Genome-Wide Study Links PNPLA3 Variant With Elevated Hepatic Transaminase After Acute Lymphoblastic Leukemia Therapy

Abstract

Remission induction therapy for acute lymphoblastic leukemia (ALL) includes medications that may cause hepatotoxicity, including asparaginase. We used a genome-wide association study to identify loci associated with elevated alanine transaminase (ALT) levels after induction therapy in children with ALL enrolled on St. Jude Children's Research Hospital (SJCRH) protocols. Germline DNA was genotyped using arrays and exome sequencing. Adjusting for age, body mass index, ancestry, asparaginase preparation, and dosage, the PNPLA3 rs738409 (C>G) I148M variant, previously associated with fatty liver disease risk, had the strongest genetic association with ALT (P = 2.5 × 10^-8 ). The PNPLA3 rs738409 variant explained 3.8% of the variability in ALT, and partly explained race-related differences in ALT. The PNPLA3 rs738409 association was replicated in an independent cohort of 2,285 patients treated on Children's Oncology Group protocol AALL0232 (P = 0.024). This is an example of a pharmacogenetic variant overlapping with a disease risk variant.

Figure 1. ALT level variation in pediatric ALL patients

(A) Total XVI patients receiving PEGylated E. coli asparaginase had higher ALT levels compared to Total XV patients receiving native E. coli asparaginase (P = 3.0×10⁻³). (B) Among Total XV and Total XVI patients, those receiving additional doses of asparaginase during induction due to a higher ALL burden at day 15–19 had higher ALT levels compared to patients receiving fewer doses of asparaginase (P = 3.5×10⁻⁶). (C) Among Total XV and Total XVI patients, whites (P = 3.3×10⁻¹⁰) and Hispanics (P = 3.3×10⁻⁷) had higher ALT levels compared to blacks. (D) ALT levels were correlated with age (yrs) in the SJCRH discovery cohort (N = 715, r = 0.20, P = 9.4×10⁻⁸). (E) ALT levels were positively correlated with BMI percentile in the SJCRH discovery cohort (N = 715, r = 0.11, P = 5.2×10⁻³). The P values indicated are from univariate analyses (Table S1).

Figure 2. Manhattan plots of inverse P values for genome-wide SNP associations with ALT levels

(A) Association between SNPs and natural logarithm ALT levels versus each chromosome for Total XV and XVI patients (N = 715). The analysis identified a variant in PNPLA3 (rs738409) associated with ALT levels. (B) Association between SNPs and ALT levels versus each chromosome for black patients in Total XV and XVI patients (n = 111). A variant near PIGV and a variant in 3′-UTR of GREB1 were associated with ALT levels with genome-wide significance.

Figure 3. Post-induction ALT levels varied by genotype in 715 SJCRH Total XV and XVI patients

(A) Boxplots of ALT levels by PNPLA3 rs738409 genotype in blacks (n = 111, P = 0.20), whites (n = 488, P = 1.5×10⁻⁶), and Hispanics (n = 60, P = 0.058) from the SJCRH discovery cohort. (B) Boxplots of ALT levels by PNPLA3 rs738409 MAF in blacks, whites and Hispanics from the SJCRH discovery cohort. (P values of whites and Hispanics vs. blacks are 3.3×10⁻¹⁰ and 3.3×10⁻⁷ respectively in univariate analysis.) (C) Boxplots of ALT levels by PIGV rs12748152 genotype in blacks (n = 102, P = 1.3×10⁻⁸), whites (n = 471, P = 0.14), and Hispanics (n = 60, P = 0.59) from the SJCRH discovery cohort. (D) Boxplots of ALT levels by GREB1 rs149940960 genotype in blacks (n = 86, P = 2.0×10⁻⁸) from the SJCRH discovery cohort. The boxes depict median with upper and lower quartiles.