Primary osteoarthritis chondrocyte map of chromatin conformation reveals novel candidate effector genes

Abstract

ObjectivesOsteoarthritis is a complex disease with a huge public health burden. Genome-wide association studies (GWAS) have identified hundreds of osteoarthritis-associated sequence variants, but the effector genes underpinning these signals remain largely elusive. Understanding chromosome organisation in three-dimensional (3D) space is essential for identifying long-range contacts between distant genomic features (e.g., between genes and regulatory elements), in a tissue-specific manner. Here, we generate the first whole genome chromosome conformation analysis (Hi-C) map of primary osteoarthritis chondrocytes and identify novel candidate effector genes for the disease.MethodsPrimary chondrocytes collected from 8 patients with knee osteoarthritis underwent Hi-C analysis to link chromosomal structure to genomic sequence. The identified loops were then combined with osteoarthritis GWAS results and epigenomic data from primary knee osteoarthritis chondrocytes to identify variants involved in gene regulation via enhancer-promoter interactions.ResultsWe identified 345 genetic variants residing within chromatin loop anchors that are associated with 77 osteoarthritis GWAS signals. Ten of these variants reside directly in enhancer regions of 10 newly described active enhancer-promoter loops, identified with multiomics analysis of publicly available chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data from primary knee chondrocyte cells, pointing to two new candidate effector genesSPRY4andPAPPA (pregnancy-associated plasma protein A)as well as further support for the geneSLC44A2known to be involved in osteoarthritis. For example, PAPPA is directly associated with the turnover of insulin-like growth factor 1 (IGF-1) proteins, and IGF-1 is an important factor in the repair of damaged chondrocytes.ConclusionsWe have constructed the first Hi-C map of primary human chondrocytes and have made it available as a resource for the scientific community. By integrating 3D genomics with large-scale genetic association and epigenetic data, we identify novel candidate effector genes for osteoarthritis, which enhance our understanding of disease and can serve as putative high-value novel drug targets.

Response eQTLs, chromatin accessibility, and 3D chromatin structure in chondrocytes provide mechanistic insight into osteoarthritis risk

“…However, a chromatin loop connects the promoter of PAP-PA to lead variants at the GWAS locus, which provides a possible mechanistic basis for this long-range regulation. This loop was recently described by Bittner et al, who provided further support for long-range communication at this locus by demonstrating that this GWAS signal colocalizes with a methylation QTL for a methylation site near the PAPPA promoter 49,50 . The PAPPA locus provides a model example of how a multi-omic approach can provide insight into the putative genes and mechanisms responsible for the contributions of particular genetic regions to OA risk.…”

“…It exhibits increased expression in OA tissue, in older donors, and in response to FN-f. The shared GWAS and eQTL signal is over 400 Kb away from the promoter of PAPPA but as we (and others 49 ) have shown, these variants are connected to the promoter of PAPPA via a chromatin loop. A recent study pinpointed PAPPA as the most consistent mediator of senescence induction in sirtuin-deficient human induced pluripotent stem cells 62 .…”