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Background: SETBP1 gene, located on 18q12.3, is a major oncogene in myeloid neoplasms. GATA2 gene, located on 3q21, is one of the six GATA transcription factors regulating gene expression via two conserved zinc finger domains (ZF). Previous data suggested that in patients with germline GATA2 mutation (m), acquisition of a somatic SETBP1 mutation (m) was associated with leukemic transformation among patients with excess blast MDS and CMML. Aim: To study the characteristics of patients with somatic SETBP1-GATA2 mutated myeloid neoplasms. Methods: This study is a retrospective study at Mayo Clinic. After obtaining IRB approval, we retrospectively reviewed the charts of patients who had myeloid NGS panel results between 2016-2023. All data were recorded at time of first NGS. Cohort 1 was defined as patients with SETBP1m and GATA2m, cohort 2; patients with SETBP1m and GATA2wt, and cohort 3; patients with SETBP1wt and GATA2m. Germline work-up was not performed in the majority of GATA2 cases. We stratified risk based on the European LeukemiaNet 2022 guidelines for AML, IPSS-M for MDS and MDS/MPN, and CPSS-M for CMML. Overall survival (OS) was calculated from date of NGS to date of last follow-up based on Kaplan-Meier estimates and Cox regression analysis. For statistical analysis, we used BlueSky Statistics V10.3.1. Results: General characteristics: 114 patients had SETBP1m (median VAF= 39%), and 63 patients had GATA2m (median VAF= 35%). Nine patients had co-occurring SETBP1m/GATA2m mutations (cohort 1). 4/9 patients in cohort 1 had MDS/MPN (44.4%), while only 13/105 in cohort 2 (12.4%) had MDS/MPN (P=0.02). AML was seen in 2 patients in cohort 1 (22.2%) compared to18 in cohort 2 (17.1%) (p=0.6). The median WBC count was 22.9 x 109 cells/L among cohort 1 compared to 9 x 109 cells/L among cohort 2 cases (p=0.09). BM blasts were higher in cohort 3 (7%) compared to cohort 1 (5%) and cohort 2 (3%) (p=0.09), while peripheral blasts tended to be lower in cohort 2 (1%) in comparison to cohort 1 (6%) and cohort 3 (4%) (p=0.48). Genetic characteristics: In cohort 1,7 GATA2m clustered in zinc finger 2 (ZF2) (77.8%), while the other two mutations were outside the ZF domains (22.2%). This was higher than the ZF2 mutated cases in cohort 3 (46.3%, p=0.1). Abnormal cytogenetics were seen in 66.7% of cohort 1 patients and 45% of cohort 2 (p= 0.3). Two cases with trisomy 8 were seen among patients in cohort 1 (22.2%), compared to only 4.9% in cohort 2 (p=0.09). Two incidences of isochromosome 17q [i(17q)] were seen in cohort 1 (22.2%), versus 5 cases in cohort 2 (4.8%) and 1 case in cohort 3 (1.9%) (p= 0.068). Co-mutations: The median number of co-mutationswas 3 in both cohort 1 and cohort 2 (p= 0.6). In cohort 1, ASXL1 and SRSF2 mutations were the most common (7/9, 77.8%) followed by NRAS (22.2%) and TET2 (22.2%). 77.8% of cohort 1 patients had SRSF2 co-mutation, compared to 44.8% in cohort 2 (p=0.08), and 27.8% in cohort 3 (p= 0.006). No isolated SETBP1m/GATA2m cases were found. Survival: Patients in cohort 1 had a numerically higher median OS compared to those in cohort 2 (19.4 vs 15.4 months, p= 0.3). When comparing with the cohort 3, patients in cohort 1 tended to have better outcomes (median OS= 19.4 vs 13.8 months, p=0.8). Among cohort 1, SRSF2 co-mutation was associated with worse survival outcomes compared to patients with SRSF2wt (median OS= 5.3 vs 19.4 months, p= 0.02); this association was not found in cohort 2 (12.5 vs 18.4 months, p= 0.3) and cohort 3 (13.2 vs 17.1 months, p= 0.4). Allogeneic hematopoietic cell transplantation was associated with favorable survival outcomes in all cohorts (cohort 1: 22.6 vs 7.8 months, p= 0.1; cohort 2: 20.9 vs 12.5 months, p= 0.04; cohort 3: 25.6 vs 13.1 months, p= 0.03). Conclusion: SETBP1m/GATA2m myeloid neoplasms included a significantly higher proportion of MDS/MPN overlap cases in comparison with the SETBP1m/GATA2wt group. The SETBP1m/GATA2m group had a higher proportion of ZF2 GATA2m and SRSF2 co-mutation compared to patients with SETBP1wt/GATA2m. Survival of SETBP1m/GATA2m patients was not worse compared to SETBP1wt/GATA2m or SETBP1m/GATA2wt.

Background Blast or accelerated phase myeloproliferative neoplasm (MPN-BP/AP) carries a dismal prognosis, with 3-year survival estimates of <5% (BCJ 2023;108). Patients with MPN-BP/AP were excluded from venetoclax (Ven) plus hypomethylating agent (HMA) clinical trials for acute myeloid leukemia (NEJM 2020;383:617). In the current retrospective study, we examined response patterns and long-term survival of newly-diagnosed MPN-BP/AP patients who received treatment with Ven+HMA, outside of clinical trials. Methods Newly-diagnosed patients with MPN-BP/AP treated with Ven+HMA at the Mayo Clinic, between March 2019 and May 2024, were retrospectively reviewed. Diagnostic criteria were according to the International Consensus Classification (Blood 2022;140:1200). Cytogenetic and molecular studies were performed by conventional karyotype and next-generation sequencing, respectively. All patients received at least one cycle of Ven+HMA (azacitidine 75 mg/m2 days 1-7 or decitabine 20 mg/m2 days 1-5). Response was assessed according to the 2022 European Leukemia Net criteria (Blood 2022;140:1345). Standard statistical analyses were performed using JMP Pro (Version 17.1.0). Results Patient characteristics 70 patients (median age 73 years, 59% males, 48% splenomegaly >14 cm, 4% isolated myeloid sarcoma) with newly-diagnosed MPN-BP (n=58) or AP (n=12) received Ven+HMA with (n=13) or without (n=57) concomitant JAK2 inhibitor. Driver mutation distribution was 69% JAK2, 21% CALR, 6% MPL, and 4% triple negative. Mutations involved ASXL1 (31%), TP53 (28%), TET2 (28%), RUNX1 (25%), SRSF2 (18%), IDH2 (12%), U2AF1 (11%), DNMT3A (9%), IDH1 (7%), and K/NRAS (7%). Karyotype was abnormal in 50 (76%) of 66 informative cases, of which 28 (56%) were complex (CK). Median TP53 mutation variant allele frequency (VAF) was 30% (8-96%) and all evaluable cases displayed CK (n=18). Response and Survival Complete remission (CR; 21%) or CR with incomplete count recovery (CRi; 19%) was documented in 28 (40%) patients with residual MPN in 18 (64%) patients. Median response duration was 5.5 months (1-60 months). After a median follow up of 7 months (1-62 months), 48 (69%) deaths, 13 relapses (46%), and 15 (21%) allogeneic stem cell transplants (ASCT; 12 in CR/CRi) were recorded. Median overall survival (OS) was 9 months and was superior with ASCT (median 22 vs. 8 months; p=0.01). In univariate analysis, transplant-censored survival was superior with CR/CRi (12 vs. 5 months; p<0.01) and IDH1 mutation (33 vs. 8 months; p=0.04) and inferior with CK (7 vs. 10 months; p=0.05), TP53 mutation (5 vs. 10 months; p<0.01), post polycythemia vera myelofibrosis (post-PV MF) (3 vs. 9 months; p=0.01), and splenomegaly >14 cm (5 vs. 16 months; p<0.01). Multivariable analysis confirmed the negative survival impact of not achieving CR/CRi (HR 3.8; p<0.01) and presence of TP53 mutation (HR 4.0; p<0.01); median survival (1/3-year survival rate) was 3 months (10%/0%) in TP53 mutated patients not achieving CR/CRi (n=11) vs. 27 months (65%/28%) in TP53 unmutated cases achieving CR/CRi (n=19) (p < 0.01). Median survival in patients with TP53 mutations or CK who achieved CR/CRi (n=7; 7 months) was inferior to that in treatment responders without TP53 mutations or CK (n=18; 23 months; p=0.01). CR/CRi rates in the presence vs. absence of TP53 mutations were 42% vs. 39% (p=0.80) and of CK (25% vs. 50% (p=0.04). Importantly, responses in the presence of TP53 mutations or CK were too short-lived to allow successful bridging to ASCT (median 2 vs. 9 months; p<0.01). Additional predictors of inferior treatment response included splenomegaly >14 cm (24% vs. 53%; p=0.01), and post-PV MF (0% vs. 46%; p<0.01) while SRSF2 (67% vs. 34%; p=0.04) and IDH2 mutations (75% vs. 35%; p=0.03) were associated with favorable response. In multivariable analysis, CK (p=0.04) and splenomegaly >14 cm (p=0.01) remained independent predictors of inferior response. The use of concomitant JAK2 inhibitor therapy did not impact treatment response (CR/CRi 46% vs. 39%; p=0.62) or survival (median 9 vs. 8 months; p=0.71). Conclusions TP53 mutations and CK undermine the value of Ven+HMA, with or without concomitant JAK2 inhibitor, in enabling successful bridging of newly-diagnosed MPN-BP/AP to ASCT. An alternative treatment approach is advised, in the particular scenario, while the observed 3-year survival rate of 28%, in treatment responders without TP53 mutations, is encouraging.

Introduction Oligomonocytic chronic myelomonocytic leukemia (OM-CMML) is defined by relative monocytosis ≥ 10% and an absolute monocyte count (AMC) between ≥ 0.5 and < 1.0 x109/L. The 5th ed WHO and International Consensus Classifications lowered the AMC threshold to ≥ 0.5 x10/9L for CMML diagnosis, thereby incorporating OM-CMML (Khoury, 2022; Arber, 2022). However, prior reports differ as to whether OM-CMML is a distinct CMML subtype. This multi-center study compares the clinical, molecular, and survival features of OM-CMML with myelodysplastic (MD, WBC < 13.0 x109/L) and myeloproliferative (MP, WBC ≥ 13.0 x109/L) CMML with an AMC ≥1.0. Methods After IRB approval, patients with CMML from Mayo Clinic (n = 400, 47%) and MD Anderson Cancer Center (n = 449, 53%) were identified retrospectively. Analyses considered clinical, laboratory, and next generation sequencing parameters at diagnosis or first referral (in chronic phase). Categorical variables were compared by Fisher exact or Pearson χ2 tests and continuous variables by Mann-Whitney U or ANOVA tests. Survival was assessed via the Kaplan-Meier method with outcomes censored at allogeneic stem cell transplantation (alloSCT). P < 0.05 was considered significant. Calculations used BlueSky Statistics (v10.3.1). Results A molecularly annotated cohort of 849 patients with CMML (median age 71 years, 32% female, 90% white, median follow up 31 months [mo]) was categorized as OM-CMML (n = 57, 7%), MD-CMML (n = 394, 46%), and MP-CMML (n = 391, 46%). There were no differences in age or sex across subtypes. No clinical differences were observed between OM-CMML and MD-CMML, with similar hematologic parameters, karyotype distributions, Mayo-Molecular (Patnaik, 2014) or CPSS-Molecular (Elena, 2016) risk stratifications, and rates of leukemic transformation (12% vs 12%, p = 0.98) and death (35% vs 43%, p = 0.27). Cases of OM-CMML had lower WBC counts (median 4.4 vs 24.7 x109/L, p < 0.0001), fewer circulating immature myeloid cells (23% vs 57%, p < 0.0001) and fewer marrow blasts (median 3% vs 4%, p = 0.0065) than MP-CMML. Comparatively, OM-CMML cases were overrepresented in the lower-risk groups of the CPSS-Molecular and Mayo-Molecular models (p < 0.0001). Leukemic transformation (12% vs 20%, p = 0.015) and death (35% vs 52%, p = 0.034) rates were higher in the MP-CMML cohort. Molecular profiles were similar between OM-CMML and MD-CMML, including median number of genes mutated (3 vs 3, p = 0.88). Frequencies of ASXL1 (39% vs 38%, p = 0.91), SRSF2 (48% vs 43%, p = 0.49), DNMT3A (7% vs 5%, p = 0.60), and SF3B1 (4% vs 7%, p = 0.48) mutations were also similar. TET2 mutation frequency was higher in OM-CMML (70% vs 55%, p = 0.031) and occurred in isolation more frequently (12% vs 6%, p = 0.048) compared to MD-CMML. Neither median number of TET2 mutations (1 vs 2, p = 0.87), nor TET2 variant allele fractions (41% vs 44%, p = 0.19) were different between the two groups. Compared to OM-CMML, patients with MP-CMML were more likely to have mutations in ASXL1 (39% vs 56%, p = 0.017), EZH2 (0% vs 9%, p = 0.019), JAK2 (0% vs 9%, p = 0.019), NRAS (7% vs 25%, p = 0.0024), and SETBP1 (2% vs 13%, p = 0.021). RAS family (CBL, BRAF, KRAS, NRAS, PTPN11; 25% vs 54%, p < 0.0001) and signaling pathway (CSF3R, FLT3, JAK2, SH2B3; 2% vs 14%, p = 0.0078) mutations were also more frequent whereas spliceosome mutations (SF3B1, SRSF2, U2AF1, ZRSR2; 61% vs 46%, p = 0.033) were less frequent in MP-CMML. The median (95% CI) overall survival (OS) of OM-CMML patients was 44 (38 - not reached) mo compared to 45 (34 - 60) mo in MD-CMML (p = 0.76) and 23 (20 - 29) mo in MP-CMML (p < 0.0032). Similar results were obtained when comparing the acute leukemia-free survival (LFS) of the OM-CMML (41 mo), MD-CMML (39 mo), and MP-CMML (19 mo) groups. At last follow up (medians 42 and 62 mo, respectively), 33% of evaluable OM-CMML patients had progressed to MD-CMML and 28% of MD-CMML patients had progressed to MP-CMML. No patient with OM-CMML progressed directly to MP-CMML. Conclusions These data show that OM-CMML and MD-CMML are a relatively homogenous subset of patients with similar clinicomolecular profiles and survival outcomes. Although OM-CMML patients are more likely to have TET2 mutations in comparison to other CMML subtypes, they have similar rates of disease progression as MD-CMML. This validates recent modifications to CMML classification criteria, in which OM-CMML cases are included as bona fide CMML.

AbstractThe current study was inspired by observations from exploratory analyses of an institutional cohort with chronic myelomonocytic leukemia (CMML; N = 398) that revealed no instances of blast transformation in the seven patients with plant homeodomain finger protein 6 (PHF6) mutation (PHF6MUT). A subsequent Mayo Clinic enterprise‐wide database search identified 28 more cases with PHF6MUT. Compared with their wild‐type PHF6 counterparts (PHF6WT; N = 391), PHF6MUT cases (N = 35) were more likely to co‐express TET2 (89% vs. 45%; p < .01), RUNX1 (29% vs. 14%; p = .03), CBL (14% vs. 2%; p < .01), and U2AF1 (17% vs. 6%; p = .04) and less likely SRSF2 (23% vs. 45%; p < .01) mutation. They were also more likely to display loss of Y chromosome (LoY; 21% vs. 2%; p < .01) and platelets <100 × 109/L (83% vs. 51%; p < .01). Multivariable analysis identified PHF6MUT (HR 0.28, 95% CI 0.15–0.50) and DNMT3AMUT (HR 5.8, 95% CI 3.3–10.5) as the strongest molecular predictors of overall survival. The same was true for blast transformation‐free survival with corresponding HR (95% CI) of 0.08 (0.01–0.6) and 9.5 (3.8–23.5). At median 20 months follow‐up, blast transformation was documented in none of the 33 patients with PHF6MUT/DNMT3AWT but in 6 (32%) of 19 with DNMT3AMUT and 74 (20%) of 374 with PHF6WT/DNMT3AWT (p < .01). The specific molecular signatures sustained their significant predictive performance in the context of the CMML‐specific molecular prognostic model (CPSS‐mol). PHF6MUT identifies a unique subset of patients with CMML characterized by thrombocytopenia, higher prevalence of LoY, and superior prognosis.

Abstract The ZRSR2 gene is a member of the spliceosome gene family which are frequently mutated in myeloid neoplasms. ZRSR2 mutations (ZRSR2m) occur in less than 5% of MDS, CMML, and AML. Our study included 164 ZRSR2m patients (98.8% males) and 98 ZRSR2wt MDS control cohort. In the ZRSR2m group, there were 53 MDS (32%), 39 CCUS (24%), 33 MPN (20%), 23 MDS/MPN overlap (14%), 15 AML (9%), and 1 MPAL (0.6%). Most MDS patients were the low blast subtype (n=37, 70%). Twenty-seven MDS patients (51%), and 23 CCUS patients (59%) had absolute monocyte count ≥0.5 x109/L and 18 of 23 MDS/MPN overlap were CMML (78%). Mutations in ZRSR2 were spread across the entire gene. The median number of co-mutations was 2, with TET2 (51%) and ASXL1 (32%) being the most common. U2AF1 and SRSF2, previously described as mutually exclusive with ZRSR2, were found in 10.4% of patients. Median overall survival (OS) was 51 months, and significantly varied among MNs (p=0.004). ZRSR2m MDS patients had better mOS than the MDS control cohort with ZRSR2wt (35 vs 22 months, p=0.013). ZRSR2m patients with isolated TET2 co-mutation and higher hemoglobin showed improved survival, while patients with RUNX1m, higher WBC count showed worse OS.

Abstract Clonal cytopenia of undetermined significance (CCUS) represents a distinct disease entity characterized by myeloid-related somatic mutations with a variant allele fraction of ≥2% in individuals with unexplained cytopenia(s) but without a myeloid neoplasm (MN). Notably, CCUS carries a risk of progressing to MN, particularly in cases featuring high-risk mutations. Understanding CCUS requires dedicated studies to elucidate its risk factors and natural history. Our analysis of 357 patients with CCUS investigated the interplay between clonality, cytopenia, and prognosis. Multivariate analysis identified 3 key adverse prognostic factors: the presence of splicing mutation(s) (score = 2 points), platelet count of &lt;100 × 109/L (score = 2.5), and ≥2 mutations (score = 3). Variable scores were based on the coefficients from the Cox proportional hazards model. This led to the development of the clonal cytopenia risk score (CCRS), which stratified patients into low- (score of &lt;2.5 points), intermediate- (score of 2.5 to &lt;5), and high-risk (score of ≥5) groups. The CCRS effectively predicted 2-year cumulative incidence of MN for low- (6.4%), intermediate- (14.1%), and high-risk (37.2%) groups, respectively, by the Gray test (P &lt; .0001). We further validated the CCRS by applying it to an independent CCUS cohort of 104 patients, demonstrating a c-index of 0.64 (P = .005) in stratifying the cumulative incidence of MN. Our study underscores the importance of integrating clinical and molecular data to assess the risk of CCUS progression, making the CCRS a valuable tool that is practical and easily calculable. These findings are clinically relevant, shaping the management strategies for CCUS and informing future clinical trial designs.