Genetic Determinants of Disease Phenotype and Clinical Outcome in Myelodysplastic Syndromes with Ring Sideroblasts

Ring sideroblasts (RS) characterize a group of myelodysplastic syndromes (MDS) categorized in the WHO classification as refractory anemia with RS (RARS) or refractory cytopenia with multilineage dysplasia and RS (RCMD-RS), according to the presence of 15% or more bone marrow RS and dysplasia in one or more myeloid lineages. A high prevalence of somatic mutations in SF3B1 was reported in MDS with RS [N Engl J Med 2011;365:1384-95], and recent unsupervised analyses suggested that MDS with SF3B1 mutation represent a homogeneous subset [Blood 2014 Jun 26]. In this study, we performed a comprehensive mutation analysis of genes implicated in myeloid disorders in a large and well-characterized cohort of myeloid neoplasms with 1% or more RS with the aim to identify mutation patterns that affect disease phenotype and clinical outcome.

The study population consisted of 309 patients (pts), including: a) 244 with MDS, of whom 160 assigned to sideroblastic categories (RARS, RCMD-RS) and 84 to other WHO categories [34 RA or RCMD, 7 MDS with isolated del(5q), 20 RAEB-1, 23 RAEB-2]; b) 51 with myelodysplastic/myeloproliferative neoplasms (MDS/MPN: 9 CMML, 42 RARS-T); c) 14 with AML-MDS.

SF3B1 mutations were observed in 151/244 pts with MDS and RS (62%). Within sideroblastic categories, SF3B1 mutation was found in 81/91 cases of RARS (89%), and 48/69 RCMD-RS (70%). Among pts classified in other MDS categories, significantly lower rate of SF3B1 mutations (22/84, P<.001) and higher prevalence of mutations in other RNA splicing factors (SRSF2, U2AF1, ZRSR2) (P<.001) were observed. Pts with MDS carrying SF3B1 mutation showed a limited pattern of recurrently co-mutated genes including those involved in DNA methylation (39%), chromatin modification (10%), and RUNX1 (5%). Variant allele frequencies (VAFs) analysis showed that in most cases (91%) SF3B1 mutation was in the dominant clone. Within SF3B1-negative MDS with RS, a significantly higher prevalence of mutations in TP53 was found (9/93, P=.001), 6 of 9 cases showing disease phenotype with multilineage dysplasia and no excess blasts.

In a multivariable analysis, pts with SF3B1 mutation showed significantly better overall survival (OS) (HR .39, P=.001) and lower risk of disease progression (HR=.40, P=.024) compared with SF3B1-unmutated cases. The independent prognostic value of SF3B1 mutations was retained when the analysis was limited to sideroblastic categories (OS: HR=.32, P=.005; risk of progression: HR=.27, P=.036).

Then, we focused on MDS associated with SF3B1 mutation (defined by SF3B1 mutation, no excess blasts or del(5q): 81 RARS, 48 RCMD-RS, 4 RA or RCMD) with the aim to identify genetic determinants of disease phenotype. We found that mutations in DNA methylation genes (TET2, DNMT3A) were significantly associated with multilineage dysplasia (P=.015). The analysis of VAFs showed that in 90% of cases there was no statistical evidence of subclonality of these gene mutations. When comparing pts with uni- or multilineage dysplasia, no significant difference was observed in hematological parameters. In addition, no significant effect of multilineage dysplasia was found on OS (P=.5) and risk of progression (P=.92). Taken together, these results suggest that MDS associated with SF3B1 mutation is indeed a homogeneous subset, and should be recognized as a distinct disease entity within MDS, irrespective of current WHO criteria.

We then used Cox regression models in SF3B1-mutant MDS with the aim to identify mutation patterns associated with relevant clinical outcomes, including RBC transfusion-dependency, risk of disease progression and survival. We found that mutations in chromatin modifiers (ASXL1, EZH2) were significantly associated with development of transfusion-dependency (HR=3.85, P=.006). In addition, mutations in RUNX1 were significantly associated with worse OS (HR=6.98, P=.012) and increased risk of progression (HR=5.63, P=.023). Unambiguous statistical evidence of subclonality of these gene mutations was obtained in 46% of cases.

In conclusion, this study shows that SF3B1 mutations identify a distinct subset of MDS with homogeneous features and favorable prognosis irrespective of current WHO classification criteria. Within MDS associated with SF3B1 mutation, concurrent or subclonal mutations in genes involved in DNA methylation, chromatin modification and RUNX1 account for variability in disease phenotype and clinical outcomes.