Background Myelodysplastic syndromes are a diverse and common group of chronic hematologic cancers. The identification of new genetic lesions could facilitate new diagnostic and therapeutic strategies. Methods We used massively parallel sequencing technology to identify somatically acquired point mutations across all protein-coding exons in the genome in 9 patients with low-grade myelodysplasia. Targeted resequencing of the gene encoding RNA splicing factor 3B, subunit 1 (SF3B1), was also performed in a cohort of 2087 patients with myeloid or other cancers. Results We identified 64 point mutations in the 9 patients. Recurrent somatically acquired mutations were identified in SF3B1. Follow-up revealed SF3B1 mutations in 72 of 354 patients (20%) with myelodysplastic syndromes, with particularly high frequency among patients whose disease was characterized by ring sideroblasts (53 of 82 [65%]). The gene was also mutated in 1 to 5% of patients with a variety of other tumor types. The observed mutations were less deleterious than was expected on the basis of chance, suggesting that the mutated protein retains structural integrity with altered function. SF3B1 mutations were associated with down-regulation of key gene networks, including core mitochondrial pathways. Clinically, patients with SF3B1 mutations had fewer cytopenias and longer event-free survival than patients without SF3B1 mutations. Conclusions Mutations in SF3B1 implicate abnormalities of messenger RNA splicing in the pathogenesis of myelodysplastic syndromes. (Funded by the Wellcome Trust and others.)

These data show that the WHO classification of MDSs has a relevant prognostic value. This classification, along with cytogenetics, might be useful in decisions regarding transplantation. MDS with isolated erythroid lineage dysplasia identifies a subset of truly low-risk patients, for whom a conservative approach is advisable.

Key Points• Mutation profiling has a high predictive value for identifying individuals with, or at high risk of developing, a myeloid neoplasm.• Patients with clonal cytopenia have a significantly higher risk of developing a myeloid neoplasm than those with no evidence of clonality.Unexplained blood cytopenias, in particular anemia, are often found in older persons. The relationship between these cytopenias and myeloid neoplasms like myelodysplastic syndromes is currently poorly defined. We studied a prospective cohort of patients with unexplained cytopenia with the aim to estimate the predictive value of somatic mutations for identifying subjects with, or at risk of, developing a myeloid neoplasm. The study included a learning cohort of 683 consecutive patients investigated for unexplained cytopenia, and a validation cohort of 190 patients referred for suspected myeloid neoplasm. Using granulocyte DNA, we looked for somatic mutations in 40 genes that are recurrently mutated in myeloid malignancies. Overall, 435/683 patients carried a somatic mutation in at least 1 of these genes. Carrying a somatic mutation with a variant allele frequency ‡0.10, or carrying 2 or more mutations, had a positive predictive value for diagnosis of myeloid neoplasm equal to 0.86 and 0.88, respectively. Spliceosome gene mutations and comutation patterns involving TET2, DNMT3A, or ASXL1 had positive predictive values for myeloid neoplasm ranging from 0.86 to 1.0. Within subjects with inconclusive diagnostic findings, carrying 1 or more somatic mutations was associated with a high probability of developing a myeloid neoplasm during follow-up (hazard ratio 5 13.9, P < .001). The predictive values of mutation analysis were confirmed in the independent validation cohort. The findings of this study indicate that mutation analysis on peripheral blood granulocytes may significantly improve the current diagnostic approach to unexplained cytopenia and more generally the diagnostic accuracy of myeloid neoplasms. (Blood. 2017;129(25):3371-3378)

In a previous study, we identified somatic mutations of SF3B1, a gene encoding a core component of RNA splicing machinery, in patients with myelodysplastic syndrome (MDS). Here, we define the clinical significance of these mutations in MDS and myelodysplastic/myeloproliferative neoplasms (MDS/MPN). The coding exons of SF3B1 were screened using massively parallel pyrosequencing in patients with MDS, MDS/MPN, or acute myeloid leukemia (AML) evolving from MDS. Somatic mutations of SF3B1 were found in 150 of 533 (28.1%) patients with MDS, 16 of 83 (19.3%) with MDS/MPN, and 2 of 38 (5.3%) with AML. There was a significant association of SF3B1 mutations with the presence of ring sideroblasts (P < .001) and of mutant allele burden with their proportion (P = .002). The mutant gene had a positive predictive value for ring sideroblasts of 97.7% (95% confidence interval, 93.5%-99.5%). In multivariate analysis including established risk factors, SF3B1 mutations were found to be independently associated with better overall survival (hazard ratio = 0.15, P = .025) and lower risk of evolution into AML (hazard ratio = 0.33, P = .049). The close association between SF3B1 mutations and disease phenotype with ring sideroblasts across MDS and MDS/MPN is consistent with a causal relationship. Furthermore, SF3B1 mutations are independent predictors of favorable clinical outcome, and their incorporation into stratification systems might improve risk assessment in MDS.

The WHO recently proposed a new classification of myelodysplastic syndromes (MDS) based on uni- or multi-lineage hematopoietic involvement, blast count and cytogenetic features. The aims of this study were to evaluate the prognostic value of the WHO classification, to assess the role of known prognostic factors in MDS within these WHO subgroups, and to estimate mortality rates and life expectancy of the patients in the subgroups. Four hundred and ninety-one consecutive patients with a diagnosis of MDS made at the IRCCS Policlinico San Matteo, University of Pavia Medical School, Italy, between 1992 and 2002 were retrospectively evaluated and reclassified according to the WHO criteria. Cox proportional hazards regression was used to identify the most significant prognostic factors. A standardized mortality ratio (SMR) was calculated to compare the mortality of MDS patients with that of the general population. Overall survival (OS) and leukemia-free survival (LFS) differed significantly between RA and RCMD (P&lt;.001 and P=.01, respectively), but not between RA and MDS with del(5q), or between MDS with or without ringed sideroblasts. There was a significant difference in LFS between RCMD and RAEB-1 (P=.006), and in both OS and LFS between RAEB-1 and -2 (P&lt;.001). Overall, age and gender had significant effects on survival (P&lt;.001), older age and male gender negatively affecting the prognosis. These effects were statistically significant for RA and RCMD patients (P values from.01 to &lt;.001), but not for those with RAEB. The mortality rate of all patients with RA/RARS aged 70 years or older and the male subgroup aged 65-70 years old did not differ from that of the general population. Cox regression analysis with time dependent covariates was applied to evaluate the prognostic value of needing transfusion. Patients with RA/RARS who became transfusion-dependent had a significantly shorter life expectancy than those who did not (P=.01) except for patients aged 70 years or older whose life expectancy was only marginally shorter than that of the general population (SMR=1.90, P=.03). Cox regression showed that IPSS significantly stratified OS and LFS of WHO subgroups (P=.005 and P=.003, respectively). Among IPSS variables, blast count and peripheral cytopenia failed to predict survival within the WHO subgroups, while karyotypic abnormalities, classified according to IPSS, significantly affected OS and LFS of MDS stratified in WHO categories (P=.03 and P=.02, respectively). In conclusion, the new WHO classification of MDS has relevant prognostic value. Cytogenetics is the only independent prognostic factor significantly affecting survival of patients classified into these WHO subgroups. MDS with uni-lineage dysplasia identifies a subset of truly low risk patients, whose survival is significantly affected by demographic characteristics. Patients with refractory anemia who are older than 70 years, as well the males aged between 65 and 70 years, have a life expectancy similar to that of the general population, and only slightly worsened by becoming transfusion-dependent. According to these results, extending curative approaches, such as non-myeloablative transplantation, to these groups of patients does not seem advisable.