Epigenetic Aspects of Systemic Lupus Erythematosus

Autoimmune diseases such as systemic lupus erythematosus (SLE), rheumatoid arthritis, multiple sclerosis, autoimmune hepatitis, and inflammatory bowel disease have complex pathogeneses and the courses of events leading to these diseases are not well understood. The immune surveillance is a delicate balance between self and foreign as well as between tolerance and immune response. Exposure to certain environmental factors may impair this equilibrium, leading to autoimmune diseases, cancer, and the so-called “lifestyle diseases” such as atherosclerosis, heart attack, stroke, and obesity, among others. These external stimuli may also alter the epigenetic status quo and may trigger autoimmune diseases such as SLE in genetically susceptible individuals. This review aims to highlight the role of epigenetic (dys-)regulation in the pathogenesis of SLE. Electronic supplementary material The online version of this article (doi:10.1007/s40744-015-0014-y) contains supplementary material, which is available to authorized users.


INTRODUCTION
One interesting hypothesis concerning autoimmune diseases is that environmental effects on immune responses could be mediated by alterations in the epigenetic profile. Indeed, there is evidence that environmental factors may be the reason for the high discordance rate for autoimmune diseases in identical twins [1][2][3][4]. Advances in molecular genetics have illustrated that genomes are not a static entity for the deposition of genetic information. These findings imply dynamic response to external stimuli and a high genomic plasticity that is affected by epigenetic gene regulation. This kind of gene regulation relies on inducible and/or heritable patterns of gene expression, which are not based on changes of the genomic

WHAT IS EPIGENETICS?
Although known before, the word ''epigenetics'' was introduced in modern science in 1942 by

Conrad
Hal Waddington, a British developmental biologist [5]. The concept of epigenetics is defined as the study of regulatory mechanisms that account for (potentially) heritable and reversible patterns in gene expression without affecting the nucleotide sequence of the genome. As the Greek prefix '' '' (epi) means ''upon, over, on top of'', the ''epigenome'' is thought to be an additional, secondary informational level on top of the genetic code. A classic example of epigenetic regulation in mammals is the dosage compensation by silencing of one X chromosome in females. A condensed chromatin configuration prevents expression of genes on the silenced X chromosome, while the other X chromosome in the same nucleus is actively transcribed [6,7]. It has been shown in humans that the silencing of individual gene loci by imprinting (in combination with micro deletions and mutations) leads to developmental abnormalities, known as Beckwith-Wiedemann, Angelman and Prader-Willi syndromes [8][9][10].
As the molecular basis of inheritance was unknown at that time, the term was initially used in an unspecific sense. This in conjunction with the description of the DNA double-helix structure by Watson and Crick, which demonstrated its eminent role in inheritance [11], ''have cast a shadow over this discipline for decades'' [12]. The term was reintroduced no more than four decades later, as studies on chromatin structure had identified the molecular basis of epigenetics.
The year 1974 marked the ''birth-year'' of modern, molecular-based epigenetics. There, Kornberg and colleagues published that chromatin is ''a repeating unit of histones and DNA'' [13]. These repetitive units were then called ''nucleosomes''. However, it took until 1996 before two studies provided the first clear connection between histone acetylation and transcriptional regulation [14,15] and it took further 4 years before a functional link between histone methylation and chromatin structure could be established [16].  The  different  combinations  of  these  modifications are thought to constitute a code, which has led to the so-called ''histone code'' hypothesis [20].  In the last three decades, major advances have been made in understanding the interaction between DNA methylation, histone modification, and gene expression. This fundamental research demonstrated that the interplay between the individual components is highly complex and opened the new field of epigenetics. In the last few years, it became evident that epigenetic changes are not only involved in cancer and developmental processes but also play a significant role in the etiopathology of autoimmune diseases.

EPIGENETIC CHANGES IN AUTOIMMUNE DISEASES
The mechanisms underlying epigenetic changes are of great importance to human autoimmune diseases. However, they are poorly understood  MHC2TA could also be observed [67]. Different blood cell populations of SLE patients are characterized by a global loss of DNA methylation [68]. For instance, persistent hypomethylation of interferon genes and interferon-regulated genes can be found in CD4? T cells [69], CD19? B cells, CD14? monocytes [70], and neutrophils [71] [80]) and IL1R2 [81], respectively) and cell lysis (perforin [82,83]), which all can increase inflammation by stimulating the immune system.
Another example concerns the overexpression of the transcription regulatory factor cAMP-responsive element modulator alpha (CREMa) in T cells of patients with SLE and lupus-prone MRL/lpr mice. It binds to the CRE site in the promoter region of genes and contributes to epigenetic remodeling through the recruitment of DNA methyltransferase DNMT3A [84]. Then, DNMT3A mediates CpG hypomethylation, remodeling the CD8 cluster [85] and silencing of IL2 and IL17A [84]. On the other hand, it has recently been shown, that an increased histone H3 lysine 27 trimethylation enrichment at the hematopoietic progenitor kinase 1 (HPK1) promoter of SLE CD4? T cells (relative to controls) inhibits the HPK1 expression and contributes to autoimmunity in SLE [86]. All these reports support a role for epigenetic DNA alterations in the pathogenesis of SLE.
However, DNA methylation is not a process whose effects are restricted to the DNA. As the methylation of DNA maintains chromatin in a condensed and hence, more inactive configuration, it acts synergistically or antagonistically on the diverse modifications of histone proteins [87]. For instance, hypomethylated CpG island chromatin is enriched in hyperacetylated histones and deficient in linker histones [88]. DNA methylation may also protect individuals from autoimmune diseases, such as SLE: as the estrogen receptor becomes hypermethylated during aging [89] A recent study detected a correlation between the 5-hydroxymethylcytosine (5-hmC) level in the peripheral blood and SLE [97]. The oxidation of 5-methylcytosine (5-mC) to 5-hmC is an epigenetic mechanism which is present in the DNA of mammalian cells. First seen in bacteriophages in 1952 [98], it was then found in high levels in neurons of the central nervous system in human and mouse as well as in embryonic stem cells [99,100]. The exact function of this sixth DNA base is not fully understood, but it is thought to regulate gene expression and prompt DNA demethylation.
This hypothesis is supported by the observation that hydroxylation of 5-mC to 5-hmC by TET1 actively promotes DNA demethylation [101].
Reduction of hmC levels in DNA is also a hallmark of cancers and, contrary to DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 h following DNA synthesis [102].

ROLE OF MICRO RNA IN SLE PATHOGENESIS
Micro RNA (miRNA) was initially discovered in 1993 [103] but little attention was given to these small RNAs until 2001 [104][105][106][107][108]. miRNAs are an important class of endogenous regulatory small RNAs [109,110] which (amongst others) regulate the expression of genes involved in immune activation [111]. For cancer, it has been demonstrated that the miR-29 family induces DNA hypomethylation by directly targeting DNA methyltransferases thereby leading to a re-expression of hypermethylated silenced tumor suppressor genes [112,113]. These studies have shown that miRNAs are involved in disease pathogenesis by targeting DNA methylation. miRNAs are also implicated in the pathology of SLE [114,115]. One of these miRNAs, miR-146a, is a negative regulator of the IFN pathway. Underexpression of miR-146a contributes to alterations in the type I IFN pathway in lupus patients by targeting the key signaling proteins [114]. Dai et al. [116] identified several miRNAs that are differentially expressed in the peripheral blood mononuclear cells of SLE patients whose expression profiling may provide a useful clue for the etiology of SLE.
Another miRNA that is upregulated in CD4? T cells from SLE patients is miR-126 [118]. is the main initiator of the blood coagulation cascade and it could be shown that monocytes of patients with SLE are characterized by a high TF expression and low miR-19b and -20a levels [122]. Reporter assays demonstrated that miR-20a binds to TF mRNA [123]. Thus, downregulation of miR-19b and miR-20a could contribute to increased TF expression provoking the hypercoagulable state characteristic of patients with SLE. Further miRNAs involved in SLE are miRNA-3148 [124], miRNA-1246 [125], and miRNA-let7A [126], respectively. Excessive activation of the innate immune system reported inflammatory targets [128,129]. It could be shown that its overexpression may contribute to hyperplasia and a proinflammatory response, including inflammatory mediator production. Recent studies have shown that a significant fraction of miRNAs themselves is regulated by epigenetic mechanisms [130][131][132], demonstrating the entire complexity of eukaryotic gene regulation.
We now know that changes in DNA methylation, mRNA, and miRNA expression are characteristic for SLE and correlate with the phenotype of this severe disease [133]. However, more studies are required to consolidate the role of miRNAs in SLE pathology. Until then, the question of if these non-coding RNAs are ''hope or hype'' [134] remains unanswered for SLE.