Numerous studies focusing on the genetic basis of autoimmunity have been performed to unravel the molecular mechanisms underlying autoimmune diseases. Although multiple risk variants associated with autoimmunity have been described, it has been proven difficult to translate these findings into novel insights of disease pathogenesis, and to demonstrate the molecular consequence of these variants. One of the reasons for this is that it has become increasingly clear that autoimmune diseases are characterized by a complex interplay of genetic as well as epigenetic mechanisms. In this thesis we sought to characterize epigenetic mechanisms, focusing on enhancer regulation, which are involved in the pathogenesis of autoimmune diseases. In addition, we studied autophagy in the context of autoimmune disease and its epigenetic and transcriptional regulation. For these studies, we utilized cells from joint, i.e. the site of inflammation, of patients suffering from the autoimmune disease juvenile idiopathic arthritis (JIA).
Enhancers are epigenetically regulated elements in the DNA, typically a few hundred base pairs in size, to which transcription factors and co-factors can bind and control transcription. Analysis of the active enhancer profile of immune cells, such as T cells and monocytes, from JIA patients demonstrated that these cells display a distinct enhancer profile compared to healthy control cells. Furthermore, we demonstrated that arthritis-associated SNPs are enriched within these enhancer regions and that the altered enhancer profile correlates with disease-associated gene expression. Inhibition of enhancer activity results in reduced disease-associated gene expression, indicating that inhibition of enhancer activity might be a potential therapeutic strategy for the treatment of autoimmune diseases. Epigenetic and transcriptomic analysis of inflammatory site-derived monocytes led to the observation that osteoclast-associated genes are increasingly expressed and highly regulated on the epigenetic level. Since osteoclasts are bone-degrading cells, increased monocytes to osteoclast differentiation could be one of the reasons for increased bone erosion as observed in the joints of patients with inflammatory arthritis. We observed that synovial fluid from the inflamed joints of JIA patients can induce the differentiation of monocytes towards osteoclasts. Together, this suggests that inhibition of enhancer activity might also inhibit osteoclast differentiation.
Additionally, we have investigated autophagy, a recycling and cell survival process, in JIA synovial fluid-derived T cells and demonstrated that autophagy is increased in these cells. Inhibition of autophagy reduces the inflammatory phenotype of these cells, suggesting that autophagy contributes to the inflammatory phenotype of JIA synovial fluid T cells. To identify novel regulators of autophagy, genome-wide transcriptomic and epigenomic profiling of nutrient-deprived cells was performed. The transcription factor EGR1 was identified as a transcriptional regulator of autophagy, since it induces autophagy-associated gene expression and enhances autophagic flux.
Taken together, the studies described in this thesis provide novel insight into transcriptional and epigenetic mechanisms in an autoimmune disease setting and demonstrate that altered enhancer regulation and autophagy is associated with autoimmunity. Furthermore, these findings indicate that targeting these molecular mechanisms could be of interest for the treatment of autoimmune diseases.