<i>U2AF1</i> mutation variants in myelodysplastic syndromes and their clinical correlates
Authors: Ayalew Tefferi, Mythri Mudireddy, Christy M. Finke, Maura Nicolosi, Terra L. Lasho, Curtis A. Hanson, Mrinal M. Patnaik, Animesh Pardanani, Naseema Gangat
Journal: American Journal of Hematology (2018)

To the Editor: In 2011, Yoshida et al. published their seminal discovery of spliceosome mutations in myelodysplastic syndromes (MDS) and other myeloid malignancies.1 These mutations were often mutually exclusive and the most frequent were splicing factor 3b subunit 1 (SF3B1), serine and arginine rich splicing factor 2 (SRSF2), U2 small nuclear RNA auxiliary factor 1 (U2AF1) and Zinc finger CCCH-type, RNA binding motif, and serine/arginine rich 2 (ZRSR2). These observations have since been validated by multiple other studies, including our own, where we reported SF3B1, SRSF2, U2AF1, and ZRSR2 mutational frequencies of 8%, 15%, 16%, and 11% in primary myelofibrosis (PMF),2 6%, 49%, 7%, and 3% in primary chronic myelomonocytic leukemia,3 and 20%, 16%, and 16% and 8% in primary MDS.4 In 2014, we discovered a significant association between U2AF1 mutations and anemia and thrombocytopenia, in PMF.5 In the same study, a univariate adverse impact on survival from U2AF1 mutations was not sustained during multivariable analysis that accounted for anemia and thrombocytopenia.5 In a more recent study in PMF,6 we were able to demonstrate phenotypic and prognostic differences between the two most frequent U2AF1 mutation types, Q157 and S34. Among U2AF1-mutated patients with PMF, 65% harbored Q157 and 34% S34 variants6; both mutation variants clustered with anemia and JAK2/MPL mutations; in addition, Q157, but not S34, mutation type was associated with thrombocytopenia, ASXL1 mutations, and inferior survival, not accounted for by anemia, thrombocytopenia, driver mutational status, ASXL1 mutations, or current prognostic models.6 In the current institutional review board approved study, we looked into the phenotypic and prognostic impact of specific U2AF1 mutation variants in primary MDS. Study inclusion required availability of next-generation sequencing (NGS)-derived mutation information. Diagnoses of primary MDS and leukemic transformation were according to the 2008 World Health Organization criteria.7 Methods of mutation screening have previously been published.8 Statistical analyses considered clinical and laboratory parameters obtained at the time of sample collection for mutation analysis, which coincided, in most instances, with the time of diagnosis. Survival analysis was computed from the date of sample collection to the date of death or last contact. Patients receiving allogenic hematopoietic stem cell transplantation (HCT) were censored at the time of their transplant. Survival curves were prepared by the Kaplan–Meier method and compared by the log-rank test. Cox proportional hazard regression model was used for multivariable analysis. Three hundred fifty-seven patients with primary MDS (median age 74 years; 70% males) had NGS information and were thus included in the study; the revised international prognostic scoring system9 risk distribution was 11% very high, 15% high, 17% intermediate, 40% low, and 16% very low. Mayo cytogenetic risk distribution was 11% high, 30% intermediate, and 59% low.8 NGS revealed SF3B1 (32%), ASXL1 (27%), TET2 (24%), and U2AF1 (15%) mutations to be the most frequent. After a median follow-up of 14 months, 217 (61%) deaths, 35 (10%) leukemic transformations, and 19 (5%) HCT were recorded. In age-adjusted multivariable analysis restricted to genetic risk factors, we have previously shown the independent prognostic contribution of high and intermediate risk karyotype, presence of ASXL1 and RUNX1 mutations, and absence of SF3B1 mutations.8 Among 52 patients with U2AF1 mutations, 28 (54%) harbored S34 (25 S34F and 3 S34Y), 22 (42%) Q157 (16 Q157P and 6 Q157R), and two R156H. Comparison of U2AF1 Q157 versus U2AF1 S34 versus U2AF1 unmutated cases revealed differences in mutational frequencies of TP53, ASXL1, IDH1, and SETBP1 mutations; 14%, 0%, and 13% (P = .02) for TP53, 55%, 32%, and 25% (P = .01) for ASXL1, 18%, 4%, and 2% (P = .01) for IDH1, and 14%, 4%, and 2% (P = .05) for SETBP1, respectively. In addition, as expected, both types of U2AF1 mutations were often mutually exclusive of SRSF2 and SF3B1 mutations. Both U2AF1 mutation variants clustered with intermediate risk karyotype (P < .001) and male sex (P = .003). We found no significant association with anemia; sex-adjusted severe anemia was present in 55%, 57%, and 45% of U2AF1 Q157, S34, and unmutated cases, respectively (P = .32). The lack of significant association with anemia was confirmed by using different hemoglobin thresholds, including presence or absence of any degree of anemia (P = .4). Platelet count of <50 × 109/L was seen in 41%, 25%, and 18% (P = .05) of patients harboring the Q157, S34, and wild-type variants, respectively. We found significant clustering of U2AF1 S34, but not Q157, variant with leukopenia (leukocyte count <2 × 109/L; P < .001) and monocytopenia (absolute monocyte count <0.1 × 109/L; P = .004). In univariate analysis, confirmed by age-adjusted re-analysis, adverse survival impact, compared to U2AF1 unmutated cases, was more evident for U2AF1 Q157 (P = .002; HR 2.4, 95% CI 1.4-3.9), as opposed to U2AF1 S34 (P = .08; HR 1.7, 95% CI 0.93-2.8), while no significant survival difference was apparent between the two variants (P = .31) (Figure 1A). Figure 1 includes Figure 1B for purposes of comparing the survival impact of U2AF1 mutation types in PMF and MDS.6 During multivariable analysis of mutations, both U2AF1 Q157P (P = .05) and S34 (P = .04) variants, as well as TP53 and ASXL1 mutations, remained significantly associated with inferior survival. However, the addition of cytogenetic risk stratification to the multivariable model resulted in loss of significance for both U2AF1 mutation variants and TP53 mutations, while ASXL1 mutations remained significant. A, Survival data on 355 patients with primary myelodysplastic syndromes, stratified by U2AF1 Q157 versus S34 versus unmutated mutation types. B, survival data on 490 patients with primary myelofibrosis stratified by U2AF1 Q157 versus S34 versus unmutated mutation types, borrowed from a recent publication A number of important observations are borne out of the current study. First, we confirm the higher frequency of U2AF1 S34 mutation variant in MDS, which is opposite of what is the case in PMF, where U2AF1 Q157 is more frequent.6, 10 Second, unlike the case with PMF,6 we found no association between the presence of either one of the two U2AF1 mutation variants and anemia.6 Similarly, a karyotype-independent prognostic impact was not evident for either one of the two U2AF1 mutation variants in MDS, while the U2AF1 Q157 variant was recently shown to carry such an effect in PMF.6 On the other hand, in both our MDS and PMF cohorts, U2AF1 Q157 variant was associated with ASXL1 mutations. Additional studies are required to clarify the discrepant observation from another MDS study, where thrombocytopenia was specifically associated with U2AF1 S34 and anemia with U2AF1 Q157 mutation types.11 All authors declare no conflict of interest regarding matters pertinent to the current manuscript. All authors have reviewed and approved the manuscript. CAH reviewed pathology data. NG, AP and MMP contributed patients. TLL and CMF were in charge of molecular studies and analysis. MM and MN were in charge of data collection and organization. AT developed the study concept and design, contributed patients, assisted in data extraction, performed statistical analysis and wrote the paper.