Clinical effect of point mutations in myelodysplastic syndromes

Abstract

Background: Myelodysplastic syndromes are clinically heterogeneous disorders characterized by clonal hematopoiesis, impaired differentiation, peripheral-blood cytopenias, and a risk of progression to acute myeloid leukemia. Somatic mutations may influence the clinical phenotype but are not included in current prognostic scoring systems.

Methods: We used a combination of genomic approaches, including next-generation sequencing and mass spectrometry-based genotyping, to identify mutations in samples of bone marrow aspirate from 439 patients with myelodysplastic syndromes. We then examined whether the mutation status for each gene was associated with clinical variables, including specific cytopenias, the proportion of blasts, and overall survival.

Results: We identified somatic mutations in 18 genes, including two, ETV6 and GNAS, that have not been reported to be mutated in patients with myelodysplastic syndromes. A total of 51% of all patients had at least one point mutation, including 52% of the patients with normal cytogenetics. Mutations in RUNX1, TP53, and NRAS were most strongly associated with severe thrombocytopenia (P<0.001 for all comparisons) and an increased proportion of bone marrow blasts (P<0.006 for all comparisons). In a multivariable Cox regression model, the presence of mutations in five genes retained independent prognostic significance: TP53 (hazard ratio for death from any cause, 2.48; 95% confidence interval [CI], 1.60 to 3.84), EZH2 (hazard ratio, 2.13; 95% CI, 1.36 to 3.33), ETV6 (hazard ratio, 2.04; 95% CI, 1.08 to 3.86), RUNX1 (hazard ratio, 1.47; 95% CI, 1.01 to 2.15), and ASXL1 (hazard ratio, 1.38; 95% CI, 1.00 to 1.89).

Conclusions: Somatic point mutations are common in myelodysplastic syndromes and are associated with specific clinical features. Mutations in TP53, EZH2, ETV6, RUNX1, and ASXL1 are predictors of poor overall survival in patients with myelodysplastic syndromes, independently of established risk factors. (Funded by the National Institutes of Health and others.).

Figure 1. Mutations and Cytogenetic Abnormalities in 223 Samples with at Least One Mutation

Mutations in the 11 most frequently mutated gene groups are shown by colored bars. Each column represents 1 of the 223 samples with a mutation in one or more of the genes listed. Darker bars indicate samples with two or more distinct mutations in that gene group. The karyotype of each of the 223 samples is also shown.

Figure 2. Hazard Ratios for Death from Any Cause, According to Presence (vs. Absence) of Mutation in Each of Seven Genes

Results are shown, on a log₁₀ scale, for univariate analyses as well as for analyses with adjustment for the International Prognostic Scoring System (IPSS) risk category (based on the percentage of blasts in bone marrow, the karyotype, and the number of cytopenias) (for details, see Table 2 in the Supplementary Appendix). CI denotes confidence interval.

Figure 3. Proportions of Patients with Mutations, According to Platelet Count, Blast Percentage, and Hemoglobin Level

Data are shown for the platelet count (Panel A), percentage of blasts in bone marrow aspirate (Panel B), and hemoglobin level (Panel C) at the time of bone marrow sample collection. The numbers in parentheses along the x axis indicate the number of patients with a mutation in the gene (patients could have >1 mutated gene). Mutations in NRAS, TP53, and RUNX1 were significantly associated with severe thrombocytopenia (defined as <50,000 platelets per cubic millimeter) (P<0.001 for each comparison) (Panel A) and elevated blast percentage (defined as ≥5%) (P<0.001, P = 0.005, and P = 0.003 for mutations in the three genes, respectively) (Panel B).

Figure 4. Overall Survival, According to International Prognostic Scoring System (IPSS) Risk Category and Mutational Status

Panel A shows the overall survival of patients within each IPSS risk group. Panel B shows the overall survival of patients with mutations in one or more of the five prognostic genes (TP53, EZH2, ETV6, RUNX1, or ASXL1) as compared with patients without such mutations. Panels C through F show the overall survival of patients according to the presence and absence of prognostic mutations and according to IPSS risk group. In Panels C, D, and E, the overall-survival curve for patients in the next-highest IPSS risk group is included for the purpose of comparison. In Panel F, the comparison curve is for patients in the next-lowest IPSS risk group. P values were calculated for the log-rank comparison of overall survival between patients with mutations and those without mutations for the given IPSS risk group. The IPSS risk classification, which is based on the percentage of blasts in bone marrow, the karyotype, and the number of cytopenias (Table 2 in the Supplementary Appendix), was recalculated for 428 of the 439 samples at the time of bone marrow sample collection (the IPSS classification could not be recalculated for 11 samples).