Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects

Abstract

Purpose: Methotrexate plasma concentration is related to its clinical effects. Our aim was to identify the genetic basis of interindividual variability in methotrexate pharmacokinetics in children with newly diagnosed acute lymphoblastic leukemia (ALL).

Patients and methods: We performed a genome-wide analysis of 500,568 germline single-nucleotide polymorphisms (SNPs) to identify how inheritance affects methotrexate plasma disposition among 434 children with ALL who received 3,014 courses of methotrexate at 2 to 5 g/m(2). SNPs were validated in an independent cohort of 206 patients.

Results: Adjusting for age, race, sex, and methotrexate regimen, the most significant associations were with SNPs in the organic anion transporter polypeptide, SLCO1B1. Two SNPs in SLCO1B1, rs11045879 (P = 1.7 x 10(-10)) and rs4149081 (P = 1.7 x 10(-9)), were in linkage disequilibrium (LD) with each other (r(2) = 1) and with a functional polymorphism in SLCO1B1, T521C (rs4149056; r(2) > 0.84). rs11045879 and rs4149081 were validated in an independent cohort of 206 patients (P = .018 and P = .017), as were other SLCO1B1 SNPs residing in different LD blocks. SNPs in SLCO1B1 were also associated with GI toxicity (odds ratio, 15.3 to 16.4; P = .03 to .004).

Conclusion: A genome-wide interrogation identified inherited variations in a plausible, yet heretofore low-priority candidate gene, SLCO1B1, as important determinants of methotrexate's pharmacokinetics and clinical effects.

Fig 1.

Average methotrexate clearance and linkage disequilibrium structure of the SLCO1B1 single-nucleotide polymorphisms (SNPs) in 434 children with acute lymphoblastic leukemia. The average methotrexate clearance for each of the 434 children in the discovery cohort is plotted from the highest to lowest (gray shaded area), and each patient's genotype at each of the SLCO1B1 SNP loci listed is indicated (colored bars below the x axis). Patients homozygous for the major allele are coded in blue, heterozygotes are coded in green, and those homozygous for the minor allele are coded in yellow.

Fig 2.

Genome-wide P values showing the association of single-nucleotide polymorphisms (SNPs) with methotrexate clearance in the discovery cohort of 434 children with acute lymphoblastic leukemia. Shown is the distribution of P values (as –log₁₀ values) for the association of 398,699 SNP genotypes with methotrexate clearance in the discovery cohort. The P value of 1.7 × 10⁻¹⁰ is for the most significant association identified between a single SNP (located in SLCO1B1 on chromosome 12) and methotrexate clearance.

Fig 3.

SLCO1B1 single-nucleotide polymorphism (SNP) rs11045879 is associated with methotrexate clearance and GI toxicity. (A) Association of SLCO1B1 SNP genotype (rs11045879) with methotrexate clearance in patients on Total XIIIB (TXIIIB), Total XV low-risk (TXVL), and Total XV standard/high-risk (TXVSH) treatment regimens. Numbers below each box plot indicate the sample size for each genotype. (B) Association of this SNP with GI toxicity. Logistic regression was used to analyze whether genotypes for SLCO1B1 SNPs were associated with toxicity as a dichotomous variable (yes or no) during the 2-week consolidation phase. The bar graphs display the percentage of patients (plotted on the y axis) per genotype (plotted on the x axis) who had grade 3 to 4 GI toxicity. Numbers above each bar represent the number of patients who had toxicity versus those who did not for the specified genotype. Similar relationships exist for SLCO1B1 SNP rs4149081 (data not shown).

Fig 4.

Incidence of toxicity based on SLCO1B1 rs11045879 genotype. Cumulative incidence of the first episode of GI toxicity significantly differed (P = .024) by SLCO1B1 rs11045879 genotype during the continuation phase of treatment during the Total XIIIB treatment regimen. Cumulative incidences of GI toxicity were compared among genotypes using Gray's test with incorporation of competing risks.