3D Chromatin Structure in Chondrocytes Identifies Putative Osteoarthritis Risk Genes

Abstract

Genome-wide association studies (GWAS) have identified over 100 loci associated with osteoarthrtis (OA) risk, but the majority of OA risk variants are non-coding, making it difficult to identify the impacted genes for further study and therapeutic development. To address this need, we used a multi-omic approach and genome editing to identify and functionally characterize potential OA risk genes. Computational analysis of GWAS and ChIP-seq data revealed that chondrocyte regulatory loci are enriched for OA risk variants. We constructed a chondrocyte specific regulatory network by mapping 3D chromatin structure and active enhancers in human chondrocytes. We then intersected these data with our previously collected RNA-seq dataset of chondrocytes responding to fibronectin fragment (FN-f), a known OA trigger. Integration of the three genomic datasets with recently reported OA GWAS variants revealed a refined set of putative causal OA variants and their potential target genes. One of the novel putative target genes identified was SOCS2, which was connected to a putative causal variant by a 170 Kb loop and is differentially regulated in response to FN-f. CRISPR-Cas9-mediated deletion of SOCS2 in primary human chondrocytes from three independent donors led to heightened expression of inflammatory markers after FN-f treatment. These data suggest that SOCS2 plays a role in resolving inflammation in response to cartilage matrix damage and provides a possible mechanistic explanation for its influence on OA risk. In total, we identified 56 unique putative OA risk genes for further research and potential therapeutic development.

The impact of omics research on our understanding of osteoarthritis and future treatments

“…However, another mechanism that has received little attention in the field of OA is three-dimensional organization of chromatin, which is highly important for higher order regulation of transcription. A recent study by Thulson et al [10 ▪ ] has used, to the best of my knowledge for the first time, a specific chromatin conformation capture (3C) approach called Hi-C to quantify contacts between different chromatin regions in a chondrocyte cell line (C-28/I2). The team identified more than 9000 chromatin loops.…”

“…This is particularly useful for genetic variants (e.g. polymorphisms) that cannot be directly associated with a particular gene, as the authors have done here for the SOCS2 gene (encoding a suppressor of cytokine signaling) [10 ▪ ]. The authors then used gene editing to inactivate the SOCS2 gene in primary human chondrocytes and validated its role as suppressor of catabolic gene expression, providing an excellent example of the pathway from genomics screens (in this case Hi-C) to functional validation.…”

Functional investigation of inherited noncoding genetic variation impacting the pharmacogenomics of childhood acute lymphoblastic leukemia treatment

“…Because promoter-distal CREs (e.g., enhancers) regulate gene expression through long-range 3D looping to the promoters of target genes (25), an attractive assay to identify gene targets of promoter-distal regulatory variants is promoter capture Hi-C (promoter CHiC) (39). Promoter capture Hi-C and related 3D chromatin interaction assays have been implemented at multiple GWAS loci to identify gene targets of promoter-distal regulatory variation (29,36,(40)(41)(42)(43).…”