The Role of Epigenetics in Autoimmune/Inflammatory Disease

Abstract

Historically, systemic self-inflammatory conditions were classified as either autoinflammatory and caused by the innate immune system or autoimmune and driven by adaptive immune responses. However, it became clear that reality is much more complex and that autoimmune/inflammatory conditions range along an "inflammatory spectrum" with primarily autoinflammatory vs. autoimmune conditions resembling extremes at either end. Epigenetic modifications influence gene expression and alter cellular functions without modifying the genomic sequence. Methylation of CpG DNA dinucleotides and/or their hydroxymethylation, post-translational modifications to amino termini of histone proteins, and non-coding RNA expression are main epigenetic events. The pathophysiology of autoimmune/inflammatory diseases has been closely linked with disease causing gene mutations (rare) or a combination of genetic susceptibility and epigenetic modifications arising from exposure to the environment (more common). Over recent years, progress has been made in understanding molecular mechanisms involved in systemic inflammation and the contribution of innate and adaptive immune responses. Epigenetic events have been identified as (i) central pathophysiological factors in addition to genetic disease predisposition and (ii) as co-factors determining clinical pictures and outcomes in individuals with monogenic disease. Thus, a complete understanding of epigenetic contributors to autoimmune/inflammatory disease will result in approaches to predict individual disease outcomes and the introduction of effective, target-directed, and tolerable therapies. Here, we summarize recent findings that signify the importance of epigenetic modifications in autoimmune/inflammatory disorders along the inflammatory spectrum choosing three examples: the autoinflammatory bone condition chronic nonbacterial osteomyelitis (CNO), the "mixed pattern" disorder psoriasis, and the autoimmune disease systemic lupus erythematosus (SLE).

Keywords: DNA methylation; autoimmune; chromatin; epigenetic; inflammasome; inflammation; lupus; psoriasis.

Figure 1

Epigenetic modifications regulate gene transcription and translation. (A) DNA methyltransferase (DNMT) enzymes maintain or generate (de novo) DNA methylation at CpG dinucleotides. DNA methylation confers repression of gene expression through reduced transcription factor accessibility. DNA Hydroxymethylation is achieved through oxidation of methylated CpG DNA and mediated by Ten-eleven translocation methylcytosine dioxygenase (TET) proteins. DNA hydroxymethylation defines an “open” chromatin structure which allows for gene transcription (similar to unmethylated CpG DNA). (B) Histone methyltransferases (HMT) can add (one to three) methyl groups to histone amino termini. Depending on the exact molecular location and the degree of histone methylation, this can lead to chromatin compaction or decompaction. Methylation of histone H3 at lysine 27 (H3K27) will lead to chromatin compaction and transcriptional repression, while methylation at H3 lysine 4 (H3K4) and H3K36 mediates “opening” and increases transcription. Histone demethylases (HDM) can counteract this by removing the methyl groups. Histone acetylation is mediated by histone acetyltransferases (HAT) and can be reversed by histone deacetylases (HDAC). Histone acetylation is associated with chromatin decompaction and transcription of genes. (C) The transcription of non-coding RNA from intergenic or intronic regions can promote coding mRNA transcription by providing an open chromatin formation. (D) Short micro-RNAs (miRNA) can mediate transcriptional repression through inhibition of the ribosome when binding to the 3'UTR region of mRNAs. Furthermore, miRNAs can induce degradation of the mRNA through initiation of the miRISC complex.

Figure 2

Monocytes from CNO/CRMO patients are epigenetically primed for inflammation. (A) In response to TLR4 activation (with lipopolysaccharide; LPS) monocytes from healthy individuals phosphorylate mitogen activated protein kinases (MAPK) extracellular signal reactive kinases (ERK)1 and 2. Kinases activate the transcriptional regulatory factor signaling protein Sp-1, which results in its translocation into the nucleus. Furthermore, ERK1/2 contribute to histone H3 phosphorylation at serine residue 10 (H3S10) resulting in an open chromatin structure at IL10 and IL19. These events together result in trans-activation of IL10 and IL19. Immune regulatory cytokine expression (IL-10 and IL-19) negatively affect the expression of the pro-inflammatory IL10 cytokine family member IL-20. Furthermore, the IL20 promoter is controlled by CpG DNA methylation. Inflammasomes are multi-protein complexes that become activated in response to “danger signals.” Furthermore, the expression of inflammasome components (NLRP3 and ASC/PYCARD) is regulated by epigenetic events. Promotors of NLRP3 and PYCARD are controlled by CpG DNA methylation. (B) In monocytes from CNO/CRMO patients, ERK1/2 activation in response to LPS stimulation is impaired which results in reduced Sp-1 activation and nuclear shuttling, and decreased H3S10 phosphorylation at IL10 and IL19 resulting in impaired gene expression. Reduced levels of immune regulatory cytokine expression allows for higher expression of the pro-inflammatory cytokine IL-20. Furthermore, impaired IL-10 and IL-19 expression promoted expression of inflammasome components, and reduced CpG DNA methylation of the PYCARD and NLRP3 genes further increase pro-inflammatory molecule expression. Thus, epigenetic events are involved in the molecular pathophysiology of CNO/CRMO.

Figure 3

Epigenetics orchestrating interactions between immune and stroma cells in psoriasis. Increased expression of miR-210 in CD4⁺ T cells from psoriasis patients reduces the expression of the immune regulatory molecule FOXP3. Together with increased histone deacetylase (HDAC) levels that contribute to increased pro-inflammatory cytokine expression (particularly IL-17A), this leads to an imbalance between effector T cells (Th17 cell) and regulatory T cells. Effector CD3⁺CD4⁻CD8⁻ “double negative” (DN) T cells in psoriasis patients are epigenetically primed for IFN-γ expression through decreased CpG DNA methylation at a distal enhancer element of the IFNG gene. Keratinocytes from psoriasis patients exhibit elevated miR-203 expression which results in reduced expression of SOCS3, a negative regulator of STAT3 signaling. This contributes to increased STAT3 phosphorylation (activation) and subsequently increases pro-inflammatory cytokine expression and effector T cell differentiation. Expression of miR-31 in keratinocytes contributes to the activation of NFκB and subsequent production of IL-1β, CXCL1,-5 and-8. Elevated levels of miR-155 induce AIM2 and NLRP3 inflammasome activation through unknown mechanisms which results in enhanced IL-1β release.

Figure 4

Epigenetic mechanisms contribute to dysregulation of innate and adaptive immune responses in SLE. Reduced CpG DNA methylation at IL10 and IL13 regulatory regions allow for increased gene expression. STAT3 recruits to IL10 regulatory elements in the proximal promoter and an intrinsic enhancer. At these elements, STAT3 co-recruits the transcriptional co-activator p300 which has histone acetylase activity and supports chromatin decompaction through H3K18ac and increased gene expression. Increased IL-10 expression in T cells promotes B cell activity in SLE, while not affecting effector T cells (likely due to reduced IL-10 receptor expression on T cells from SLE patients). The transcription factor cAMP response element mediator (CREM)α promotes effector T cells in SLE. It induces H3K18 acetylation and CpG DNA demethylation across the IL17 gene cluster while recruiting DNMT3 to the IL2 locus instructing DNA methylation. Furthermore, CREMα co-recruits histone deacetylase (HDAC)1 to the IL2 gene, which results in decreased H3K18ac and stable gene silencing. Furthermore, B and T cells are stimulated by increased type I IFN (IFN-α and –β) expression in dendritic cells and neutrophils. Neutrophils exhibit reduced CpG DNA methylation of type I IFNs and associated genes. Dendritic cells are primed for type I IFN release through stimulation of endosomal TLR9 through augmented NETosis of neutrophils. Neutrophils from SLE patients release hypomethylated DNA, which binds to TLR9 more potently when compared to methylated DNA.