Purpose: Osteoarthritis (OA) has a considerable genetic component and genetic research has resulted in many insights into underlying disease pathways. Most recent large-scale genomic association studies have identified TGFA , MGP, CHADL as compelling genes involved in the aetiology of OA. The functions of these genes confirm that deviations in both cartilage and bone maintenance processes are major pathways underlying OA pathology in humans. Moreover, follow-up studies have shown that risk SNPs frequently modulate pathology due to altering transcription of the genes in cis both in bone and cartilage. Nonetheless, follow up study of these genes towards underlying biological mechanisms, preclinical studies on target discovery and eventually drug testing have thus far focused on gene expression profiling in articular cartilage. The aim of the current study was to characterize interactive pathophysiological processes of subchondral bone and articular cartilage in human osteoarthritis (OA) in large human cohort RNA sequencing. Methods: We performed RNA sequencing on macroscopically preserved and lesioned OA subchondral bone of patients that underwent a joint replacement surgery due to OA (N=24 pairs; 6 hips, 18 knees, RAAK-study). Unsupervised hierarchical clustering and differential expression analysis were performed on the data. Gene enrichment was performed using the online tool DAVID. Moreover, we compared the differentially expressed genes identified here to our previously reported differentially expressed genes in OA articular cartilage. Results: Upon performing cluster analysis we identified two clusters; one representing hips and the other representing knees. Due to the low hip sample size, differential expression analysis was performed on knee samples only. As shown in Figure 1, we identified 1757 significantly differentially expressed genes between lesioned and preserved subchondral bone. The most significantly downregulated gene was FRZB (FC=0.48, FDR=3.07x10-12), encoding the frizzled receptor protein and is a well-known cartilage OA gene. The most significantly upregulated gene was CNTNAP2 (FC=2.90, FDR=3.38x10-6), encoding the contactin-associated protein-like 2 protein (CASPR2). Among the 1757 differentially expressed genes, 102 genes showed an absolute foldchange of 2 or higher. The highest upregulated gene was STMN2 (FC=23.0, FDR=1.8x10-4), encoding stathmin 2, while the most downregulated gene was CHRDL2 (FC=0.09, FDR=4.13x10-6), encoding chordin-like protein 2 and is also known to be involved in OA in cartilage. Enrichment of the differentially expressed genes resulted in significant enrichment of GO-terms regarding the extracellular matrix. To investigate whether the subchondral bone and the articular cartilage show similarities in the OA pathophysiological processes, we compared the results presented here with our previously reported results on differentially expressed genes in OA articular cartilage. As a result, we identified 398 genes that were differentially expressed in both tissues, of which 361 showed similar directions of effect, including the genes IL11, encoding Interleukin 11, and CHADL, encoding Chondroadherin-Like Protein. Conclusions: To our knowledge, we are the first to report on the differential expression pattern of OA subchondral bone using RNA sequencing on a large sample size while integrating these with differential expression patterns of cartilage of the same individuals. By performing cluster analysis on our RNA sequencing data, we identified two clusters representing hips and knees, respectively. These clusters indicate distinct OA pathophysiological processes in the subchondral bone between the two joint sites, which was not previously seen with similar analyses of the cartilage. Among the most consistently differentially expressed genes with OA pathophysiology in bone and cartilage are IL11, and CHADL. Notably, these genes were recently found in large GWA studies on OA indicating also their causal involvement in the OA pathophysiology. Moreover, IL11 was recognized as being targeted by FDA approved drugs. As such, we advocate that IL11 could be an attractive potential drug for OA patients with a therapeutic effect both in cartilage and subchondral.
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