Functional testing of thousands of osteoarthritis-associated variants for regulatory activity.
Jason C KleinAidan KeithSarah J RiceColin ShepherdVikram AgarwalJohn LoughlinJay ShendurePublished in: Nature communications (2019)
To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and the mechanisms by which they contribute to disease risk have yet to be pinpointed. Here, we functionally test 1,605 single nucleotide variants associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identify six single nucleotide polymorphisms (SNPs) with differential regulatory activity between the major and minor alleles. We show that the most significant SNP, rs4730222, exhibits differential nuclear protein binding in electrophoretic mobility shift assays and drives increased expression of an alternative isoform of HBP1 in a heterozygote chondrosarcoma cell line, in a CRISPR-edited osteosarcoma cell line, and in chondrocytes derived from osteoarthritis patients. This study provides a framework for prioritization of GWAS variants and highlights a role of HBP1 and Wnt signaling in osteoarthritis pathogenesis.
Keyphrases
- genome wide
- copy number
- rheumatoid arthritis
- genome wide association
- knee osteoarthritis
- crispr cas
- end stage renal disease
- transcription factor
- dna methylation
- genome editing
- chronic kidney disease
- ejection fraction
- binding protein
- prognostic factors
- small molecule
- patient reported outcomes
- men who have sex with men
- high density
- protein protein
- extracellular matrix
- case control