Cindy Boer

Epigenomics in bone and cartilage disease | 53 1.2 miRNAs or genetically/epigenetically engineered MSCs. The local nature of the disease and the therapy may help to avoid generalized undesired effects. In this line, antisense oligonucleotides of miRNA 181a‐5p attenuate cartilage destruction when injected into the knees of rats and mice with experimentally induced OA[138]. The task of revealing the role of epigenomic variants and pathways is even more difficult because, unlike the genome, the epigenome is cell‐ and tissue‐specific and may change over time. Thus, studies may need to be done using skeletal samples, which pos- es obvious difficulties for human studies and particularly for those requiring sampling at multiple time points. For studies on developmental processes for bone and cartilage in humans, model systems such as human stem cells and IPSCs might prove a good al- ternative. In addition, organ on a chip technology is promising for studying early disease processes. In this regard, recent findings that suggest that some molecules circulating in blood may be used as biomarkers of the status of solid tissues, if confirmed, may facilitate using epigenetic elements as biomarkers. In the skeletal field, miRNAs have been mostly studied from this perspective. However, methylation marks in circulating cell‐free DNA are also being actively explored in cancer and other disorders. Technical advances to facilitate high‐throughput analysis of epigenomic marks at decreasing costs are emerging and will facilitate larger‐scale applications. Sequencing costs are continuously going down, making it possible to generate increasing amounts of data. The bottleneck for these “big data” studies is the data analysis, which in general requires the same costs as generation of the raw data itself. An emerging technique is single‐molecule sequencing, with Pac Bio's single‐molecule real‐time sequencing (SMRT) and Oxford Nanopore's (ON) nanopore sequencing as the most prominent play- ers in the field. SMRT and ON are able to directly sequence native DNA or RNA, making it possible to directly measure chemical groups attached to the nucleic acid sequence (such as methylation), avoiding the bias of other techniques due to the necessary ampli- fication and/or bisulphite treatment. Although single‐molecule sequencing is still in a developmental stage, more and more applications are being developed, indicating that the technique is almost ready for wider‐scale applications. Another important technical advance is single‐cell epigenomics, which is devel- oping rapidly. Single‐cell “omic” technologies have emerged as powerful tools to explore cellular heterogeneity at individual cell resolution. Previous scientific knowledge in cell biology is largely limited to data generated by bulk profiling methods, which only provide averaged read‐outs that generally mask cellular heterogeneity. Single‐cell tech- nology has recently led to the identification of a self‐renewing skeletal stem cell that generates progenitors of bone, cartilage, and stroma but not fat[139]. In addition, the first study applying single‐cell RNAseq on OA cartilage identified seven chondrocyte