IVs were screened according to the conditions described above. The details of the SNPs that were eventually included in the TSMR analysis of the plasma lipidome and allergic rhinitis (AR) are presented in Supplementary Table 1. After harmonization, the number of SNPs involved in each pair of lipid species and allergic rhinitis ranged from 10 to 34. The F-statistics of all SNPs ranged from 18.79 to 1969.17, indicating that there are no weak IVs. In the reverse Mendelian randomization analysis, SNPs related to allergic rhinitis as the exposure were also screened using a genome-wide significance threshold of P < 5 × 10-8. The number of SNPs after clumping ranged from 23 to 31. To identify suitable IVs for this study, we utilized the PhenoScanner website. Any SNPs of exposure found to be directly associated with the outcomes were excluded ahead of the MR analysis. Furthermore, we comprehensively assessed the selected SNPs to evaluate their potential pleiotropic effects, utilizing the MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test. Fortunately, none of the SNPs exhibited any indications for removal after undergoing this evaluation.
Causal effects of lipidomes and AR
Through FDR correction (PFDR <0.05), we identified several lipid phenotypes as risk factors for allergic rhinitis (AR): Sterol ester (27:1/20:4) levels, Phosphatidylcholine (18:0_20:4) levels, Phosphatidylcholine (18:0_22:5) levels, Sterol ester (27:1/20:5) levels, and Phosphatidylcholine (20:4_0:0) levels. Notably, Phosphatidylcholine (18:0_20:4) levels remained significant after FDR correction when using FinnGen data for AR outcomes as auxiliary validation (PFDR = 0.017, P = 0.0003). For detailed data, refer to Table S1-S4. For Sterol ester (27:1/20:4) levels in relation to AR (UK Biobank data), the IVW method estimated the risk (OR) as 1.009 (95% CI = 1.004-1.014, PFDR = 0.027, P = 0.0003). Similarly, for Phosphatidylcholine (18:0_20:4) levels in relation to AR (UK Biobank data), the IVW method estimated the risk (OR) as 1.009 (95% CI = 1.004-1.014, PFDR = 0.027, P = 0.0003). Consistent results were obtained from the MR Egger, weighted median, and Bayesian Weighted Mendelian Randomization (BWMR) methods, further validating these findings (Figures 2 and 3). For Phosphatidylcholine (18:0_20:4) levels in relation to AR (FinnGen data), the IVW method estimated the risk (OR) as 1.068 (95% CI = 1.03-1.106, PFDR = 0.017, P = 0.0003). For Phosphatidylcholine (18:0_22:5) levels in relation to AR (FinnGen data), the IVW method estimated the risk (OR) as 1.115 (95% CI = 1.055-1.178, PFDR = 0.010, P = 0.0001). The consistent results from other methods reinforced these associations. For Sterol ester (27:1/20:5) levels in relation to AR (FinnGen data), the IVW method estimated the risk (OR) as 1.084 (95% CI = 1.035-1.134, PFDR = 0.025, P = 0.0006). Finally, for Phosphatidylcholine (20:4_0:0) levels in relation to AR (FinnGen data), the IVW method estimated the risk (OR) as 1.081 (95% CI = 1.04-1.123, PFDR = 0.010, P = 0.0001) (Figure 2).
Sensitivity analysis results
To validate the robustness of our findings, sensitivity analyses were performed using the stricter P < 5 × 10-8 threshold. Although this stricter threshold resulted in fewer SNPs (ranging from 2 to 8), the positive associations identified with the P < 1 × 10-5 threshold remained significant after FDR correction, reinforcing the reliability of our causal inferences. Interestingly, using the P < 5 × 10-8 threshold allowed us to identify more positive results, which was crucial for maintaining sufficient statistical power. However, using fewer SNPs with the stricter threshold increased the risk of results being influenced by individual SNP effects. Therefore, the more inclusive threshold was preferred to ensure a robust Mendelian Randomization (MR) analysis (Table S7-8).
For all associations, the MR-Egger intercept test excluded the notion of horizontal pleiotropy, indicating no pleiotropic bias. The MR-Egger intercept test showed no significant evidence of directional pleiotropy (P values > 0.05), suggesting minimal influence of genetic pleiotropy on the IVs' impact on AR through lipidomes. Cochran's Q test was used to evaluate the heterogeneity of the IVs, with Q_pval values ranging from 0.207 to 0.955, indicating no substantial heterogeneity (Table 2). The leave-one-out analysis confirmed that no single SNP significantly influenced the overall results, reinforcing the stability of our findings (Figures 4 and 5). Additionally, funnel plots and scatter plots demonstrated a high degree of association and a lack of heterogeneity, further validating the robustness of the identified causal relationships.
Table 2 Assessment of Pleiotropy and Heterogeneity in MR Analysis
Exposure
|
Outcome
|
Pleiotropy
|
Heterogeneity
|
MR-Egger intercept
|
MR-PRESSO
|
Cochrane’s Q P-value
|
egger_intercept
|
pval
|
Global Test`$Pvalue
|
IVW
|
MR-Egger
|
Sterol ester (27:1/20:4) levels
|
AR(ukb)
|
-0.0008
|
0.352
|
0.346
|
0.211
|
0.210
|
Phosphatidylcholine (18:0_20:4) levels
|
AR(ukb)
|
-0.0003
|
0.651
|
0.364
|
0.207
|
0.176
|
Phosphatidylcholine (18:0_20:4) levels
|
AR(finngen)
|
0.0010
|
0.859
|
0.304
|
0.230
|
0.190
|
Phosphatidylcholine (18:0_22:5) levels
|
AR(finngen)
|
-0.0138
|
0.070
|
0.272
|
0.215
|
0.331
|
Sterol ester (27:1/20:5) levels
|
AR(finngen)
|
-0.0023
|
0.705
|
0.810
|
0.749
|
0.706
|
Phosphatidylcholine (20:4_0:0) levels
|
AR(finngen)
|
-0.0002
|
0.976
|
0.962
|
0.955
|
0.938
|
MR-Egger intercept and p-values are used to assess pleiotropy, where non-significant p-values indicate no pleiotropic bias. The MR-PRESSO Global Test's p-values further evaluate pleiotropy. Cochrane’s Q p-values assess heterogeneity, with non-significant values indicating no substantial heterogeneity. AR: Allergic Rhinitis.
Additionally, for Phosphatidylcholine (18:0_20:4) levels, which remained significant after FDR correction in both UK Biobank and FinnGen datasets, we conducted a meta-analysis of the outcomes. As shown in the attached figure, the random effects model estimated an overall odds ratio (OR) of 1.0351 (95% CI = 0.9799-1.0933, P = 0.2169), indicating a consistent association across both cohorts despite the observed heterogeneity (I² = 89%, τ² = 0.001, P < 0.01) (Figure 6).
Reverse Mendelian Randomization Analysis
In our exploration of the causal effects of AR on the plasma lipidome, we utilized the IVW method as the principal analysis in a two-sample MR study. Despite conducting multiple test adjustments via the FDR method, we identified two lipid traits in the UK Biobank cohort with suggestive significance: Phosphatidylcholine (18:2_20:3) levels (beta = -0.5165, P = 0.0449, 95% CI = -1.0213 to -0.0117) and Phosphatidylinositol (18:0_20:3) levels (beta = -0.5020, P = 0.0450, 95% CI = -0.9929 to -0.0112). However, these associations did not retain significance after FDR correction (PFDR = 0.993). For the FinnGen cohort, no lipid traits were identified at a significance level of P < 0.05, even before FDR correction (Table S5,S6). This suggests that AR does not have a robust causal effect on the plasma lipidome in the FinnGen dataset. These results imply that while there may be suggestive associations between AR and specific lipid traits in the UK Biobank data, they do not meet the stringent criteria for statistical significance after correction for multiple testing. The lack of significant findings in the FinnGen cohort further supports the conclusion that the observed effects of AR on the plasma lipidome are not robust.