Cindy Boer

42 | Chapter 1.2 Epigenomewide studies in osteoarthritis A relatively large number of EWAS have been done focusing on the differences in the methylome of diseased versus preserved cartilage[43-47], cartilage from hip frac- ture[48, 49], controls[48, 50], or neocartilage engineered from MSCs[51] ( Table 1 ). Although the exact genes that are identified in the studies can differ, the identified path- ways that emerge are robust. They involve skeletal development and morphogenesis and known signalling pathways (such as the TGFβ, Wnt, HOX ) involved in skeletal devel- opment. Also, inflammation seems to be a pathway that is identified by multiple studies and two studies have also shown the possibility of clustering a subset of patients char- acterized by methylation differences in (or near) inflammatory genes[50, 52]. It is in- teresting to note that genome-wide methylation studies consistently found enrichment of differentially methylated CpGs in enhancer regions[53]. This suggests that modifica- tions of DNA methylation marks may be more important in distant regulatory regions than in proximal promoters. This observation is consistent with other EWAS of complex diseases, where most of the associations found have been highly enriched in enhancer regions. Good annotation and interpretation of these enhancers are therefore of great importance. Methylation patterns can also be used to calculate a so‐called “epigenetic age,” which is thought to reflect biological aging and has been linked to a whole range of age‐related diseases and time of death[54, 55]. One study examined the relation be- tween this “epigenetic clock” and osteoarthritis and observed accelerated aging in OA cartilage[56]. Epigenomewide studies in osteoporosis The number of EWAS studies that examine osteoporosis as an endpoint is much lower than the cartilage studies described above. The first study examined femoral head bone tissue from hip fracture and OA patients using a limited set of methylation sites, and showed among a number of pathways, differentially methylated regions in the family of HOX‐genes[57]. A second, more recent study, examined MSCs in fracture versus OA patients and identified a number of differentially methylated genes in stem cell and os- teoblast differentiation pathways[58]. In another study using bone biopsies of women with low (osteoporotic) or normal BMD[63]. differentially methylated CpGs were found at a lenient false discovery rate (FDR<0.1)[59]. Because bone is a multicellular tissue, methylation differences could also reflect the changes in cell‐type proportions, which was not accounted for in the published studies. Methylation signatures in the circulation can potentially be powerful biomarkers for disease. A large EWAS examining methylation patterns of circulating leukocytes was