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Li J, Li L, Wang Y, Huang G, Li X, Xie Z, Zhou Z. Insights Into the Role of DNA Methylation in Immune Cell Development and Autoimmune Disease. Front Cell Dev Biol 2021; 9:757318. [PMID: 34790667 PMCID: PMC8591242 DOI: 10.3389/fcell.2021.757318] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/07/2021] [Indexed: 12/26/2022] Open
Abstract
To date, nearly 100 autoimmune diseases have been an area of focus, and these diseases bring health challenges to approximately 5% of the population worldwide. As a type of disease caused by tolerance breakdown, both environmental and genetic risk factors contribute to autoimmune disease development. However, in most cases, there are still gaps in our understanding of disease pathogenesis, diagnosis, and treatment. Therefore, more detailed knowledge of disease pathogenesis and potential therapies is indispensable. DNA methylation, which does not affect the DNA sequence, is one of the key epigenetic silencing mechanisms and has been indicated to play a key role in gene expression regulation and to participate in the development of certain autoimmune diseases. Potential epigenetic regulation via DNA methylation has garnered more attention as a disease biomarker in recent years. In this review, we clarify the basic function and distribution of DNA methylation, evaluate its effects on gene expression and discuss related key enzymes. In addition, we summarize recent aberrant DNA methylation modifications identified in the most important cell types related to several autoimmune diseases and then provide potential directions for better diagnosing and monitoring disease progression driven by epigenetic control, which may broaden our understanding and contribute to further epigenetic research in autoimmune diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimeng Wang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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Chi M, Ma K, Li Y, Quan M, Han Z, Ding Z, Liang X, Zhang Q, Song L, Liu C. Immunological Involvement of MicroRNAs in the Key Events of Systemic Lupus Erythematosus. Front Immunol 2021; 12:699684. [PMID: 34408748 PMCID: PMC8365877 DOI: 10.3389/fimmu.2021.699684] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/19/2021] [Indexed: 12/21/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an archetype autoimmune disease characterized by a myriad of immunoregulatory abnormalities that drives injury to multiple tissues and organs. Due to the involvement of various immune cells, inflammatory cytokines, and related signaling pathways, researchers have spent a great deal of effort to clarify the complex etiology and pathogenesis of SLE. Nevertheless, current understanding of the pathogenesis of SLE is still in the early stages, and available nonspecific treatment options for SLE patients remain unsatisfactory. First discovered in 1993, microRNAs (miRNAs) are small RNA molecules that control the expression of 1/3 of human genes at the post-transcriptional level and play various roles in gene regulation. The aberrant expression of miRNAs in SLE patients has been intensively studied, and further studies have suggested that these miRNAs may be potentially relevant to abnormal immune responses and disease progression in SLE. The aim of this review was to summarize the specific miRNAs that have been observed aberrantly expressed in several important pathogenetic processes in SLE, such as DCs abnormalities, overactivation and autoantibody production of B cells, aberrant activation of CD4+ T cells, breakdown of immune tolerance, and abnormally increased production of inflammatory cytokines. Our summary highlights a novel perspective on the intricate regulatory network of SLE, which helps to enrich our understanding of this disorder and ignite future interest in evaluating the molecular regulation of miRNAs in autoimmunity SLE.
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Affiliation(s)
- Mingxuan Chi
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Kuai Ma
- Department of Nephrology, Osaka University, Suita, Japan
| | - Yunlong Li
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Min Quan
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhongyu Han
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhaolun Ding
- Department of Emergency Surgery, Shannxi Provincial People's Hospital, Xi'an, China
| | - Xin Liang
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qinxiu Zhang
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Linjiang Song
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chi Liu
- Reproductive & Women-Children Hospital, School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Department of Nephrology, Sichuan Clinical Research Center for Kidney Disease, Sichuan Provincial People's Hospital, University of Electronic Science and Technology, Chengdu, China
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The Impact of Protein Acetylation/Deacetylation on Systemic Lupus Erythematosus. Int J Mol Sci 2018; 19:ijms19124007. [PMID: 30545086 PMCID: PMC6321219 DOI: 10.3390/ijms19124007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/30/2018] [Accepted: 12/10/2018] [Indexed: 02/08/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic inflammatory autoimmune disease in which the body’s immune system mistakenly attacks healthy cells. Although the exact cause of SLE has not been identified, it is clear that both genetics and environmental factors trigger the disease. Identical twins have a 24% chance of getting lupus disease if the other one is affected. Internal factors such as female gender and sex hormones, the major histocompatibility complex (MHC) locus and other genetic polymorphisms have been shown to affect SLE, as well as external, environmental influences such as sunlight exposure, smoking, vitamin D deficiency, and certain infections. Several studies have reported and proposed multiple associations between the alteration of the epigenome and the pathogenesis of autoimmune disease. Epigenetic factors contributing to SLE include microRNAs, DNA methylation status, and the acetylation/deacetylation of histone proteins. Additionally, the acetylation of non-histone proteins can also influence cellular function. A better understanding of non-genomic factors that regulate SLE will provide insight into the mechanisms that initiate and facilitate disease and also contribute to the development of novel therapeutics that can specifically target pathogenic molecular pathways.
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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: 42] [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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Weeding E, Sawalha AH. Deoxyribonucleic Acid Methylation in Systemic Lupus Erythematosus: Implications for Future Clinical Practice. Front Immunol 2018; 9:875. [PMID: 29740453 PMCID: PMC5928134 DOI: 10.3389/fimmu.2018.00875] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/09/2018] [Indexed: 01/19/2023] Open
Abstract
Differential deoxyribonucleic acid (DNA) methylation has emerged as a critical feature of systemic lupus erythematosus (SLE). Genome-wide DNA methylation studies have revealed methylation patterns characteristic of SLE—in particular, robust hypomethylation of interferon-regulated genes is a prominent finding in all cells of the immune system studied to date. These patterns reliably distinguish individuals with SLE from healthy controls and from individuals with other autoimmune diseases. For example, hypomethylation within IFI44L is both highly sensitive and highly specific for SLE, superior to currently available biomarkers. Furthermore, methylation status of other genetic loci has been associated with clinically relevant features of SLE including disease severity and organ-specific manifestations. Finally, DNA methylation studies have provided important insights into the pathophysiology of SLE. Most recently, there is a growing body of evidence that the transcription factor enhancer of zeste homolog 2 (EZH2) plays an important role in triggering SLE disease activity via epigenetic mechanisms, and that EZH2 blockade may be a future treatment option in SLE. In this short review, we discuss the DNA methylation patterns associated with SLE, their relationship to clinically significant features of SLE, and their implications in the development of novel diagnostic and therapeutic approaches to this complex disease.
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Affiliation(s)
- Emma Weeding
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
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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: 48] [Impact Index Per Article: 6.9] [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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Sharma R, Harris VM, Cavett J, Kurien BT, Liu K, Koelsch KA, Fayaaz A, Chaudhari KS, Radfar L, Lewis D, Stone DU, Kaufman CE, Li S, Segal B, Wallace DJ, Weisman MH, Venuturupalli S, Kelly JA, Pons-Estel B, Jonsson R, Lu X, Gottenberg JE, Anaya JM, Cunninghame-Graham DS, Huang AJW, Brennan MT, Hughes P, Alevizos I, Miceli-Richard C, Keystone EC, Bykerk VP, Hirschfield G, Nordmark G, Bucher SM, Eriksson P, Omdal R, Rhodus NL, Rischmueller M, Rohrer M, Wahren-Herlenius M, Witte T, Alarcón-Riquelme M, Mariette X, Lessard CJ, Harley JB, Ng WF, Rasmussen A, Sivils KL, Scofield RH. Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sjögren's Syndrome. Arthritis Rheumatol 2017; 69:2187-2192. [PMID: 28692793 DOI: 10.1002/art.40207] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 07/06/2017] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Sjögren's syndrome (SS) and systemic lupus erythematosus (SLE) are related by clinical and serologic manifestations as well as genetic risks. Both diseases are more commonly found in women than in men, at a ratio of ~10 to 1. Common X chromosome aneuploidies, 47,XXY and 47,XXX, are enriched among men and women, respectively, in either disease, suggesting a dose effect on the X chromosome. METHODS We examined cohorts of SS and SLE patients by constructing intensity plots of X chromosome single-nucleotide polymorphism alleles, along with determining the karyotype of selected patients. RESULTS Among ~2,500 women with SLE, we found 3 patients with a triple mosaic, consisting of 45,X/46,XX/47,XXX. Among ~2,100 women with SS, 1 patient had 45,X/46,XX/47,XXX, with a triplication of the distal p arm of the X chromosome in the 47,XXX cells. Neither the triple mosaic nor the partial triplication was found among the controls. In another SS cohort, we found a mother/daughter pair with partial triplication of this same region of the X chromosome. The triple mosaic occurs in ~1 in 25,000-50,000 live female births, while partial triplications are even rarer. CONCLUSION Very rare X chromosome abnormalities are present among patients with either SS or SLE and may inform the location of a gene(s) that mediates an X dose effect, as well as critical cell types in which such an effect is operative.
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Affiliation(s)
- Rohan Sharma
- Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Department of Veterans Affairs Medical Center, Oklahoma City
| | - Valerie M Harris
- Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City
| | - Joshua Cavett
- Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City
| | - Biji T Kurien
- Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Department of Veterans Affairs Medical Center, Oklahoma City
| | - Ke Liu
- Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, Ohio
| | - Kristi A Koelsch
- Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Department of Veterans Affairs Medical Center, Oklahoma City
| | - Anum Fayaaz
- Department of Veterans Affairs Medical Center, Oklahoma City, Oklahoma
| | | | - Lida Radfar
- University of Oklahoma Health Sciences Center, Oklahoma City
| | - David Lewis
- University of Oklahoma Health Sciences Center, Oklahoma City
| | - Donald U Stone
- Johns Hopkins University, Baltimore, Maryland, and King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - C Erick Kaufman
- University of Oklahoma Health Sciences Center, Oklahoma City
| | - Shibo Li
- University of Oklahoma Health Sciences Center, Oklahoma City
| | | | | | | | | | | | | | - Roland Jonsson
- University of Bergen and Haukeland University Hospital, Bergen, Norway
| | - Xianglan Lu
- University of Oklahoma Health Sciences Center, Oklahoma City
| | | | | | | | | | | | | | - Ilias Alevizos
- National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD
| | - Corinne Miceli-Richard
- Department of Rheumatology, Université Paris-Sud, AP-HP, INSERM U1012, Le Kremlin-Bicêtre, France
| | - Edward C Keystone
- Mount Sinai Hospital and University of Toronto, Toronto, Ontario, Canada
| | | | | | | | | | | | - Roald Omdal
- Stavanger University Hospital, Stavanger, Norway
| | | | - Maureen Rischmueller
- The Queen Elizabeth Hospital, Woodville South, and University of Adelaide, Adelaide, South Australia, Australia
| | | | | | | | - Marta Alarcón-Riquelme
- Pfizer-University of Granada-Andalusian Regional Government, Granada, Spain, and Karolinska Institutet, Stockholm, Sweden
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Sud, AP-HP, INSERM U1012, Le Kremlin-Bicêtre, France
| | | | - John B Harley
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, and Ohio Department of Veterans Affairs Medical Center, Cincinnati
| | - Wan-Fai Ng
- Newcastle University, Newcastle upon Tyne, UK
| | | | - Kathy L Sivils
- Oklahoma Medical Research Foundation and University of Oklahoma Health Sciences Center, Oklahoma City
| | - R Hal Scofield
- Oklahoma Medical Research Foundation, University of Oklahoma Health Sciences Center, and Department of Veterans Affairs Medical Center, Oklahoma City
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The Upregulation of Genomic Imprinted DLK1-Dio3 miRNAs in Murine Lupus Is Associated with Global DNA Hypomethylation. PLoS One 2016; 11:e0153509. [PMID: 27070142 PMCID: PMC4829153 DOI: 10.1371/journal.pone.0153509] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 03/30/2016] [Indexed: 12/20/2022] Open
Abstract
Epigenetic factors such as DNA methylation and microRNAs (miRNAs) are now increasingly recognized as vital contributors to lupus etiology. In this study, we investigated the potential interaction of these two epigenetic factors in lupus-prone MRL-lpr mice. We recently reported dysregulated expression of miRNAs in splenocytes of MRL-lpr mice. Here, we report that a majority of the upregulated miRNAs in MRL-lpr mice is located at the genomic imprinted DLK1-Dio3 domain. Further, we show a differential magnitude of upregulation of DLK1-Dio3 miRNA cluster in purified splenic CD4+ T, CD19+ B, and splenic CD4-CD19- cells from MRL-lpr lupus mice when compared to control MRL mice. MRL-lpr splenocytes (especially CD19+ and CD4-CD19- subsets) were hypomethylated compared to cells from control, MRL mice. We further show that deliberate demethylation of splenocytes from control MRL mice, but not from MRL-lpr lupus mice, with specific DNA methylation inhibitor 5-Aza-2'-deoxycytidine significantly augmented DLK1-Dio3 miRNAs expression. These findings strongly indicate that the upregulation of DLK1-Dio3 miRNAs in lupus splenic cell subsets is associated with reduced global DNA methylation levels in lupus cells. There was a differential upregulation of DLK-Dio3 miRNAs among various demethylated splenic cell subsets, which implies varied sensitivity of DLK1-Dio3 miRNA cluster in these cell subsets to DNA hypomethylation. Finally, inhibition of select DLK1-Dio3 miRNA such as miR-154, miR-379 and miR-300 with specific antagomirs significantly reduced the production of lupus-relevant IFNγ, IL-1β, IL-6, and IL-10 in lipopolysaccharide (LPS) activated splenocytes from MRL-lpr mice. Our study is the first to show that DNA methylation regulates genomic imprinted DLK1-Dio3 miRNAs in autoimmune lupus, which suggests a connection of DNA methylation, miRNA and genomic imprinting in lupus pathogenesis.
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Shi L, Zhang Z, Song L, Leung YT, Petri MA, Sullivan KE. Monocyte enhancers are highly altered in systemic lupus erythematosus. Epigenomics 2015; 7:921-35. [PMID: 26442457 DOI: 10.2217/epi.15.47] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVE Histone modifications set transcriptional competency and can perpetuate pathologic expression patterns. We defined systemic lupus erythematosus (SLE)-specific changes in H3K4me3 and K3K27me3, histone marks of gene activation and repression, respectively. METHODS We used ChIP-seq to define histone modifications in monocytes from SLE patients and controls. RESULTS Both promoters and enhancers exhibited significant changes in histone methylation in SLE. Regions with differential H3K4me3 in SLE were significantly enriched in potential interferon-related transcription factor binding sites and pioneer transcription factor sites. CONCLUSION Enhancer activation defines the character of the cell and our data support extensive disease effects in monocytes, a particularly plastic lineage. Type I interferons not only drive altered gene expression but may also alter the character of the cell through chromatin modifications.
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Affiliation(s)
- Lihua Shi
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Zhe Zhang
- The Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 1910, USA
| | - Li Song
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Yiu Tak Leung
- Division of Rheumatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michelle A Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kathleen E Sullivan
- Division of Allergy & Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
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Strickland FM, Li Y, Johnson K, Sun Z, Richardson BC. CD4(+) T cells epigenetically modified by oxidative stress cause lupus-like autoimmunity in mice. J Autoimmun 2015; 62:75-80. [PMID: 26165613 DOI: 10.1016/j.jaut.2015.06.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/01/2015] [Accepted: 06/07/2015] [Indexed: 10/23/2022]
Abstract
Lupus develops when genetically predisposed people encounter environmental agents such as UV light, silica, infections and cigarette smoke that cause oxidative stress, but how oxidative damage modifies the immune system to cause lupus flares is unknown. We previously showed that oxidizing agents decreased ERK pathway signaling in human T cells, decreased DNA methyltransferase 1 and caused demethylation and overexpression of genes similar to those from patients with active lupus. The current study tested whether oxidant-treated T cells can induce lupus in mice. We adoptively transferred CD4(+) T cells treated in vitro with oxidants hydrogen peroxide or nitric oxide or the demethylating agent 5-azacytidine into syngeneic mice and studied the development and severity of lupus in the recipients. Disease severity was assessed by measuring anti-dsDNA antibodies, proteinuria, hematuria and by histopathology of kidney tissues. The effect of the oxidants on expression of CD40L, CD70, KirL1 and DNMT1 genes and CD40L protein in the treated CD4(+) T cells was assessed by Q-RT-PCR and flow cytometry. H2O2 and ONOO(-) decreased Dnmt1 expression in CD4(+) T cells and caused the upregulation of genes known to be suppressed by DNA methylation in patients with lupus and animal models of SLE. Adoptive transfer of oxidant-treated CD4(+) T cells into syngeneic recipients resulted in the induction of anti-dsDNA antibody and glomerulonephritis. The results show that oxidative stress may contribute to lupus disease by inhibiting ERK pathway signaling in T cells leading to DNA demethylation, upregulation of immune genes and autoreactivity.
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Affiliation(s)
- Faith M Strickland
- Department of Internal Medicine, Rheumatology Division, The University of Michigan, Ann Arbor, MI 48109, USA.
| | - YePeng Li
- Department of Internal Medicine, Rheumatology Division, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Kent Johnson
- Department of Pathology, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhichao Sun
- Department of Biostatistics, School of Public Health, The University of Michigan, Ann Arbor, MI 48109, USA
| | - Bruce C Richardson
- Department of Internal Medicine, Rheumatology Division, The University of Michigan, Ann Arbor, MI 48109, USA; Department of Medicine, Ann Arbor VA Medical Center, USA
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Coit P, Jeffries M, Altorok N, Dozmorov MG, Koelsch KA, Wren JD, Merrill JT, McCune WJ, Sawalha AH. Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients. J Autoimmun 2013; 43:78-84. [PMID: 23623029 DOI: 10.1016/j.jaut.2013.04.003] [Citation(s) in RCA: 251] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 02/06/2023]
Abstract
Systemic lupus erythematosus is an autoimmune disease characterized by multi-system involvement and autoantibody production. Abnormal T cell DNA methylation and type-I interferon play an important role in the pathogenesis of lupus. We performed a genome-wide DNA methylation study in two independent sets of lupus patients and matched healthy controls to characterize the DNA methylome in naïve CD4+ T cells in lupus. DNA methylation was quantified for over 485,000 methylation sites across the genome, and differentially methylated sites between lupus patients and controls were identified and then independently replicated. Gene expression analysis was also performed from the same cells to investigate the relationship between the DNA methylation changes observed and mRNA expression levels. We identified and replicated 86 differentially methylated CG sites between patients and controls in 47 genes, with the majority being hypomethylated. We observed significant hypomethylation in interferon-regulated genes in naïve CD4+ T cells from lupus patients, including IFIT1, IFIT3, MX1, STAT1, IFI44L, USP18, TRIM22 and BST2, suggesting epigenetic transcriptional accessibility in these genetic loci. Indeed, the majority of the hypomethylated genes (21 out of 35 hypomethylated genes) are regulated by type I interferon. The hypomethylation in interferon-regulated genes was not related to lupus disease activity. Gene expression analysis showed overexpression of these genes in total but not naïve CD4+ T cells from lupus patients. Our data suggest epigenetic "poising" of interferon-regulated genes in lupus naïve CD4+ T cells, argue for a novel pathogenic implication for abnormal T cell DNA methylation in lupus, and suggest a mechanism for type-I interferon hyper-responsiveness in lupus T cells.
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Affiliation(s)
- Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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12
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Abstract
Idiosyncratic drug reactions are a significant cause of morbidity and mortality for patients; they also markedly increase the uncertainty of drug development. The major targets are skin, liver, and bone marrow. Clinical characteristics suggest that IDRs are immune mediated, and there is substantive evidence that most, but not all, IDRs are caused by chemically reactive species. However, rigorous mechanistic studies are very difficult to perform, especially in the absence of valid animal models. Models to explain how drugs or reactive metabolites interact with the MHC/T-cell receptor complex include the hapten and P-I models, and most recently it was found that abacavir can interact reversibly with MHC to alter the endogenous peptides that are presented to T cells. The discovery of HLA molecules as important risk factors for some IDRs has also significantly contributed to our understanding of these adverse reactions, but it is not yet clear what fraction of IDRs have a strong HLA dependence. In addition, with the exception of abacavir, most patients who have the HLA that confers a higher IDR risk with a specific drug will not have an IDR when treated with that drug. Interindividual differences in T-cell receptors and other factors also presumably play a role in determining which patients will have an IDR. The immune response represents a delicate balance, and immune tolerance may be the dominant response to a drug that can cause IDRs.
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Affiliation(s)
- Jack Uetrecht
- Faculties of Pharmacy and Medicine, University of Toronto, Toronto, Canada M5S3M2.
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