The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation

AUTREV-01841; No of Pages 6 Autoimmunity Reviews xxx (2016) xxx–xxx

Contents lists available at ScienceDirect

Autoimmunity Reviews journal homepage: www.elsevier.com/locate/autrev

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Haijing Wu 1, Ming Zhao 1, Lina Tan, Qianjin Lu ⁎

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The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation

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Hunan Key Laboratory of Medical Epigenomics, Department of Dermatology, Second Xiangya Hospital, Central South UniversityChangsha, Hunan, China

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Article history: Received 22 February 2016 Accepted 28 February 2016 Available online xxxx

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Keywords: SLE Epigenetics DNA methylation T cells

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Contents

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Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Role of aberrant DNA methylation in the pathogenesis of SLE . . . . . . . . . . . . 2.1. Abnormal DNA methylation and T cell dysfunction in SLE . . . . . . . . . . 2.2. The molecular mechanisms of DNA hypomethylation in lupus T cells . . . . . 2.2.1. Environmental factors . . . . . . . . . . . . . . . . . . . . . . 2.2.2. Aberrant expression of transcription factors and miRNAs . . . . . . 2.2.3. Defect of the ERK signaling pathway . . . . . . . . . . . . . . . 2.2.4. DNA hydroxymethylcytosine . . . . . . . . . . . . . . . . . . . 2.3. Aberrant DNA methylation and B cell abnormalities in SLE . . . . . . . . . . 3. Potential epigenetic biomarkers and therapies by interfering DNA methylation for SLE Author contributions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Conflicts of interest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Take-home message . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Acknowledgments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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1. Introduction

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Systemic lupus erythematosus (SLE) is an autoimmune disease with multiple organ involvement. It is characterized by abundant autoantibodies that form immune complex with autoantigens and deposit in organs and cause tissue damage by inducing inflammation. The pathogenesis of SLE has been intensively studied but remains unclear. B and T lymphocyte abnormalities, dysregulation of apoptosis, defects in the clearance of apoptotic materials, and various genetic and epigenetic factors are believed to contribute to the initiation and development of SLE. The up-to-date research findings point to the relationship between abnormal DNA methylation and SLE, which has attracted considerable interest worldwide. Besides the global hypomethylation on lupus T and B cells, the gene specific and site-specific methylation has been identified and documented to be responsible for SLE. The purpose of this review was to present and summarize the association between aberrant DNA methylation of immune cells and SLE, the possible mechanisms of immune dysfunction caused by DNA methylation, and to better understand the roles of aberrant DNA methylation in the initiation and development of SLE and to provide an insight into the related diagnosis biomarkers and therapeutic options in SLE. © 2016 Published by Elsevier B.V.

SLE is a multi-systemic, autoimmune disorder that predominately affects women during their reproductive years [1,2]. The prevalence and the incidence of SLE have been shown to vary across geographic regions around the world. It has been found more frequently in non-white ⁎ Corresponding author. E-mail address: [email protected] (Q. Lu). 1 These two authors contribute equally to this work.

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populations compared to Caucasians, and the highest prevalence is reported among Afro-Caribbeans [3,4]. SLE is characterized by autoreactive T and B lymphocytes [5,6], together with a presence of a diverse set of autoantibodies in the circulation of affected patients [7], such as antinuclear antibodies (ANAs), anti-double-strand DNA (dsDNA) antibody, and anti-Smith (Anti-Sm) antibody, which have been used as conventional serological markers in patients with SLE [8]. Although the direct cause of SLE remains unclear, many factors are revealed to contribute to the pathogenesis of SLE, including genetic susceptibility, epigenetics, hormones, and

http://dx.doi.org/10.1016/j.autrev.2016.03.002 1568-9972/© 2016 Published by Elsevier B.V.

Please cite this article as: Wu H, et al, The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation, Autoimmun Rev (2016), http://dx.doi.org/10.1016/j.autrev.2016.03.002

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2.1. Abnormal DNA methylation and T cell dysfunction in SLE

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The role of DNA methylation in SLE first attracted attention in the 1960s and has since become a very hot research topic [25]. Two epigenetic drugs, procainamide and hydralazine, which are inhibitors of DNA methylation, were found to induce a lupus-like disease after long-term administration in wild-type mice, and the disease disappeared after the withdrawal of these drugs. Methylation levels in thymus and lymphatic nodules of a murine model of lupus (MRL/lpr) were lower than those found in the control mice [26,27]. To extrapolate this information to humans, DNA demethylation has been found in SLE CD4+ T cells, but not in CD8+ T cells, and peripheral blood mononuclear cells (PBMCs) [28,29]. CD4+ T cells from lupus patients with active disease activity display hypomethylated DNA and over-express LFA-1 on an autoreactive subset, which spontaneously lyses autologous macrophages [30,31]. Genome-wide DNA methylation study revealed epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients [32], as well as from lupus patients with different clinical manifestations, such as malar rash versus discoid rash [33] and renal involvement versus non-renal involvement [34]. However, the global DNA methylation status may not reflect actual specific gene expression patterns but may instead indicate the activation status of cells in general. Thus, the most recent research has focused on specific cell types as well as certain SLE relevant genes. T helper (Th) cells, as a major component of the adaptive immune system, have a critical function of “helping” B cells in the production of antibodies. Th cells are not a single population but can be divided into several subsets, such as Th1, Th2, Th17, Th9, Th22, follicular T (Tfh), and regulatory T (Treg) cells, based on their unique cytokines and transcription factors [35]. More importantly, these different subsets of Th cells are not automatically differentiated; their developmental trajectories from naïve T cells depend on the antigens presenting on major histocompatibility complex (MHC) molecules on dendritic cells and/or macrophages as well as the cytokine milieu provided by antigenpresenting cells (APCs). These processes occur in T cell zones in secondary lymphoid tissues after naïve T cells leave the thymus [36]. A mild dysregulation of any type of Th cells can result in severe immune disorders. It has been well documented that circulating CD4+ T cells are flexible; an imbalance of Th17 and Treg, Th1 and Th2, or even increased levels of Tfh cells may contribute to SLE [37–40]. In addition to the unique transcription factors of these cells, recent studies have revealed that DNA methylation plays a role in controlling this sophisticated differentiation process. Previously, Richardson et al. reported that DNA hypomethylation on lupus CD4+ T cells is associated with T cell autoreactivity in lupus [30]. That study was the first attempt to explore the role of epigenetics in lupus, and it has prompted the coming of a new era of epigenetics in the study of pathogenesis. Their finding was supported by the induction of autoreactivity of healthy CD4+ T cells by the addition of 5-azacytidine [30,41], which followed prior evidence of the induction of IL-2 and IFN-γ by the same agent [42]. An increasing number of studies have focused on the role of DNA methylation in the activation and differentiation of T cells at specific loci in individual genes. IFN-γ and IL-4 are well-described cytokines for Th1 and Th2 processes, respectively, and impaired DNA methylation has been found at Ifng and Il4 loci during Th1 and Th2 differentiation [43,44]. DNA hypomethylation is observed at the FOXP3 locus in regulatory T cells compared to naïve T cells [45]. In a very recent report, BCL-6, a key transcription factor for Tfh cell, is found to bind in Tfh cell associated with a decrease in 5hmC [46], indicating that the differentiation of Tfh cell is regulated by DNA methylation.

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DNA methylation is a biochemical process in which a methyl group is added to a cytosine or adenine at the 5′ position of a CpG dinucleotide, converting the cytosine to methylcytosine [17]. The CpG dinucleotides tend to cluster in regions called CpG islands, defined as regions of more than 200 bases with a G + C content of at least 50% and a ratio of observed to statistically expected CpG frequencies of at least 0.6. Approximate 60% of gene promoters are associated with CpG islands and are normally unmethylated, although some of them (about 6%) become methylated in a tissue-specific manner during early development or in differentiated tissues [18]. This may explain why all cell in an organism share the same genetic information, but they show different phenotypes. In general, CpG island methylation is associated with gene silencing. Methylation serves as a mark that indicates repression of gene expression, and DNA methylation is therefore involved in many biological processes, such as cell differentiations and immune responses. DNA methylation inhibits gene expression via various mechanisms. For example, methyl-CpG-binding domain (MBD) proteins can be recruited by methylated DNA, and MBD family members recruit histone modifying and chromatin-remodeling complexes to methylated sites in turn [19,20]. Moreover, DNA methylation can also directly inhibit transcription by precluding the recruitment of DNA-binding proteins from their target sites [21]. However, DNA methylation does not occur exclusively at CpG islands, and CpG island shores, which refer to regions of lower density of CpG and lie close to CpG, is associated with transcriptional inactivation. Most tissue-specific DNA methylation occurs not at CpG islands but at CpG island shores [22]. In mammalian cells, DNA methylation is restricted to regions of CpG islands, which are typically present in promoter regions [23]. The process of DNA methylation is mediated by methyltransferases, such as DNMT1, DNMT3a, and DNMT3b, and each displays capacity

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different functional capacity. For example, DNMT1 maintains the methylation status during cell replication, whereas DNMT3a and 3b usually induce de novo methylation [24]. By contrast, DNA demethylation re-activates or re-expresses silenced genes, a process that is also regulated by enzymes, such as ten-eleven translocation methylcytosine dioxygenase 1 (TET1), TET2, and TET3.

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environmental factors [9]. SLE occurs when an individual with genetic susceptibility to lupus encounters environmental triggers such as sunlight, drugs, or infection. Immune tolerance is broken down such that T cells recognize self-antigens and provide help to autoreactive B cells, which produce abundant autoantibodies. These autoantibodies bind to self-antigens and reside in multiple organs, leading to organ inflammation, dysfunction, and failure. SLE can affect various organ systems, including skin, joint, kidney, central nervous system, and bone marrow [10–13]. Epigenetics is a study of the reversible and potentially heritable changes in gene expression without genetic code alterations, including DNA methylation, histone modification, and microRNA (miRNA). Recently, epigenetics becomes a new area of investigation into the pathogenesis of SLE [14]. Even before DNA was identified as the inheritable molecules, it was known that not every gene in an organism can be active in each cell at all times. Indeed, epigenetics provides an additional explanation for how genetics can contribute to health and disease and is being increasingly recognized as an important factor contributing to SLE. For example, only 20% of concordance for SLE has been found in homozygotic twins, suggesting that there are roles of environmental and epigenetic factors in the onset of disease [15]. Further indirect evidence of the role of epigenetics is that SLE is found predominantly in females and that it can be accelerated by environmental triggers (e.g., infection, UV, drugs) and/or internal factors (hormones and stress). In addition, certain types of drugs, which have been reported to induce SLE, are also known to cause epigenetic modifications, including 5azacytidine and procainamide [16]. However, the precise mechanism by which these and many other environmental agents initiate lupus flares in genetically predisposed individuals has not been elucidated. Among these epigenetic modifications, DNA methylation received global attention and has been intensively studied by our group and others. Thus, this review summarizes up-to-date data showing the immune abnormalities induced by DNA methylation in SLE patients and provides insight into the possibility of relevant diagnosis biomarkers and therapies.

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Please cite this article as: Wu H, et al, The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation, Autoimmun Rev (2016), http://dx.doi.org/10.1016/j.autrev.2016.03.002

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2.2.2. Aberrant expression of transcription factors and miRNAs In addition to the linage-specific cytokines and transcription factors, other genes such as HTR1A [53], LFA-1 [54], CD70 [55,56], perforin [57], and CD40L [58] have been found to be demethylated in lupus CD4+ T cells and have been associated with the pathogenesis of SLE. These genes, which are also related to autoreactivity of T cells, are overexpressed in conjunction with DNA hypomethylation. CD40L on T cells is a ligand for CD40, which is expressed on B cells and DCs. The joining of the CD40L-CD40 pathway provides the “secondary signal” to B cells and/or DCs, promoting the activation of these cells, which then may lead to a higher production of antibodies [59]. Recently, upstream factors of DNA methylation have also been explored. Zhao et al. observed that RFX1, a regulation factor for the X-Box protein family, is decreased in SLE and regulates DNA methylation in CD4+ T cells [55]. In addition, the level of DNA Damage-Inducible 45 alpha (Gadd45a), which is thought to have demethylation capability, is reportedly enhanced in lupus patients and positively correlates with CD11a/CD70 expression [60]. Furthermore, high mobility group box protein 1 (HMGB1) has been found to be involved in DNA methylation by binding to Gadd45a [61]. In a large-scale DNA methylation investigation, DNA hypomethylation was found in interferon-regulated genes in lupus naïve T cells, including IFI44L, IFIT1, IFIT3, MX1, STAT1, USP18, BST2, and TRIM22, suggesting abnormalities in T cell progenitors [32]. More important is that the DNA methylation level on IFI44L promoter is identified as a sensitive and specific biomarker for lupus diagnosis [62]. Lupus-associated and inflammatory cytokine genes, such as IL4, IL6, IL10, and IL13, are demethylated in lupus T cells and may contribute to disease progression [45,63,64]. In addition, microRNAs have been identified as regulators for DNA methylation. Not surprisingly, critical associations between miRNAs and DNA methylation patterns in lupus CD4+ T cells have also been reported. It is demonstrated that expression of miR-21 and miR-148a increased in both lupus patients and lupusprone MRL/lpr mice, which may inhibit DNMT1 expression and thus

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2.2.4. DNA hydroxymethylcytosine 5-Hydroxymethylcytosine (5-hmC), the oxidative derivatives of 5-methylcytosine (5-mC) that are generated by TET proteins, including TET1, 2, and 3, advances our understanding of DNA demethylation mechanisms [66]. DNA hydroxymethylation is reported as a mechanism that regulates human T cells [73] and stem cells [74,75]. The deletion of TET2 in T cells reduced 5-hmc content and key transcription factors binding, resulting in reduction of cytokine expression by Th1 and Th17 cells [76]. In an unpublished study, we report that the global DNA hydroxymethylation levels are increased significantly, along with the upregulated methylcytosine dioxygenase TET2 and TET3 expression, in CD4+ T cells from SLE patients compared to healthy controls, indicating that gain of 5-hmC in genome DNA may be a novel mechanism of the global DNA hypomethylation and increased self-reactivity of CD4+ T cells in SLE. We propose that DNA hydroxymethylation may be responsible for aberrant DNA methylation contributing to the pathogenesis of SLE.

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2.3. Aberrant DNA methylation and B cell abnormalities in SLE

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As the source of autoantibodies, B cells have a direct and central role in the pathogenesis of SLE. Therefore, a growing number of clinical trials have targeted B cell therapies, without a complete understanding of the mechanisms leading to SLE. DNA methylation is clearly involved in B cell differentiation, as it is in T cells as described in the above section. For example, at the early stage of B cell differentiation, PAX-5, and Pu-1 regulation regions are demethylated [77,78]; by contrast, CD19 promoter demethylation occurs in pre-pro-B cells, and the CD21 promoter is demethylated in mature B cells [79]. However, in contrast to T cell, fewer studies have addressed DNA methylation in B cell abnormalities in SLE. DNA demethylation has been observed in lupus B cells, especially in CD5-nonexpressing (B2) cells [80], promoting the autoreactivity of B cells. Renaudineau et al. also detected an alteration in the regulation of HRES1/p28 expression in lupus B cells by DNA methylation [81]. In

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2.2.3. Defect of the ERK signaling pathway In addition to T cell differentiation, epigenetic abnormalities may play a role in the various signaling pathways that are involved in SLE. Richardson et al. demonstrated that blocking the ERK signaling pathway in lupus CD4+ T cells resulted in the downregulation of DNMT1 activity and DNA demethylation in daughter cells [57]. The autoreactivity of ERK inhibitor (hydralazine)-treated CD4+ T cells was confirmed by the finding that injection into syngeneic mice caused lupus-like symptoms, similar to the 5-azacytidine treatments [67]. In addition, the inhibition of PKCδ, which is a step in the ERK pathway (PKC-ras–raf-MEK–ERK), causes hypomethylation of the CD70 promoter and enhances CD70 expression, resembling that seen in lupus or 5-azacytidine-treated T cells [68,69]. More convincing evidence of ERKs role in the pathogenesis of SLE is shown in PKCδ “knockout” mice, which develop lupus-like symptoms [70,71], as well as dnMEK mouse model with autoimmune phenotype by inhibiting ERK signaling [72], indicating a critical role of this signaling pathway and the subsequent potential effect of epigenetic changes.

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2.2.1. Environmental factors It is generally believed that DNA methylation or demethylation does not occur spontaneously, i.e., there must be a trigger or external factor that leads to alterations in DNA methylation. Many environmental factors have previously been implicated as triggers of SLE, and it is becoming more apparent that the mechanism by which these environmental insults exert their effects is through epigenetics. For example, oxidative stress, which may be caused by UV light, smoking, infections, mercury exposure, and even air pollution, is capable of lowering DNMT1 levels in T cells, as well as causing demethylation and overexpression of genes previously shown to be suppressed by DNA methylation in T cells from patients with active lupus [47]. In addition, sera from patients with active lupus are nitrated, caused by superoxide (O− 2 ) reacting with nitric oxide (NO) to form peroxynitrite (ONOO−), which reacts with tyrosine to form 3-nitro-tyrosine [48,49], and the level of nitration is directly related to disease activity [49]. Other external factors that can act synergistically include dietary deficiencies in vitamin B, folate, methionine (Met), choline, and Zn [50], all of which have been shown to be necessary to maintain a normal level of DNMT1 [51]. How do these dietary factors contribute to SLE via epigenetic modifications? For example, varying dietary Met levels had no effect on T cell DNA methylation or disease manifestations in normal conditions. However, when T cell DNMT1 levels were decreased by doxycycline, a diet high in methyl donors decreased anti-DNA antibody levels and kidney damages, while a diet poor in methyl donors displayed reverse effects [52]. More and more environmental agents are being targeted as potential triggering factors for autoimmunity, but only a subset of these truly have a causal relationship. Further studies are necessary to delineate which environmental factors are true triggers of autoimmune disease and how epigenetics may play a role in pathogenesis.

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contribute to demethylation of lupus-relevant methylation-sensitive genes such as CD70 and CD11a [65]. miR-126 has been reported to regulate DNA methylation in lupus T cells by targeting DNMT1 [49], supporting the idea that lupus T cells are switched on by DNA hypomethylation via miRNAs. In more recent report, miR-29b has also been reported to promote DNA hypomethylation of lupus CD4+ T cells by indirectly targeting DNMT1 [66]. Although it is known that epigenetics plays a critical role in T cell differentiation in general, our knowledge of how this impacts abnormalities in T cell differentiation in specific autoimmune diseases such as SLE is incomplete. However, further studies on the epigenetic regulation in specific pathogenic mechanisms known to occur in SLE are required before specific epigenetic treatments can be applied to the clinical setting.

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Please cite this article as: Wu H, et al, The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation, Autoimmun Rev (2016), http://dx.doi.org/10.1016/j.autrev.2016.03.002

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Table 1 DNA methylation status in lupus

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The current available laboratory markers for SLE diagnosis have been restricted. For example, ANA tests have a very high sensitivity (100%) but a relatively low specificity (65%) [90]. In the contrast, anti-dsDNA antibody is highly specific for SLE (94%); however, low sensitivity was due to the transient appearance [91]. Same phenomena have been found in anti-Sm antibodies (high specificity and low sensitivity) [92]. Thus, a more reliable biomarker for SLE is in great need. In our very recent report, the methylation level on two CpG sites within IFI44L promoter, Site1 (Chr1: 79 085 222) and Site2 (Chr1: 79 085 250; cg06872964), has been identified as a biomarker with high sensitivity (~ 93%) and high specificity (~ 96%). This finding is validated on 1144 lupus patients, 1350 healthy controls, 429 RA patients, and primary Sjogren's syndrome patients [62]. DNA methylation has been intensively investigated as biomarkers in cancer [93–96]; however, for autoimmune disorder, this is the first time

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identified as a biomarker. Due to the high sensitivity, specificity, feasibility, and reliability, we believe that more and more DNA methylation biomarkers will bloom. Unlike anti-cancer therapies, the strategies for lupus treatment are demethylation inhibitors. MBD2 might be a good first target, proposed by Moshe Szyf [97]. He and his colleagues previously developed antisense oligonucleotide inhibitors of MBD2 and therefore reduced MBD2 level and tumorigenesis of a human tumor xenoplant in nude mice [98]. It would be interesting to investigate whether MBD2 inhibitor would reverse the hypomethylation of cytokines and genes in lupus CD4+ T cells. Another candidate for DNA demethylation inhibition is the methyl donor of the DNA methylation reaction: S-adenosylmethionine (SAM). It is reported that SAM has been shown to inhibit MDB2/demethylase activity in vitro and to reverse gene demethylation [99]. Although SAM is highly unstable under physiological conditions, dietary supplementation with SAM has displayed some effect on osteoarthritis in clinical trails [100]. Therefore, developing SAM analogs with higher stability and potency in inhibiting demethylation might provide a value option for lupus therapy. However, by now none of DNA methylation drugs has been proven for SLE treatment. Only DNMT inhibitor (5-aza-2′-deoxyxytidine) has been applied in rheumatoid arthritis and multiple sclerosis studies [101]. Total glucosides of peony (TGP), an extracted component from Peony root, have been shown to possess anti-inflammatory and immuno-regulatory activities [102] and therapeutic effects in SLE [103]. TGP has been found to down-regulate Foxp3 promoter methylation levels and enhance the expression of Foxp3 in lupus CD4+ T cells [103]. These findings indicate that TGP may improve SLE by altering DNA methylation status in T cells. Author contributions

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addition, direct evidence of DNA hypomethylation in B cells at the onset on SLE was provided by treating B cells ex vivo with DNMT1 inhibitors and then adoptively transferring them into syngeneic mice, which developed then antinuclear antibodies [82]. Although several evidence showing the DNA hypomethylation in V (D) J and lgh 3′-LCR, which contribute to autoantibody production [83,84], little has been revealed in this aspect in SLE. In addition, lupus B cells have been found to be defective in their capacity to methylate DNA [85], and this defect has been associated with a blockage in the PKC delta/Erk pathway, which regulates DNMTs expression [68]. As the epigenome revolution unfolds, additional evidence will be available in the near future to reveal the factors that regulate DNA methylation in lupus B cells and how these demethylated genes contribute to SLE. It has also been postulated that DNA methylation in X chromosomal silencing may serve as a potential explanation for the sex bias in lupus [86]. Moreover, dendritic cells (DCs) have also been implicated in the pathogenesis of SLE [87–89]. It is believed that the role of DCs in a normal functioning immune system involves their ability to clear apoptotic debris, recognize self-DNA and RNA via Toll-like receptor (TLR) 9 and 7 expression in their cytoplasm, promote B cell maturation and proliferation through IFN-α secretion, and polarize naïve T cells into different effector T cells via the cytokine milieu and surface markers they provide. Unfortunately, to this date, little research has been focused on the DNA methylation of DCs in lupus. Indeed, investigations have so far been restricted to hypomethylation- and methyltransferase-level observations for certain genes and the global levels of DNA methylation in lupus T and B cells (summarized in Table 1). With the advent of the epigenetic era, additional informative results, especially in a linagespecific manner, will be available in the near future.

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Cell subsets, molecules, genes, or pathways

Methylation status

Ref.

t1:4 t1:5 t1:6 t1:7 t1:8 t1:9 t1:10 t1:11 t1:12 t1:13 t1:14 t1:15 t1:16 t1:17 t1:18

Global methylation status in T and B cells DNMT expression in CD4+ T cells: DNMT1, DNMT3a, DNMT3b GADD45a in T cells Methylation status of co-stimulatory molecules: CD6, CD11a, CD70, CD40L, CD5 Methylation status of cytokine genes: IL4, IL6, IL10, IL13 Methylation status of pro-inflammatory genes: IFGNR2, MMP14, LNC2, CSF3R, AIM2, IFI44L, IFIT1, IFIT3, MX1, STAT1, USP18, BST2, TRIM22 Methylation status of HERV element LINE-1 in CD4+ T, CD8+ T, and B cells Blocking the ERK signaling pathway The inhibition of PKCδ

Decreased Decreased

[30,58,105] [58,105–107]

Increased Decreased

[60] [54,80,108–110]

Decreased

[45,63,64]

Decreased

[32,62]

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Decreased

[111,112]

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[57,67] [68,69]

Haijing Wu and Lina Tan conducted the manuscript writing. Ming 402 Zhao conducted editing, and Qianjin Lu revised the manuscript. 403 Conflicts of interest The authors declare no conflict of interest. Take-home message • Accumulating evidence suggests the involvement of epigenetic mechanisms in immune regulation and the pathogenesis of lupus. DNA hypomethylation has been identified to play a role in the pathogenesis of lupus. Besides the findings on CD4+ T cells, including Th1, Th2, Th17, and Treg cells, increasing evidence has confirmed the important role of DNA methylation in SLE. For example, Tfh cells, which are critical in SLE, have been newly proven that the key transcription factor BCL-6 is regulated by DNA methylation [46]. Moreover, recent studies have been focused on identifying the upstream and downstream factors that affect or impact DNA methylation. RFX1 is an example that recruits DNMT1 and regulates CD70 and CD11a expression [55]. Efforts have been made, for example, to explore how environmental triggers promote DNA demethylation and contribute to diseases, investigate the interaction of epigenetic modifications, and elucidate the relationship between transcription factors and DNA methylation. In a recent report, 111 reference human epigenomes has been identified and analyzed, including 1821 histone modification data sets, 360 DNA accessibility data sets, 277 DNA methylation data sets, and 166 RNA-seq data sets [104], and the first DNA methylation biomarker for SLE [62], implying the real advent of the epigenomics era. Based on these findings and future expected results, researchers will continue to broaden and deepen our understanding of pathogenesis of SLE and establish more individually optimized therapeutic strategies for lupus patients.

Please cite this article as: Wu H, et al, The key culprit in the pathogenesis of systemic lupus erythematosus: Aberrant DNA methylation, Autoimmun Rev (2016), http://dx.doi.org/10.1016/j.autrev.2016.03.002

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This work was supported by the National Natural Science Foundation of China (grant no. 81220108017, no. 81430074, no. 81373205, and no. 81270024), the Specialized Research Fund for the Doctoral Program of Higher Education (grant no. 20120162130003), the Hunan Natural Science Funds for Distinguished Young Scientists (no. 14JJ1009), and the Programs of Science-Technology Commission of Hunan province (2013FJ4202).

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