Causality Between T2D and OA
For T2D, we used forty genomewide significant (p<5E−08) SNPs associated with increased T2D risk identified in the largest meta-analysis of T2D GWAS studies [9]. For each of the susceptibility variants for T2D, we sought summary-level data for OA from the GWAS performed by arcOGEN Consortium. After removing three T2D variants (rs1333039, rs6494307, rs7619041) that were palindromic with intermediate allele frequencies, thirty-seven SNPs remained to perform the MR analysis for hip and knee OA. None of the thirty-seven SNPs were significantly associated with OA outcomes (p<6.76E-04) (e.g., 0.05/74). Seven of the thirty-seven T2D variants (rs1061813, rs13239186, rs1801214, rs2493394, rs6066138, rs6515236 and rs7240767) was absent from the arcOGEN study. Therefore, we used seven proxy SNPs (rs1353258, rs10276758, rs1046314, rs5025718, rs6066149, rs6048114 and rs9948462) respectively that were in high LD (r2>0.8) with the seven SNPs of interest in our analysis (Table S2). For these IVs, all the F values were larger than 10, ranging from 30.6746 to 256.3266, with an average F value of 51.9134.
In our analysis using the full set of 37 SNPs, we did not find causal associations of per unit increase in the log-odds of having T2D with risk changes of having OA, based on IVW, WM, MR-Egger regression, and MR.RAPS methods at the Bonferroni-corrected significance threshold p<0.025 (e.g., 0.05/2). (For hip OA, MR-Egger OR=0.9536, 95% CI 0.5585 to 1.6283, p=0.8629; IVW OR = 0.9086, 95% CI 0.7596 to 1.0869, p=0.2945; WM OR=0.9210, 95% CI 0.7010 to 1.2100, p=0.5545; MR.RAPS OR=0.8970, 95% CI 0.7337 to 1.0967, p=0.2892. For knee OA, MR-Egger OR=1.3162, 95% CI 0.8010 to 2.1628, p=0.2856; IVW OR=1.0085, 95% CI 0.8521 to 1.1921, p=0.9208; WM OR=1.0000, 95% CI 0.7673 to 1.3032, p=1.0000; MR.RAPS OR=1.0076, 95% CI 0.8464 to 1.1996, p=0.9319.) (Table 1 and Figure 1). We assessed the horizontal pleiotropy by checking the association of T2D associated SNPs with confounders, and no significant association signal was detected among the thirty-seven SNPs we selected at the Bonferroni-corrected significance threshold p<3.38E-04 (e.g., 0.05/148) (Table S3). We also assessed the horizontal pleiotropy with the MR-Egger regression and found no horizontal pleiotropy would bias the causality with hip OA (intercept=-0.0032, p=0.8518) and knee OA (intercept=-0.0176, p=0.2720) (Table 2). The heterogeneity test demonstrated that there is no evidence of heterogeneity in the MR analysis. (For hip OA, MR-Egger Q=40.5481, I2=0.1368, p=0.2389; IVW Q=40.5892, I2=0.1131, p=0.2752; Maximum likelihood Q=40.5675, I2=0.1126, p=0.2759. For knee OA, MR-Egger Q=30.9104, I2<0.0001, p=0.6659; IVW Q=32.1561, I2<0.0001, p=0.6520; Maximum likelihood Q=32.1560, I2<0.0001, p=0.6520.) (Table 2). The MR-Steiger results supported the causal direction between T2D and OA traits (Table 1).
Causality Between FG in non-diabetic individuals and OA
Based on independent and LD analyses, we selected fifteen genomewide significant (p<5E−08) SNPs associated with FG in non-diabetic individuals to analyze the causality with hip and knee OA, no palindromic SNPs were found. None of the fifteen SNPs were significantly associated with OA outcomes (p<0.0017) (e.g., 0.05/30) (Table S4). Five target FG variants (rs2191349, rs3783347, rs479661, rs6072275 and rs6975024) were not available in the arcOGEN study. Therefore, we used five proxy SNPs (rs6947830, rs12882934, rs525428, rs2228246 and rs2908282) respectively that were in high LD (r2>0.8) with the five SNPs of interest in our analysis (Table S4). The F values of the fifteen SNPs ranged from 32.6531 to 806.5600, with an average value of 150.5130.
No evidence supported that the genetically-increased FG was causally associated with the hip and knee OA risk changes in non-diabetic individuals based on IVW, WM, MR-Egger regression and MR.RAPS methods (p<0.025). (For hip OA, MR-Egger OR=0.5584, 95% CI 0.1741 to 1.7909, p=0.3450; IVW OR=0.5675, 95% CI 0.3143 to 1.0248, p=0.0603; WM OR=0.4772, 95% CI 0.2400 to 0.9487, p=0.0348; MR.RAPS OR=0.5712, 95% CI 0.3099 to 1.0527, p=0.0726. For knee OA, MR-Egger OR=0.4623, 95% CI 0.1447 to 1.4771, p=0.2156; IVW OR=0.7278, 95% CI 0.3947 to 1.3418, p=0.3087; WM OR=0.4896, 95% CI 0.2446 to 0.9802, p=0.0438; MR.RAPS OR=0.7247, 95% CI 0.3682 to 1.4265, p=0.3514.) (Table 1 and Figure 2). None of the fifteen SNPs were significantly associated with known confounders at the Bonferroni-corrected significance threshold (p<8.33E-04) (e.g., 0.05/60) (Table S5). We also conducted the MR-Egger regression to assess the horizontal pleiotropy, and the results revealed that the horizontal pleiotropy was unlikely to bias the causality with hip OA (intercept=0.0006, p=0.9748) and knee OA (intercept=0.0170, p=0.3830) (Table 2).
We also found no significant heterogeneity between FG and OA. (For hip OA, MR-Egger Q=17.7654, I2=0.2682, p=0.1666; IVW Q=17.7668, I2=0.2120, p=0.2176; Maximum likelihood Q=17.7374, I2=0.2107, p=0.2190. For knee OA, MR-Egger Q=19.7632, I2=0.3437, p=0.1013; IVW Q=21.0027, I2=0.3334, p=0.1016; Maximum likelihood Q=20.9936, I2=0.3331, p=0.1018.) (Table 2). The MR-Steiger directionality test showed that the direction of the IV estimates between higher level of FG and OA risk in non-diabetic individuals remained largely unchanged (Table 1).
Causality Between 2hGlu in non-diabetic individuals and OA
We chose three independent SNPs associated with 2hGlu in European ancestry from summary statistics data sets of GWAS meta-analyses, and no palindromic SNPs were found. None of the three SNPs were significantly associated with OA outcomes (p<0.0083) (e.g., 0.05/6). Two target SNPs (rs1019503 and rs6975024) were unavailable in the outcome database. Therefore, two proxy SNPs (rs1981846 and rs2908282) were chosen in the 1000 Genomes Project-imputed genotype data that were in high LD (r2>0.8) with the two target SNPs respectively (Table S6). The F values of the three SNPs were 32.8017, 33.5180 and 39.0625, with an average value of 35.1274.
Our results did not suggest causal associations of genetically-increased 2hGlu with hip and knee OA risk changes in non-diabetic individuals (p<0.025). (For hip OA, MR-Egger OR=0.2509, 95% CI 0.0338 to 1.8614, p=0.4054; IVW OR=0.8368, 95% CI 0.5154 to 1.3586, p=0.2473; WM OR=0.7844, 95% CI 0.4320 to 1.4242, p=0.4249; MR.RAPS OR=0.8311, 95% CI 0.4939 to 1.3985, p=0.4860. For knee OA, MR-Egger OR=0.4928, 95% CI 0.0759 to 3.1997, p=0.5938; IVW OR=0.8362, 95% CI 0.5292 to 1.3212, p=0.4433; WM OR=0.8345, 95% CI 0.4847 to 1.4368, p=0.5140; MR.RAPS OR=0.8356, 95% CI 0.5210 to 1.3402, p=0.4562.) (Table 1 and Figure 3). We conducted the MR-Egger regression to assess the pleiotropy, and the results revealed that the horizontal pleiotropy was unlikely to bias the causality with hip OA (intercept=0.1051, p=0.4386) and knee OA (intercept=0.0451, p=0.6695) (Table 1).
The associations between these genetic variants and confounding factors were analyzed. None of the three genetic variants were significantly associated with the confounding factors mentioned above at the Bonferroni-corrected significance threshold (p<0.0042) (e.g., 0.05/12) (Table S7). Cochran’s Q value and the I2 value indicated no evidence of heterogeneity between IV estimates with IVW, MR-Egger and maximum likelihood methods (For hip OA, MR-Egger Q=0.5059, I2<0.0001, p=0.4769; IVW Q=1.9800, I2<0.0001, p=0.3716; Maximum likelihood Q=1.9699, I2<0.0001, p=0.3735. For knee OA, MR-Egger Q=0.0485, I2<0.0001, p=0.8257; IVW Q=0.3749, I2< 0.0001, p=0.8291; Maximum likelihood Q =0.3730, I2<0.0001, p=0.8299.) (Table 2). The MR-Steiger results supported the causal direction between the exposures and outcomes (Table 1).