The WT1 synonymous SNP rs16754 Is Associated with Higher mRNA Expression and Predicts Significantly Improved Outcome In Favorable-Risk Pediatric AML: a Report From the Children's Oncology Group

Abstract 950

SNP rs16754, a synonymous single nucleotide polymorphism of the WT1 gene, has recently been reported to have prognostic implications in adult normal-karyotype acute myeloid leukemia (AML). We sought to determine the prevalence and clinical implications of WT1 SNP rs16754 in a large cohort of unselected pediatric AML patients. Available diagnostic bone marrow specimens (N=790) from patients treated on 3 consecutive CCG / COG trials (CCG-2941, CCG-2961, and COG AAML03P1) were analyzed for the presence of SNP rs16754 via direct sequencing of exon 7 of the WT1 gene. SNP status was correlated with disease characteristics, WT1 quantitative mRNA expression level, and clinical outcome. At least 1 copy of the minor SNP allele was detected in 229 (29.0%) patients, 38 (16.6%) of whom were homozygous for the SNP. SNP rs16754 was significantly more common in Asian and Hispanic patients than in Caucasian patients (P<0.001). The SNP was also less common in patients with inv(16) (P=0.043) and more common in patients with -5/del(5q) (P=0.047). Although FLT3/ITD, NPMc, and CEBPA mutations occurred at comparable frequencies in patients with or without the WT1 SNP, WT1 mutations were significantly less common in SNP-positive patients (3.2% vs. 10.4%, P=0.002). WT1 expression levels were evaluated by quantitative RT-PCR in 114 unselected patient samples with known WT1 SNP and mutation status (SNP-positive, n=31; WT1-mutation positive, n=13; one patient harbored both the SNP and a WT1 mutation). Median WT1 expression in WT1 wild-type patients (without SNP rs16754 and negative for a WT1 mutation, n=71) was 40.61 times that of normal marrow controls (range 0.00–2949.42). Median WT1 expression levels were significantly higher in both patients with SNP rs16754 (215.76 fold normal marrow, range 0.00–1399.23, P=0.0214) and in patients with a WT1 mutation (327.14 fold normal marrow, range 54.17–902.3, P=0.0005). Five-year overall survival (OS) for patients with or without the SNP was 60% ± 7% and 50% ± 5%, respectively (P=0.031). In multivariate analysis, the presence of the SNP was an independent predictor of improved OS (HR 0.64, 95% CI 0.47–0.86, P=0.004). Relapse rates were comparable between the 2 groups, but OS after relapse was significantly higher in SNP-positive patients (31% ± 11% vs. 24% ± 6% at 5 years, P=0.034) suggesting a higher rate of salvage success. The prognostic impact was most pronounced in patients with low-risk disease (those with CBF-AML, CEBPA mutation, or NPMc mutation), where five-year OS for those with or without the SNP was 90% ± 8% vs. 64% ± 9% (P=0.001) with a corresponding disease-free survival of 72% ± 13% vs. 53% ± 10% (P=0.041). The high prevalence of WT1 SNP rs16754, and its association with improved outcome, identifies WT1 SNP rs16754 as a potentially important molecular marker of prognosis in pediatric AML. WT1 SNP status, WT1 mutation status, and WT1 expression levels should be evaluated together prospectively in future pediatric AML clinical trials.