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In this issue of Arthritis & Rheumatism, Zhao et al (1) provide further insight into the influence of certain microRNA on the promoter methylation status regulated by DNA methyltransferases (Dnmt). In recent years, there has been increased interest in the role of epigenetic modifications of DNA and the pathogenetic mechanisms of human diseases such as systemic lupus erythematosus (SLE) (2).

Epigenetics is linked to stable and potentially heritable changes in gene expression that do not entail a change in the DNA sequence. DNA methylation and histone modifications are the 2 major changes that contribute to the epigenome of a cell. The first mechanism usually occurs in the context of CpG dinucleotides at the 5′ position of cytosine in the promoter region, leading to functional consequences such as transcription repression. In fact, some tissue-specific genes are silenced by promoter methylation (2). Posttranslational modifications that occur in histones make up a second group of epigenetic modifications. Both DNA methylation and histone modifications are coupled through different machineries, including Dnmt as well as histone-modifying enzymes in multiprotein complexes (2). Three main types of Dnmt are involved in genomic DNA methylation: Dnmt1, Dnmt3A, and Dnmt3B. Whereas Dnmt1 preferentially replicates existing methylation patterns and maintains DNA methylation, Dnmt3A and Dnmt3B are responsible for establishing new DNA methylation markers, therefore referred to as de novo DNA methyltransferase (3).

A remarkable example of disease in which epigenetic DNA methylation abnormalities and patterns of inheritance are extremely complex is SLE, which is characterized by the production of a variety of autoantibodies against nuclear and cytoplasmic components associated with inflammation and injury of multiple organs. The high incidence of twin pairs in which SLE develops in only one of the siblings supports the notion that environmental factors and their involvement in epigenetic modifications could affect the onset of disease. The influence on SLE onset could occur at several levels. The epigenetic dysregulation of genes can contribute to, or increase, the activation of apoptosis. Moreover, it may lead to exacerbated activation of T cells and B cells (2). In fact, the DNA extracted from the T cells of patients with SLE is hypomethylated compared with the DNA extracted from normal T cells (3). The mechanisms by which hypomethylated T cells induce SLE are not well understood. Additional evidence of the role of global methylation changes in the development of SLE comes from studies with DNA-demethylating drugs, such as 5-azacytidine, procainamide, and hydralazine (2). In all cases, exposing T cells to demethylating drugs results in the demethylation-dependent induction of lupus-like disease (2).

MicroRNA are small, noncoding RNAs, usually 21–23 nucleotides long, which mediate posttranscriptional silencing of target genes (4). MicroRNA usually bind to partially complementary sites in the 3′–untranslated region (3′-UTR) of target messenger RNAs (mRNA), and efficient mRNA targeting requires continuous basepairing of microRNA nucleotides 2–8, the so-called “seed sequence” (4). In this way, microRNA can regulate target gene expression by translational inhibition, mRNA degradation, or both (3, 4). Dysregulation of microRNA by several mechanisms has been described in various disease states, including SLE (5, 6). Only recent studies have suggested that microRNA can regulate DNA methylation by targeting the DNA methylation machinery in SLE (3) (Figure 1A). The discovery of the association between microRNA and methylation regulation provides an insight into the role of microRNA in lupus CD4+ T cell hypomethylation and the pathogenesis of SLE.

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Figure 1. MicroRNA-21 (miR-21), miR-126, and miR-148a directly or indirectly regulate Dnmt1 in CD4+ T cells from patients with systemic lupus erythematosus (SLE). A, MiR-148a and miR-126 directly regulate Dnmt1, as validated experimentally. In particular, miR-148a binds to the Dnmt1 coding sequence, as predicted by the program RNA22 (a pattern-based method for identifying microRNA-target sites and their corresponding RNA/RNA complexes [8]), while miR-126 binds to the 3′–untranslated region (3′-UTR) of Dnmt, as predicted by the program MicroCosm (http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/). B, Dnmt is directly or indirectly regulated in CD4+ T cells from patients with SLE and triggers the overexpression of autoimmune-associated methylation-sensitive genes involved in SLE. In normal human T cells, gene hypermethylation controlled by Dnmt1 blocks the transcription activity of RNA polymerase II (RNA pol II), thus silencing autoimmune-related methylation-sensitive genes such as CD70, lymphocyte function–associated antigen 1 (LFA-1; CD11a), and EGFL7. In CD4+ T cells from patients with SLE, promoter hypomethylation allows binding of transcription factors (TFs) and recruiting of RNA polymerase II (step 1). This leads to the overexpression of autoimmune-related genes, including EGFL7 (step 2). Interestingly, miR-126 is encoded in the seventh intron of EGFL7. Thus, the expression of EGFL7 leads to elevated levels of miR-126, which down-regulates the production of Dnmt1 in a reciprocal negative feedback (amplification) loop (step 3). Low-level Dnmt1 leads to the hypomethylation status that maintains the aberrant autoimmune response (step 4). Other microRNA contributing to decreased Dnmt1 activity are miR-148a, through direct inhibition, and miR-21, which indirectly regulates Dnmt1 by targeting Ras guanyl-releasing protein 1 (RASGRP1) in the Ras–mitogen-activated protein kinase pathway and thus also influencing Dnmt1 protein levels. CH3 = methyl group.

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Pan et al (3) recently identified 2 microRNA, microRNA-21 (miR-21) and miR-148a, as being up-regulated in CD4+ T cells in both patients with lupus and MRL/lpr mice. Moreover, both microRNA down-regulate the protein level of the enzyme Dnmt1, one of the major components in the demethylation of DNA, thus resulting in hypomethylation status in CD4+ T cells. In particular, miR-21 indirectly down-regulates Dnmt1 by targeting its upstream regulator, Ras guanyl-releasing protein 1, while miR-148a directly down-regulates Dnmt1 by targeting the protein-coding region of its transcript (Figure 1B). The final result is the de-repression of autoimmune-associated methylation-sensitive genes in CD4+ T cells, such as CD70 and lymphocyte function–associated antigen 1 (LFA-1; CD11a). These investigators were also able to induce the potential alleviation of hypomethylation in CD4+ T cells from patients with lupus by transfection with miR-21 and miR-148a inhibitors.

The study by Zhao et al (1) further expands the role of microRNA and epigenetic changes in SLE. The novel finding is that, among the 11 microRNA that were observed to have increased or decreased expression in CD4+ T cells from patients with SLE, miR-126 was significantly overexpressed, and its up-regulation was inversely correlated with Dnmt1 protein levels (Figure 1B). Zhao and colleagues were then able to demonstrate that miR-126 can directly inhibit Dnmt1 translation by interacting with its 3′-UTR, leading to a significant reduction in Dnmt1 protein levels (Figure 1B). Through this mechanism, overexpression of miR-126 causes demethylation and up-regulation of genes encoding for LFA-1 (CD11a) and CD70, 2 autoimmune-related proteins, which are directly proportional to disease activity. The inhibition of miR-126 in CD4+ T cells from patients with SLE has opposite effects. The miR-126 host gene EGFL7 was also overexpressed in SLE CD4+ T cells, in a hypomethylation-dependent manner.

Another interesting point regarding the current study is that Zhao et al focused their attention not only on the influence of the DNA methylation machinery on lupus CD4+ T cells but also on the costimulation between active T cells and B cells, leading to IgG overproduction. They were also able to show that knocking down miR-126 in SLE CD4+ T cells reduced their autoimmune activity and their stimulatory effect on IgG production in the cocultured B cells.

The main differences in the reports by Pan et al (3) and Zhao et al (1) focusing on the role of microRNA overexpression affecting the DNA methylation mechanism in SLE T cells are shown in Table 1. Pan et al and Zhao et al detected different microRNA involved in the DNA methylation machinery. One possible explanation is that Pan and associates performed the microarray analysis of microRNA in splenic CD4+ T cells and B cells isolated from MRL/lpr mice and normal control mice but not in CD4+ T cells from patients with SLE. In contrast, in the present study, Zhao and colleagues performed their analysis using CD4+ T cells from patients with SLE and healthy control subjects. However, even though the initial microarray analyses were performed on different substrates, only CD4+ T cells from patients with SLE were used in the microRNA analysis, as shown in Table 1. Moreover, it is well known that SLE is a very heterogeneous disease, so it is possible that the different altered microRNA detected in the 2 studies can be associated with patient selection, disease subsets, autoantibody expression, immunosuppressive therapy, and phases of disease activity. Ethnic background is usually another important aspect to consider when studying patients with SLE, but it does not seem to play a role in this situation, because SLE patients in both studies are from a Chinese population.

Table 1. Main differences between 2 recent studies focusing on the role of microRNA overexpression affecting the DNA methylation mechanism in SLE T cells*
 Study authors (ref)
Pan et al (3)Zhao et al (1)
  • *

    MiR-21 = microRNA-21; SLEDAI = Systemic Lupus Erythematosus Disease Activity Index; anti-dsDNA = anti–double-stranded DNA; LFA-1 = lymphocyte function–associated antigen 1.

Overexpressed microRNAMiR-21, miR-148aMiR-126
Cell substrate used for microarray analysisSplenic CD4+ T cells and B cells isolated from MRL/lpr mice and controlsCD4+ T cells from SLE patients and healthy controls, no mouse model
No. of SLE patients studied for microRNA expression36 (33 female, 3 male)30 (all female)
SLE patient informationComplete (male:female ratio, age, disease duration, SLEDAI score, anti-dsDNA antibodies, lupus nephritis, treatment with steroids and secondary agents)Limited (age, sex, SLEDAI score, medications)
Overexpressed methylation-sensitive gene targetsLFA-1 (CD11a), CD70LFA-1 (CD11a), CD70, EGFL7
Cell types examined for microRNA overexpressionCD4+ T cellsCD4+ T cells and B cells

One possible limitation of the study by Zhao et al is the lack of information on the patients with SLE, in terms of clinical features and immunosuppressive therapy. Patients were recruited from an in-patient ward and a dermatology department, and it is not clear whether these SLE patients had predominantly dermatologic manifestations, which could be a reason for the different microRNA expression in the 2 studies. Moreover, Pan et al (3) provide more detailed information on SLE patients, including disease duration, anti–double-stranded DNA titer, number of patients affected by lupus nephritis, detection of proteinuria, and use of immunosuppressive therapy.

Both studies analyzed the influence of DNA methylation on the expression of genes that are linked to T cell autoreactivity. The CD70 and LFA-1 (CD11a) genes are the targets investigated in both studies, because they are demethylated genes overexpressed posttreatment with hypomethylating agents in CD4+ T cells (3). Zhao et al (1) further studied a new target, the miR-126 host gene EGFL7, which is also overexpressed in CD4+ T cells from patients with SLE. Up-regulation of miR-126 is associated with a reduction in EGFL7 promoter methylation and thus also with T cell autoreactivity in SLE, leading to an amplification cycle that further contributes to the disease.

Zhao and colleagues (1) studied the regulation of miR-126 on Dnmt1 at the 3′-UTR level using information from the miRBase microRNA version 11.0 database. However, this prediction was not confirmed by other algorithms, such as TargetScan or PicTar, which are commonly used in bioinformatic analyses. This may be particularly important because, in the present work, the 5′ interaction of miR-126 and the 3′-UTR of Dnmt1 only involve 4 bases. It is generally known that the seed sequence is expected to be 7–8 bases for most strong microRNA–mRNA interactions. Thus, it could be possible that the proposed interaction is weak, and the in vivo biologic relevance needs to be further examined.

It is also clear that microRNA can regulate the immune response through pathways independent from the DNA-methylation machinery (7). In fact, recent studies have shown that miR-146a is a negative regulator of the interferon pathway in patients with lupus, and that underexpression of miR-125 contributes to elevated expression of the proinflammatory cytokine RANTES in lupus (5–7).

A number of analytical techniques are now available for studying epigenetic modifications in a genome-wide manner. The systematic use of these genomic techniques will serve to provide a full profile of epigenetic dysregulation in SLE. Unlike genetic alterations, which are permanent, epigenetic alterations are reversible. This opens the possibility of using epigenetic drugs to reverse the pattern of epigenetic alterations to relieve the phenotype. To date, histone deacetylase inhibitors such as suberoylanilide hydroxamic acid and trichostatin A (TSA) have proved to be useful for relieving lupus disease in mice (2). The effects of TSA on human T cells are predominantly immunosuppressive and reminiscent of the signaling aberrations that have been described in patients with SLE (2). Current evidence indicates that most of the genes that exhibit aberrant patterns of DNA methylation are hypomethylated, although gene–gene–specific hypermethylation cannot be ruled out (2). Therefore, the detailed analysis of DNA methylation at the gene level will serve to evaluate how useful histone deacetylase inhibitors and DNA-demethylating drugs could be. It is not clear whether the increased expression of specific microRNA is an indirect effect rather than the cause of SLE, and this point also needs further investigation in future studies.

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