Phenome-wide Mendelian randomization identifies causal exposures for nonsyndromic cleft lip with or without cleft palate.

Objective: To systematically investigate the causal effects of exposure factors on nonsyndromic cleft lip with or without cleft palate (NSCL/P) using a phenome-wide Mendelian randomization (MR-PheWAS) framework and identify pleiotropic loci. Methods: This study integrated genome-wide association study (GWAS) data for NSCL/P, including 1 069 cases and 1 724 controls, and systematically evaluated causal associations between exposures and NSCL/P using the MR-PheWAS framework. GWAS summary data for 2 106 Asian population-exposure phenotypes were obtained from the IEU OpenGWAS database. The inverse-variance weighted (IVW) method served as the core causal inference model, supplemented by weighted median and MR-Egger regression to verify the robustness of causal associations. Additionally, multivariable MR analysis was conducted to adjust for confounding effects, alongside sensitivity tests (Cochran's Q and MR-PRESSO). Genetic correlations were analyzed using LD Score regression, and cross-phenotype pleiotropy analysis (PLACO/CPASSOC) was employed to identify shared genetic loci. Pathway enrichment and gene annotation data were integrated to explore potential biological mechanisms. Results: MR analysis identified serum calcium (OR=0.12, P=0.019), high-density lipoprotein (HDL, OR=0.61, P=0.039), and mean corpuscular hemoglobin concentration (MCHC, OR=0.39, P=0.032) as protective factors, whereas serum sodium (OR=21.41, P=0.013) was a risk factor. Furthermore, in subsequent analyses of genetic correlation and genetic overlap, a strong association was observed between serum calcium and NSCL/P. Cross-trait analysis localized pleiotropic loci to 16q24.2 and 3q21.1, involving CASR and CSTA, with significant enrichment in vitamin D response pathways. Conclusions: Numerous environmental exposure factors may have a causal impact on the outcomes of NSCL/P, and metabolic homeostasis (especially calcium signaling) plays a significant role in the pathogenesis of NSCL/P. Further genetic analyses identified potential pleiotropic loci primarily located at 16q24.2 and 3q21.1, involving key genes such as CASR and CSTA, and enriched in vitamin D response pathways. This study highlights the crucial position of genetic-environmental factors in the development of cleft lip and palate.