Genetic risk of osteoarthritis operates during human fetal development

Abstract

Osteoarthritis (OA) is a polygenic disease of older people resulting in the breakdown of cartilage within articular joints. Although a leading cause of disability, there are no disease-modifying therapies. Evidence is emerging to support the origins of OA in skeletogenesis. Whilst methylation QTLs (mQTLs) co-localizing with OA GWAS signals have been identified in aged human cartilage and used to identify effector genes and variants, such analyses have never been conducted during human development. Here, for the first time, we have investigated the developmental origins of OA genetic risk at seven well-characterized OA risk loci, comprising 39 OA-mQTL CpGs, in human fetal limb (FL) and cartilage (FC) tissues using a range of molecular genetic techniques. We compared our results to aged cartilage samples (AC) and identified significant OA-mQTLs at 14 CpGs and 29 CpGs in FL and FC tissues, respectively. Differential methylation was observed at 26 sites between fetal and aged cartilage, with the majority becoming actively hypermethylated in old age. Notably, 6/9 OA effector genes showed allelic expression imbalances during fetal development. Finally, we conducted ATAC-sequencing in cartilage from the developing and aged hip and knee to identify accessible chromatin regions, and found enrichment for transcription factor-binding motifs including SOX9 and FOS/JUN. For the first time, we have demonstrated the activity of OA-mQTLs and expression imbalance of OA effector genes during skeletogenesis. We show striking differences in the spatiotemporal function of these loci, contributing to our understanding of OA etiology, with implications for the timing and strategy of pharmacological interventions.

Epigenetic mechanisms of osteoarthritis risk in human skeletal development

“…Allelic expression imbalance at the locus showed a decrease in gene expression driven by the OA risk allele, which was present in osteochondral tissue from the trapezium, along with cartilage from the hip and knee 55,56 . This effect was also replicated in our targeted analysis of human foetal cartilage 21 . Furthermore, an OA-mQTL was identified at cg12031962, where the minor and effect allele, C, correlated with a decrease in DNAm 11 .…”

“…At 7 of the loci, OA-mQTLs were identified which have previously been reported in investigations of aged adult cartilage. We overlapped the physical location of the CpGs with open chromatin regions in foetal and OA knee chondrocytes 21 , regions of H3K27ac enrichment in foetal limb tissues 38 , and with designated chromatin states in mesenchymal stem cells (MSCs) and chondrocytes 39 . Through this, we compiled in silico evidence of functional impact for the identified mQTLs restricted to development (D) or throughout the life course (L).…”

“…This includes both the shape of the joint [18][19][20] (which affects the biomechanical properties and weight-bearing capacity) and the biochemical composition of the articular cartilage (which affects the resilience of the tissue to withstand stresses throughout the life course). Our recent targeted study of 39 CpGs investigated the presence of OA mQTLs in human foetal limbs, at seven well-characterised OA genetic risk loci 21 . We identified that at 85% of the CpGs, the significant OA-mQTLs replicated in the foetal tissues, demonstrating for the first time that functional epigenetic mechanisms associated with a musculoskeletal disease of older age operate from the start of life 21 .…”

“…DNA methylating enzymes are expressed in proliferating chondrocytes during embryonic development and persist in articular chondrocytes during post-natal development 24 . Investigation of the methylome of human developmental cartilage has been limited to two studies to date, which utilised small sample numbers (n=8) falling within a narrow developmental window (14-19pcw) 25 , or, in the case of our previous study, applying targeted approaches which captured only a handful of CpGs 21 . Here, we present a comprehensive study of the methylomic trajectory of human articular cartilage in a broader window of development to capture novel risk loci for joint disease.…”

“…Our recent targeted study of 39 CpGs investigated the presence of OA mQTLs in human foetal limbs, at seven well-characterised OA genetic risk loci 21 . We identified that at 85% of the CpGs, the significant OA-mQTLs replicated in the foetal tissues, demonstrating for the first time that functional epigenetic mechanisms associated with a musculoskeletal disease of older age operate from the start of life 21 .…”