Study design. (A) Overview of the process and principal assumptions of MR. (B) Data sources of the GWASs. (C) Methods performed in the present study.

Abbreviations and Notes: BCC, Blood Cell Consortium; BMA, Bayesian model averaging, a high-throughput method based on non-linear regression; BMI, body mass index; FPG, fasting plasma glucose; FUSION, functional summary-based imputation; GLIDE, Gene-Lifestyle Interactions in Dental Endpoints collaboration consortium; GWAS, genome-wide association study; IVW, inverse variance weighted, the primary method in MR to explore the association between exposure and outcome; LOO, leave-one-out, a method for detecting potential influential SNPs; SNP, single nucleotide polymorphism, as genetic instrumental variables for the exposure and outcome; MACE, model-averaged causal estimate; MIP, marginal probability of inclusion; MR, Mendelian randomization; MR-PRESSO, Mendelian Randomization Pleiotropy RESidual Sum and Outlier, a method for assessing and rectifying pleiotropic SNPs; MSCE, model-specific causal estimate; MVMR, multivariable Mendelian randomization, a MR model for adjusting confounding and mutual correction; Neu, neutrophil; NKT, Natural Killer T cell; pDC, plasmacytoid dendritic cell; PP, posterior probability; TWAS, transcriptome-wide association study; UVMR, univariable Mendelian randomization.

Characteristics of the GWAS data for MR.

Results of the UVMR. (A) A circular heatmap representing the MR analyses for the associations between circulating immune cells and the risk of periodontitis. Lines, from outermost to innermost, represent IVW, MR-WM, MR-ML, MR-Egger, and MR-PRESSO respectively. The color scale of the heatmap is based on the OR. * P < 0.05. (B) A forest plot of the MR analyses for significant results in Figure 2A (P < 0.05). The effects are quantified using OR with 95% CI. (C-E) The effect estimate for each individual variant in Natural Killer T cell (C), neutrophil (D), and plasmacytoid DC (E) is provided by plotting SNP-outcome associations against SNP-exposure associations. The regression slope fitted by different MR methods is represented by lines with different colors.

Abbreviations: CI, confidence interval; DC, dendritic cell; F-stat, F-statistic; IVW, inverse variance weighted; Het, heterogeneity; MR, Mendelian randomization; MR-ML, Mendelian randomization weighted median; MR-WM, Mendelian randomization maximum likelihood; MR-PRESSO, Mendelian Randomization Pleiotropy RESidual Sum and Outlier; OR, odds ratio; Pleio, pleiotropy; SNP, single nucleotide polymorphism; UVMR, univariable Mendelian randomization.

Forest plot analysis of the MVMR of significant results following mutual adjustment and confounder correction. The effects are quantified using OR with 95% CI.

Abbreviations: CI, confidence interval; DC, Dendritic Cell; IVW, inverse variance weighted; Het, heterogeneity; LASSO, least absolute shrinkage and selection operator; MVMR, multivariable Mendelian randomization; OR, odds ratio; Pleio, pleiotropy; SNP, single nucleotide polymorphism.

Ranking of risk factors and models for periodontitis in MR-BMA analysis.

Results of the subgroup and reverse MR. (A) A circular heatmap illustrates the results of the subgroup analysis and reverse MR. Lines in the heatmap represent periodontitis (GLIDE), chronic periodontitis (FinnGen), chronic gingivitiss (FinnGen), gingival hyperplasia (FinnGen), and reverse MR analysis, progressing from outside to inside. The color scale of the heatmap is determined by the odds ratio (OR). * P < 0.05. (B) A forest plot of the MR analyses for significant results in Figure 4A (P < 0.05). The effects are quantified using OR with 95% CI. (C-F) The effect estimates for each individual variant in B cell (CP) (C), plasmacytoid DC (CP) (D), B cell (GH) (E) and CD4+ T cell (CG) (F) is provided by plotting SNP-outcome associations against SNP-exposure associations. The regression slope fitted by different MR methods is represented by lines with different colors.

Abbreviations: CG, chronic gingivitiss; CI, confidence interval; CP, chronic periodontitis; DC, dendritic cell; F-stat, F-statistic; GH, gingival hyperplasia; GLIDE, Gene-Lifestyle Interactions in Dental Endpoints collaboration consortium; Het, heterogeneity; IVW, inverse variance weighted; MR-PRESSO, Mendelian Randomization Pleiotropy RESidual Sum and Outlier; OR, odds ratio; PD, periodontitis; Pleio, pleiotropy; SNP, single nucleotide polymorphism.

Results of the TWAS and colocalization analysis. (A) A Venn diagram illustrates the intersecting genes shared by multiple traits (P < 0.05). (B) A heatmap representing the TWAS and colocalization analysis for five genes interacting among neutrophil, Natural Killer T cell, plasmacytoid DC, and periodontitis. The TWAS Z-score is used as the color scale for the heatmap. * PP.H3 + PP.H4 > 0.5; ** PP.H3 + PP.H4 > 0.8; *** PP.H4 > 0.8. (C) Manhattan plot of gene-traits associations for periodontitis. The X-axis represents genomic positions. Blue lines indicate a Z-score of 1.96. Red circles represent significant gene-trait associations (P < 0.05). Six genes satisfy a multiple corrected threshold of P < 5×10−4. (D) Regional Manhattan plot of conditional analysis for S100A9, S100A12 in periodontitis. Grey bars indicate the location of genes on chromosome 1. Genes colored in orange and green on the graph indicate the marginally and jointly significant genes that best explain the GWAS signals. Gray and blue dots respectively indicate GWAS p-values before and after conditioning on the jointly significant gene.

Abbreviations: DC, dendritic cell; GWAS, genome-wide association study; PP, posterior probability; TWAS, transcriptome-wide association study.

TWAS and colocalization analysis identified genes involved in multiple phenotypes.