Genetic and epigenetic interplay regulates COLGALT2, contributing to osteoarthritis genetic risk.

Objective The osteoarthritis (OA)-associated single nucleotide polymorphism (SNP) rs11583641 is located within COLGALT2, encoding a post-translational modifier of collagen. In cartilage, the SNP genotype correlates with DNA methylation (DNAm) within a putative enhancer. We used patient samples and a chondrocyte cell model to characterise the mechanistic relationship between rs11583641, the putative enhancer, and COLGALT2 expression. Methods Nucleic acids were extracted from patient cartilage (n=137). Samples were genotyped and DNAm was quantified at 12 CpGs by pyrosequencing. The putative enhancer was deleted in Tc28a2 chondrocytes using CRISPR-Cas9, and the impact upon nearby gene expression was determined by RT-qPCR. Targeted modulation of the epigenome using dCas9-DNMT3a and -TET1 constructs allowed investigation of a causal relationship between DNAm and enhancer activity. Results Genotype at rs11583641 correlated with DNAm at three CpGs, with the OA effect allele, C, corresponding with reduced methylation. Deletion of the enhancer resulted in a 2.7-fold reduction in COLGALT2 expression. Targeted methylation and demethylation of the CpGs had antagonistic effects upon COLGALT2 expression. An allelic imbalance in the expression of COLGALT2 was identified in patient cartilage, with a relative over-expression of the OA risk allele. Allelic expression ratios correlated with DNAm at four CpGs. Conclusion We have demonstrated that COLGALT2 is a target of OA genetic risk at this locus. Genotype at rs11583641 impacts DNAm within a gene enhancer, which, in turn, modulates COLGALT2 expression. COLGALT2 encodes an enzyme which initiates the post-translational glycosylation of collagens, and is therefore a compelling osteoarthritis susceptibility target.