Pathway Based Pharmacogenomics of Cytarabine In Pediatric Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is the second most common form of childhood leukemia and has the worst prognosis of all major childhood cancers. The mainstay of AML chemotherapy is the nucleoside analog cytarabine (ara-C). Numerous studies suggest that the intracellular concentrations of the ara-C active metabolite, ara-CTP, vary widely among patients, and in turn, are associated with variability in clinical response to AML treatment. In the present study, we have taken a pathway directed approach to identify genetic predictors of ara-C response in pediatric patients treated with ara-C based antileukemic chemotherapy in the AML02 (n=187) and AML97 (n=55) clinical trials. The AML02 trial enrolled AML patients <22 years of age excluding APL or Down's syndrome patients, but those with all other subtypes of de novo or secondary AML, as well as patients with mixed-lineage leukemia, were eligible. Patients were randomized to receive induction I therapy containing high-dose cytarabine or low-dose cytarabine plus daunorubicin and etoposide. We genotyped the genomic DNA from patients enrolled in AML02 study for potentially significant single nucleotide polymorphisms (SNPs) in 10 key ara-C pathway genes and screened for association with 3 endpoints in AML02 study: in vitro ara-C LC50 determined in diagnostic leukemic cells, event free survival (EFS) and overall survival (OS). In samples from St. Jude AML97 study, we screened for association of SNPs with 4 endpoints: intracellular ara-CTP levels after start of induction, DNA synthesis relative to baseline, morphological response after induction I, and EFS. In the St Jude AML 97 study patients were randomly assigned to receive ara-C as either a short daily infusion (500 mg/m²/dose intravenously over 2 hrs daily for 5 days) or a continuous infusion (500 mg/m²/day as a continuous infusion over 5 days). Bone marrow was collected at the end of the ara-C infusion on day 1 for patients receiving the short daily infusion (n=27), and at 10 hrs after the start of the infusion for those receiving the continuous infusion (n=28). Ara-CTP levels in leukemia cells were analyzed by HPLC. Intracellular accumulation of ara-CTP was significantly higher when given as short daily infusion, as compared to continuous infusion (p = 0.01). The inter-patient variability for blast ara-CTP concentrations was 40-fold in the short infusion arm and 101-fold in the continuous infusion arm. We found significant correlations between SNPs in ara-C pathway genes (such as DCK, DCTD, CMPK, CTPS, CDA and NT5C2) and various clinical parameters (after adjusting for arm and/or risk group), some of which are listed below.

These results suggest that genetic variation in key candidate genes in ara-C metabolic pathway could in?uence and predict the variability observed in cellular sensitivity and treatment response. The pharmacogenomic factors identi?ed in the present study could be potentially used for tailoring medications to better individualize cytarabine based AML therapy.

No relevant conflicts of interest to declare.