Identification of a novel, methylation-dependent, RUNX2 regulatory region associated with osteoarthritis risk

Abstract

Osteoarthritis (OA) is a common, multifactorial and polygenic skeletal disease that, in its severest form, requires joint replacement surgery to restore mobility and to relieve chronic pain. Using tissues from the articulating joints of 260 patients with OA and a range of in vitro experiments, including CRISPR-Cas9, we have characterized an intergenic regulatory element. Here, genotype at an OA risk locus correlates with differential DNA methylation, with altered gene expression of both a transcriptional regulator (RUNX2), and a chromatin remodelling protein (SUPT3H). RUNX2 is a strong candidate for OA susceptibility, with its encoded protein being essential for skeletogenesis and healthy joint function. The OA risk locus includes single nucleotide polymorphisms (SNPs) located within and flanking the differentially methylated region (DMR). The OA association SNP, rs10948172, demonstrates particularly strong correlation with methylation, and two intergenic SNPs falling within the DMR (rs62435998 and rs62435999) demonstrate genetic and epigenetic effects on the regulatory activity of this region. We therefore posit that the OA signal mediates its effect by modulating the methylation of the regulatory element, which then impacts on gene expression, with RUNX2 being the principal target. Our study highlights the interplay between DNA methylation, OA genetic risk and the downstream regulation of genes critical to normal joint function.

Role of Epigenomics in Bone and Cartilage Disease

“…This suggests that the genetic association with various skeletal phenotypes might arise due to a difference in control of RUNX2 expression. Recent studies have shown that regulation of RUNX2 is tightly regulated by multiple epigenetic mechanisms, such as miR‐204/211 and other miRNAs, HDAC, and DNA methylation . Also, some of the genetic association signals near RUNX2 exert effects on epigenetics.…”

“…Also, some of the genetic association signals near RUNX2 exert effects on epigenetics. For the osteoarthritis‐associated SNP, rs10948172, it has been shown to operate as a methylation quantitative trait loci (mQTL) for 4 CpG sites in the RUNX2 locus . Nevertheless, the GWAS signals are positioned at a relative large distance from RUNX2, and chromatin interaction from regulatory region to gene promoter is needed.…”

Discovery and analysis of methylation quantitative trait loci (mQTLs) mapping to novel osteoarthritis genetic risk signals

“…These CpGs are known as methylation quantitative trait loci, or mQTLs. At several OA loci, including GDF5 and RUNX2, genotype at the associated SNP correlates not only with DNA methylation but also with gene expression 11,12 . This indicates that chondrocytes use DNA methylation as an intermediary between genotype and phenotype, with this epigenetic mechanism underpinning a large proportion of OA disease risk.…”

Role of Signal Transduction Pathways and Transcription Factors in Cartilage and Joint Diseases

“…Recently, the progression of osteoarthritis was found to be accelerated in chondrocyte-specific Runx2-overexpressing mice [37]. Furthermore, methylation level of the RUNX2 gene has been correlated with the risk for osteoarthritis [38]. However, there is some debate regarding the pathogenic effects of RUNX2 in osteoarthritis because no reported evidence suggests the altered occurrence of osteoarthritis in patients with cleidocranial dysplasia compared with other populations (personal communication).…”