Proteome-wide Mendelian randomization implicates TIMP2 as a putative causal protein for bone mineral density and fracture risk

Abstract

Osteoporosis is a prevalent cause of fractures in older adults and remains a source of morbidity that requires efforts to develop therapeutics. Circulating proteins play a critical role in the pathophysiology of osteoporosis and offer opportunities to identify new causal determinants of bone health. We therefore performed a large-scale proteome-wide Mendelian randomization (MR) analysis to estimate the effects of genetically determined circulating proteins levels on bone mineral density (BMD) and fracture risk. Genetic instruments were derived from cis-protein quantitative trait loci (cis-pQTLs) for 2,110 plasma proteins across four European ancestry cohorts and applied to genome-wide association studies (GWAS) of heel estimated BMD, femoral neck BMD, lumbar spine BMD, any fracture, and forearm fracture in up to 426,824 individuals of European ancestry. Across proteins and outcomes, 192 protein-skeletal outcome associations showed MR evidence of association, without evidence for heterogeneity or horizontal pleiotropy, and 128 of these further showed strong colocalization with osteoporosis-related loci. We then prioritized proteins that replicated across cohorts, exhibited concordant effect directions, and were likely to be active in circulation, yielding 18 high-confidence causal proteins for BMD and fracture risk. These included established skeletal regulators such as sclerostin (SOST) and R-spondin-3 (RSPO3), which showed opposing effects consistent with their known biology, along with less well-characterized proteins. Higher genetically predicted tissue inhibitor of metalloproteinases 2 (TIMP2) levels was associated with lower BMD and increased forearm fracture risk. Gene-level and variant-level phenome-wide association analyses converged on skeletal traits, and rare predicted damaging or loss-of-function variants in TIMP2 were associated with higher BMD at the heel, spine and hip. Our findings implicate several circulating proteins as putatively causal factors for osteoporosis and, among them, provide multiple layers of evidence supporting TIMP2 as a genetically supported candidate for further functional and translational evaluation. Lay summaryOsteoporosis is characterized by decreased bone density, and despite available medications, it remains a key risk factor for fractures, requiring continued effort for development of new therapeutics. We used genetic data to estimate the effect of genetically predicted levels of 2,110 blood proteins on strength and fracture risk. We found 18 proteins with effects on bone mineral density and fractures. One protein, tissue inhibitor of metalloproteinases 2 (TIMP2), showed robust evidence linking its higher levels to decreased bone density and increased risk of forearm fracture, highlighting TIMP2 as a promising new treatment target for osteoporosis.