Purpose: Genetic studies can help to identify novel genes involved in OA and in that way elucidate OA etiological pathways. However to date, GWAS (genome-wide association studies) in OA have yielded only few loci, which is partly explained by the phenotypic and ethiological heterogeneity of OA. Therefore, we have stratified OA definitions into endophenotypes, which help to identify underlying disease etiology. We have focused on separate radiographic features of the OA process: radiographic measured joint space width (JSW), Joint space narrowing (JSN) and osteophytosis as proxies for the separate biological processes underlying OA pathology. Methods: Using the Rotterdam Study cohorts (RS1, RS2, RS3) as a discovery, we conducted GWAS on 30 OA endophenotypes based on radiographic measurements. We have used the following radiographic measurements to create (semi)-quantitative endophenotypes for the hip, knee, hand, finger and thumb joints: JSN, JSW, Osteophytes, and the quantitative KL score. GWAS were carried out under an additive model in RV-test using HRC v1.0 imputations, with adjustment for age, sex and the first 4 principle components. EasyQC was used to conduct quality control across cohorts (excluded: MAF<0.05). Cleaned results were combined in a joint meta-analysis using METAL. Functional assessed of the identified loci was done by examining if the identidied SNPs changed RNA expression in multiple tissues (GTEX), Pathway analysis (GO biological functions, reactome, KEGG, WIKIPathways), and to see if there were DNA interactions at the identified SNPs (3D genome browser). Results: In total we defined 30 different OA endophenotypes for the hip, knee, and hand joints in the Rotterdam Study cohorts. On average each GWAS performed has a relative small sample size of ∼8000 individuals. We have identified 94 different loci (100 SNPs) with a P<1E-6 of which 16 loci (20 SNPs) reached genome-wide significance (P<5E-8), We find 3 known (DOT1L , MGP and CCD91 ) and 14 novel loci to be genome-wide significantly associated to thumb, hand and knee OA endophenotypes. The most significant novel locus is located on chr1, associated to thumb OA endophynotypes, Knee JSN and (nominal significant) hip cartilage thickness. Within the same topological associated domain in this locus is WNT9A and WNT3A. WNT9A plays a central role in early synovial joint development, as ectopic expression of WNT9a in early differentiating chondrocytes induces joint formation. The other novel loci are located near DAB1, KCNK1-SLC25F3, KCND3-CTTNBP2NL, DCBLD2, COL25A1, FIP1L1-PDGFRA, ESR1, CCDC82-CNTN5, TLE3-UACA, MT1G, DYM, and MYPOP genes. Gene-function enrichment and pathway analysis using the 17 top loci shows enrichment for i.a. Regulation of growth (Padj = 4.21E-5), Female sex differentiation (Padj = 4.73E-5) and Skeletal development (Padj = 7.99E-3). Pathway enrichments is seen for i.a. differentiation Pathways ( Padj = 1.55E-3) and Wnt-signaling (Padj = 2.49E-2), in addition we also see an enrichment for height associated loci (Padj = 1.87E-5). In addition, we have examined all known OA loci in our endophenotype dataset and found striking patterns of endophenotype association. For example, the established GDF5 locus shows strong signals with all osteophytosis endophenotypes, but not with cartilage endophenotypes. Conclusions: We have identified 14 novel loci associated to different aspects of OA pathology. In addition we have identified another 80 loci with suggestive evidence for association (P<1E-6). Examination of known genetic OA loci showed striking patterns of association, and suggests that the GDF5 association is driven by bone formation pathways rather then cartilage driven pathways. Our findings highlight the potential of endophenotypes in OA genetic studies. Future analysis will consist of validation in other cohorts, and further functional assessment of the identified loci to gain etiological insight into the biological mechanism underlying the relationship between genetic variation and OA.
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