Shared Genetic Architecture Between Epigenetic Aging and Musculoskeletal Diseases

The directional relationship between epigenetic age acceleration (EAA) and musculoskeletal disease remains unresolved. This study integrated bidirectional Mendelian randomization (MR) with multi-layer genomic evidence to evaluate directionality, shared genetic architecture, and robustness to instrument definition.

Four EAA clocks (IEAA, PhenoAA, HannumAA, and GrimAA) and ten musculoskeletal phenotypes were analyzed in a 10 × 4 bidirectional two-sample MR design. EAA instruments underwent GRCh37 functional annotation, genome-wide-significant external-association screening for the index variants and European linkage-disequilibrium proxies, pair-specific Steiger filtering, and conservative Set A/B/C sensitivity analyses. The juvenile-arthritis reverse models underwent instrument-flow reconstruction, strength assessment, liability-scale directionality testing, and minimum-detectable-effect analysis. Additional analyses comprised LD score regression (LDSC), PLACO+ cross-trait locus mapping, Bayesian colocalization, multivariable MR (MVMR) with exact-SNP matched univariable comparators, and integrated evidence synthesis.

Forward MR yielded two nominal HannumAA associations. The inverse HannumAA-spondyloarthritis estimate remained directionally consistent across the original, Steiger-filtered, and conservative external-association-filtered sets, whereas the HannumAA-pain-in-thoracic-spine estimate lost nominal significance in the conservative set; no forward result survived correction across 40 tests. GrimAA forward estimates were sensitive to use of the fallback instrument threshold. Reverse MR identified ten nominal associations. For juvenile arthritis, three harmonized instruments had F statistics of 51.25-102.35; liability-scale Steiger comparisons supported the tested direction under all 16 outcome-by-prevalence combinations, although the 788-case discovery GWAS and possible winner's curse remained important limitations. LDSC identified FDR-significant positive genetic correlations of GrimAA with hip osteoarthritis (r_g = 0.267, p = 8.49 × 10^-5, q = 0.0019) and knee osteoarthritis (r_g = 0.269, p = 9.52 × 10^-5, q = 0.0019). PLACO+ identified 738 genome-wide-significant cross-trait variants and 65 independent loci; six of 37 evaluable loci showed strong colocalization. Of 96 MVMR models, 43 had primary-exposure conditional F ≥ 10, and 32 also had candidate-trait conditional F ≥ 10. After exact-SNP matching, the 43 primary-strength models were operationally classified as 35 partially attenuated and eight independent-signal models, with no fully attenuated model; no adjusted association survived multiplicity correction.

The results support a prioritized genomic map with substantial instrument- and model-specific uncertainty. Disease-to-clock signals were richer than clock-to-disease signals, GrimAA shared polygenic architecture with osteoarthritis, and selected loci showed strong shared-variant evidence, while the MR and MVMR findings remained unsuitable for definitive causal or mediation claims.