DNA methylation-regulated ZDHHC5 and PPT1 in the pathogenesis of osteoporosis

While osteoporosis (OP) affects over 200 million people globally, the causal roles of protein palmitoylation and its upstream epigenetic regulation in the pathogenesis of the disease remain undefined. We aimed to investigate whether DNA methylation causally influences OP risk by modulating the expression of palmitoylation-related genes. We employed an integrated multi-omics causal inference framework, combining 2-sample Mendelian randomization (MR), summary-data-based MR, Bayesian colocalization, and 2-step mediation MR analyses. Data were sourced from large-scale consortia: the FinnGen study (genome-wide association study: 10,461 cases, 473,264 controls), eQTLGen, GTEx (expression quantitative trait loci), and the GoDMC database (methylation quantitative trait loci). Two-sample MR identified ZDHHC5 as a protective factor (odds ratio = 0.81, 95% confidence interval: 0.76-0.87; P = 6.8 × 10-9) and the depalmitoylase PPT1 as a risk factor (odds ratio = 1.06, 95% confidence interval: 1.03-1.08; P = 7.9 × 10-5) for OP. These findings were corroborated by summary-data-based analysis, and colocalization confirmed a shared causal variant at the ZDHHC5 locus (posterior probability of H4 = 0.947). Mediation analysis revealed that DNA methylation is a central mechanistic link: methylation at site cg13473383 mediated 92.7% of ZDHHC5's protective effect, while sites cg04560534 and cg07033722 mediated 74.8% and 43.4%, respectively, of PPT1's risk effect. This study is the first to establish a causal epigenetic-palmitoylation axis in OP. The genes ZDHHC5 and PPT1, regulated by specific DNA methylation sites, represent novel potential therapeutic targets and biomarkers, offering fresh insights for precision medicine strategies against bone loss.