Converging evidence from exome sequencing and common variants implicates target genes for osteoporosis

In this study, we leveraged the combined evidence of rare coding variants and common alleles to identify therapeutic targets for osteoporosis. We undertook a large-scale multiancestry exome-wide association study for estimated bone mineral density, which showed that the burden of rare coding alleles in 19 genes was associated with estimated bone mineral density ( P < 3.6 × 10 –7 ). These genes were highly enriched for a set of known causal genes for osteoporosis (65-fold; P = 2.5 × 10 –5 ). Exome-wide significant genes had 96-fold increased odds of being the top ranked effector gene at a given GWAS locus ( P = 1.8 × 10 –10 ). By integrating proteomics Mendelian randomization evidence, we prioritized CD109 (cluster of differentiation 109) as a gene for which heterozygous loss of function is associated with higher bone density. CRISPR–Cas9 editing of CD109 in SaOS-2 osteoblast-like cell lines showed that partial CD109 knockdown led to increased mineralization. This study demonstrates that the convergence of common and rare variants, proteomics and CRISPR can highlight new bone biology to guide therapeutic development.