Recent updates to monocyte count thresholds recognize oligomonocytic chronic myelomonocytic leukemia (OM-CMML) as an early form of CMML. However, the clinical validity of these changes remains uncertain without incorporating biological and genomic factors. In this study, we analyzed a cohort of 911 patients (249 with OM-CMML, 359 with overt CMML, and 303 with myelodysplastic syndromes) using unsupervised clustering to evaluate the role of genomic determinants in refining CMML diagnosis. Our findings show that CMML molecular signatures (biallelic TET2 mutations or SRSF2-TET2 comutations) are linked to a distinct transcriptome, monocytic bias, classical monocytosis, and a higher risk of progression to overt CMML in OM-CMML cases. We developed a weighted genomic model and diagnostic workflow showing that combining genomic signatures with bone marrow monocyte frequencies in OM-CMML more accurately predicts progression to overt CMML. These findings support integrating genomic determinants and our clinic-ready diagnostic workflow into the CMML diagnostic framework to improve accuracy. SIGNIFICANCE:Through comprehensive clinical and genomic profiling of a large patient cohort, alongside immunophenotypic and transcriptional cellular analyses, this study provides evidence that incorporating genomic determinants into the diagnostic criteria for OM-CMML improves diagnostic accuracy and refines the identification of early-stage CMML, thereby preventing misclassification.

Heatmap of patients with active disease at study theray initiation, showing CBF subtype, ACA, treatment group and mutational groups

Association of biTET2/SRSF2 and monocytic differentiation parameters in a validation cohort.

Penalized time-to-event model for CMML progression (cumulative incidence of CMML).

Numbers at risk by survival time point by genomic group (Figure 4N).

Cox multivariate for overall survival in the full cohort with backward model selection not including DNMT3A-ASXL1-TET2 (DAT) and TRANSCRIPTION FACTORS

Representativeness of study participants

6531 Background: Outcomes of patients (pts) with ND AML with myelodysplasia related gene mutations (MRMs), while traditionally adverse, appear to be better with LIT regimens + venetoclax (Ven). The impact of MRMs as a minimal residual disease (MRD) marker warrants investigation. Methods: We retrospectively analyzed the impact of persistence/clearance of MRM at VAF <2% at best response of CR/CRi, in pts with LIT treated ND AML (with available genomic data), treated at our institution between 2017 – 2025 and had ≥1 MRM ( ASXL1, BCOR, EZH2, STAG2, SF3B1, SRSF2, U2AF1 , and/or ZRSR2 ) at diagnosis, at a VAF of ≥2%. We excluded pts with CBF-AML, APL, or treated secondary AML. MRM dynamics were tracked at baseline and best response (CR/CRi) and correlated with relapse free/overall survival (RFS/OS). Results: A total of 185 pts, median (med) age 69 yrs (range, 56-87 yrs), were included; 96% were ≥ 60 yrs. The common baseline MRM were SRSF2 (54%), ASXL1 (32%), STAG2 (16%) and BCOR (14%); 16% had >1 MRM. Overall, 17% had concurrent NPM1 mutation (mut), 9% FLT3 -ITD (AR>0.05), 22% RAS , 32% RUNX1 , 8% TP53 , and 32/183 pts (17%) had ELN2017 adverse cytogenetics (CTG). 171 pts (92%) were treated with LIT+Ven and 14 (8%) LIT without Ven; 105 (57%) received hypomethylating agents based, and the rest (43%) received cladribine + low-dose cytarabine based LIT. Overall, 148 (80%) achieved CR and 37 (20%) CRi. 117/168 (70%) pts with available data were MRD negative (-) by flow cytometry (FCM; <0.01%) at CR/CRi. At CR/CRi, 49 (26%) cleared their MRMs (MRM-) while 136 (74%) retained MRMs (MRM+); among pts with FCM MRD- CR/CRi, 33/117 (28%) were MRM- and 84/117 (72%) MRM+. Med cycle to CR/CRi was 1 (IQR 1-2). Pts with MRM- at CR/CRi had superior med RFS (24 [95% CI 9-18] vs. 14 mos [16-NR], p=0.008) and OS (54 [25-NR] vs. 21 mos [15-27], p=0.01) compared to MRM+ pts. Among 117 FCM MRD- pts, med RFS (NR vs. 14 mos [9-23], p=0.001) and med OS (NR vs. 19 mos [14-36], p=0.003) was still superior among MRM- pts (n=33) vs. MRM+ (n=84). 67 pts (36%) underwent a hematopoietic stem cell transplantation (HSCT) in CR1, 26/49 (53%) MRM- and 41/136 (30%) MRM+. Among FCM MRD- pts who did not undergo HSCT, 2-yr OS rate (86% vs. 48%, p=0.04) was better in MRM- pts (n=15) vs. MRM+ pts (n=58); among FCM MRD- pts who had HSCT, 2-yr OS rate trended to favor MRM- pts (n=18) (77% vs. 55%, p=.14) vs. MRM+ pts (n=26). On backward selected Cox MVA, clearance of MRMs at CR/CRi was independently associated with favorable OS (HR=0.54, 95% CI 0.31-0.95, p=0.03), along with BCOR, IDH2 mut, and HSCT, while RAS mut, FLT3 -ITD, and adverse CTG were unfavorable. Finally, among FCM-MRD- pts at CR/CRi, using the same Cox model, clearance of MRMs was independently favorable for OS (HR=0.42, 95%CI 0.20-0.93, p=0.03). Conclusions: In our analysis, the status of MRM clearance at CR/CRi in LIT treated AML with baseline MRM affected survival outcomes, including in pts FCM MRD- at CR/CRi.

PURPOSE:As risk stratification for patients with AML treated with lower-intensity venetoclax-based therapy remains suboptimal, we developed and validated a prognostic model integrating clinical, cytogenetic, and molecular features. METHODS:We assembled a multinational data set comprising 2,092 adults with newly diagnosed AML treated with hypomethylating agents plus venetoclax (HMA + VEN). One thousand nine hundred eighteen patients with complete data were randomly divided into training (70%) and internal validation (30%) cohorts. Two independent external validation cohorts were assembled (n = 500 and n = 222). Modeling overall survival (OS), Elastic Net regression was applied in 1,000 bootstrap samples from the training cohort to select variables for a Ridge regression, which generated a continuous Prognostic Risk Integration for Survival Modeling (PRISM) score and risk categories based on tertiles (PRISM-3: low, moderate, high). These PRISM indices were then computed for the validation cohorts and compared with the 4-gene classifier (based on mutations in FLT3-ITD, N/KRAS, and TP53). RESULTS:PRISM integrated 17 clinical and genomic variables and demonstrated a linear association with OS. PRISM-3 stratified survival consistently across all cohorts (median OS: 25.1-28.8 months for low risk, 12.5-14.7 months for moderate risk, and 5.8-6.7 months for high risk; P < .001). Compared with the 4-gene classifier, PRISM-3 reassigned approximately 40% of patients (and >50% of those with favorable risk) and demonstrated significantly better discrimination in validation cohorts (C-index 0.63-0.65 v 0.59-0.61; P < .05). CONCLUSION:PRISM is a validated prognostic model for patients with AML receiving HMA + VEN that improves survival risk stratification beyond current standard tools and supports individualized, risk-adapted clinical decision making. The model, the PRISM-AML Risk Calculator, is publicly available.

Comparison of SF3B1-mutated MDS with del(5q) to subclonal SF3B1-mutated MDS without del(5q). (A-F) No significant differences in baseline clinical demographics or SF3B1 VAF were observed between cases with vs. without del(5q). (G,H) Whilst survival was superior in patients with clonal SF3B1 mutations, no significant difference in leukemia-free or overall survival was identified between cases of SF3B1-mutated MDS with del(5q) vs. subclonal SF3B1-mutated MDS without del(5q), suggesting survival outcomes in such cases are influenced by alternative molecular driver events. Reported p-values utilized the cox model Wald test.

Correlation between RAS pathway mutation variant allele frequencies and monocytic parameters.

Cox regression univariate analysis for overall survival

Cytogenetic abnormalities and somatic mutations among all patients included in the validation cohort.

Cox multivariate model for relapse free survival for the full cohort

We report a unique case in a 67-year-old male patient in whom melanoma tumor sequencing identified DNMT3A and SF3B1 mutations suggesting tumor-infiltrating clonal hematopoiesis. Following comprehensive bone marrow evaluation, the patient was discovered to have a well-differentiated (WD) systemic mastocytosis with an associated myeloid neoplasm (SM-AMN) best classified as myelodysplastic syndrome with SF3B1 mutation. Notably, the SM component was negative for KIT D816V mutation, as expected for WD-SM; however, the immunophenotype was atypical with aberrant expression of CD25. This case highlights the potential for solid tumor genomics to expose occult myeloid neoplasms incidentally and underscores the importance of a comprehensive workup, including bone marrow examination, in distinguishing between incidental clonal hematopoiesis and bona fide myeloid neoplasms.

Acquired resistance to targeted, non-intensive therapies is common in myeloid malignancies. However, the kinetics of selection, the hematopoietic cell compartments where selection occurs, and the molecular mechanisms underlying selection remain open questions. To address this, we studied the kinetics of clonal and transcriptional responses to ivosidenib + venetoclax ± azacitidine combination therapy across hematopoiesis in 8 patients with IDH1-mutant myeloid malignancy. All 8 patients initially responded to treatment but 6 relapsed while 2 remained in sustained remission for >4 years. We performed combined high-sensitivity single-cell (sc) genotyping and scRNA-seq in index-sorted sequential patient samples. In all patients, clonal selection occurred rapidly, within 1-3 treatment cycles. Clonal selection preceded treatment failure by months to years. Relapse was associated with expansion of either clones harboring newly-detected myeloid driver mutations or pre-existing minor clones that underwent differentiation delay upon treatment exposure. In both cases, clonal selection occurred within immature cell populations previously shown to contain leukemic stem cell (LSC) potential. Different genetic alterations within relapse-associated clones converged onto common upregulated transcriptional programs of stemness, branched-chain amino acid catabolism, and genes sensitive to menin inhibition. Importantly, this relapse-associated transcriptional signature was selected within 3 cycles of therapy. In contrast, in both patients remaining in remission, leukemic clones were rapidly eradicated and replaced by clonal and wild-type hematopoiesis. Overall, in patients treated with ivosidenib combination therapy, rapid clonal selection occurs within the first treatment cycles. In those patients destined to relapse, genetically heterogeneous resistant clones are characterized by common transcriptional programs.

Survival stratified by CBF subtype and treatment arm