Impact of polymorphisms in drug pathway genes on disease-free survival in adults with acute myeloid leukemia

Abstract

Acute myeloid leukemia (AML) is a clinically heterogeneous disease, with a 5-year disease-free survival (DFS) ranging from under 10% to over 70% for distinct groups of patients. At our institution, cytarabine, etoposide and busulfan are used in first or second remission patients treated with a two-step approach to autologous stem cell transplantation (ASCT). In this study, we tested the hypothesis that polymorphisms in the pharmacokinetic and pharmacodynamic pathway genes of these drugs are associated with DFS in AML patients. A total of 1659 variants in 42 genes were analyzed for their association with DFS using a Cox-proportional hazards model. One hundred and fifty-four genetically European patients were used for the primary analysis. An intronic single nucleotide polymorphism (SNP) in ABCC3 (rs4148405) was associated with a significantly shorter DFS (hazard ratios (HR)=3.2, P=5.6 × 10(-6)) in our primary cohort. In addition, a SNP in the GSTM1-GSTM5 locus, rs3754446, was significantly associated with a shorter DFS in all patients (HR=1.8, P=0.001 for 154 European ancestry; HR=1.7, P=0.028 for 125 non-European patients). Thus, for the first time, genetic variants in drug pathway genes are shown to be associated with DFS in AML patients treated with chemotherapy-based autologous ASCT.

Figure 1

Schematic of workflow applied to determine the association of genetic variations in 42 candidate genes with disease free survival (DFS) in AML patients treated with a two-step treatment protocol prior to autologous stem cell transplantation. The workflow begins with phenotype data collection and genotyping of DNA samples using a genomewide SNP array. Candidate genes were selected based on their roles in the: drugs' pharmacokinetic/pharmacodynamics pathway; DNA mismatch repair mechanism; association with the drug cytotoxicity in lymphoblastoic cell lines previously identified in literatures; and pharmacogenomics studies of AML drug response. After association of each SNPs with disease-free survival in the 154 AML patients of European ancestry, the SNPs with p<0.01 and their tag-SNPs were examined for their potential functional roles using databases to identify eQTL SNPs and predicted regulatory elements such as binding sites of transcription factors and for their replications of previous studies. The SNPs with p<0.01 were also examined for their associations with DFS in 125 non-European ancestry. Finally, imputation was performed to identify other SNPs with stronger associations with DFS in European ancestry.

Figure 2

Plot showing the significance (-log10 of the P-value) of associations of the 1659 SNPs with DFS in 154 AML patients of European ancestries. Only SNPs with minor allele frequencies of ≥1% in the selected 42 candidate genes are shown. Each dot represents a SNP. SNPs above the black dotted line are SNPs with p<0.01, and the SNP above the red dotted line reached a p-value,which was significant after correction for multiple testing (p<3x10^-5).

Figure 3a – d

Kaplan-Meier estimate of disease-free survival (DFS) stratified by the top SNPs (a) rs4148405 ABCC3 (b) rs10805074 DCK (c) rs3754446 GSTM1 and (d) rs505802 SLC22A12 genotypes in patients of European ancestry.

Figure 3a – d

Kaplan-Meier estimate of disease-free survival (DFS) stratified by the top SNPs (a) rs4148405 ABCC3 (b) rs10805074 DCK (c) rs3754446 GSTM1 and (d) rs505802 SLC22A12 genotypes in patients of European ancestry.

Figure 3a – d

Kaplan-Meier estimate of disease-free survival (DFS) stratified by the top SNPs (a) rs4148405 ABCC3 (b) rs10805074 DCK (c) rs3754446 GSTM1 and (d) rs505802 SLC22A12 genotypes in patients of European ancestry.

Figure 3a – d

Kaplan-Meier estimate of disease-free survival (DFS) stratified by the top SNPs (a) rs4148405 ABCC3 (b) rs10805074 DCK (c) rs3754446 GSTM1 and (d) rs505802 SLC22A12 genotypes in patients of European ancestry.

Figure 4

Plot showing the association of the genotyped and imputed SNPs with MAF ≥1% in the selected top 8 candidate genes (ABCC3, DCK, SLC28A3, SLC22AA12, MSH3, RRM1, GSTM1, GSTT1). Each colored diamond (not gray or black) represents a genotyped SNP and the grey/black dots represent imputed SNPs.