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
Authors: Ho Phoenix A. , Kuhn Julia , Gerbing Robert B. , Pollard Jessica A. , Zeng Rong , Miller Kristen L. , Heerema Nyla A. , Raimondi Susana C. , Hirsch Betsy A. , Franklin Janet , Lange Beverly , Gamis Alan S. , Alonzo Todd A. , Meshinchi Soheil 
Published: October 2019

Abstract
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.

Disclosures:
No relevant conflicts of interest to declare.