Abstract: The study of epigenetic mechanisms in the pathogenesis of autoimmune diseases is receiving unprecedented attention from clinicians and researchers in the field. Autoimmune disorders comprise a wide range of genetically complex diseases, including systemic lupus erythematosus, rheumatoid arthritis, type 1 diabetes, and multiple sclerosis. Together they affect a significant proportion of the population and have a great economic impact on public health systems. Epigenetic mechanisms control gene expression and are influenced by external stimuli, linking environment and gene function. A variety of environmental agents, such as viral infection, hormones, certain drugs, and pollutants, have been found to influence the development of autoimmune diseases. On the other hand, there is considerable evidence of epigenetic changes, particularly DNA methylation alterations, in diseases like systemic lupus erythematosus, rheumatoid arthritis, or multiple sclerosis. However, the gap in our understanding between the specific effects of external agents and the influence on epigenetic profiles has not yet been filled. Here we review a number of studies describing epigenetic alterations in autoimmune diseases and a range of environmental factors that influence the development of autoimmune diseases. We also discuss potential mechanisms linking environment and epigenetics, consider the prospects for future epigenetic studies addressing the relationship between environment and epigenetics, and comment on the use of drugs with an epigenetic-reversing effect in the clinical management of these diseases.

Autoimmune Disorders: Interplay Between Environmental and Genetic Factors

Autoimmune disorders constitute a group of more than 80 different diseases characterized by immune attack of components of a person’s own body, mediated by autoantibodies and autoreactive T cells. Specifically, the common feature that defines autoimmune diseases is the breakdown of immune tolerance and the subsequent malfunction of the immune system, resulting in inflammation and tissue destruction (Cho and Gregersen, 2011). Despite their heterogeneity, autoimmune diseases share epidemiological, etiopathogenic, and clinical features. Most autoimmune disorders affect more women, frequently of reproductive age, than men. This observation draws attention to the environmental etiology, especially the role of sex hormones and X-chromosome genes in autoimmune disorders. On the other hand, autoimmune diseases are treated with immunosuppressive strategies. Finally, people frequently suffer from more than one autoimmune disorder at the same time or during different stages of their lives. Also, patients with chronic inflammatory diseases, such as systemic lupus erythematosus (SLE) or rheumatoid arthritis (RA), are at higher risk than the general population of developing specific types of lymphoma (Hansen et al., 2007).

Autoimmune diseases can be classified into two canonical groups, depending on whether the effect is organ-specific or systemic. In the former case, the immune response specifically reacts against autoantigens located in a specific organ. Some examples of organ-specific autoimmune disorders are diabetes mellitus type 1, multiple sclerosis (MS), primary biliary cirrhosis, Hashimoto’s thyroiditis, and Grave’s disease, among others. On the other hand, systemic autoimmune disorders, such as RA, SLE, Sjögren’s syndrome, and psoriasis, are characterized by a multi-organ attack arising from the systemic distribution of the autoantigens (Javierre et al., 2008).

Autoimmune diseases affect around 5% of the world population, particularly people from developed countries. This biased distribution is explained by the existing differences in the genetic background and environmental agents. Autoimmune processes, like other complex diseases such as cancer, arise from a combination of genetic susceptibility and environmental factors. It is therefore critical not only to study them separately but also to understand their interactions in order to define risk levels and to develop therapeutic strategies.

Genetic susceptibility has a major role in autoimmunity development. In fact, polymorphisms in over 200 bona fide loci have been identified as contributors to autoimmune disorders and many of these are common to various autoimmune diseases (Cho and Gregersen, 2011). The combination of multiple polymorphisms of relatively small effect individually can generate a physiological context in which the threshold for attaining an autoimmune response is lower. The majority of susceptibility loci affected by polymorphisms fall into one of three main groups: innate immune response, cytokine signaling, and lymphocyte activation. A clear example of a group of susceptibility genes related with lymphocyte activation is the major histocompatibility complex (MHC) family. Polymorphisms affecting these sequences significantly contribute to type 1 diabetes, MS, celiac disease, psoriasis, RA, and SLE. Another classic example of a susceptibility gene related with the innate immune response is Interferon regulatory factor 5 (IRF5). This gene is involved in the interferon-mediated signaling, featuring many polymorphisms that are associated with RA, SLE, systemic sclerosis, and primary biliary cirrhosis.

However, genetics cannot fully explain the hereditary patterns of autoimmune disorders. In fact, genome-wide association studies have shown that genetic polymorphisms account for only 20% of the phenotypic variance (Wallace, 2010). In addition, monozygotic (MZ) twins show moderate rates of concordance for autoimmune disorders (Ballestar, 2010). For example MZ twins are highly concordant for psoriasis or celiac disease. In contrast, ulcerative colitis, RA, and type 1 diabetes have stronger environmental influences, as reflected by low concordance rates of around 10%. All of these data highlight the different contributions and interactions between genetic and environmental factors in various autoimmune diseases. Temporal associations between some environmental exposures and autoimmunity onset, and relationships between seasonality patterns in birth dates and autoimmunity development have been observed (Samuelsson and Carstensen, 2003; Sarkar et al., 2005). Occurrence of geographic and occupational clustering of autoimmune patients provides further evidence of the environmental determinants of these diseases. Many environmental factors, including exposure to tobacco smoke, infectious agents, radiation, ultraviolet (UV) light, and chemical compounds, among other external conditions, are significantly associated with the development of autoimmune disorders. The majority of these environmental factors can directly or indirectly induce epigenetic changes, which modulate gene expression and therefore associate with changes in immune cell function. For this reason, epigenetics provides a source of molecular mechanisms that can explain the environmental effects on the development of autoimmune disorders. The close relationship between environment and epigenetic status is exemplified by the ability to acquire DNA methylation alterations induced by a specific maternal diet in descendent mice (Cooney et al., 2002; Sandovici et al., 2011; Waterland et al., 2006; 2010). This relationship has not only been determined in mice; there is also a great deal of evidence of epigenetic changes induced by environment in humans (Heijmans et al., 2008; Katari et al., 2009; Waterland et al., 2010).

Other potential mechanisms underlying the induction of autoimmunity by environmental factors have been proposed. One model is the “hapten hypothesis” which proposes that certain chemical products may react with self components of the body to generate novel antigenic molecules (Mintzer et al., 2009). For example, tobacco smoke can convert arginine into citrulline. Interestingly, RA patients are frequently characterized by the presence of autoantibodies against citrullinated proteins (Klareskog et al., 2006). Environmental factors, such as UV radiation, can also alter the abundance and localization of some autoantigens (Casciola-Rosen et al., 1994; Kuhn and Beissert, 2005). Another theory emphasizes the molecular mimicry based on the cross-reaction between environmental antigens with self antigens. This is highlighted by the detection of serum autoantibodies that also recognize pathogenic epitopes such as the anti-SM autoantibody obtained from SLE patients that also reacts against the Epstein-Barr virus antigen EBNA-1 (Harley and James, 2006). All these possibilities are compatible with the thesis that environmental factors induce epigenetic-mediated expression changes as discussed below in further detail.

Epigenetic Deregulation in Autoimmune Diseases

Epigenetics has become an essential area of research for investigating mechanisms that lead to human disease. Epigenetics focuses on the study of mechanisms and chemical marks that influence gene activity and ultimately cell function. There are two main epigenetic modifications: DNA methylation and histone modifications, both of which are associated with transcriptional regulation and determination of the cellular transcriptome, thereby contributing to cell identity and function (Portela and Esteller, 2010). The breakdown of epigenetic regulation is now known to play a key role in the development of diseases. Exploiting the reversibility of epigenetic marks opens up the possibility of developing novel targets for therapeutic treatment. Although a large amount of information about the mechanisms of epigenetic deregulation in cancer and other diseases has been accumulated, these mechanisms have been less well studied in relation to autoimmune processes. The importance of epigenetics in autoimmunity was first evidenced by the observation that DNA demethylating agents result in drug-induced autoimmunity (Quddus et al., 1993; Richardson, 1986). Defects in some factors involved in epigenetic mechanisms have also been described in autoimmune processes. For instance, transgenic or knockout mice for Gadd45a (Salvador et al., 2002) or the histone acetyltransferase p300 (Forster et al., 2007) develop different autoimmune syndromes. On the other hand, although MZ twins are genetically identical, they are often discordant for autoimmune disorders. This discordance is the result of environmental influences, frequently operating through epigenetic mechanisms. In fact, a recent study showed that MZ discordant for SLE display differences in DNA methylation and expression in a number of genes associated with immune function (Javierre et al., 2010).

Figure 1. Epigenetic gene regulation. DNA methylation and histone modifications determine gene expression and genomic stability. DNA is represented in the context of chromatin structure, where nucleosomes are represented as grey cylinders. Each nucleosome contains two copies of each core histone (H2A, H2B, H3, and H4). Histone N-terminal tails are represented by protruding grey segments. CpG methylation and different histone modifications are presented as indicated in the box. Unmethylated gene promoters allow gene expression, in contrast with methylated promoters that result in gene repression. In repetitive sequences, methylation provides genomic stability and endoparasitic silencing. Active histone marks at gene promoters (trimethylation of the lysine 4 of the histone H3, or H3K4me3, and acetylation of the histones H3 and H4, or H3/H4 ac) associate with gene expression, while inactive histone marks at these regions (trimethylation of the lysines 9 and 27 of the histone H3, or H3K9me3 and H3k27me3, respectively) associate with gene silencing.

As mentioned above, DNA methylation is one of the main epigenetic marks. In vertebrates, DNA methylation consists of the addition of a methyl group in the 5′ position of cytosines followed by guanines (CpGs). DNA methylation is catalyzed by a group of enzymes named DNA methyltransferases (DNMTs) using S-adenosylmethionine as the donor substrate. CpG sites are under-represented in the mammalian genome as a whole, although they cluster in repetitive sequences as well as in regions known as CpG island, many of which overlap with the promoter of RNA polymerase II-transcribed genes. Except those associated with tissue-specific, X-chromosome, or imprinted genes, most promoter CpG islands are demethylated in physiological situations, allowing transcription to proceed (Figure 1). Conversely, CpG islands located in repetitive sequences are methylated contributing to genomic stability (Figure 1). Alteration of DNA methylation profiles can occur at the global or sequence-specific level (Portela and Esteller, 2010).

The global deregulation of the DNA methylation content is affected in many cell types in a range of autoimmune disorders (Table 1). This phenomenon has been best studied in SLE (Lei et al., 2009), RA (Neidhart et al., 2000), progressive systemic sclerosis (Lei et al., 2009), ulcerative colitis (Gloria et al., 1996), and psoriasis (Zhang et al., 2010). Global changes of DNA methylation content can have different effects, including gene expression alteration, imprinting signature modification, and reactivation of endoparasitic sequences (Figure 1), all of which contribute to the breakdown of the immune tolerance checkpoints. CD4+ T cells of SLE patients are characterized by a significant loss in the total content of 5-methylcytosine (Lei et al., 2009) that correlates with decreased levels of DNMTs. Interestingly, the symptomatology is directly associated with the reduction in the level of this epigenetic mark (Richardson et al., 1990).

The global decrease of DNA methylation is also supported by the generation of autoreactivity in vitro and lupus-like disease in vivo as consequence of hydralazine treatment, a drug that decreases DNA methylation levels (Mazari et al., 2007). Furthermore, global DNA hypomethylation has been detected in blood cells and synovial tissue of RA patients. In the specific case of RA synovial fibroblasts (RASFs), global hypomethylation correlates with retrotransposable Line 1 overexpression and altered gene expression (Neidhart et al., 2000). In progressive systemic sclerosis and ulcerative colitis, T lymphocytes and affected mucosa of the rectum all show lower levels of 5-methylcytosine than control donors (Gloria et al., 1996; Lei et al., 2009). Conversely, peripheral blood mononuclear cells from psoriatic patients are characterized by an increase in DNA methylation accompanied by DNMT1 up-regulation; the presence of these features is directly associated with Psoriasis Area and Severity Index scores (Zhang et al., 2010). Global alterations in the content of 5-methylcytosine suggests changes in repetitive elements because they are the major contributors of CpG dinucleotides to the genome (Wilson et al., 2007). Despite this evidence, there is little information about the specific repetitive elements that are affected in autoimmunity. In the case of SLE, the 18S and 28S regions of the ribosomal RNA genes that are represented in several hundred copies have been demonstrated to be demethylated (Javierre et al., 2010). These patients overexpress the pre-RNA and the 18S RNA. This overproduction could be related to an increase in the number of ribosomal molecules in SLE, which could stimulate the generation of the autoantibodies against these particles, which are frequently detected in these patients (Isenberg et al., 2007; Sawalha and Harley, 2004). On the other hand, chromatin is chemically modified during apoptosis, generating new epitopes that may be recognized by the immune system (Boix-Chornet et al., 2006). Interestingly, this type of cell death is a typical feature of autoimmunity due to the increased rate of this event as well as the insufficient clearance of apoptotic debris noted in many autoimmune disorders. Moreover, cell death causes these new intracellular autoantigens to be released into the extracellular medium, explaining why the majority of autoantibodies mainly react against intracellular components. A recognized apoptosis-induced change in the chromatin is the generalized loss of methylation (Emlen et al., 1994; Kaplan et al., 2002). It is important to mention that injection of apoptotic DNA into a healthy mouse generates a lupus-like disorder, but this autoimmune response is not obtained by the use of methylated DNA (Wen et al., 2007). Non-methylated DNA is more antigenic than the methylated form, so the immune system can interpret the apoptotic DNA as microbial material, and so react against it (Krieg, 1995; Yung et al., 1995).

DNA methylation alterations have been identified in specific genomic regions (Table 1). Genes important for immune homeostasis and cellular biology are affected by this epigenetic deregulation mechanism. Specifically, many gene promoters are hypomethylated in autoimmune disorders. Some examples are PRF1, CSF3R, TNFSF7, ITGAL, and IFNGR2 in SLE (Javierre et al., 2010; Kaplan et al., 2004; Lu et al., 2002), MAPK13 and MET in RA (Neidhart et al., 2000), PAD2 in MS (Mastronardi et al., 2007), and SHP1, p15, p16, and p21 in psoriasis (Chen et al., 2008; Ruchusatsawat et al., 2006; Zhang et al., 2010; 2007). On the other hand, other gene promoters are hypermethylated, including DR3 in RA (Takami et al., 2006), BP230 in Sjögren’s syndrome (Gonzalez et al., 2011), FLI1 in scleroderma (Wang et al., 2006), and PAR2 and MDR1 in ulcerative colitis (Tahara et al., 2009; 2009). All of these findings highlight the need for further DNA methylation screening studies to determine the range of these alterations in autoimmune disorders.

The enzymatic addition or elimination of chemical groups, including acetyl, methyl, or phosphate groups among others, to the histone tails, determines the interaction of chromatin with different nuclear factors, regulating nuclear organization, gene expression, and genomic stability (Kouzarides, 2007) (Figure 1). The alteration of the histone modification profile can generate alterations in cellular phenotype and genomic stability, collaborating to produce the loss of immune tolerance in immune cells. Although the important role of histone modification deregulation in autoimmunity has been accepted, not many examples have been identified. In fact, the majority of these deregulating events have been described in SLE patients. Monocytes obtained from these patients undergo histone H4 hyperacetylation, affecting gene promoters, consequently giving rise to aberrant overexpression (Zhang et al., 2010). Conversely, CD4+ T cells are characterized by global histone H3 and H4 hypoacetylation (Mishra et al., 2001). These lymphocytes overproduce interleukin-10 (IL-10) and cell-surface CD40 ligand (CD154), but under-produce interferon-gamma (IFN-γ). The treatment based on the histone deacetylase inhibitor trichostatin A (TSA) has the ability to revert this skewed expression (Hu et al., 2008). Although the role of histone modifications in autoimmunity is far from being completely understood, evidence from the use of epigenetic drugs supports the notion that the deregulation of this regulatory mechanism is essential in the breakdown of immune tolerance checkpoints. In-depth analysis of histone modification profiles of different cell populations obtained from autoimmune patients and chromatin immunoprecipitation combined with high-throughput sequencing would provide an excellent starting point for confronting this medical challenge.

Environmental Factors Triggering Autoimmunity: Potential Mechanisms Linking Environment with Epigenetic Regulation

Figure 2. Cellular pathways linking environmental factors with epigenetic gene control. A variety of external factors, such as drugs, pollutants, UV light, pathogens, stress, and hormones among others, have the ability of impact on epigenetic marks and gene expression. Regulation can be mainly driven by two basic mechanisms: regulating transcriptional machinery (RNA polymerase II, co-activators, co-repressors) or controlling epigenetic enzymes (DNA methyltransferases and histone modification enzymes). Abbreviations: AHR, aryl hydrocarbon receptor; ARNT, aryl hydrocarbon receptor nuclear translocator; DNMT, DNA methyltransferase; EBV, Epstein-Bar virus; NF-κB, nuclear factor-kappaB; TCR, T cell receptor; UV, ultraviolet light; TCDD, 2,3,7,8-tetrachlorodibenzo-p-dioxin.

Accumulated data suggest that environmental factors have a variable influence on epigenetic profiles associated with autoimmune disorders. Although there is evidence for these relationships, it is difficult to establish a direct link between one particular environmental factor and the development of the disease. In fact, it is almost impossible to identify all the environmental factors to which individuals are exposed at one given time. The most widely accepted environmental conditions that trigger autoimmunity through epigenetic mechanisms are drugs, pollutants, viruses and other pathogens, sex hormones, radiation, heavy metals, and stress (Figure 2). These specific environmental conditions will be discussed below.

Many medications have side effects such as the generation of drug-induced autoimmune reactions or the exacerbation of pre-existing autoimmune disorders. Several of these drug-induced autoimmune manifestations frequently have similarities with SLE. In fact, around 10% of SLE cases are drug-induced. Additionally, more than 100 drugs are known to cause lupus-like disease after long-term exposure, the disorder disappearing once the exposure ceases. Most of these chemical products are characterized by the ability to induce epigenetic modifications, suggesting a possible mechanism of autoimmunity generation. The medications that most commonly induce drug-induced autoimmune syndromes are 5-azacytidine, procainamide, hydralazine, quinidine, isoniazid, methyldopa, minocycline, chlorpromazine, and phenytoin (Dedeoglu, 2009). The first evidence of drug-induced autoimmunity was reported in 1950 in people treated with hydralazine (for a review see Wiik, 2008). Although this observation was made early on, the first experimental verification of the effect of a demethylating drug in inducing autoimmunity came many years later, by Richardson and co-workers. They confirmed the induction of self-reactivity in CD4+ and CD8+ lymphocytes by treatment with the DNA methylation inhibitor 5-azacytidine (Richardson, 1986). This drug is a cytosine analogue that contains a nitrogen atom at the 5 position of the pyrimidine ring that it is incorporated into the newly synthesized DNA strand, generating genome-wide hypomethylation. 5-azacytidine, commercially known as Vidaza^®, has been used to treat myelodysplastic syndromes since 2004, and some patients receiving this treatment experienced lupus-like syndrome. Other experiments have confirmed these results. In fact, murine and human T cells treated with 5-azacytidine, procainamide (an inhibitor of the ERK signaling pathway that lowers levels of DNMTs during mitosis), or other demethylating agents can be activated by autologous macrophages alone, responding to self-major histocompatibility complex II molecules without antigen requirement (Cornacchia et al., 1988). Furthermore, the injection of T lymphocytes treated with demethylating agent into syngeneic mice or the direct treatment of these animals with these drugs induces a lupus-like disease (Quddus et al., 1993). All of these data indicate a key role for DNA methylation in autoimmunity.

Autoimmunity induction by pollutants, as with drugs, can trigger autoimmune response by different mechanisms. A toxic exposure can result in aberrant cell death and the released cellular material can activate Nod-like receptors (NLRs) and Toll-like receptors (TLRs), key mediators of innate immune response. NLR activation leads to NLRP3-inflammasome activation and production of pro-inflammatory cytokines, including IL-1β, IL-6, and IFN-γ. Conversely, activation of TLRs by nuclear material is essential for producing an autoantibody response to nuclear antigens such as chromatin and RNA-protein complexes. In these cases, the T cell response is increased and promotes the activation of autoantibody producing B cells. These autoantibodies to self-antigens stimulate immune-complex formation and tissue damage that can generate cellular material release, promoting the immune response. Tetramethylpentadecane (TMPD) is an example of a chemical that induces autoimmunity. TMPD, commonly known as pristane, is used in processed food for human consumption (Reeves et al., 2009). Compelling evidence shows that TMPD can induce chronic inflammatory response in organs such as liver, spleen, and lymph nodes (Cruickshank and Thomas, 1984). The effects of TMPD in inducing chromatin changes, and potentially changes in gene expression, have been described (Garrett and Cuchens, 1991). Another example is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a highly potent dioxin as well as a contaminant of the herbicide Agent Orange (Young et al., 2004). TCDD has an important immunosuppressive action due to the activation of aryl hydrocarbon receptor (AHR) and the generation of CD4+ CD25+ T regulatory cells (Funatake et al., 2005). AHR is known to physically associate with elements of the epigenetic machinery (Gomez-Duran et al., 2008) and epigenetically regulate gene transcription (Figure 2) (Singh et al., 2011). Another example is that of the common industrial solvent trichloroethylene (TCE), which is known to be able to exacerbate autoimmunity in mice (Cai et al., 2008). TCE has also been reported to influence DNA methylation patterns (Palbykin et al., 2011). Finally, the fungicide hexachlorobenzene (HCB) is associated with the porphyria turcica related with altered porphyrin metabolism (Michielsen et al., 1999). Exposure to HCB can induce hepatomegaly, splenomegaly, hyperpigmentation, hirsutism, painless arthritic changes of the hands, and enlarged lymph nodes and thyroid (Michielsen et al., 1999). Recent data have also shown the epigenetic effects of HCB (Plante et al., 2006).

Infectious agents can also induce autoimmunity. Throughout our life we are exposed to infections caused by different pathogens, such as viruses and bacteria. These pathogens use several mechanisms that result in initiation or perpetuation of autoimmunity. These mechanisms affect the processing and presentation of self-antigens, immune cell activation, cytokine release, apoptotic death, and the process of necrosis. Several mechanisms are antigen-specific but others are non-specific and related with the “bystander activation.” Molecular mimicry, expression of modified proteins and cryptic antigens and production of superantigens by a variety of microorganisms account for the most common antigen-specific mechanisms. Finally, pathogens can use cellular pathways that result in alteration of cell identity, through the induction of epigenetic and expression changes. There are several examples of infectious agents that use these mechanisms to induce autoimmunity.

One of the best known examples is the Epstein-Barr virus (EBV). EBV infects B lymphocytes and is associated with a panel of common autoimmune diseases, like RA, SLE, and MS (Niller et al., 2008). EBV has also been associated with the development of Sjögren’s syndrome (Padalko and Bossuyt, 2001), autoimmune thyroiditis (Vrbikova et al., 1996), autoimmune hepatitis (Vento et al., 1995), and Kawasaki disease. To infect B cells, the major envelope glycoprotein of EBV binds the complement receptor type 2 (CD21) on the cell surface. This binding is sufficient to trigger nuclear factor kappaB (NF-κB) activation and ultimately results in nuclear accumulation of p50 and p65 hetero- and homodimers. As NF-κB is activated, the viral DNA enters the cell nucleus and transcription of several viral products is initiated. Both NF-κB proteins p65 and p50 and virus-encoded transcription factors regulate transcription (Figure 2) and are able to associate to epigenetic machinery. Another example of an infectious agent associated with autoimmunity is Parvovirus B19. Parvovirus B19 has been detected in patients with arthritis and skin rashes (Lunardi et al., 2008). Another pathogen that induces autoimmunity is the human cytomegalovirus (HCMV). This virus infects around 70-100% of world’s population and establishes life-long latency in the host. A positive correlation between HCMV infection, presence of viral proteins, and development of disease has been detected in RA, Sjögren’s syndrome, dermatopolymyositis, psoriasis, Wegener’s granulomatosis, ulcerative colitis, and Crohn’s disease (Einsele et al., 1992; Kantor et al., 1970). Apart from viruses, bacteria also represent a big group of infectious agents that cause autoimmunity. For example, Streptococcus pyogenes leads to rheumatic fever. Systematic studies on the specific effects of these infectious agents on epigenetic and expression profiles are needed to understand their mechanisms of action in inducing autoimmunity.

Sex hormones are another type of environmental factor that can trigger the autoimmune response. Estrogens are able to enhance humoral autoimmunity and stimulate the T cell response (Cutolo et al., 2004), while androgens and progesterone suppress these immune characteristics (Cutolo et al., 2006). In general, females have stronger humoral and cellular immunity than men, owing to the detection of higher levels of circulating antibodies, greater numbers of circulating CD4+ T cells, and enhanced cytokine production (Nalbandian and Kovats, 2005). Sex hormones can directly affect the function of immune cells by binding to the steroid receptors expressed by the cells of the immune system. Estrogen receptors are expressed in CD8+ T lymphocytes, monocytes, neutrophils, and natural killer cells. B lymphocytes, apart from estrogen receptors, also express androgen receptors (Rubtsov et al., 2010). Changes in the levels of sex hormones generate a number of alterations in innate and adaptive immune cells. Unfortunately, the stronger immunity of females has a down-side in that they are more susceptible to autoimmune diseases. Many hormone receptors translocate to the nucleus upon binding with their corresponding ligands, being able to translate the external signal into transcriptional change (Figure 2), in general, in association with elements of the epigenetic machinery.

Radiation is another important environmental factor that induces autoimmunity. Although, in some cases, UV light induces essential chemical reactions such as formation of pre-vitamin D3. In other cases it may cause local and systemic immune suppression. Exposure to UV radiation induces the activation of NF-κB. This in turn induces the secretion of a variety of inflammatory mediators including IL-1 or IL-6, the TNF-α molecule, and the VEGF transcriptional factor (Abeyama et al., 2000). In keratinocytes, UV light provokes an inflammatory response causing DNA damage, apoptosis, and release of autoantigens from these cells. UV radiation can also cause redistribution of these autoantigens, alter self-proteins to make them more immunogenic, and enhance the immunogenicity (Maverakis et al., 2010).

Heavy metals are also related with autoimmune diseases. Among these, mercury, silver, and gold have the greatest ability to induce autoimmunity. Silver and gold induce the production of antinuclear antibodies, especially the generation of an autoantibody against the nucleolar protein fibrillarin (Baserga et al., 1991). Mercury can induce autoimmunity by inducing necrosis of somatic cells. There is growing evidence that exposure to heavy metals can induce aberrant gene deregulation through a variety of epigenetic mechanisms (Martinez-Zamudio and Ha, 2011).

Finally, physical and psychological stresses have been suggested as being potential modulators in the development of autoimmune diseases. The possible role of psychological stress in the pathogenesis of autoimmune disease has been related with the major stress-related hormones, which ultimately influence epigenetic control through its corresponding receptors.

Future Challenges of Epigenetic Research in Autoimmunity

Undoubtedly, we are far from understanding not only the extent of epigenetic alterations in autoimmune disorders but also the direct impact of specific environmental factors in immune cells’ epigenetic and expression profiles. High-throughput studies of affected cell types in different autoimmune diseases will allow us to identify characteristic epigenetic deregulation events. Such a meticulous analysis will improve our understanding of the autoimmune process as well as allowing us to evaluate the potential of therapeutic approaches to revert these alterations. One important step towards achieving this aim is the use of adequate model systems. Due to the complexity of autoimmune disorders, it is important to control the heterogeneity so that we may easily identify the specific epigenetic defect. For this reason, the use of MZ twins discordant for the autoimmune disorders is an appropriate approach to control for the genetic influence among all the other factors that determine the origin and course of the disease. The small number of these matched patients, the limited amount of sample that can be obtained from them, and the need for fractionation, make it important also to consider the use of animal models. The development and characterization of these autoimmune models is another intermediate objective. Moreover, due to the difficulty of acquiring samples, it is important to promote interdisciplinary relationships. Collaborations between clinicians and researchers, as well as the dialogue between epigenetics and immunology experts are essential to ensure advances in the epigenetic study of autoimmunity.

The possibility of reverting epigenetic modifications opens new prospects for therapeutic treatment of these diseases. Several epigenetic drugs are used in the treatment of myelodysplastic syndromes. Better knowledge on the extent of epigenetic alterations and how this can be influenced by drug treatment will surely help to determine the true potential of epigenetic therapeutic compounds.

Acknowledgments

E.B. is supported by grant SAF2011-29635 from the Spanish Ministry of Science and Innovation (MICINN) and grant 2009SGR184 from AGAUR (Catalan Government).

Disclosure

The authors declare no conflicts of interest.

Corresponding Author

Esteban Ballestar, Ph.D., Chromatin and Disease Group, Cancer Epigenetics and Biology Programme (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, 08908, Spain.

References

Abeyama K, Eng W, Jester JV, Vink AA, Edelbaum D, Cockerell CJ, Bergstresser PR, Takashima A. A role for NF-kappaB-dependent gene transactivation in sunburn. J Clin Invest 105(12):1751-1759, 2000.

Ballestar E. Epigenetics lessons from twins: prospects for autoimmune disease. Clin Rev Allergy Immunol 39(1):30-41, 2010.

Baserga SJ, Yang XD, Steitz JA. An intact Box C sequence in the U3 snRNA is required for binding of fibrillarin, the protein common to the major family of nucleolar snRNPs. EMBO J 10(9):2645-2651, 1991.

Boix-Chornet M, Fraga MF, Villar-Garea A, Caballero R, Espada J, Nunez A, Casado J, Largo C, Casal JI, Cigudosa JC, Franco L, Esteller M, Ballestar E. Release of hypoacetylated and trimethylated histone H4 is an epigenetic marker of early apoptosis. J Biol Chem 281(19):13540-13547, 2006.

Cai P, Konig R, Boor PJ, Kondraganti S, Kaphalia BS, Khan MF, Ansari GA. Chronic exposure to trichloroethene causes early onset of SLE-like disease in female MRL +/+ mice. Toxicol Appl Pharmacol 228(1):68-75, 2008.

Casciola-Rosen LA, Anhalt G, Rosen A. Autoantigens targeted in systemic lupus erythematosus are clustered in two populations of surface structures on apoptotic keratinocytes. J Exp Med 179(4):1317-1330, 1994.

Cooney CA, Dave AA, Wolff GL. Maternal methyl supplements in mice affect epigenetic variation and DNA methylation of offspring. J Nutr 132(8 Suppl):2393S-2400S, 2002.

Cornacchia E, Golbus J, Maybaum J, Strahler J, Hanash S, Richardson B. Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity. J Immunol 140(7):2197-2200, 1988.

Cruickshank B, Thomas MJ. Mineral oil (follicular) lipidosis: II. Histologic studies of spleen, liver, lymph nodes, and bone marrow. Hum Pathol 15(8):731-737, 1984.

Cutolo M, Capellino S, Sulli A, Serioli B, Secchi ME, Villaggio B, Straub RH. Estrogens and autoimmune diseases. Ann N Y Acad Sci 1089:538-547, 2006.

Cutolo M, Sulli A, Capellino S, Villaggio B, Montagna P, Seriolo B, Straub RH. Sex hormones influence on the immune system: basic and clinical aspects in autoimmunity. Lupus 13(9):635-638, 2004.

Chen M, Chen ZQ, Cui PG, Yao X, Li YM, Li AS, Gong JQ, Cao YH. The methylation pattern of p16INK4a gene promoter in psoriatic epidermis and its clinical significance. Br J Dermatol 158(5):987-993, 2008.

Cho JH, Gregersen PK. Genomics and the multifactorial nature of human autoimmune disease. N Engl J Med 365(17):1612-1623, 2011.

Dedeoglu F. Drug-induced autoimmunity. Curr Opin Rheumatol 21(5):547-551, 2009.

Einsele H, Steidle M, Muller CA, Fritz P, Zacher J, Schmidt H, Saal JG. Demonstration of cytomegalovirus (CMV) DNA and anti-CMV response in the synovial membrane and serum of patients with rheumatoid arthritis. J Rheumatol 19(5):677-681, 1992.

Emlen W, Niebur J, Kadera R. Accelerated in vitro apoptosis of lymphocytes from patients with systemic lupus erythematosus. J Immunol 152(7):3685-3692, 1994.

Forster N, Gallinat S, Jablonska J, Weiss S, Elsasser HP, Lutz W. p300 protein acetyltransferase activity suppresses systemic lupus erythematosus-like autoimmune disease in mice. J Immunol 178(11):6941-6948, 2007.

Funatake CJ, Marshall NB, Steppan LB, Mourich DV, Kerkvliet NI. Cutting edge: activation of the aryl hydrocarbon receptor by 2,3,7,8-tetrachlorodibenzo-p-dioxin generates a population of CD4+ CD25+ cells with characteristics of regulatory T cells. J Immunol 175(7):4184-4188, 2005.

Garrett LR, Cuchens MA. Pristane induced effects on chromatin of rat lymphoid cells. J Cell Biochem 45(3):311-316, 1991. Based on changes made above (name initials and journal name abbreviations), please make similar changes to the rest of the references.

Gloria L, Cravo M, Pinto A, De Sousa LS, Chaves P, Leitao CN, Quina M, Mira FC, Soares J. DNA hypomethylation and proliferative activity are increased in the rectal mucosa of patients with long-standing ulcerative colitis. Cancer 78(11):2300-2306, 1996.

Gomez-Duran A, Ballestar E, Carvajal-Gonzalez JM, Marlowe JL, Puga A, Esteller M, Fernandez-Salguero PM. Recruitment of CREB1 and histone deacetylase 2 (HDAC2) to the mouse Ltbp-1 promoter regulates its constitutive expression in a dioxin receptor-dependent manner. J Mol Biol 380(1):1-16, 2008.

Gonzalez S, Aguilera S, Alliende C, Urzua U, Quest AF, Herrera L, Molina C, Hermoso M, Ewert P, Brito M, Romo R, Leyton C, Perez P, Gonzalez Mj. Alterations in type I hemidesmosome components suggestive of epigenetic control in the salivary glands of patients with Sjogren’s syndrome. Arthritis Rheum 63(4):1106-1115, 2011.

Hansen A, Lipsky PE, Dorner T. B-cell lymphoproliferation in chronic inflammatory rheumatic diseases. Nat Clin Pract Rheumatol 3(10):561-569, 2007.

Harley JB, James JA. Epstein-Barr virus infection induces lupus autoimmunity. Bull NYU Hosp Jt Dis 64(1-2):45-50, 2006.

Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A 105(44):17046-17049, 2008.

Hu N, Qiu X, Luo Y, Yuan J, Li Y, Lei W, Zhang G, Zhou Y, Su Y, Lu Q. Abnormal histone modification patterns in lupus CD4+ T cells. J Rheumatol 35(5):804-810, 2008.

Isenberg DA, Manson JJ, Ehrenstein MR, Rahman A. Fifty years of anti-ds DNA antibodies: are we approaching journey’s end? Rheumatology (Oxford) 46(7):1052-1056, 2007.

Javierre BM, Esteller M, Ballestar E. Epigenetic connections between autoimmune disorders and haematological malignancies. Trends Immunol 29(12):616-623, 2008.

Javierre BM, Fernandez AF, Richter J, Al-Shahrour F, Martin-Subero JI, Rodriguez-Ubreva J, Berdasco M, Fraga MF, O’hanlon TP, Rider LG, Jacinto FV Lopez-Longo FJ, Dopazo J, Forn M, Peinado MA, Carreno L, Sawalha AH, Harley JB Siebert R, Esteller M, et al. Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus. Genome Res 20(2):170-179, 2010.

Kantor GL, Goldberg LS, Johnson BL, Jr, Derechin MM, Barnett EV. Immunologic abnormalities induced by postperfusion cytomegalovirus infection. Annals of internal medicine 73(4):553-558, 1970.

Kaplan MJ, Lewis EE, Shelden EA, Somers E, Pavlic R, Mccune WJ, Richardson BC. The apoptotic ligands TRAIL, TWEAK, and Fas ligand mediate monocyte death induced by autologous lupus T cells. J Immunol 169(10):6020-6029, 2002.

Kaplan MJ, Lu Q, Wu A, Attwood J, Richardson B. Demethylation of promoter regulatory elements contributes to perforin overexpression in CD4+ lupus T cells. J Immunol 172(6):3652-3661, 2004.

Katari S, Turan N, Bibikova M, Erinle O, Chalian R, Foster M, Gaughan JP, Coutifaris C, Sapienza C. DNA methylation and gene expression differences in children conceived in vitro or in vivo. Hum Mol Genet 18(20):3769-3778, 2009.

Klareskog L, Stolt P, Lundberg K, Kallberg H, Bengtsson C, Grunewald J, Ronnelid J, Harris HE, Ulfgren AK, Rantapaa-Dahlqvist S, Eklund A, Padyukov L, Alfredsson L. A new model for an etiology of rheumatoid arthritis: smoking may trigger HLA-DR (shared epitope)-restricted immune reactions to autoantigens modified by citrullination. Arthritis Rheum 54(1):38-46, 2006.

Kouzarides T. Chromatin modifications and their function. Cell 128(4):693-705, 2007.

Krieg AM. CpG DNA: a pathogenic factor in systemic lupus erythematosus? J Clin Immunol 15(6):284-292, 1995.

Kuhn A, Beissert S. Photosensitivity in lupus erythematosus. Autoimmunity 38(7):519-529, 2005.

Lei W, Luo Y, Lei W, Luo Y, Yan K, Zhao S, Li Y, Qiu X, Zhou Y, Long H, Zhao M, Liang Y, Su Y, Lu Q. Abnormal DNA methylation in CD4+ T cells from patients with systemic lupus erythematosus, systemic sclerosis, and dermatomyositis. Scand J Rheumatol 38(5):369-374, 2009.

Lu Q, Kaplan M, Ray D, Ray D, Zacharek S, Gutsch D, Richardson B. Demethylation of ITGAL (CD11a) regulatory sequences in systemic lupus erythematosus. Arthritis Rheum 46(5):1282-1291, 2002.

Lunardi C, Tinazzi E, Bason C, Dolcino M, Corrocher R, Puccetti A. Human parvovirus B19 infection and autoimmunity. Autoimmunity reviews 8(2):116-120, 2008.

Martinez-Zamudio R, Ha HC. Environmental epigenetics in metal exposure. Epigenetics 6(7):820-827, 2011.

Mastronardi FG, Noor A, Wood DD, Paton T, Moscarello MA. Peptidyl argininedeiminase 2 CpG island in multiple sclerosis white matter is hypomethylated. J Neurosci Res 85(9):2006-2016, 2007.

Maverakis E, Miyamura Y, Bowen MP, Correa G, Ono Y, Goodarzi H. Light, including ultraviolet. J Autoimmun 34(3):J247-257, 2010.

Mazari L, Ouarzane M, Zouali M. Subversion of B lymphocyte tolerance by hydralazine, a potential mechanism for drug-induced lupus. Proc Natl Acad Sci U S A 104(15):6317-6322, 2007.

Michielsen CC, Van Loveren H, Vos JG. The role of the immune system in hexachlorobenzene-induced toxicity. Environ Health Perspect 107(Suppl 5):783-792, 1999.

Mintzer Dm, Billet Sn, Chmielewski L. Drug-induced hematologic syndromes. Adv Hematol 2009:495863, 2009.

Mishra N, Brown Dr, Olorenshaw Im, Kammer Gm. Trichostatin A reverses skewed expression of CD154, interleukin-10, and interferon-gamma gene and protein expression in lupus T cells. Proceedings of the National Academy of Sciences of the United States of America 98(5):2628-2633, 2001.

Nalbandian G, Kovats S. Understanding sex biases in immunity: effects of estrogen on the differentiation and function of antigen-presenting cells. Immunol Res 31(2):91-106, 2005.

Neidhart M, Rethage J, Kuchen S, Kunzler P, Crowl RM, Billingham ME, Gay RE, Gay S. Retrotransposable L1 elements expressed in rheumatoid arthritis synovial tissue: association with genomic DNA hypomethylation and influence on gene expression. Arthritis Rheum 43(12):2634-2647, 2000.

Niller HH, Wolf H, Minarovits J. Regulation and dysregulation of Epstein-Barr virus latency: implications for the development of autoimmune diseases. Autoimmunity 41(4):298-328, 2008.

Padalko EY, Bossuyt X. Anti-dsDNA antibodies associated with acute EBV infection in Sjogren’s syndrome. Ann Rheum Dis 60(10):992, 2001.

Palbykin B, Borg J, Caldwell PT, Rowles J, Papoutsis AJ, Romagnolo DF, Selmin OI. Trichloroethylene induces methylation of the Serca2 promoter in H9c2 cells and embryonic heart. Cardiovasc Toxicol 11(3):204-214, 2011.

Plante I, Charbonneau M, Cyr DG. Activation of the integrin-linked kinase pathway downregulates hepatic connexin32 via nuclear Akt. Carcinogenesis 27(9):1923-1929, 2006.

Portela A, Esteller M. Epigenetic modifications and human disease. Nat Biotechnol 28(10):1057-1068, 2010.

Quddus J, Johnson KJ, Gavalchin J, Amento EP, Chrisp CE, Yung RL, Richardson BC. Treating activated CD4+ T cells with either of two distinct DNA methyltransferase inhibitors, 5-azacytidine or procainamide, is sufficient to cause a lupus-like disease in syngeneic mice. J Clin Invest 92(1):38-53, 1993.

Reeves WH, Lee PY, Weinstein JS, Satoh M, Lu L. Induction of autoimmunity by pristane and other naturally occurring hydrocarbons. Trends Immunol 30(9):455-464, 2009.

Richardson B. Effect of an inhibitor of DNA methylation on T cells. II. 5-Azacytidine induces self-reactivity in antigen-specific T4+ cells. Hum Immunol 17(4):456-470, 1986.

Richardson B, Scheinbart L, Strahler J, Gross L, Hanash S, Johnson M. Evidence for impaired T cell DNA methylation in systemic lupus erythematosus and rheumatoid arthritis. Arthritis Rheum 33(11):1665-1673, 1990.

Rubtsov AV, Rubtsova K, Kappler JW, Marrack P. Genetic and hormonal factors in female-biased autoimmunity. Autoimmun Rev 9(7):494-498, 2010.

Ruchusatsawat K, Wongpiyabovorn J, Shuangshoti S, Hirankarn N, Mutirangura A. SHP-1 promoter 2 methylation in normal epithelial tissues and demethylation in psoriasis. J Mol Med (Berl) 84(2):175-182, 2006.

Salvador JM, Hollander MC, Nguyen AT, Kopp JB, Barisoni L, Moore JK, Ashwell JD, Fornace AJ, Jr. Mice lacking the p53-effector gene Gadd45a develop a lupus-like syndrome. Immunity 16(4):499-508, 2002.

Samuelsson U, Carstensen J. Space-time clustering at birth and at diagnosis of type 1 diabetes mellitus in relation to early clinical manifestation. J Pediatr Endocrinol Metab 16(6):859-867, 2003.

Sandovici I, Smith NH, Nitert MD, Ackers-Johnson M, Uribe-Lewis S, Ito Y, Jones RH, Marquez VE, Cairns W, Tadayyon M, O’Neill LP, Murrell A, Ling C, Constancia M, Ozanne SE. Maternal diet and aging alter the epigenetic control of a promoter-enhancer interaction at the Hnf4a gene in rat pancreatic islets. Proc Natl Acad Sci U S A 108(13):5449-5454, 2011.

Sarkar K, Weinberg CR, Oddis CV, Medsger TA, Jr, Plotz PH, Reveille JD, Arnett FC, Targoff IN, Genth E, Love LA, Miller FW. Seasonal influence on the onset of idiopathic inflammatory myopathies in serologically defined groups. Arthritis Rheum 52(8):2433-2438, 2005.

Sawalha AH, Harley JB. Antinuclear autoantibodies in systemic lupus erythematosus. Curr Opin Rheumatol 16(5):534-540, 2004.

Singh NP, Singh UP, Singh B, Price RL, Nagarkatti M, Nagarkatti PS. Activation of aryl hydrocarbon receptor (AhR) leads to reciprocal epigenetic regulation of FoxP3 and IL-17 expression and amelioration of experimental colitis. PLoS One 6(8):e23522, 2011.

Tahara T, Shibata T, Nakamura M, Yamashita H, Yoshioka D, Okubo M, Maruyama N, Kamano T, Kamiya Y, Fujita H, Nakagawa Y, Nagasaka M, Iwata M, Takahama K, Watanabe M, Nakano H, Hirata I, Arisawa T. Promoter methylation of protease-activated receptor (PAR2) is associated with severe clinical phenotypes of ulcerative colitis (UC). Clin Exp Med 9(2):125-130, 2009.

Tahara T, Shibata T, Nakamura M, Yamashita H, Yoshioka D, Okubo M, Maruyama N, Kamano T, Kamiya Y, Nakagawa Y, Fujita H, Nagasaka M, Iwata M, Takahama K, Watanabe M, Hirata I, Arisawa T. Effect of MDR1 gene promoter methylation in patients with ulcerative colitis. Int J Mol Med 23(4):521-527, 2009.

Takami N, Osawa K, Miura Y, Komai K, Taniguchi M, Shiraishi M, Sato K, Iguchi T, Shiozawa K, Hashiramoto A, Shiozawa S. Hypermethylated promoter region of DR3, the death receptor 3 gene, in rheumatoid arthritis synovial cells. Arthritis Rheum 54(3):779-787, 2006.

Vento S, Guella L, Mirandola F, Cainelli F, Di Perri G, Solbiati M, Ferraro T, Concia E. Epstein-Barr virus as a trigger for autoimmune hepatitis in susceptible individuals. Lancet 346(8975):608-609, 1995.

Vrbikova J, Janatkova I, Zamrazil V, Tomiska F, Fucikova T. Epstein-Barr virus serology in patients with autoimmune thyroiditis. Exp Clin Endocrinol Diabetes 104(1):89-92, 1996.

Wallace DC. Bioenergetics and the epigenome: interface between the environment and genes in common diseases. Dev Disabil Res Rev 16(2):114-119, 2010.

Wang Y, Fan PS, Kahaleh B. Association between enhanced type I collagen expression and epigenetic repression of the FLI1 gene in scleroderma fibroblasts. Arthritis Rheum 54(7):2271-2279, 2006.

Waterland RA, Dolinoy DC, Lin JR, Smith CA, Shi X, Tahiliani KG. Maternal methyl supplements increase offspring DNA methylation at Axin Fused. Genesis 44(9):401-406, 2006.

Waterland RA, Kellermayer R, Laritsky E, Rayco-Solon P, Harris RA, Travisano M, Zhang W, Torskaya MS, Zhang J, Shen L, Manary MJ, Prentice AM. Season of conception in rural gambia affects DNA methylation at putative human metastable epialleles. PLoS Genet 6(12):e1001252, 2010.

Wen ZK, Xu W, Xu L, Cao QH, Wang Y, Chu YW, Xiong SD. DNA hypomethylation is crucial for apoptotic DNA to induce systemic lupus erythematosus-like autoimmune disease in SLE-non-susceptible mice. Rheumatology (Oxford) 46(12):1796-1803, 2007.

Wiik A. Drug-induced vasculitis. Curr Opin Rheumatol 20(1):35-39, 2008.

Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta 1775(1):138-162, 2007.

Young AL, Giesy JP, Jones PD, Newton M. Environmental fate and bioavailability of Agent Orange and its associated dioxin during the Vietnam War. Environ Sci Pollut Res Int 11(6):359-370, 2004.

Yung RL, Quddus J, Chrisp CE, Johnson KJ, Richardson BC. Mechanism of drug-induced lupus. I. Cloned Th2 cells modified with DNA methylation inhibitors in vitro cause autoimmunity in vivo. J Immunol 154(6):3025-3035, 1995.

Zhang K, Zhang R, Li X, Yin G, Niu X. Promoter methylation status of p15 and p21 genes in HPP-CFCs of bone marrow of patients with psoriasis. Eur J Dermatol 19(2):141-146, 2009.

Zhang K, Zhang R, Li X, Yin G, Niu X, Hou R. The mRNA expression and promoter methylation status of the p16 gene in colony-forming cells with high proliferative potential in patients with psoriasis. Clin Exp Dermatol 32(6):702-708, 2007.

Zhang P, Su Y, Chen H, Zhao M, Lu Q. Abnormal DNA methylation in skin lesions and PBMCs of patients with psoriasis vulgaris. J Dermatol Sci 60(1):40-42, 2010.

Zhang Z, Song L, Maurer K, Petri MA, Sullivan KE. Global H4 acetylation analysis by ChIP-chip in systemic lupus erythematosus monocytes. Genes Immun, 11(2):124-133, 2010.

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