Point Mutations In Myelodysplastic Syndromes Are Associated with Clinical Features and Are Independent Predictors of Overall Survival

Abstract 300

Myelodysplastic syndromes (MDS) are clonal hematopoietic disorders with highly variable clinical features. Much of this heterogeneity is likely driven by the diverse set of genetic lesions associated with MDS. Prognostic scoring systems help stratify patients into risk groups based on clinical measures, bone marrow blast counts, and common cytogenetic abnormalities. However, the presence or absence of point mutations is not considered by the prognostic scoring systems used in clinical practice. Since more than half of MDS cases have a normal karyotype, genetic abnormalities do not contribute to prognostic risk in the majority of patients. In order to better understand the frequency, overlap, and clinical impact of point mutations in MDS, we examined samples from a cohort of 438 patients for mutations in cancers genes. First we screened 191 samples for the presence of 1233 known oncogenic mutations in over 130 cancer-related genes using a high-throughput, mass spectroscopic genotyping platform (OncoMap). Somatic mutations were validated in 7 genes. Known oncogenic mutations in these genes were then sought in an expanded cohort of 438 MDS patient samples. Additional mutated samples were identified for 6 of these 7 genes, including NRAS, KRAS, BRAF, and JAK2. Our second approach utilized next-generation 454-pyrosequencing of several tumor suppressor genes and MDS-related genes not covered with OncoMap, including TET2, RUNX1, TP53, CBL, NPM1, PTEN and CDNK2A. This was complemented by Sanger sequencing of additional genes including IDH1, IDH2, ASXL1, and KDM6A. In aggregate, 50.9% of samples were found to carry at least one mutation, including 50.8% of samples with normal cytogenetics. The most frequently mutated genes were TET2 (18%), ASXL1 (14%), RUNX1 (8%), and TP53 (7%). Recurring mutations in NRAS, JAK2, IDH1, IDH2, CBL, NPM1, KDM6A, and KRAS were identified at lower frequency. TP53 mutations were largely exclusive of all other mutations except for those in TET2 and TP53 mutations were highly associated with complex cytogenetics and abnormalities of chromosome 17. TET2 mutations were overrepresented in cases of normal cytogenetics but not predictive of survival, even after stratification by mutant allele burden. Mutations of RUNX1, NRAS, and TP53 were each associated with a lower platelet count (p<0.001 for each comparison). Mutations in these genes and CBL were also associated with a higher bone marrow blast count (p≤0.01 for each comparison). Several genes, including NRAS, RUNX1, TP53, CBL, IDH2, and ASXL1 were associated with decreased overall survival (p=0.01, p<0.001, p<0.001, p=0.02, p=0.03, p=0.01, respectively). In a multivariable model including age, sex, and International Prognostic Scoring System risk group, RUNX1 (hazard ratio [HR], 1.61; 95% confidence interval [CI], 1.10–2.35), TP53 (HR, 2.34; 95% CI, 1.50–3.64), and ASXL1 (HR, 1.42; 95%, CI1.05-1.92) were independent predictors of decreased overall survival. In summary, we performed a broad survey for gene mutations associated with myeloid neoplasms or other cancers. In our cohort of 438 clinically annotated MDS patient samples, we identified point mutations in over 15 genes with more than 50% of samples harboring at least one mutation. Mutations in several genes were associated with clinical features of MDS including thrombocytopenia and elevated blast counts. Mutations of RUNX1, TP53, and ASXL1 (present in 26.3% of samples) are independent predictors of decreased survival, demonstrating that incorporation of point mutations adds information to the risk stratification systems used in clinical practice.