NPM1-mutated (NPM1-mut) acute myeloid leukemia (AML) is generally associated with a more favorable outcome, although the presence of additional gene mutations can influence patient prognosis. We analyzed intensively-treated adult NPM1-mut AML patients included in the HARMONY Alliance database. A newly developed risk classification, which included combinations of co-mutations in FLT3-ITD, DNMT3A, IDH1/IDH2, and TET2 genes, was applied to a training cohort of NPM1-mut AML patients included in clinical trials (n = 1001), an internal validation cohort more representative of real-world settings (n = 762), and an external validation cohort enrolled in UK-NCRI trials (n = 585). The HARMONY classification considered 51.8% of the NPM1-mut AML training cohort patients as favorable, 24.8% as intermediate, and 23.4% as adverse risk, with median overall survival (OS) of 14.4, 2.2, and 0.9 years, respectively; p < 0.001), thereby reclassifying 42.7% of NPM1-mut patients into a different European LeukemiaNet (ELN) 2022 risk category. These results were confirmed both in an internal and external validation cohort. Allogeneic hematopoietic stem cell transplantation (allo-HSCT) in first complete remission (CR1) showed the highest benefit in the NPM1-mut adverse-risk subgroup. The HARMONY classification provides the basis for a refined genetic risk stratification for adult NPM1-mut AML with potential clinical impact on allo-HSCT decision-making.

Abstract The increasing availability of genomic and transcriptomic sequencing has uncovered diverse genomic alterations and distinct gene expression profiles driving hematologic diseases, yet a data integration and sharing platform dedicated to hematology remains lacking. We developed the American Society of Hematology (ASH) HematOmics Program (ASHOP; ashop.hematology.org), a resource for exploring somatic alterations and gene fusions, transcriptomic results, and clinical data from 5960 patients spanning B-cell precursor and T-cell acute lymphoblastic leukemia, acute myeloid leukemia, myelodysplastic syndromes, and chronic lymphocytic leukemia. Users can explore genomic alteration landscapes and comutation patterns via lollipop and matrix plots and analyze significantly altered genes in user-defined subcohorts. Transcriptomes can be explored through interactive uniform manifold approximation and projections, clustering, differential expression, and pathway enrichment. Genomic, transcriptomic features, and clinical outcomes can be correlated in a user-driven manner or combined to precisely define study cohorts. We illustrate the following 4 use cases of ASHOP: (1) stratification of DUX4-rearranged B-cell leukemias into Early/Multipotent and Committed subgroups with distinct outcomes, (2) characterization of HOXA/HOXB expression patterns in acute myeloid leukemias, (3) correlating mutational burden with mismatch repair deficiency and mutational signatures, and (4) investigation of TP53 alteration landscape. ASHOP is an open-access resource to inform genomic and transcriptomic data interpretation for hematologic malignancies and will expand to support additional diseases and data modalities from the ASH community.

Monotherapy with hypomethylating agents (HMA) remains the standard of care for patients with higher-risk myelodysplastic neoplasms (HR-MDS). Recently, the randomized phase III VERONA study evaluating azacitidine plus venetoclax (VEN) versus azacitidine plus placebo in newly diagnosed HR-MDS showed no difference in overall survival (OS) between the two arms. However, whether the addition of VEN to HMA improves outcomes among subsets of patients with HR-MDS remains debated. We analyzed 1907 patients with HR-MDS from 31 centers in 9 countries who were treated with HMA monotherapy or HMA/VEN in the frontline setting (HMA monotherapy: n = 1773; HMA/VEN: n = 134). Responses were assessed centrally by two investigators using the IWG 2023 response criteria. Addition of VEN improved composite complete remission (cCR) rates (48.8% vs. 27.7%; p < 0.001) but not CR rates (17.1% vs. 11.7%; p = 0.16). In multivariable logistic regression analysis, cCR remained favorable for HMA/VEN vs. HMA monotherapy (Odds Ratio [OR]: 2.49; 95% CI: 1.56-3.96; p < 0.001). However, we did not observe a statistically significant difference in OS for HMA/VEN vs. HMA monotherapy (Hazard Ratio [HR]: 0.83; 95% CI: 0.64-1.07; p = 0.15). In subgroup analyses, patients with TP53 wild-type disease (HR: 0.47; 95% CI: 0.29-0.74; p = 0.002) had a significant improvement in OS and those with ≥10% bone marrow blasts (HR: 0.73; 95% CI: 0.53-1.01; p = 0.06) had a trend towards OS benefit with HMA/VEN.

Background The advent of B-cell maturation antigen (BCMA)-targeted immunotherapies has markedly transformed the prognosis for patients with relapsed/refractory multiple myeloma (r/r MM). However, the emergence of therapeutic resistance, frequently driven by tumor-intrinsic alterations in the TNFRSF17 (tumor necrosis factor receptor superfamily member 17) gene encoding BCMA, remains a critical clinical challenge. While the event of complete antigen loss via biallelic gene deletion is well-described, the functional impact of novel, non-truncating variants of uncertain significance (VUS) discovered through comprehensive sequencing is often unclear, complicating therapeutic decisions. Methods Whole-genome sequencing (WGS) was performed on purified CD138 + plasma cells from two patients with r/r MM who experienced disease progression after treatment with the anti-BCMA chimeric antigen receptor (CAR) T-cell therapy idecabtagene vicleucel (ide-cel) or ciltacabtagene autoleucel (cilta-cel). We developed a novel AI-based computational workflow to assess the impact of identified TNFRSF17 mutations on protein structure response to treatment across a panel of clinically relevant BCMA-directed agents. Our method combines AI-based protein-complex structure prediction with binding free energy calculations. Results WGS revealed a monoallelic deletion of 16p13, encompassing the TNFRSF17 gene locus, in both patients, accompanied by distinct subclones on the remaining allele: three VUS (p.Cys37Tyr, p.Cys24_Cys28del, and p.Pro23delins9) in patient #1, and the p.Cys8Trp VUS in patient #2. All detected variants in the protein sequence are localized within the extracellular, epitope-bearing domain of BCMA. Our AI-driven structural analysis predicted that these mutations induce significant conformational changes, primarily by disrupting the stabilizing disulfide bond network. Quantitative energetic calculations demonstrated that these variants would severely impair or completely abrogate binding of specific therapeutic agents, including ide-cel and belantamab cilta-cel, consistent with the patients’ clinical course of relapse. Notably, our analysis showed differential effects across various agents, with the binding affinity of some therapeutics predicted to remain robust to the structural changes. Conclusion The integration of WGS into diagnostics with AI-driven structural and energetic modeling provides a powerful framework for the functional interpretation of VUS in TNFRSF17 . This approach can rapidly elucidate patient-specific, epitope-dependent resistance mechanisms and has the potential to guide the rational sequencing of BCMA-targeted therapies. By transforming VUS from a diagnostic challenge into an actionable clinical biomarker, this methodology represents a critical step toward precision immunotherapy in MM.

Deletion of chromosome 5q [del(5q)] is the most common cytogenetic abnormality in myelodysplastic neoplasms (MDS) and results in haploinsufficiency of multiple genes, including CSNK1A1. Recurrent CSNK1A1 mutations, predominantly affecting the E98 hotspot, occur almost exclusively in del(5q) MDS and are associated with adverse outcomes, yet their impact on CK1ɑ function remains unclear. Using integrated transcriptomic, (phospho)proteomic, and kinome activity profiling in hematopoietic stem and progenitor cells (HSPCs), combined with in vivo serial transplantation assays, we show that Csnk1a1 E98V represents a change-of-function rather than a loss-of-function mutation. Unlike Csnk1a1 haploinsufficiency, Csnk1a1 E98V preserves long-term hematopoietic reconstitution and does not enhance clonal expansion in vivo. Instead, the mutation induces suppression of kinase signaling networks, leading to coordinated repression of ribosomal gene expression, protein translation, and cell cycle programs. This signaling rewiring is accompanied by metabolic reprogramming characterized by reduced mitochondrial respiration, increased glycolytic flux, and an inability to adapt to metabolic challenges, creating a stress-tolerant but inflexible cellular state. Notably, Csnk1a1 E98V cells exhibit impaired megakaryopoiesis and increased vulnerability to iron overload, as well as RSL-3-mediated ferroptosis. Analysis of del(5q) MDS patients confirmed that CSNK1A1 mutations are associated with distinct clinical features, including thrombocytopenia, elevated myeloblasts, and reduced bone marrow iron levels. Together, our findings support a two-step model in which del(5q)-associated CSNK1A1 haploinsufficiency drives clonal expansion, followed by acquisition of CSNK1A1 mutations that promote stress tolerance rather than increased proliferation. This adaptive rewiring exposes metabolic and iron-dependent vulnerabilities that may be therapeutically exploited.

Prognostication in chronic myelomonocytic leukemia (CMML) remains a challenge due to the biological complexity and variable clinical course of the disease. This study aimed to evaluate the prognostic utility of the International Prognostic Scoring System-Molecular (IPSS-M) in CMML and its applicability across the myelodysplastic and myeloproliferative subsets of the disease. We conducted a multicenter, retrospective study including 511 patients diagnosed with CMML. Clinical, cytogenetic, and molecular data were collected at diagnosis, including targeted NGS. Patients were stratified using IPSS-M, CPSS-Mol, and the recently developed iCPSS. IPSS-M effectively stratified patients into risk groups with significantly different overall survival (OS) and cumulative incidence of acute myeloid leukemia (AML) progression. Discrimination was maintained after merging overlapping intermediate risk categories, yielding a four-tier model with a c-index of 0.678 for OS and 0.628 for AML progression. This model retained its prognostic performance in both MD-CMML and MP-CMML subsets, with higher discrimination for OS in the MD-CMML group. When compared with CPSS-Mol and iCPSS, adapted IPSS-M showed comparable prognostic performance to iCPSS and improved discrimination compared with CPSS-Mol. These findings support the applicability of an adapted IPSS-M to CMML, extending its use beyond myelodysplastic syndromes and highlighting its potential utility in guiding clinical decision-making and therapeutic strategies. Moreover, this study also provides an external validation of the iCPSS in an independent and genetically well-characterized CMML cohort, reinforcing its clinical utility.

Myelodysplastic neoplasms (MDS) with TP53 multihit alterations are associated with dismal outcomes. MDS with isolated del(5q) present favorable prognosis but is defined by the absence of TP53 multihit alterations. However, whether TP53 multihit alterations exert the same adverse impact in this genetic context remains uncertain. We retrospectively analyzed the characteristics and outcome of 43 patients with MDS with isolated del(5q) harboring TP53 multihit alterations (MDS-del(5q) TP53 multihit) and compared with 68 patients with low-blast MDS with TP53 multihit and without isolated del(5q) (MDS-LB TP53 multihit). Patients with MDS-del(5q) TP53 multihit showed significantly higher platelet counts, more frequent SF3B1 mutations, were less often classified as high-risk by IPSS-R or IPSS-M, and had significantly better outcomes than patients with MDS-LB TP53 multihit: overall survival of 70.2 vs 13.9 months, and time to acute myeloid leukemia progression (AML) of 31.9 vs 7.2 months, respectively. Moreover, the superior outcomes of MDS-del(5q) TP53 multihit patients persisted significant even when compared with MDS-LB TP53 multihit cases without complex karyotype (survival of 70.2 vs 39.9 months; time to AML progression of 31.9 vs 11.4 months). These findings indicate that, in MDS-del(5q) the adverse impact of TP53 multihit alterations may be less important than in other MDS subtypes.

Acute myeloid leukemia (AML) is a complex hematological malignancy with multiple disease sub-groups defined by somatic mutations and heterogeneous outcomes. Although genome-wide association studies (GWAS) have identified a small number of common genetic variants influencing AML risk, the heritable component of this disease outside of familial susceptibility remains largely undefined. Here we perform a meta-analysis of four published GWAS plus two new GWAS, totalling 4710 AML cases and 12938 controls. We identify a new genome-wide significant risk locus for pan-AML at 2p23.3 (rs4665765; P=1.35x10-8; EFR3B, POMC, DNMT3A, DNAJC27) which also significantly associates with patient survival (P=6.09x10-3). Our analysis also identifies three new genome-wide significant risk loci for disease sub-groups, including AML with deletions of chromosome 5 and/or 7 at 1q23.3 (rs12078864; P=7.0x10-10; DUSP23) and cytogenetically complex AML at 2q33.3 (rs12988876; P=3.28x10-8; PARD3B) and 2p21 (rs79918355; P=1.60x10-9; EPCAM). We also investigated loci previously associated with risk of clonal hematopoiesis (CH) or clonal hematopoiesis of indeterminate potential (CHIP) and identified several variants associated with risk of AML. Our results further inform on AML etiology and demonstrate the existence of disease sub-group specific risk loci.

Myelodysplastic syndromes with isolated deletion of chromosome 5q [MDS-del(5q)] constitute a distinct biological entity traditionally associated with favorable outcomes, although up to one quarter of patients progress to acute myeloid leukemia (AML). Existing prognostic models, developed in heterogeneous MDS populations, may not adequately capture risk within this subgroup. We assembled an international cohort of 682 patients with MDS-del(5q) to evaluate the performance of the IPSS-R and IPSS-M, identify prognostic variables, and develop a disease-specific prognostic tool, the IPSS-del(5q). Most patients were classified as lower-risk by IPSS-R (94.4%) and IPSS-M (85.5%), yet both systems showed limited discriminatory ability (C-indices ≈0.5). Independent adverse prognostic factors included age ≥70 years, male sex, anemia (hemoglobin ≤10 g/dL), thrombocytopenia (platelets ≤100×10⁹/L), the presence of one additional chromosomal abnormality, ≥2 gene mutations, SF3B1 mutations, and high-risk TP53 status. Six variables were included in the IPSS-del(5q), stratifying patients into standard-risk (74.3%) and high-risk (25.7%) groups with significantly different LFS (69.2 vs. 32.0 months; p<0.01). Moreover, this model reclassified 19.1% of lower-risk IPSS-R and 14.6% of lower-risk IPSS-M patients into the high-risk IPSS-del(5q) group. However, its discriminative power remained modest, with a C-index of 0.60. Overall, this study provides the most comprehensive prognostic evaluation of MDS-del(5q) to date, demonstrates the limited discriminatory capacity of existing MDS scores in this entity, and underscores the need to develop refined disease-specific prognostic approaches for this MDS subtype.

Baseline IPSS-M risk, response to hypomethylating agent (HMA) therapy, and receipt of allogeneic stem cell transplant (allo-HCT) have all been individually shown to impact overall survival (OS) in patients with myelodysplastic syndromes (MDS). However, the prognostic impact of response when adjusting for IPSS-M risk and treatment strategy remains unclear. Hence, we used the VALIDATE database of the International Consortium for MDS (icMDS) to evaluate the impact of International Working Group (IWG) 2023 best response on OS in 715 HMA-treated, higher-risk MDS patients stratified by baseline IPSS-M risk and their treatment strategy (subsequent allo-HCT vs. medical therapy alone) treating both best response and allo-HCT as time-dependent variables. Baseline IPSS-M risk (hazard ratio (HR): 0.5, p < 0.001) and receipt of allo-HCT (HR: 0.5, p < 0.001) were the strongest independent predictors of OS, whereas achievement of composite complete response (cCR) had a more modest impact on OS (HR: 0.8, p = 0.004). Among patients treated with medical therapy alone, achieving cCR improved OS significantly (HR: 0.7, p = 0.006). In contrast, among transplanted patients, cCR did not retain independent prognostic value for post-transplant survival after adjusting for baseline IPSS-M (HR: 0.9, p = 0.634). Achieving cCR did not fully overcome adverse disease biology as OS continued to segregate according to baseline IPSS-M risk. In summary, achieving cCR improves outcomes in non-transplanted patients, but it does not significantly impact post-transplant OS, suggesting that failure to achieve cCR with HMA may not warrant delay or preclude allo-HCT. Clinical trials should consider response in the context of IPSS-M risk distribution and treatment strategy (subsequent allo-HCT vs. medical therapy alone) to avoid overinterpretation of high response rates.

ABSTRACT:Mutations in the isocitrate dehydrogenase (IDH) genes, IDH1 and IDH2, are recurrently found in patients with myeloid neoplasms (MN) and clinically targeted by small-molecule inhibitors. We aimed to comprehensively study the genetic pattern and underlying clonal architecture in a large cohort of 12 071 patients (acute myeloid leukemia [AML], n = 4113; myelodysplastic neoplasms [MDS], n = 6316; or chronic myelomonocytic leukemia [CMML], n = 1642). IDH mutations were found in 28% of patients with AML (IDH1, 10%; IDH2, 18%), 6.3% of patients with MDS (IDH1, 1.8%; IDH2, 4.6%), and 5.2% of patients with CMML (IDH1, 0.8%; IDH2, 4.4%). IDH mutations were enriched in subgroups with increased blasts but almost absent within MDS with biallelic TP53 inactivation. The comutational pattern differed by age, between MN, and between mutation hot spots. The underlying clonal hierarchy suggested that IDH mutations were present in the founder clone in many, but not all, patients. Finally, the high frequencies of IDH1 mutations in secondary AML and myelodysplasia-related AML (both 9.5%), compared with MDS (1.8%) and CMML (0.8%), indicate a frequent acquisition of this mutation at the transition to AML, which was directly confirmed in a subset of patients analyzed before and after progression. Overall, our findings have potential implications for sequential molecular testing and targeted treatment decisions.