bims-tremyl Biomed News
on Therapy resistance biology in myeloid leukemia
Issue of 2025–03–23
thirty-one papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London



  1. Blood. 2025 Mar 19. pii: blood.2024028000. [Epub ahead of print]
      'Non-classical' Myeloproliferative Neoplasms (MPNs) and Myelodysplastic/Myeloproliferative Neoplasms (MDS/MPNs) represent a heterogeneous group of malignancies characterized by a wide range of clinical manifestations. Unlike classical MPNs, there is no standardized management approach for these conditions, particularly concerning the indications for and management of allogeneic hematopoietic cell transplantation (HCT). To address this gap, the EBMT Practice Harmonization and Guidelines (PH&G) Committee and the Chronic Malignancies Working Party (CMWP) have collaborated to develop shared guidelines aimed at optimizing the selection and management of patients with these rare forms of neoplasms. A comprehensive review of the literature from the publication of the revised 4th edition of the (2016) WHO classification onward was conducted. A multidisciplinary group of experts in the field convened to produce this document, which was developed through multiple rounds of draft circulation. Key recommendations include the early identification of potential transplant candidates, particularly in cases of chronic neutrophilic leukemia (CNL), chronic eosinophilic leukemia (CEL) / CEL, not otherwise specified (CEL-NOS), myeloid/lymphoid neoplasm with eosinophilia and tyrosine kinase gene fusions (MLN-TK) with FGFR1, JAK2, ABL1, and FLT3 rearrangements, MDS/MPN with neutrophilia / atypical chronic myeloid leukemia (aCML), and MDS/MPN, NOS. For patients with MPN, NOS / MPN unclassifiable, standard recommendations for myelofibrosis (MF) should be applied. Similarly, in MDS/MPN with thrombocytosis, transplantation is recommended based on established MDS guidelines. Given the current lack of robust evidence, this document will serve as a valuable resource to guide future research activities, providing a framework for addressing critical unanswered questions and advancing the field.
    DOI:  https://doi.org/10.1182/blood.2024028000
  2. J Clin Invest. 2025 Mar 20. pii: e184021. [Epub ahead of print]
      Mutations and deletions in TP53 are associated with adverse outcomes in patients with myeloid malignancies and developing improved therapies for TP53-mutant leukemias is of urgent need. Here we identify mutations in TET2 as the most common co-occurring mutation in TP53 mutant acute myeloid leukemia (AML) patients. In mice, combined hematopoietic-specific deletion of TET2 and TP53 resulted in enhanced self-renewal compared to deletion of either gene alone. Tp53/Tet2 double knockout mice developed serially transplantable AML. Both mice and AML patients with combined TET2/TP53 alterations upregulated innate immune signaling in malignant granulocyte-monocyte progenitors (GMPs), which had leukemia-initiating capacity. A20 governs the leukemic maintenance by triggering aberrant non-canonical NF-κB signaling. Mice with Tp53/Tet2 loss had expansion of monocytic myeloid-derived suppressor cells (MDSCs), which impaired T cell proliferation and activation. Moreover, mice and AML patients with combined TP53/TET2 alterations displayed increased expression of the TIGIT ligand, CD155, on malignant cells. TIGIT blocking antibodies augmented NK cell-mediated killing of Tp53/Tet2 double-mutant AML cells, reduced leukemic burden, and prolonged survival in Tp53/Tet2 double knockout mice. These findings uncover a leukemia-promoting link between TET2 and TP53 mutations and highlight therapeutic strategies to overcome the immunosuppressive bone marrow environment in this adverse subtype of AML.
    Keywords:  Hematology; Inflammation; Leukemias; Mouse models; Oncology; p53
    DOI:  https://doi.org/10.1172/JCI184021
  3. Cancer Res Commun. 2025 Mar 20.
      Overall survival of acute myeloid leukemia (AML) remains limited. Inhibitors of the master mitotic kinase PLK1 have emerged as promising therapeutics, demonstrating efficacy in an undefined subset of AML patients. However, the clinical success of PLK1 inhibitors remains hindered by a lack of predictive biomarkers. The Fanconi anemia (FA) pathway, a tumor-suppressive network comprised of at least 22 genes, is frequently mutated in sporadic AML. Here, we demonstrate that FA pathway disruption sensitizes AML cells to PLK1 inhibition. Mechanistically, we identify novel interactions between PLK1 and both FANCA and FANCD2 at mitotic centromeres. We demonstrate that PLK1 inhibition impairs recruitment of FANCD2 to mitotic centromeres, induces damage to mitotic chromosomes, and triggers mitotic collapse in FANCA-deficient cells. Our findings indicate that PLK1 inhibition targets mitotic vulnerabilities specific to FA pathway-deficient cells and implicate FA pathway mutations as potential biomarkers for the identification of patients likely to benefit from PLK1 inhibitors.
    DOI:  https://doi.org/10.1158/2767-9764.CRC-24-0260
  4. Nat Commun. 2025 Mar 18. 16(1): 2641
      Targeting the dependency of MLL-rearranged (MLLr) leukemias on menin with small molecule inhibitors has opened new therapeutic strategies for these poor-prognosis diseases. However, the rapid development of menin inhibitor resistance calls for combinatory strategies to improve responses and prevent resistance. Here we show that leukemia stem cells (LSCs) of MLLr acute myeloid leukemia (AML) exhibit enhanced guanine nucleotide biosynthesis, the inhibition of which leads to myeloid differentiation and sensitization to menin inhibitors. Mechanistically, targeting inosine monophosphate dehydrogenase 2 (IMPDH2) reduces guanine nucleotides and rRNA transcription, leading to reduced protein expression of LEDGF and menin. Consequently, the formation and chromatin binding of the MLL-fusion complex is impaired, reducing the expression of MLL target genes. Inhibition of guanine nucleotide biosynthesis or rRNA transcription further suppresses MLLr AML when combined with a menin inhibitor. Our findings underscore the requirement of guanine nucleotide biosynthesis in maintaining the function of the LEDGF/menin/MLL-fusion complex and provide a rationale to target guanine nucleotide biosynthesis to sensitize MLLr leukemias to menin inhibitors.
    DOI:  https://doi.org/10.1038/s41467-025-57544-9
  5. bioRxiv. 2025 Mar 07. pii: 2025.03.03.641255. [Epub ahead of print]
      Enhanced glycolysis plays a pivotal role in fueling the aberrant proliferation, survival and therapy resistance of acute myeloid leukemia (AML) cells. Here, we aimed to elucidate the extent of glycolysis dependence in AML by focusing on the role of lactate dehydrogenase A (LDHA), a key glycolytic enzyme converting pyruvate to lactate coupled with the recycling of NAD+. We compared the glycolytic activity of primary AML patient samples to protein levels of metabolic enzymes involved in central carbon metabolism including glycolysis, glutaminolysis and the tricarboxylic acid cycle. To evaluate the therapeutic potential of targeting glycolysis in AML, we treated AML primary patient samples and cell lines with pharmacological inhibitors of LDHA and monitored cell viability. Glycolytic activity and mitochondrial oxygen consumption were analyzed in AML patient samples and cell lines post-LDHA inhibition. Perturbations in global metabolite levels and redox balance upon LDHA inhibition in AML cells were determined by mass spectrometry, and ROS levels were measured by flow cytometry. Among metabolic enzymes, we found that LDHA protein levels had the strongest positive correlation with glycolysis in AML patient cells. Blocking LDHA activity resulted in a strong growth inhibition and cell death induction in AML cell lines and primary patient samples, while healthy hematopoietic stem and progenitor cells remained unaffected. Investigation of the underlying mechanisms showed that LDHA inhibition reduces glycolytic activity, lowers levels of glycolytic intermediates, decreases the cellular NAD+ pool, boosts OXPHOS activity and increases ROS levels. This increase in ROS levels was however not linked to the observed AML cell death. Instead, we found that LDHA is essential to maintain a correct NAD+/NADH ratio in AML cells. Continuous intracellular NAD+ supplementation via overexpression of water-forming NADH oxidase from Lactobacillus brevis in AML cells effectively increased viable cell counts and prevented cell death upon LDHA inhibition. Collectively, our results demonstrate that AML cells critically depend on LDHA to maintain an adequate NAD+/NADH balance in support of their abnormal glycolytic activity and biosynthetic demands, which cannot be compensated for by other cellular NAD+ recycling systems. These findings also highlight LDHA inhibition as a promising metabolic strategy to eradicate leukemic cells.
    DOI:  https://doi.org/10.1101/2025.03.03.641255
  6. Blood Cancer J. 2025 Mar 15. 15(1): 40
      Although treatment with standard frontline therapies, including a FLT3 inhibitor (FLT3i) reduces AML burden and achieves clinical remissions, most patients with AML with FLT3 mutation relapse due to therapy-resistant stem/progenitor cells. The core ATPases, BRG1 (SMARCA4) and BRM (SMARCA2) of the canonical (c) BAF (BRG1/BRM-associated factor) complex is a dependency in AML cells, including those harboring FLT3 mutations. We have previously reported that treatment with FHD-286, a BRG1/BRM ATPases inhibitor, induces differentiation and loss of viability of AML stem/progenitor cells. Findings of present studies demonstrate that treatment with FHD-286 induces lethality in AML cells, regardless of sensitivity or resistance to FLT3i. This efficacy is associated with the induction of gene-expression perturbations responsible for growth inhibition, differentiation, as well as a reduced AML-initiating potential of the AML cells. Additionally, co-treatment with FHD-286 and FLT3i exerts superior pre-clinical efficacy against AML cells and patient-derived (PD) xenograft (PDX) models of AML with FLT3 mutations.
    DOI:  https://doi.org/10.1038/s41408-025-01251-7
  7. Cancer. 2025 Apr 01. 131(7): e35806
      Focused research in acute myeloid leukemia (AML) biology and treatment has led to the identification of new therapeutic targets and several new drug approvals over the last decade. Progressive improvements in response and survival have mirrored these improvements in treatment options. Traditionally adverse subtypes such as FLT3-internal tandem duplication-positive AML now have better outcomes with potent FLT3 inhibitors, and menin inhibitors in KMT2A-rearranged and other MEIS/HOX-dependent leukemias hold promise toward improving outcomes. More patients with AML are now able to undergo a consolidative allogeneic hematopoietic stem cell transplantation (HSCT), and the rates of nonrelapse mortality with or without HSCT have also decreased. Comprehensive genomic interrogation of AML has elucidated mechanisms of response and resistance to treatments, which has enabled more precise decision algorithms and better prognostication. Deep levels of measurable residual disease assessment in some AML subsets hold the potential to dynamically modify treatment on the basis of these responses. Improving frontline intensive and low-intensity therapies, by incorporating venetoclax and other targeted agents, is the most important intervention to improve AML outcomes. Despite these developments, a sizeable percentage of AML, such as AML with TP53 or MECOM aberrations, postmyeloproliferative neoplasm AML, and so forth, remains as subsets without significant improvement in outcomes and no targeted options. Evolving strategies with natural killer cell-based approaches, novel antibody-drug conjugates, bispecific T-cell engagers, and engineered chimeric antigen receptor T-cell therapies are being evaluated, and may fill the therapeutic vacuum for some of the high-risk AML subtypes.
    Keywords:  TP53; acute myeloid leukemia; acute promyelocytic leukemia; menin inhibitors; venetoclax
    DOI:  https://doi.org/10.1002/cncr.35806
  8. Blood. 2025 Mar 19. pii: blood.2024027376. [Epub ahead of print]
      Phosphoinositide 3-kinase gamma (PI3Kγ), the only class IB PI3 kinase, is a cell-extrinsic immunotherapy target in solid tumors. PI3Kγ inhibition reprograms immunosuppressive myeloid cells to acquire immunostimulatory phenotypes, which promote antitumor cytotoxic T cell activity. Although PI3Kγ inhibition has no direct effect on solid tumor cells, several new studies have nominated PI3Kγ as a cell-intrinsic target in various leukemias, particularly acute myeloid leukemia (AML). Intrinsic dependency on PI3Kγ is present at baseline in leukemias with specific pathologic characteristics, is inducible by extrinsic inflammation in others, and may also be acquired with resistance to certain therapies. The discovery of leukemia PI3Kγ dependency has generated enthusiasm for immediate clinical trial evaluation of inhibitor monotherapy and combinations. Parallel laboratory evaluation is needed to develop an improved understanding of leukemia disease features associated with clinical inhibitor sensitivity that might suggest biomarker-directed patient enrichment strategies. In this review, we discuss recent progress credentialling PI3Kγ as a bona fide target in leukemia. We also highlight open questions, including a need to understand the mechanism of acquired resistance to PI3Kγ inhibition, how to optimally prioritize combination therapies to enhance PI3Kγ inhibitor utility, and how cell-extrinsic effects of PI3Kγ inhibition in the leukemia microenvironment might also contribute to clinical activity.
    DOI:  https://doi.org/10.1182/blood.2024027376
  9. Leukemia. 2025 Mar 17.
      We investigated the clinical and functional role of the miR-106a-363 cluster in adult acute myeloid leukemia (AML). LAML miRNA-Seq TCGA analyses revealed that high expression of miR-106a-363 cluster members was associated with inferior survival, and miR-106a-5p and miR-20b-5p levels were significantly elevated in patients with adverse risk AML. Overexpression of the miR-106a-363 cluster and its individual members in a murine AML model significantly accelerated leukemogenesis. Proteomics analysis of leukemic bone marrow cells from these models emphasized the deregulation of proteins involved in intracellular transport, protein complex organization and mitochondrial function, driven predominantly by miR-106a-5p. These molecular alterations suggested mitochondrial activation as a potential mechanism for the observed increase in leukemogenicity. High-resolution respirometry and STED microscopy confirmed that miR-106a-5p enhances mitochondrial respiratory activity and increases mitochondrial volume. These findings demonstrate that the miR-106a-363 cluster, and particularly miR-106a-5p, contribute to AML progression through modulation of mitochondrial function and deregulation of mitochondria-coordinated pathways.
    DOI:  https://doi.org/10.1038/s41375-025-02558-x
  10. bioRxiv. 2025 Mar 03. pii: 2025.02.28.640879. [Epub ahead of print]
      Clonal hematopoiesis (CH) is characterized by expanding blood cell clones carrying somatic mutations in healthy aged individuals and is associated with various age-related diseases and all-cause mortality. While CH mutations affect diverse genes associated with myeloid malignancies, their mechanisms of expansion and disease associations remain poorly understood. We investigate the relationship between clonal fitness and clinical outcomes by integrating data from three longitudinal aging cohorts (n=713, observations=2,341). We demonstrate pathway-specific fitness advantage and clonal composition influence clonal dynamics. Further, the timing of mutation acquisition is necessary to determine the extent of clonal expansion reached during the host individual's lifetime. We introduce MACS120, a metric combining mutation context, timing, and variant fitness to predict future clonal growth, outperforming traditional variant allele frequency measurements in predicting clinical outcomes. Our unified analytical framework enables standardized clonal dynamics inference across cohorts, advancing our ability to predict and potentially intervene in CH-related pathologies.
    DOI:  https://doi.org/10.1101/2025.02.28.640879
  11. Clin Lymphoma Myeloma Leuk. 2025 Feb 23. pii: S2152-2650(25)00072-2. [Epub ahead of print]
      
    Keywords:  Anemia; Lower risk MDS; Red blood cell transfuion dependency; Response to treatment; myelodysplastic neoplasms
    DOI:  https://doi.org/10.1016/j.clml.2025.02.010
  12. Blood Adv. 2025 Mar 18. pii: bloodadvances.2025015793. [Epub ahead of print]
      Allogeneic hematopoietic cell transplantation (allo-HCT) is potentially curative for older adults with hematologic malignancies. Concerns about non-relapse mortality (NRM) in older adults limit allo-HCT utilization. We executed a prospective, observational study (BMT-CTN 1704) enrolling allo-HCT recipients aged ≥60 years from 49 centers in the U.S. We analyzed associations between 13 measurements of older adult health and NRM within 1-year to construct a comprehensive health assessment risk model (primary-CHARM) using amultivariate Fine-Gray model and grouped penalized variable selection. Two (Cox and pseudovalue Boosting) Machine-Learning (ML) models were also explored. Models' performances were compared using area under the receiver operating curve (AUC), with bootstrap and crossvalidation sampling to correct for optimism, decision-curve analysis (DCA), calibration, and Brierscores. Among 1105 patients with median age of 67 years (range 60-82) who received alloHCT, NRM was 14.4% and overall survival (OS), 71.7% at 1-year. Factors statistically selected for inclusion in primary-CHARM were: higher comorbidity-burden, lower albumin, higher Creactive protein, older age, higher weight loss percentage, lower patient-reported performance score, and cognitive impairment. Primary-CHARM scores were independently associated with higher NRM (hazard ratio [HR]:2.72, p<0.0001) and worse OS (HR:2.09, p<0.0001). Bootstrap bias-corrected AUC for primary-CHARM was 0.591. Comparing primary-CHARM to HCTcomorbidity index and 2 ML-CHARM models, calibration, Brier score, and DCA analysis favored primary-CHARM. The primary-CHARM, comprised of mostly simple and readily available parameters, risk-stratifies older adults for allo-HCT. Adopting primary-CHARM in practice maypromote broader use of HCT by quantifying risk and enhance the design of strategies to improve outcomes. Clinicaltrials.gov number: (NCT03992352).
    DOI:  https://doi.org/10.1182/bloodadvances.2025015793
  13. Transplant Cell Ther. 2025 Mar 17. pii: S2666-6367(25)01096-6. [Epub ahead of print]
       BACKGROUND: Myeloablative conditioning (MAC) and reduced intensity conditioning (RIC) regimens are both used before allogeneic haematopoietic stem cell transplantation (allo-HCT) for myelofibrosis (MF). The median age of patients with MF treated with allo-HCT is increasing and a high non-relapse mortality (NRM), especially to MAC, has increased utilisation of lesser intense non-myeloablative (NMA) regimens. NMA is used as the standard conditioning regimen before allo-HCT for MF at all transplantation centres in Denmark.
    OBJECTIVES: To describe the outcomes of a highly homogenously treated, population derived cohort of MF-patients who received NMA conditioning prior to allo-HCT, and identify factors associated to transplantation outcomes.
    STUDY DESIGN: The study is a retrospective cohort study of MF-patients treated with NMA prior to allo-HCT at Copenhagen University Hospital, Rigshospitalet from 2007 to 2023.
    RESULTS: Of 70 patients with MF who were treated with allo-HCT for MF from 2007 to 2023, 67 patients received NMA conditioning with fludarabine 90 mg/m2 and total body irradiation of 2-4 Gray. These 67 patients had a median age of 61.1 years, 22 patients (33%) had a Karnofsky performance status below 90, and 28 patients (44%) had a haematopoietic-stem-cell-transplantation comorbidity index (HCT-CI) above 2. With a median follow-up time of 3.4 years (range 0.16-15.58 years), 39 patients (58%) were still alive. Eighteen patients (27%) relapsed and of the 28 patients (42%) that died during the study period, 12 (43%) died from relapse, and 16 (57%) from NRM. Median time to neutrophil engraftment, transfusion independency and platelet engraftment was 21 days (range 11 - 119 days), 69 days (range 0 - 470 days) and 17 days (range 0 - 308 days) respectively with primary graft failure identified in 13 patients (19.7%). Overall survival (OS) after 1, 3, and 5 years was 77%, 68%; 61% %, whereas the NRM was 15%, 15% and 21%. The cumulative incidence of relapse (CIR) was 24% after 1 year, 28 % after 3 years and 28% after 5 years. Multivariable analysis showed that male sex (HR= 5.43, p<0.001), graft from unrelated donor (HR= 3.58, p=0.018) and HCT-CI above 2 (HR= 2.5, p=0.025) remained associated to OS, whereas for progression-free survival, only NRAS mutations remained as an independent factor (HR= 5.88, p=0.013). Both male sex (HR= 8.41, p=0.037) and graft from unrelated donor (HR= 3.15, p=0.043) were associated to NRM in multivariable analysis.
    CONCLUSION: NMA conditioning in the form of low dose TBI and fludarabine before allo-HCT for MF is feasible. Patients show low 1-year NRM but a relatively high 1-year CIR. Differentiated conditioning with more intensive RIC regiments for younger and fit patients could be considered to reduce the early relapse rate without increasing NRM. In survival analysis, donor-patient relation, patient comorbidity burden and patient sex were independently associated to OS.
    Keywords:  Haematopoietic stem cell transplantation; NRAS; myelofibrosis; myeloproliferative neoplasms; reduced intensity conditioning
    DOI:  https://doi.org/10.1016/j.jtct.2025.03.006
  14. Eur J Haematol. 2025 Mar 18.
       OBJECTIVES: Mixed phenotype acute leukemia (MPAL) often poses challenges in diagnosis and clinical management. This is the first study to assess the lineage/immunophenotype-genotype association and the significance of AML-myelodysplasia-related changes (MR, cytogenetic abnormalities and gene mutations, AML-MR-CG-Gene) in MPAL classification.
    METHODS: We conducted a clinicopathologic and genomic evaluation of 25 MPAL cases by the WHO-HEM5/ICC classification criteria, except for retaining those MPAL cases with AML-MR-CG-Gene (Conditional-MPAL).
    RESULTS: The majority of MPAL cases (22/25, 88%) showed distinct genotypes that overlapped with those of lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). The genomic profile of ALL-like and AML-like was associated with immunophenotypically lymphoid and myeloid lineage predominance, respectively. The lineage/immunophenotype-genotype association may provide a rationale to develop a lineage-immunophenotypically/biologically guided therapy selection. Additionally, 64% of MPAL cases carried AML-MR-CG-Gene, half of which were MPAL with lymphoid-lineage predominance and had ALL-like molecular signatures, and most of these patients responded well to the ALL-based induction regimens. These results support that Conditional-MPAL with AML-MR-CG-Gene may be better diagnosed as MPAL rather than AML-MR.
    CONCLUSION: Genomic landscape of AML-like or ALL-like MPAL is associated with the immunophenotypic lineage predominance, and such association could impact treatment decisions and provide supporting evidence to refine MPAL diagnostic criteria in future studies.
    Keywords:  ALL; AML; MPAL; diagnostic criteria; genomic profile; lineage‐immunophenotype/genotype association; mixed phenotype acute leukemia; myelodysplasia‐related changes; treatment
    DOI:  https://doi.org/10.1111/ejh.14414
  15. Blood. 2025 Mar 19. pii: blood.2024028005. [Epub ahead of print]
      Despite recent advances in graft-versus-host disease (GVHD) prophylaxis, novel approaches to effective prevention of chronic GVHD (cGVHD) remain of high importance. In this prospective, multicenter phase II trial (NCT03286530), ruxolitinib, an oral inhibitor of JAK 1 & 2, was administered as maintenance therapy after reduced-intensity allogeneic hematopoietic cell transplantation (HCT). GVHD prophylaxis consisted of tacrolimus and methotrexate. Ruxolitinib began between Day +30-100 and was administered continuously in 28-day cycles for up to 24 cycles. Seventy-eight participants were enrolled prior to HCT; 63 participants received the intervention. The median start date of ruxolitinib after HCT was Day +45. The most common grade ≥3 adverse events were neutropenia, thrombocytopenia, and anemia. Seven participants experienced grade ≥3 infectious events. GVHD-free, relapse-free survival at 1-year after HCT, the primary endpoint, was 70%. Grade III-IV acute GVHD at 6-months was 4.8% and moderate-severe cGVHD at 2-years was 16%. cGVHD requiring systemic therapy was 9.5% at 1-year and 13% at 2-years. Overall survival and progression-free survival at 2-years were 76% and 68%, respectively. Prolonged administration of ruxolitinib following HCT is associated with low rates of clinically significant cGVHD. The incorporation of JAK inhibition into GVHD prevention approaches warrants further investigation.
    DOI:  https://doi.org/10.1182/blood.2024028005
  16. Blood. 2025 Mar 16. pii: blood.2024027270. [Epub ahead of print]
      The critical role of leukemic initiating cells as a therapy-resistant population in myeloid leukemia is well established, however, the molecular signatures of such cells in acute lymphoblastic leukemia remain underexplored. Moreover, their role in therapy response and patient prognosis is yet to be systematically investigated across various types of acute leukemia. We employed single-cell multiomics to analyze diagnostic specimens from 96 pediatric patients with acute lymphoblastic, myeloid, and lineage ambiguous leukemias. Through the integration of single-cell multiomics with extensive bulk RNA-Seq and clinical datasets, we uncovered a prevalent, chemotherapy-resistant subpopulation that resembles hematopoietic stem and progenitor cells (HSPC-like) and is associated with poor clinical outcomes across all subtypes investigated. We identified a core transcriptional regulatory network (TRN) in HSPC-like blasts that is combinatorically controlled by HOXA/AP1/CEBPA. This TRN signature can predict chemotherapy response and long-term clinical outcomes. We identified shared potential therapeutic targets against HSPC-like blasts, including FLT3, BCL2, and the PI3K pathway. Our study provides a framework for linking intra-tumoral heterogeneity with therapy response, patient outcome and discovery of new therapeutic targets for pediatric acute leukemias.
    DOI:  https://doi.org/10.1182/blood.2024027270
  17. Sci Adv. 2025 Mar 21. 11(12): eads8351
      Galectin-9 is overexpressed in a variety of cancers and associated with worse clinical outcome in some cancers. However, the regulators driving Galectin-9 expression are unknown. Here, we defined the transcriptional regulators and epigenetic circuitry of Galectin-9 in pediatric T cell acute lymphoblastic leukemia (T-ALL), as an example of a disease with strong Galectin-9 expression, in which higher expression was associated with lower overall survival. By performing a genome-wide CRISPR screen, we identified the transcription factors IRF1 and TFAP4 as key regulators for Galectin-9 expression by binding its regulatory elements. Whereas IRF1 was observed exclusively on the promoter, TFAP4 binding was detected at an enhancer solely in T-ALL cells associated with higher Galectin-9 levels. Together, our results show that IRF1 is responsible and indispensable for Galectin-9 expression and TFAP4 further fine-tunes its expression. Our approach, a flow-based genome-wide CRISPR screen complemented by transcription factor binding and enhancer mapping, creates innovative opportunities for understanding and manipulating epigenetic transcriptional regulation in cancer.
    DOI:  https://doi.org/10.1126/sciadv.ads8351
  18. JAMA. 2025 Mar 17.
       Importance: Chronic myeloid leukemia (CML) has an annual incidence of 2 cases per 100 000 people and is newly diagnosed in approximately 9300 individuals per year in the US. Approximately 150 000 people in the US and 5 million worldwide have CML.
    Observations: Chronic myeloid leukemia is a myeloproliferative neoplasm characterized by the presence of the Philadelphia chromosome, which is defined by the BCR::ABL1 oncogene that develops after fusion of the ABL1 proto-oncogene to the constitutively active BCR gene. Approximately 90% of people with CML present with an indolent chronic phase of CML, defined as blasts of less than 10% in the blood or bone marrow, absence of extramedullary evidence of leukemia, basophils of less than 20%, and platelet counts of 100 to 1000 × 109/L. The most advanced stage is CML blastic phase (CML-BP), characterized by the World Health Organization as 20% or more blasts/immature cells and by the MD Anderson Cancer Center and European LeukemiaNet as 30% or more. Approximately 1% to 2% of patients with CML present with CML-BP. Since 2000, first-generation tyrosine kinase inhibitors (TKIs) targeting BCR::ABL1, such as imatinib, and second-generation TKIs, such as bosutinib, dasatinib, and nilotinib, have improved CML-related mortality from 10% to 20% per year to 1% to 2% per year, such that patients with CML have survival rates similar to those of a general age-matched population. Six BCR::ABL1 TKIs have been approved by the US Food and Drug Administration, including 5 that are first-line treatment (imatinib, dasatinib, bosutinib, nilotinib, and asciminib) and 5 approved for treatment after disease progression despite initial therapy (dasatinib, bosutinib, nilotinib, ponatinib, asciminib). Effects on improved survival are similar with all TKIs, although more patients are able to promptly achieve and maintain BCR::ABL1 clearance with second- and third-generation TKIs. Medication adherence is important to maintain treatment responsiveness. All TKIs are associated with hematologic toxicity, such as myelosuppression, with additional agent-specific adverse effects, such as pleural effusion (dasatinib), arterio-occlusive events such as myocardial infarction, stroke, and peripheral artery disease (nilotinib, ponatinib), gastrointestinal disturbance (bosutinib), or increased amylase and lipase with pancreatitis (ponatinib, asciminib, nilotinib). These adverse effects should be considered when selecting a TKI. Allogeneic hematopoietic stem cell transplant is a reasonably safe therapy, with cure rates ranging from 20% to 60% based on the stage of CML at the time of transplant. Stem cell transplant is reserved for patients with CML who do not respond to second-generation TKIs, those with intolerance to multiple TKIs, or those with accelerated-phase CML or CML-BP.
    Conclusions and Relevance: Chronic myeloid leukemia is a myeloproliferative neoplasm that can typically be effectively treated with TKIs, improving survival similar to that of a general age-matched population. Many patients require continuous TKI therapy. Therefore, TKI therapy should be selected with consideration of adverse effects, and patients should be helped to maximize adherence to TKI treatment.
    DOI:  https://doi.org/10.1001/jama.2025.0220
  19. bioRxiv. 2025 Mar 03. pii: 2025.02.27.640600. [Epub ahead of print]
      Cancer cells adapt to treatment, leading to the emergence of clones that are more aggressive and resistant to anti-cancer therapies. We have a limited understanding of the development of treatment resistance as we lack technologies to map the evolution of cancer under the selective pressure of treatment. To address this, we developed a hierarchical, dynamic lineage tracing method called FLARE (Following Lineage Adaptation and Resistance Evolution). We use this technique to track the progression of acute myeloid leukemia (AML) cell lines through exposure to Cytarabine (AraC), a front-line treatment in AML, in vitro and in vivo. We map distinct cellular lineages in murine and human AML cell lines predisposed to AraC persistence and/or resistance via the upregulation of cell adhesion and motility pathways. Additionally, we highlight the heritable expression of immunoproteasome 11S regulatory cap subunits as a potential mechanism aiding AML cell survival, proliferation, and immune escape in vivo. Finally, we validate the clinical relevance of these signatures in the TARGET-AML cohort, with a bisected response in blood and bone marrow. Our findings reveal a broad spectrum of resistance signatures attributed to significant cell transcriptional changes. To our knowledge, this is the first application of dynamic lineage tracing to unravel treatment response and resistance in cancer, and we expect FLARE to be a valuable tool in dissecting the evolution of resistance in a wide range of tumor types.
    DOI:  https://doi.org/10.1101/2025.02.27.640600
  20. iScience. 2025 Mar 21. 28(3): 112010
      The hierarchical organization of hematopoietic stem cells (HSCs) governing adult hematopoiesis has been extensively investigated. However, the dynamic epigenomic transition from fetal to adult hematopoiesis remains incompletely understood, particularly regarding the involvement of epigenetic factors. In this study, we investigate the roles of BRD9, an essential component of the non-canonical BAF (ncBAF) complex known to govern the fate of adult HSCs, in fetal hematopoiesis. Consistent with observations in adult hematopoiesis, BRD9 loss impairs fetal HSC stemness and disturbs erythroid maturation. Intriguingly, the impact on myeloid lineage was discrepant: BRD9 loss inhibited and promoted myeloid differentiation in fetal and adult models, respectively. Through comprehensive transcriptomic and epigenomic analysis, we elucidate the differential roles of BRD9 in a context- and lineage-dependent manner. Our data uncover how BRD9/ncBAF complex modulates transcription in a stage-specific manner, providing deeper insights into the epigenetic regulation underlying the transition from fetal to adult hematopoiesis.
    Keywords:  Cell biology; Molecular biology; Omics
    DOI:  https://doi.org/10.1016/j.isci.2025.112010
  21. Leuk Res. 2025 Mar 17. pii: S0145-2126(25)00039-6. [Epub ahead of print]152 107679
      Tyrosine kinase domain mutations (TKDMs) plays an important role in prognosis of chronic myeloid leukemia (CML). The aim of the present study was to identify the TKDMs associated with imatinib mesylate (IM) drug resistant in CML, following European leukemia Net (ELN) guidelines. Direct sequencing analysis revealed point mutations in 69.44 % (50/72), compound/ polyclonal mutations in 11.11 % (8/72) and large deletions in 4.16 % (3/72) of IM non-responder CML patients. Additionally, we have identified low level mutations in 30.55 % of warning group patients through NGS analysis, that include singly occurring point mutations (5) and polyclonal (6) mutations with mutant allele frequency ranging from 1.1 % to 14.70 %. The low-level mutations detected through NGS in warning group patients; may be responsible for suboptimal response in our study. However, follow-up studies are important to understand the mechanism of clonal evolution. We also identified 5 novel mutations that had not been reported in public databases which expands the spectrum of known mutations in BCR::ABL1 fusion gene. Our study also highlighted the impact on patient outcomes following the implementation of ELN guidelines underscores the importance of adherence to standardized protocols in clinical practice.
    Keywords:  BCR::ABL1 gene mutations; CML, ELN guidelines; Mutant allele; NGS; Warning group
    DOI:  https://doi.org/10.1016/j.leukres.2025.107679
  22. Blood. 2025 Mar 16. pii: blood.2024024956. [Epub ahead of print]
      Inherited bone marrow failure syndromes (IBMFS) are genetic disorders of impaired hematopoiesis that manifest in childhood with both cytopenias and extra-hematologic findings. While several IBMFS are categorized as ribosomopathies due to shared underlying ribosomal dysfunction, there is a broader disruption of the protein homeostasis (proteostasis) network across both classic and emerging IBMFS. Precise regulation of the proteostasis network, including mechanisms of protein synthesis, folding, trafficking, and degradation as well as associated stress response pathways, has emerged as essential for maintaining hematopoietic stem cell (HSC) function, providing new potential mechanistic insights into IBMFS pathogenesis. Furthermore, the varied clinical trajectories of patients with IBMFS with possible divergent outcomes of malignancy and spontaneous remission may reflect developmental and temporal changes in proteostasis activity and be driven by strong selective pressures to restore proteostasis. These new insights are spurring fresh therapeutic approaches to target proteostasis. Thus, further evaluation of proteostasis regulation and the consequences of proteostasis disruption in IBMFS could aid in developing new biomarkers, therapeutic agents, and preventative approaches for patients.
    DOI:  https://doi.org/10.1182/blood.2024024956
  23. EJHaem. 2025 Apr;6(2): e1097
       Introduction: Myeloproliferative neoplasms (MPNs), such as polycythaemia vera (PV), essential thrombocythemia (ET) and myelofibrosis (MF), are primarily treated by managing blood counts to reduce the thrombotic risk using cytoreductive agents. Busulphan, an oral alkylating agent, has been historically used for MPN management due to its myelosuppressive effects, but concerns about its risk of leukaemic transformation have limited its use.
    Methods: This real-world retrospective study evaluated the safety and efficacy of busulphan in 115 MPN patients across 13 UK hospitals. Responses in patients with ET and PV only were assessed using European LeukemiaNet (ELN) criteria.
    Results: With a median age of 78 years, the overall response rate was 78.1%, with 29% of PV and 18% of ET patients achieving complete responses. Dosing regimens were similarly distributed between repeated single doses of busulphan (31%), courses of treatment lasting 1-4 weeks (30%) and continuous therapy for more than 4 weeks (35%). No cases of disease progression to acute leukaemia or myelofibrosis were recorded during the median follow-up of 23 months. Adverse events were infrequent, with fatigue and cytopaenia being the most common (4% each).
    Conclusion: Busulphan demonstrated a favourable safety profile and is a viable cytoreductive option, particularly for elderly patients who are intolerant to hydroxycarbamide.
    Trial Registration: The authors have confirmed clinical trial registration is not needed for this submission.
    Keywords:  essential; myelofibrosis; myeloproliferative disease; polycythaemia vera; thrombocythaemia
    DOI:  https://doi.org/10.1002/jha2.1097
  24. Expert Rev Anticancer Ther. 2025 Mar 21.
       INTRODUCTION: Telomerase reactivation allows cancer cells to maintain telomere length and evade senescence, making it an appealing therapeutic target. Imetelstat, an antisense oligonucleotide, is the first clinically effective telomerase inhibitor approved by the FDA and the European Commission for treating anemia in transfusion-dependent low-risk myelodysplastic syndromes (MDS).
    AREAS COVERED: Sources for this review were identified through searches of PubMed, ClinicalTrials.gov and conference abstracts. This review highlights the pharmacology, efficacy and ongoing trials of imetelstat in treating MDS, myelofibrosis, essential thrombocythemia and other malignancies. In the IMerge trial, imetelstat induced durable transfusion independence in heavily transfused LR-MDS patients. Pilot trials in myelofibrosis suggest imetelstat's potential disease-modifying properties and survival benefit, warranting further studies of imetelstat as a monotherapy or in combination therapies. Imetelstat can cause thrombocytopenia, leukopenia, elevated liver enzymes, and infusion reactions, which are mostly reversible but may rarely lead to fatal events.
    EXPERT OPINION: Future clinical trials in LR-MDS should focus on optimal sequencing and combination strategies for imetelstat with other agents, and identifying biomarkers that can predict responses. Monitoring real-world outcomes will offer valuable insights into imetelstat's safety and efficacy in patient populations underrepresented in clinical trials. Imetelstat's role in other malignancies, especially myelofibrosis, is being explored.
    Keywords:  Imetelstat; myelodysplastic syndromes/neoplasms (MDS); myeloproliferative neoplasms, myelofibrosis, essential thrombocythemia, clinical trials; telomerase
    DOI:  https://doi.org/10.1080/14737140.2025.2482721
  25. Haematologica. 2025 Mar 20.
      We compared long-term outcomes in 78 patients with steroid-refractory acute graft-versushost disease (SR-aGVHD) treated at the University Medical Center Hamburg, Germany between December 2015 and August 2022 who received either ruxolitinib alone (Ruxo, n=29) or Ruxo plus extracorporeal photopheresis (Ruxo-ECP, n=49). Patients were well balanced between both arms except for SR-aGVHD grade IV which was higher in the Ruxo-ECP group (45% vs. 14%, p.
    DOI:  https://doi.org/10.3324/haematol.2024.286824
  26. Blood. 2025 Mar 16. pii: blood.2024025975. [Epub ahead of print]
      Paroxysmal nocturnal hemoglobinuria (PNH) is a non-malignant clonal hematopoietic disorder. There are two components to the pathogenesis of PNH: (i) a mutant stem cell, (ii) expansion of the mutant clone. Component (i) is straightforward: there is almost always an inactivating somatic mutation of the X-linked gene PIGA. As for (ii), different mechanisms may be involved. In rare cases expansion may be driven by independently arisen mutations (e.g. in JAK2): however, in the large majority of PNH patients such mutations are not found. Instead, clonal expansion may result from the escape of GPI-negative (PIGA mutant) stem cells from a T cell-mediated autoimmune attack on non-mutant stem cells. Several lines of evidence support this mechanism. (1) PNH is closely related to aplastic anemia (AA). (2) PIGA mutant microclones exist in normal people but they do not expand. (3) In PNH patients receiving syngeneic bone marrow transplantation PNH remission has occurred only when immunosuppressive conditioning was applied. (4) After targeted inactivation of piga in mice, large populations of GPI-negative blood cells are produced, but they gradually disappear rather than expanding. (5) There is evidence that cytotoxic T cells may spare GPI(-) stem cells, and CD1d-restricted GPI-specific T cells have been demonstrated in patients with PNH and with AA. Thus, the pathogenesis of PNH conforms to a Darwinian model within somatic cell populations: it results from a somatic mutation and from a specific selective environment. The findings in PNH are also highly relevant to the pathogenesis of AA.
    DOI:  https://doi.org/10.1182/blood.2024025975
  27. Nat Cancer. 2025 Mar 17.
      The spleen plays a critical role in the pathogenesis of leukemia. However, our understanding of the splenic niche is very limited. Herein, we report that induced expression of the secreted protein Gremlin 1 in a mouse model restrains chronic myeloid leukemia (CML) progression and synergizes with tyrosine kinase inhibitor treatment, whereas blockade of Gremlin 1 promotes CML development. Intriguingly, the effect of Gremlin 1 is most evident in the spleen but not in the bone marrow. Gremlin 1 induces apoptosis of leukemic stem cells via antagonizing the BMP pathway. Single-cell RNA sequencing and experimental validation together show that Gremlin 1 marks a unique stromal cell population in the spleens of both mice and humans. Genetic ablation of Gremlin 1+ cells leads to accelerated CML progression. Collectively, Gremlin 1 and Gremlin 1+ cells are key defensive niche components in the spleen that limit CML progression, revealing an unprecedented mechanism for the body to fight off leukemia.
    DOI:  https://doi.org/10.1038/s43018-025-00933-2
  28. Nat Cell Biol. 2025 Mar 18.
      Tyrosine kinase inhibitors (TKIs) targeting the BCR-ABL1 fusion tyrosine kinase have revolutionized the treatment of chronic myeloid leukaemia (CML). However, the development of TKI resistance and the subsequent transition from the chronic phase (CP) to blast crisis (BC) threaten patients with CML. Accumulating evidence suggests that translational control is crucial for cancer progression. Our high-throughput CRISPR-Cas9 screening identified poly(A) binding protein cytoplasmic 1 (PABPC1) as a driver for CML progression in the BC stage. PABPC1 preferentially improved the translation efficiency of multiple leukaemogenic mRNAs with long and highly structured 5' untranslated regions by forming biomolecular condensates. Inhibiting PABPC1 significantly suppressed CML cell proliferation and attenuated disease progression, with minimal effects on normal haematopoiesis. Moreover, we identified two PABPC1 inhibitors that inhibited BC progression and overcame TKI resistance in murine and human CML. Overall, our work identifies PABPC1 as a selective translation enhancing factor in CML-BC, with its genetic or pharmacological inhibition overcoming TKI resistance and suppressed BC progression.
    DOI:  https://doi.org/10.1038/s41556-024-01607-4
  29. Blood. 2025 Mar 18. pii: blood.2024027944. [Epub ahead of print]
      Tyrosine kinase inhibitors (TKIs) are the mainstay of treatment for patients with chronic myeloid leukemia (CML). The standard dose has been established for each drug according to the indication for the various stages of the disease and whether as initial therapy or after failure of prior therapies. The recommended doses are fixed for all patients and dose adjustments are mostly recommended for management of adverse events. The standard doses have been derived largely from phase 1 studies, but as we discuss in this review, the current model may not be optimal for this purpose for drugs such as TKIs that are meant to be used for extended periods of time. Subsequent studies have led to changes in the initial recommendations for some drugs. In others, experience and real-world data have led to the use of TKIs using doses and adjustments that may be different than what clinical trials have recommended. In other scenarios, available data suggests that the current standard dose may need to be revisited. It may also be time to reconsider the standard approach of starting therapy with the standard dose and adjusting merely based on adverse events. We propose a flexible model that perhaps reflects more accurately what is being done frequently in the clinic.
    DOI:  https://doi.org/10.1182/blood.2024027944