An Integrated Clinical and Genetic Prediction Model for Tacrolimus Levels in Pediatric Solid Organ Transplant Recipients

Abstract

Background: There are challenges in achieving and maintaining therapeutic tacrolimus levels after solid organ transplantation (SOT). The purpose of this genome-wide association study was to generate an integrated clinical and genetic prediction model for tacrolimus levels in pediatric SOT.

Methods: In a multicenter prospective observational cohort study (2015-2018), children <18 years old at their first SOT receiving tacrolimus as maintenance immunosuppression were included (455 as discovery cohort; 322 as validation cohort). Genotyping was performed using a genome-wide single nucleotide polymorphism (SNP) array and analyzed for association with tacrolimus trough levels during 1-y follow-up.

Results: Genome-wide association study adjusted for clinical factors identified 25 SNPs associated with tacrolimus levels; 8 were significant at a genome-wide level (P < 1.025 × 10-7). Nineteen SNPs were replicated in the validation cohort. After removing SNPs in strong linkage disequilibrium, 14 SNPs remained independently associated with tacrolimus levels. Both traditional and machine learning approaches selected organ type, age at transplant, rs776746, rs12333983, and rs12957142 SNPs as the top predictor variables for dose-adjusted 36- to 48-h posttacrolimus initiation (T1) levels. There was a significant interaction between age and organ type with rs776476*1 SNP (P < 0.05). The combined clinical and genetic model had lower prediction error and explained 30% of the variation in dose-adjusted T1 levels compared with 18% by the clinical and 12% by the genetic only model.

Conclusions: Our study highlights the importance of incorporating age, organ type, and genotype in predicting tacrolimus levels and lays the groundwork for developing an individualized age and organ-specific genotype-guided tacrolimus dosing algorithm.

Conflict of interest statement

The authors declare no conflicts of interest.

Copyright © 2021 The Author(s). Published by Wolters Kluwer Health, Inc.

Figures

Graphical abstract

FIGURE 1.

A, Box plot of tacrolimus levels by time after transplant (n = 455 recipients; 2375 tacrolimus levels). The x-axis shows tacrolimus levels at 6 posttransplant time points (36–48 h post-Tac initiation (n = 398), 7 d (n = 410), 14 d (n = 409), 30 d (n = 403), 3 mo (n = 398), and 12 mo posttransplant (n = 357) in kidney (purple), heart (red), liver (blue), and lung (green) transplant recipients. The boxes represent medians and interquartile ranges, the whiskers represent minimum and maximum values, and the dots represent outliers. B, Forest plot of variables associated with tacrolimus trough levels during 1-y follow-up posttransplant using linear-mixed effects model. Tacrolimus levels were higher in liver, heart, and lung recipients compared with kidney recipients. Tacrolimus levels were higher with increasing age, concomitant CYP3A4 inhibitor use, and higher tacrolimus dosage. Dots represent parameter estimate for tacrolimus levels, and bars represent 95% confidence intervals. *P < 0.05; **P < 0.01; ***P < 0.001. †Posttacrolimus initiation. PC1, first principal component; PC2, second principal component; TAC, tacrolimus.

FIGURE 2.

GWAS SNPs associated with tacrolimus trough levels. A, Manhattan plot showing SNPs associated with tacrolimus levels on GWAS analysis with majority of the significantly associated SNPs residing on chromosome 7. The red line represents genome-wide significance at P < 1.025 × 10−7, and the blue line represents P < 1 × 10−5. B, Q-Q plot of the observed vs expected P for SNP association with tacrolimus levels. C, Forest plot of SNPs independently associated with tacrolimus levels during 1-y follow-up posttransplant. Colored dots represent parameter estimate for tacrolimus levels, and bars represent 95% confidence intervals. GWAS, genome-wide association study; SNP, single nucleotide polymorphism.

FIGURE 3.

Interaction of age and organ type with association of rs776746*1 SNP with T1 levels. A, Interaction plot of age and rs776746*1 SNP (adjusted for organ type). Blue dots represent log-transformed dose-adjusted T1 levels in CYP3A5 nonexpressors, red dots represent log-transformed dose-adjusted T1 levels in CYP3A5 expressors, and bars represent 95% CI in 3 age groups. The difference in log-transformed dose-adjusted T1 levels between CYP3A5 nonexpressors and expressors was higher in infants (n = 238; effect size 0.73; P < 0.001) and adolescents (n = 219; effect size 0.67; P < 0.001) and lower in children (n = 234; effect size 0.34; P < 0.01) (P < 0.05 between children and other age groups). B, Interaction plot of organ type and rs776746*1 SNP (adjusted for age). Blue dots represent log-transformed dose-adjusted T1 levels in CYP3A5 nonexpressors, red dots represent log-transformed dose-adjusted T1 levels in CYP3A5 expressors, and bars represent 95% CI in 3 different organ types. The difference in log-transformed dose-adjusted T1 levels between CYP3A5 nonexpressors and CYP3A5 expressors was higher in heart (effect size 0.92; P < 0.001) than in kidney (effect size 0.42; P < 0.001) or liver recipients (effect size 0.46; P < 0.001) (P < 0.01 between heart and other organ recipients). ***P < 0.001, and **P < 0.01. SNP, single nucleotide polymorphism.

FIGURE 4.

Model performance for dose-adjusted T1 level prediction. A, Coefficient path of lasso model with a red vertical line indicating selected λ = 0.23, which has smallest out of sample MSE. The y-axis indicates standardized coefficient. Each colored line represents the independent variable and its coefficient. The variable with the largest standardized coefficient has highest impact on dose-adjusted T1 levels. As variables enter the model from left to right, the variable which enters the model first (ie, diverges from the 0 line) is the most important predictor and the variable which enters last is the least important variable. The x-axis represents the tuning parameter (λ) of lasso model. B, Standardized coefficient plot of the lasso model showing the relationship between the variables and dose-adjusted T1 levels with the variables above the zero line being positively related while those below the line being negatively associated with dose-adjusted T1 levels. C, Plot of observed vs dose-adjusted T1 levels predicted by clinical only model (blue), SNP only model (red), and combined clinical and SNP model (green) in the validation cohort. The dotted line represents a 45-degree perfect fitted line. (D) Plot of observed vs dose-adjusted T1 levels predicted by the combined clinical and SNP model in heart (orange), liver (gray), and kidney (magenta) recipients. The dotted line represents a 45-degree perfect fitted line. MSE, mean squared error; SNP, single nucleotide polymorphism.