheumatoid arthritis. We examine the degree of epigenetic sharing between different diseases and the possible mediating role of epigenetic associations in genetic and environmental risks. Finally, we also shed light into the use of epigenetic markers towards a better precision medicine regarding disease prediction, prevention and personalized treatment in systemic autoimmunity.
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Affiliation(s)
- Elena Carnero-Montoro
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain.
| | - Marta E Alarcón-Riquelme
- Pfizer - University of Granada - Andalusian Government Center for Genomics and Oncological Research (GENYO), Granada, Spain; Unit of Inflammatory Chronic Diseases, Institute of Environmental Medicine, Karolinska Institutet, Solna, Sweden.
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38
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Epigenetic Variability in Systemic Lupus Erythematosus: What We Learned from Genome-Wide DNA Methylation Studies. Curr Rheumatol Rep 2018; 19:32. [PMID: 28470479 DOI: 10.1007/s11926-017-0657-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PURPOSE OF REVIEW DNA methylation has emerged as an important contributing factor in the pathogenesis of systemic lupus erythematosus (SLE). Here, we describe the DNA methylation patterns identified in SLE and how these epigenetic changes can influence disease susceptibility, clinical heterogeneity, and disease flares. RECENT FINDINGS Several genome-wide DNA methylation studies have been recently completed in SLE. Important observations include robust demethylation of interferon-regulated genes, which is consistent across all cell types studied to date, and is independent of disease activity. This interferon epigenetic signature was shown to precede interferon transcription signature in SLE, suggesting it might be an early event in the disease process. Recent studies also revealed DNA methylation changes specific for renal and skin involvement in SLE, providing a proof of principle for a value of DNA methylation studies in exploring mechanisms of specific disease manifestations, and potentially as prognostic biomarkers. Inherited ethnicity-specific DNA methylation patterns have also been shown to possibly contribute to differences in SLE susceptibility between populations. Finally, a recent study revealed that DNA methylation levels at IFI44L can accurately distinguish SLE patients from healthy controls, and from patients with other autoimmune diseases, promising to be the first epigenetic diagnostic marker for SLE. Genome-wide DNA methylation studies in SLE have provided novel insights into disease pathogenesis, clinical heterogeneity, and disease flares. Further studies promise to reveal novel diagnostic, prognostic, and therapeutic targets for SLE.
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Abstract
The type I interferon pathway has been implicated in the pathogenesis of a number of rheumatic diseases, including systemic lupus erythematosus, Sjögren syndrome, myositis, systemic sclerosis, and rheumatoid arthritis. In normal immune responses, type I interferons have a critical role in the defence against viruses, yet in many rheumatic diseases, large subgroups of patients demonstrate persistent activation of the type I interferon pathway. Genetic variations in type I interferon-related genes are risk factors for some rheumatic diseases, and can explain some of the heterogeneity in type I interferon responses seen between patients within a given disease. Inappropriate activation of the immune response via Toll-like receptors and other nucleic acid sensors also contributes to the dysregulation of the type I interferon pathway in a number of rheumatic diseases. Theoretically, differences in type I interferon activity between patients might predict response to immune-based therapies, as has been demonstrated for rheumatoid arthritis. A number of type I interferon and type I interferon pathway blocking therapies are currently in clinical trials, the results of which are promising thus far. This Review provides an overview of the many ways in which the type I interferon system affects rheumatic diseases.
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Affiliation(s)
- Theresa L. Wampler Muskardin
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Timothy B. Niewold
- Colton Center for Autoimmunity, Department of Medicine, New York University School of Medicine, New York, NY, USA
- Division of Rheumatology, Department of Medicine and Pediatrics, New York University School of Medicine, New York, NY, USA
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40
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Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, Alexsson A, Nordmark G, Eloranta ML, Rantapää-Dahlqvist S, Bengtsson AA, Jönsen A, Padyukov L, Gunnarsson I, Svenungsson E, Sjöwall C, Rönnblom L, Syvänen AC, Sandling JK. DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus. Ann Rheum Dis 2018; 77:736-743. [PMID: 29437559 PMCID: PMC5909746 DOI: 10.1136/annrheumdis-2017-212379] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/11/2018] [Accepted: 01/15/2018] [Indexed: 11/18/2022]
Abstract
Objectives Systemic lupus erythematosus (SLE) is a chronic autoimmune condition with heterogeneous presentation and complex aetiology where DNA methylation changes are emerging as a contributing factor. In order to discover novel epigenetic associations and investigate their relationship to genetic risk for SLE, we analysed DNA methylation profiles in a large collection of patients with SLE and healthy individuals. Methods DNA extracted from blood from 548 patients with SLE and 587 healthy controls were analysed on the Illumina HumanMethylation 450 k BeadChip, which targets 485 000 CpG sites across the genome. Single nucleotide polymorphism (SNP) genotype data for 196 524 SNPs on the Illumina ImmunoChip from the same individuals were utilised for methylation quantitative trait loci (cis-meQTLs) analyses. Results We identified and replicated differentially methylated CpGs (DMCs) in SLE at 7245 CpG sites in the genome. The largest methylation differences were observed at type I interferon-regulated genes which exhibited decreased methylation in SLE. We mapped cis-meQTLs and identified genetic regulation of methylation levels at 466 of the DMCs in SLE. The meQTLs for DMCs in SLE were enriched for genetic association to SLE, and included seven SLE genome-wide association study (GWAS) loci: PTPRC (CD45), MHC-class III, UHRF1BP1, IRF5, IRF7, IKZF3 and UBE2L3. In addition, we observed association between genotype and variance of methylation at 20 DMCs in SLE, including at the HLA-DQB2 locus. Conclusions Our results suggest that several of the genetic risk variants for SLE may exert their influence on the phenotype through alteration of DNA methylation levels at regulatory regions of target genes.
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Affiliation(s)
- Juliana Imgenberg-Kreuz
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Dag Leonard
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Andrei Alexsson
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Gunnel Nordmark
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Maija-Leena Eloranta
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | | | - Anders A Bengtsson
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Andreas Jönsen
- Department of Clinical Sciences, Section of Rheumatology, Lund University, Skane University Hospital, Lund, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elisabet Svenungsson
- Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christopher Sjöwall
- Department of Clinical and Experimental Medicine, Rheumatology/Division of Neuro and Inflammation Sciences, Linköping University, Linköping, Sweden
| | - Lars Rönnblom
- Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johanna K Sandling
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Section of Rheumatology, Department of Medical Sciences, Uppsala University, Upssala, Sweden
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Foma AM, Aslani S, Karami J, Jamshidi A, Mahmoudi M. Epigenetic involvement in etiopathogenesis and implications in treatment of systemic lupus erythematous. Inflamm Res 2017; 66:1057-1073. [DOI: 10.1007/s00011-017-1082-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/22/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022] Open
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