bims-tremyl 2025-11-23 papers

on Therapy resistance biology in myeloid leukemia

Issue of 2025–11–23
twenty-six papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.
Oncogenic activation of EVC/EVC2 defines a therapeutically targetable subset of acute myeloid leukemia.
Risk stratification of low-dose cytarabine and venetoclax in patients with AML ineligible for intensive chemotherapy.
An inflammatory T-cell-stromal axis contributes to hematopoietic stem/progenitor cell failure and clonal evolution in human myelodysplastic syndrome.
Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.
Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia.
PSP-0119: Targeted IRAK4 Degradation as a Novel Therapeutic Strategy for FLT3-Mutant AML.
Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells.
Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.
JAK inhibitor selection in challenging scenarios of myelofibrosis: a review.
Long-term survival outcomes of allo-HCT in AML with fludarabine/melphalan conditioning and tacrolimus/sirolimus GVHD prophylaxis.
Nilotinib versus imatinib with early switch from imatinib to nilotinib to obtain treatment-free remission in newly diagnosed chronic myeloid leukemia patients: the analysis of the first co-primary endpoint.
Genomic and transcriptomic characterization of acute myeloid leukaemia with IL3RA overexpression: Prognostic and therapeutic implications revisited.
Fancl-mutant mice reveal central role of monoubiquitination in Fanconi anemia and a model for therapeutic gene editing.
CHARM is Prognostic of Geriatric Morbidity and Toxicity after Allogeneic Transplant for Older Adults: BMT CTN 1704 Study.
NPM1-mutated acute myeloid leukemia with marked erythroid and megakaryocytic differentiation.
ET occurring in NPM1-mutated AML during molecular complete remission: A further potential evolution of a complex disease.
Human iPSCs-based modeling unveils SETBP1 as a driver of chromatin rewiring in GATA2 deficiency.
Impaired IL-10 Receptor Signaling Leads to Inflammation Induced Exhaustion in Hematopoietic Stem Cells.
Effectiveness of Gilteritinib Beyond Second-Line Therapy in Relapsed/Refractory FLT3-Mutated Acute Myeloid Leukemia: A Real-World Multicenter Study of 171 Patients.
Clonal megakaryocyte dysplasia with normal blood values: a covert, thrombosisprone, early myeloproliferative neoplasm.
Long read nanopore DNA sequencing with adaptive sampling to identify tyrosine kinase fusion genes.
Decitabine plus all-trans retinoic acid versus decitabine monotherapy for myelodysplastic syndromes with excess blasts: a multicenter, randomized controlled trial.
Clonal hematopoiesis activates pro-calcific pathways in macrophages and promotes aortic valve stenosis.
High-Dimensional Spatiotemporal Single-Cell and 3D Atlas of the Bone Marrow Microenvironment during Leukemic Progression.
Prime editing-installed suppressor tRNAs for disease-agnostic genome editing.

Cancer Discov. 2025 Nov 20.

DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.

Thomas Köhnke, Daiki Karigane, Eleanor Hilgart, Amy C Fan, Kensuke Kayamori, Masashi Miyauchi, Cailin T Collins, Fabian P Suchy, Athreya Rangavajhula, Yang Feng, Yusuke Nakauchi, Eduardo Martinez-Montes, Jonas L Fowler, Kyle M Loh, Hiromitsu Nakauchi, Michael A Koldobskiy, Andrew P Feinberg, Ravindra Majeti.

Genetic mutations are being thoroughly mapped in human cancers, yet a fundamental question in cancer biology is whether such mutations are functionally required for cancer initiation, maintenance of established cancer, or both. Here, we study this question in the context of human acute myeloid leukemia (AML), where DNMT3AR882 missense mutations often arise early, in pre-leukemic clonal hematopoiesis, and corrupt the DNA methylation landscape to initiate leukemia. We developed CRISPR-based methods to directly correct DNMT3AR882 mutations in leukemic cells obtained from patients. Surprisingly, DNMT3AR882 mutations were largely dispensable for disease maintenance. Replacing DNMT3AR882 mutants with wild-type DNMT3A did not impair the ability of AML cells to engraft in vivo, and minimally altered DNA methylation. Taken together, DNMT3AR882 mutations are initially necessary for AML initiation, but are largely dispensable for disease maintenance. The notion that initiating oncogenes differ from those that maintain cancer has important implications for cancer evolution and therapy.

DOI: https://doi.org/10.1158/2159-8290.CD-24-1604
Leukemia. 2025 Nov 17.

Oncogenic activation of EVC/EVC2 defines a therapeutically targetable subset of acute myeloid leukemia.

Pinpin Sui, Ying Li, Juyeong Hong, Caroline R Delma, Shi Chen, Juan Wang, Peng Zhang, Songmi Han, Asra Noor, Hui Yang, Yakun Pang, Yu Luan, Mingjiang Xu, Jihoon Lee, Feng-Chun Yang.

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy characterized by high incidence, poor prognosis, and marked genetic and clinical heterogeneity. This heterogeneity poses a significant challenge to effective treatment and underscores the urgent need for tailored therapeutic strategies. Here, we identified the EvC ciliary complex subunits EVC and EVC2 as aberrantly overexpressed in a subset of AMLs, particularly those harboring ASXL1 mutations or the t(8;21) translocation, with elevated expression correlating with poor patient prognosis. Functional studies demonstrated that EVC/EVC2 are essential for maintaining the leukemogenic properties of AML cells, while being dispensable for the function of normal hematopoietic stem/progenitor cells. Loss of EVC/EVC2 impairs leukemia cell proliferation, promotes differentiation, and effectively blocks AML progression in vivo. Mechanistically, we revealed that elevated EVC/EVC2 expression is associated with gained AML1-ETO occupancy or enhanced chromatin interactions at EVC/EVC2 promoter regions in AML cells carrying t(8;21) or ASXL1 mutations, respectively. Notably, we demonstrate that the leukemogenic role of EVC/EVC2 is mediated through MYC pathway activation, independent of their canonical role in Hedgehog signaling. Collectively, our findings demonstrate an oncogenic event of overexpressed EVC/EVC2, identifying novel therapeutic vulnerabilities in AML.

DOI: https://doi.org/10.1038/s41375-025-02803-3
Blood Adv. 2025 Nov 21. pii: bloodadvances.2025017083. [Epub ahead of print]

Risk stratification of low-dose cytarabine and venetoclax in patients with AML ineligible for intensive chemotherapy.

Andrew H Wei, Panayiotis Panayiotidis, Pau Montesinos, Karim Laribi, Vladimir Ivanov, Inho Kim, Jan Novak, Rebecca Champion, Walter Fiedler, Maria Pagoni, Julie Bergeron, Stephen B Ting, Jing-Zhou Hou, Takahiro Yamauchi, Jianxiang Wang, Stephen A Strickland, Michael R Savona, Tara L Lin, Anoop K Enjeti, Ing Soo Tiong, Sangmin Lee, Gail J Roboz, Relja Popovic, Qi Jiang, Zihuan Liu, Yan Sun, Wellington L Mendes, Brenda Chyla, Courtney D DiNardo.

Prognostic risk categorization aids treatment selection for patients with acute myeloid leukemia (AML). Although the European LeukemiaNet (ELN) classifications (2017, 2022) for AML have been used to stratify outcomes for patients receiving intensive chemotherapy, application to patients receiving less intensive therapy, like azacitidine plus venetoclax, has been less satisfactory. In response, a 4-gene classifier that stratifies older patients with AML unfit for intensive chemotherapy into those with higher benefit (wild type), intermediate benefit (FLT3-internal tandem duplication [ITD] or NRAS/KRAS mutation) or lower benefit (TP53 mutation) after azacitidine plus venetoclax treatment was developed. We hypothesized that this 4-gene classifier may also have prognostic utility in patients receiving low-dose cytarabine (LDAC) plus venetoclax. Surprisingly, neither the ELN 2022 criteria nor the 4-gene azacitidine-venetoclax classifier model adequately stratified prognosis in a cohort of 139 patients receiving LDAC plus venetoclax. Patients with concurrent NPM1 and FLT3-ITD/RAS variants performed surprisingly well with LDAC plus venetoclax (92% complete remission [CR]/CR with incomplete blood count recovery [CRi] rate and 29.67 months median overall survival [OS]). Data driven (sequential bootstrapping and tree based) and empirical analyses identified complex karyotype and/or presence of TP53 mutation as prognostically relevant molecular/cytogenetic risk markers. Patients with complex karyotype and/or TP53 mutation displayed poor clinical outcomes (25% CR/CRi and 3.48 months median OS). Notably, 74% of the study population lacked these poor prognostic markers and had 67% CR/CRi with 14.92 months median OS. Overall, these data support the importance of molecular sub-classification in defining treatment outcomes to venetoclax-based therapies. NCT02287233; NCT03069352.

DOI: https://doi.org/10.1182/bloodadvances.2025017083
Nat Commun. 2025 Nov 18. 16(1): 10041

An inflammatory T-cell-stromal axis contributes to hematopoietic stem/progenitor cell failure and clonal evolution in human myelodysplastic syndrome.

Lanpeng Chen, Yujie Bian, Eline Pronk, Claire van Dijk, Tim V D van Tienhoven, Remco M Hoogenboezem, Eric M Bindels, Dennis Bosch, Sadaf Fazeli, Aniek O de Graaf, Theresia M Westers, Maksim Kholmatov, Judith B Zaugg, Pedro L Moura, Eva Hellström-Lindberg, Arjan A van de Loosdrecht, Joop H Jansen, Mathijs A Sanders, Marc H G P Raaijmakers.

Myelodysplastic syndrome (MDS) is characterized by bone marrow failure, clonal evolution and leukemic progression, but the pathophysiologic processes driving these events remain incompletely understood. Here, by establishing a comprehensive single-cell transcriptional taxonomy of human MDS, we reveal that inflammatory remodeling of bone marrow stromal niches is a common early feature, irrespective of the genetic driver landscape. We identify an activated CD8-T-cell subset as a source of stromal inflammation via TNF-receptor signaling, which prompts the inflammatory rewiring and loss of repopulating ability of residual normal hematopoietic stem/progenitor cells (HSPC). Mutant HSPCs display relative resistance to this inflammatory stress and reside predominantly in a transcriptional 'high output' state, providing a biological framework to their competitive advantage in an inflammatory microenvironment. Consistent with this, stromal inflammation associates with leukemic progression and reduced survival. Our data thus support a model of immune-stromal inflammatory signaling driving tissue failure and clonal evolution in the hematopoietic system. Mechanisms of clonal evolution in myeloid neoplasms remain incompletely understood. Darwinian theory predicts that the (micro)environment of clone-propagating stem cells may contribute to clonal selection. Here, we provide data fitting this model, establishing a relationship between stromal niche inflammation, inflammatory stress in HSPCs, clonal resistance and leukemic evolution in human MDS.

DOI: https://doi.org/10.1038/s41467-025-65802-z
Cancer Res. 2025 Nov 21.

Single-Cell Lineage Tracing Uncovers Resistance Signatures and Sensitizing Strategies to FLT3 Inhibitors in Acute Myeloid Leukemia.

Johanna Eriksson, Shuyu Zheng, Mihaela Popa, Jie Bao, Jun Dai, Wenyu Wang, Emmet McCormack, Anna Vähärautio, Jing Tang.

While FLT3 inhibitors have significantly improved the treatment of aggressive FLT3-mutated acute myeloid leukemia (AML), the emergence of resistance remains as a major challenge. Here, we applied our recently developed single-cell lineage tracing method ReSisTrace to identify cells that are intrinsically resistant or sensitive to the FLT3 inhibitors midostaurin and quizartinib in AML with FLT3-ITD mutations. Comparison of the gene expression profiles of these cells revealed transcriptional resistance signatures, including upregulation of GSPT1. Depletion of GSPT1 with CRISPR-Cas9-mediated knockout resulted in increased sensitivity of AML cells to quizartinib treatment. Further, targeting GSPT1 with the small molecule CC-90009 exhibited strong synergistic effects when combined with FLT3 inhibitors in the FLT3-ITD cell lines and primary AML patient samples. In addition, in an FLT3-ITD-positive AML patient-derived xenograft (PDX) mouse model, the CC-90009 and quizartinib combination showed significantly higher anti-tumor efficacy and prolonged overall survival compared to either treatment alone. Furthermore, compounds that induced transcriptomic changes opposite to the resistance signatures prompted cells to acquire FLT3 inhibitor-sensitive states. Vistusertib (mTOR inhibitor), linsitinib (IGF1R and insulin receptor inhibitor), and meisoindigo (IGF1R and Src family kinase inhibitor), all inhibiting pathways parallel to or downstream of oncogenic FLT3 signaling, were predicted and validated to sensitize FLT3-mutated cell lines and primary cells to FLT3 inhibitors. Collectively, these findings demonstrate the ability of ReSisTrace to unveil pre-existing transcriptional features of treatment vulnerability in hematological cancers and elucidate strategies for enhancing FLT3 inhibitor treatment efficacy in FLT3-ITD-mutated AML.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-3753
Nat Commun. 2025 Nov 18. 16(1): 10042

Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia.

Karin D Prummel, Kevin Woods, Maksim Kholmatov, Eric C Schmitt, Evi P Vlachou, Mayssa Labyadh, Rebekka Wehner, Gereon Poschmann, Kai Stühler, Susann Winter, Uta Oelschlaegel, Manja Wobus, Logan S Schwartz, Pedro L Moura, Eva Hellström-Lindberg, Krishnaraj Rajalingam, Matthias Theobald, Jennifer J Trowbridge, Clémence Carron, Thierry Jaffredo, Marc Schmitz, Uwe Platzbecker, Judith B Zaugg, Borhane Guezguez.

Somatic mutations in hematopoietic stem/progenitor cells (HSPCs) can lead to clonal hematopoiesis of indeterminate potential (CHIP) and progression to myelodysplastic syndromes (MDS). Using single-cell and anatomical profiling of a large cohort of human bone marrow (BM), we show that the HSPC BM niche in CHIP and MDS is undergoing inflammatory remodeling. This includes loss of CXCL12⁺ adipogenic stromal cells and the emergence of a distinct population of inflammatory mesenchymal stromal cells (iMSCs), which arise in CHIP and become more prevalent in MDS. Functional studies in primary BM HSPC-MSC co-cultures reveals that healthy aged and CHIP HSPCs activate stromal support, while MDS HSPCs fail to do so. In contrast, MDS blasts further suppress HSPC support and trigger inflammation, indicating disease-stage-specific stromal disruption. In parallel, we show that iMSCs retain partial support and angiogenic potential in MDS, coinciding with expanded BM vasculature. Additionally, we identify IFN-responsive T cells that preferentially interact with iMSCs, potentially reinforcing local inflammation. These findings position iMSCs as central mediators of early BM niche dysfunction and potential therapeutic targets for intercepting pre-malignant hematopoiesis.

DOI: https://doi.org/10.1038/s41467-025-65803-y
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679569. [Epub ahead of print]

PSP-0119: Targeted IRAK4 Degradation as a Novel Therapeutic Strategy for FLT3-Mutant AML.

Negar Khazan, Cameron Wa Snyder, Chandhana Ravi, Elizabeth Lamere, Niloy A Singh, Manoj K Khera, Jane Liesveld, Srinivasan Ekambaram, Nikolay V Dokholyan, Myla Strawderman, Kyu Kwang Kim, Rachael Rowswell-Turner, Michael W Becker, Richard G Moore, Rakesh K Singh.

Acute Myeloid Leukemia (AML) is a life-threatening hematologic malignancy. Despite recent therapeutic advances, rising incidence rates emphasize the urgent need for identification of new targets and therapies. Roles of interleukin receptor-associated kinases IRAK1/4 are emerging in hematologic and solid malignancies. In AML, IRAK4 mRNA is overexpressed at diagnosis, relapses, in residual disease, and in FLT3-ITD-mutant cells, MDS, MPN, and MDS/MPN-negative subtypes. Compared with hematopoietic stem cells, IRAK4 is elevated in t(15;17), inv(16)/t(16;16), and t(11q23)/MLL subtypes, correlating with poor survival. Here, we disclose anti-AML activity of PSP-0119, a novel IRAK4 PROTAC degrader. PSP-0119, inhibited IRAK4 kinase activity, NF-κβ activity, and IL-1β-induced IRAK4 phosphorylation. In-silico docking revealed interactions in CRBN/IRAK4/PSP-0119 ternary complex. PSP-0119 degraded IRAK4 in FLT3-mutant AML cell lines sparing FLT3-wild-type AML cells, FLT3-wild-type patient samples, and normal bone-marrow. Bulk-seq of PSP-0119 treated MOLM-13 cells revealed downregulation of eNOS, a poor AML prognosticator. PSP-0119 suppressed colony formation, cell viability, and MOLM-13 xenograft growth, and synergized with IRAK1 covalent inhibitor JH-X-119-01. PSP-0119 is metabolically stable, retaining 71% of parent compound at 60 minutes in human liver microsomes. In summary, IRAK4 degradation via PSP-0119 as a promising therapeutic strategy for treatment of FLT3-mutant AML.

DOI: https://doi.org/10.1101/2025.09.30.679569
Nat Cell Biol. 2025 Nov 18.

Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells.

Lucrezia Della Volpe, Andrew J Lee, Mateusz Antoszewski, Amy A Deik, Ksenia R Safina, Teng Gao, Chun-Jie Guo, Tianyi Ye, Peng Lyu, Jorge D Martin-Rufino, Nicole Castano, Jonathan Good, Yaniris Molina-Aponte, Jiawei Zhao, Clary B Clish, Peter van Galen, Vijay G Sankaran.

Improved ex vivo expansion of human haematopoietic stem cells (HSCs) would considerably advance transplantation and genome-engineered therapies, yet existing culture methods still allow substantial HSC loss. Here we show that this attrition is driven largely by ferroptosis, a metabolically regulated, iron-dependent cell-death pathway, and that it can be blocked to augment HSC expansion. Inhibiting ferroptosis with liproxstatin-1 or ferrostatin-1 markedly increases the expansion of cord blood and adult HSCs consistently across donors in both widely used serum-free cultures and recently reported chemically defined conditions. The expanded cells retain phenotypic and molecular stem cell identity and mediate improved durable, multilineage engraftment in xenotransplanted mice without genotoxicity or aberrant haematopoiesis. Mechanistically, ferroptosis blockade is accompanied by upregulated ribosome biogenesis and cholesterol synthesis, increasing levels of 7-dehydrocholesterol-a potent endogenous ferroptosis inhibitor that itself promotes HSC expansion. Crucially, this approach enhances yields of therapeutically genome-modified HSCs, paving a path for clinical applications.

DOI: https://doi.org/10.1038/s41556-025-01814-7
Cell. 2025 Nov 19. pii: S0092-8674(25)01233-4. [Epub ahead of print]

Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.

Alexander C Lewis, Emily Gruber, Rheana Franich, Jessica Armstrong, Madison J Kelly, Carlos M Opazo, Yau C Low, Léa Flippe, Kevin Wijanarko, Caitlin L Rowe, Celeste H Mawal, Alexandra Birrell, Joan So, Srimayee Vaidyanathan, Keziah Ting, Liana N Semcesen, Karena Last, Ching-Seng Ang, Giovanna Pomilio, Fiona C Brown, Andrew H Wei, Jason A Powell, Elizabeth S Ng, Ann E Frazier, Kate McArthur, Najoua Lalaoui, David A Stroud, Kristin K Brown, Ricky W Johnstone, Lev M Kats.

  The ubiquitous metabolite heme has diverse enzymatic and signaling functions in most mammalian cells. Through integrated analyses of mouse models, human cell lines, and primary patient samples, we identify de novo heme biosynthesis as a selective dependency in acute myeloid leukemia (AML). The dependency is underpinned by a propensity of AML cells, and especially leukemic stem cells (LSCs), to downregulate heme biosynthesis enzymes (HBEs), which promotes their self-renewal. Inhibition of HBEs causes the collapse of mitochondrial Complex IV and dysregulates the copper-chaperone system, inducing cuproptosis, a form of programmed cell death brought about by the oligomerization of lipoylated proteins by copper. Moreover, we identify pathways that are synthetic lethal with heme biosynthesis, including glycolysis, which can be leveraged for combination strategies. Altogether, our work uncovers a heme rheostat that is connected to gene expression and drug sensitivity in AML and implicates HBE inhibition as a trigger of cuproptosis.

Keywords:  acute myeloid leukemia; cuproptosis; heme biosynthesis; metabolic vulnerability; metabolism; mitochondrial Complex IV

DOI:  https://doi.org/10.1016/j.cell.2025.10.028
Haematologica. 2025 Nov 20.

JAK inhibitor selection in challenging scenarios of myelofibrosis: a review.

Pankit Vachhani, Ruben Mesa, John Mascarenhas, Raajit Rampal, Stephen T Oh, Alessandro Maria Vannucchi, Maria Laura Fox, Francesca Palandri, Francesco Passamonti, Jean-Jacques Kiladjian, Mahshid Azimi, Claire Harrison, Prithviraj Bose.

Myelofibrosis is a progressive myeloproliferative neoplasm characterized by dysregulated Janus kinase (JAK)/signal transducer and activator of transcription signaling. Common clinical manifestations include constitutional symptoms, splenomegaly, and anemia, which can significantly impact quality of life and survival. Although hematopoietic stem cell transplant is the only curative treatment modality in myelofibrosis, JAK inhibitors have transformed management by providing symptom relief and reducing spleen size in many patients; newer JAK inhibitors also offer anemia-related benefits. A total of four JAK inhibitors-ruxolitinib, fedratinib, pacritinib, and momelotinib-are now available for the treatment of myelofibrosis, each with distinct profiles and safety considerations that may inform selection. However, head-to-head trial comparisons are limited, and real-world experience with most of these JAK inhibitors is only just emerging; therefore, first-line selection and optimal sequencing in particular patients can be challenging. This review summarizes the current data surrounding available JAK inhibitors for the treatment of patients with myelofibrosis and examines how individual patient characteristics can help guide selection among them. To illustrate the diverse clinical factors and key considerations associated with JAK inhibitor selection in practice, we discuss these data in the context of four hypothetical patient cases representing possible real-world scenarios, offering treatment recommendations based on our collective expertise in the field. As the myelofibrosis therapeutic landscape continues to evolve, a thorough understanding of the strengths and limitations of each JAK inhibitor relative to a given patient's presentation will support individualized treatment decisions for optimal long-term outcomes.

DOI: https://doi.org/10.3324/haematol.2025.288654
Bone Marrow Transplant. 2025 Nov 18.

Long-term survival outcomes of allo-HCT in AML with fludarabine/melphalan conditioning and tacrolimus/sirolimus GVHD prophylaxis.

Amandeep Salhotra, Dongyun Yang, Monzr M Al Malki, Sally Mokhtari, Diana Knobler, Vaibhav Agarwal, Karamjeet Sandhu, Gabriel Park, Ahmed Aribi, Haris Ali, Ibrahim Aldoss, Salman Otoukesh, Shukaib Arslan, Brian Ball, Paul Koller, Idoroenyi Amanam, Hoda Pourhassan, Amanda Blackmon, Pamela Becker, Vinod Pullarkat, Andrew S Artz, Eileen Smith, Guido Marcucci, Stephen Forman, Anthony Stein, Ryotaro Nakamura.

Allogeneic hematopoietic cell transplantation (allo-HCT) is increasingly offered as a consolidation strategy for older/infirm patients with acute myeloid leukemia (AML). Fludarabine/melphalan (Flu/Mel) conditioning is associated with effective disease control but results in significant toxicity and non-relapse mortality (NRM) when combined with calcineurin-inhibitors plus methotrexate or mycophenolate mofetil. Flu/Mel with alternative graft-versus-host disease (GVHD) prophylaxis may be better tolerated and result in superior outcomes in patients with AML. In this single-center retrospective analysis, we analyzed long-term outcomes of patients with AML (n = 342) who underwent allo-HCT with Flu/Mel conditioning and tacrolimus/sirolimus (Tac/Sir)-based GVHD prophylaxis from 2008-2019 at City of Hope. Patient median age was 63 years (range: 23-78), with 37% having high-very high Disease Risk Index (DRI) and 42% with HCT-Comorbidity Index (CI) ≥ 3. Five-year overall survival (OS: primary objective) was 55% (95% CI: 49-61%) among all patients and 70% (95% CI: 55-81%) in patients ≥70 years old. Only presence of active disease correlated with lower 5-year OS on multivariate analysis (HR = 1.95; p < .001). Five-year NRM was 24% (95% CI: 19-29%) among all patients and 21% (95% CI: 11-34%) in those ≥70 years old. In conclusion, Flu/Mel conditioning with Tac/Sir GVHD prophylaxis is associated with favorable OS and acceptable NRM, even in older/infirm patients with AML.

DOI: https://doi.org/10.1038/s41409-025-02738-4
Leukemia. 2025 Nov 18.

Nilotinib versus imatinib with early switch from imatinib to nilotinib to obtain treatment-free remission in newly diagnosed chronic myeloid leukemia patients: the analysis of the first co-primary endpoint.

Fausto Castagnetti, Massimo Breccia, Elisabetta Abruzzese, Renato Bassan, Gianni Binotto, Massimiliano Bonifacio, Giovanni Caocci, Isabella Capodanno, Francesco Cavazzini, Giuseppe Cimino, Paola Fazi, Antonella Gozzini, Alessandra Iurlo, Jeroen J W M Janssen, Monia Lunghi, Roberto Marasca, Bruno Martino, Monica Messina, Francesco Muriano, Francesca Paoloni, Alfonso Piciocchi, Gianantonio Rosti, Antonella Russo Rossi, Giuseppe Saglio, Simona Sica, Simona Soverini, Agostino Tafuri, Daniele Vallisa, Peter E Westerweel, Fabrizio Pane.

Treatment-free remission is one of the most important goals of CML treatment but so far, the best treatment to reach this aim is still undefined, even though it is widely accepted that a sustained DMR is the prerequisite to discontinue TKI. Here we report on the depth of the molecular response, the first co-primary end point of the SUSTRENIM study, in a cohort of newly diagnosed CP-CML patients randomized 1:1 to be treated with nilotinib or with imatinib followed by switching to nilotinib in absence of optimal response. Of the 448 enrolled patients, 228 and 220 were randomized to the nilotinib (NIL) and imatinib (IM) arms, respectively, and followed for a median of 45.9 months. Eighty-two (37.2%) of the 220 patients on the IMarm did not fulfill the ELN criteria for optimal response of treatment and switched to nilotinib therapy. At the 24 months of follow-up, 107 of the 448 patients reached an MR4.5 response with a significantly higher frequency within the patients on the nilotinib arm (65 vs 42; p = 0.02). The analysis of the first primary endpoint indicates that, despite the early switch in the IM-randomized patients, NIL therapy is more effective to induce DMR.

DOI: https://doi.org/10.1038/s41375-025-02796-z
Br J Haematol. 2025 Nov 18.

Genomic and transcriptomic characterization of acute myeloid leukaemia with IL3RA overexpression: Prognostic and therapeutic implications revisited.

Chi-Yuan Yao, Chia-Lang Hsu, Yi-Tsung Yang, Feng-Ming Tien, Chien-Chin Lin, Yu-Hung Wang, Xavier Cheng-Hong Tsai, Wan-Hsuan Lee, Jia-Hua Liu, Yueh-Chwen Hsu, Chein-Jun Kao, Yen-Ling Peng, Yong-Huai Yi, Li-Tan Yang, Cheng-Chang Chen, Hsin-An Hou, Hwei-Fang Tien, Wen-Chien Chou.

  CD123 (encoded by IL3RA) is intricately linked to the maintenance of haematopoietic progenitors. In acute myeloid leukaemia (AML), as CD123 is overexpressed on the leukaemic stem cells (LSC), several CD123-directed therapies are currently undergoing active clinical evaluation. However, a major gap remains in understanding which AML genetic subgroups would benefit most from interventions targeting CD123 in the context of the contemporary International Consensus Classification (ICC). Therefore, in this study, we first demonstrated the strong correlation between IL3RA mRNA and CD123 protein levels and then characterized IL3RA expression patterns across various molecularly defined subgroups within the ICC framework. We discovered that IL3RA was particularly overexpressed in AML with FUS::ERG, CBFB::MYH11, high-risk KMT2A fusions, NPM1 mutations and DEK::NUP214. Patients with IL3RA overexpression exhibited significantly worse overall and event-free survivals, which could be externally validated. Biologically, IL3RA-high AML was characterized by upregulated HOX family genes as well as LSC and IL-3 signalling transcriptional programmes. Pharmaco-transcriptomic analysis revealed that IL3RA-high AML exhibited selective sensitivity to venetoclax and sapanisertib, suggesting potential synergistic opportunities. In conclusion, IL3RA overexpression defines a clinically and biologically distinct subgroup of AML, with unique therapeutic vulnerabilities. Continued research efforts are warranted to integrate CD123-directed therapies into the upfront AML treatment paradigm.

Keywords:   IL3RA ; acute myeloid leukaemia; gene expression profiling; leukaemic stem cell; targeted therapy

DOI:  https://doi.org/10.1111/bjh.70252
Blood Adv. 2025 Nov 19. pii: bloodadvances.2025017217. [Epub ahead of print]

Fancl-mutant mice reveal central role of monoubiquitination in Fanconi anemia and a model for therapeutic gene editing.

Lu Liu, Astrid Glaser, Abdulsalam I Isiaku, Kirsten Fairfax, Debora A Casolari, Angelina Ristovski, Vincent J Murphy, Sylvie van Twest, Sarah S Henrikus, Jacki Heraud-Farlow, Elissah Granger, Stevan Novakovic, Sophie F Monks O'Byrne, Vanessa Tsui, Rachel Conyers, Thomas J Gonda, Wayne Crismani, Richard J D'Andrea, Jörg Heierhorst, Andrew J Deans.

Fanconi anemia (FA) is a rare genetic disorder causing progressive loss of hematopoietic stem cells (HSCs) and bone marrow failure. Most cases result from deficient monoubiquitination of FANCD2 by the FA core complex. However, as additional functions for the complex have been proposed, it remains unclear whether loss of FANCD2 monoubiquitination is the sole cause of all FA phenotypes. Here, we generated a murine allele (FanclTAT∆) that mimics a FA patient allele. This 3bp deletion removes a catalytic cysteine in the RING E3 ligase domain of the FANCL subunit. Biochemical assays show that the mutant FA core complex retains structural integrity but lacks FANCD2 monoubiquitination activity. Homozygous FanclTAT∆/TAT∆ mice phenocopy classical human FA features, including infertility, craniofacial anomalies, DNA damage hypersensitivity, and progressive HSC loss with age. Correcting the mutation using CRISPR-Cas9 or Prime editing technology restores FANCD2 monoubiquitination and normal DNA damage resistance in myeloid cells. Collectively, our mouse model demonstrates that loss of RING E3 ubiquitin ligase activity of the FA core complex explains developmental defects and hematopoietic failure in FA, and provides a new animal model for testing potentially therapeutic gene editing.

DOI: https://doi.org/10.1182/bloodadvances.2025017217
Blood Adv. 2025 Nov 21. pii: bloodadvances.2025018340. [Epub ahead of print]

CHARM is Prognostic of Geriatric Morbidity and Toxicity after Allogeneic Transplant for Older Adults: BMT CTN 1704 Study.

Andrew S Artz, Brent R Logan, Wael Saber, Nancy Geller, Anna Bellach, Jianqun Kou, William A Wood, John McCarty, Thomas G Knight, Lyndsey Runaas, Laura Johnston, Jeremy D Walston, Ryotaro Nakamura, Asmita Mishra, Joseph Uberti, Parastoo B Dahi, Jennifer N Saultz, Shannon R McCurdy, Lawrence E Morris, Philip Imus, William J Hogan, Kalyan V Nadiminti, Vijayaraj R Bhatt, Rebecca L Olin, Joseph E Maakaron, Ronald M Sobecks, Sarah A Wall, Deborah Mattila, Bailey Protz, Steven M Devine, Mary M Horowitz, Mohamed L Sorror.

Despite concerns about the toxicity of allogeneic hematopoietic cell transplantation (alloHCT) in older patients, prospective data are limited characterizing prevalence or risk-stratification for geriatric morbidity such as disability or frailty. We prospectively assessed the prognostic impact of the novel composite health assessment risk model (CHARM), a score established to predict 1-year non-relapse mortality (NRM), among 1105 patients aged ≥60 years enrolled on the Bone Marrow Transplant-Clinical Trials Network Study 1704. Secondary endpoints were assessed post-alloHCT at day (D) 100, 180 and 365 in multivariable models adjusted with predetermined clinical variables. Among alloHCT survivors, the prevalence of disability by instrumental activities of daily living (IADL), frailty by the Physical Frailty Phenotype and physical function impairment by PROMIS was highest at D100, and lower D180 and D365. Higher CHARM scores were independently associated with greater IADL disability [coefficient=-0.64, 95% confidence interval (CI): -0.85 to -0.43, p<0.001], increased frailty (coefficient=0.19, CI: 0.081 to 0.31, p<0.001), worse PROMIS physical function, greater PROMIS depression, increased serious organ toxicity by D100, more cognitive decline at D100, higher mortality after acute GVHD but not significantly associated with PROMIS anxiety or acute GVHD. Higher CHARM score predicted for worse disability-free survival (OR = 2.03, CI: 1.66 - 2.48, p<0.001) and lower frailty-free survival (OR =2.00, CI: 1.61 - 2.49). In summary, CHARM is an independent prognostic scoring system not only for NRM, but also for geriatric morbidity and functional limitation-free survival through 1-year after alloHCT. Pre-alloHCT CHARM is a novel tool to aid shared decision-making for older patients. NCT03992352.

DOI: https://doi.org/10.1182/bloodadvances.2025018340
Blood. 2025 Nov 20. 146(21): 2612

NPM1-mutated acute myeloid leukemia with marked erythroid and megakaryocytic differentiation.

Xenia Parisi, Sanam Loghavi.

DOI: https://doi.org/10.1182/blood.2025030468
Br J Haematol. 2025 Nov;207(5): 2153-2157

ET occurring in NPM1-mutated AML during molecular complete remission: A further potential evolution of a complex disease.

Diego Bertoli, Carlotta Giupponi, Giuseppe Rossi, Mariella D'Adda, Valeria Cancelli, Chiara Cattaneo, Lorenzo Masina, Beatrice De Marco, Annalisa Peli, Giorgio Biasiotto, Alessandra Tucci, Erika Borlenghi.

  Nucleophosmin 1 (NPM1)mut acute myeloid leukaemia (AML) patients may experience different disease evolutions after achieving complete remission. Essential thrombocythaemia (ET) may arise in ≈3% of NPM1mutAML patients achieving molecular remission after treatment. The presence of JAK2V617F mutation within the persisting clonal haematopoietic background of NPM1mutAML favours the development of ET among other myeloid malignancies during NPM1wtAML remission.

Keywords:  leukaemia markers; molecular diagnostics; myeloid leukaemia

DOI:  https://doi.org/10.1111/bjh.70076
Nat Commun. 2025 Nov 17. 16(1): 10035

Human iPSCs-based modeling unveils SETBP1 as a driver of chromatin rewiring in GATA2 deficiency.

Joan Pera, Damia Romero-Moya, Eric Torralba-Sales, Rebecca Andersson, Violeta García-Hernández, Maria Magallon-Mosella, Maximiliano Distefano, Clara Berenguer Balaguer, Julio Castaño, Francesca De Giorgio, Zhichao Qiu, Arnau Iglesias, Paulina Spurk, Sara Montserrat-Vazquez, Lorenzo Pasquali, Zhuobin Liang, Albert Català, M Carolina Florian, Marcin W Wlodarski, Anna Bigas, Oskar Marin-Bejar, Alessandra Giorgetti.

Patients with GATA2 deficiency are predisposed to developing myelodysplastic neoplasms (MDS), which can progress to acute myeloid leukemia. This progression is often associated with cytogenetic and somatic alterations. Mutations in SETBP1 and ASXL1 genes are recurrently observed in GATA2 patients, although their roles remain poorly understood. Here we develop a hiPSC-based system to investigate the impact of SETBP1 and ASXL1 mutations in GATA2 deficiency. Using precise genome editing, we recreate stepwise mutational trajectories observed in GATA2-related MDS. We demonstrate that GATA2 mutation has limited impact on hematopoietic progenitors, while the co-occurrence of SETBP1 or ASXL1 mutations impairs myeloid differentiation. The combination of all three mutations severely depletes myeloid progenitors, recapitulating GATA2-related MDS and highlighting their synergistic interplay. Notably, SETBP1 mutation plays a dominant role in establishing a stable chromatin accessibility landscape, even when co-occurring with ASXL1. Our study establishes an iPSC-based model of GATA2 deficiency, offering new insights into myeloid disease progression and a platform for testing future therapeutic strategies.

DOI: https://doi.org/10.1038/s41467-025-65806-9
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679613. [Epub ahead of print]

Impaired IL-10 Receptor Signaling Leads to Inflammation Induced Exhaustion in Hematopoietic Stem Cells.

William Lucas Wadley, Helen Huang, Hew Yeng Lai, Jianhong Heidmann, Jane Chen, Eli Soyfer, Kalei Guillermo, Eshika Arora, Lauren Chen, Brianna Hoover, Angela Fleischman.

Hematopoietic stem cells require tight regulation to rapidly initiate emergency hematopoiesis in response to pathogens, but chronic activation leads to proliferation induced exhaustion. Timely reentry into quiescence after inflammatory stimuli is essential for long term sustained HSC maintenance. We identify IL-10R signaling, an established negative feedback regulator in mature myeloid cells, as critical for returning HSCs to quiescence. IL-10R blockade prolongs HSC cycling and sustains activated transcriptional programs after acute inflammation. With chronic exposure, blockade increases cumulative divisions and accelerates aging hallmarks, including myeloid bias, loss of polarity, and functional defects, under conditions that do not otherwise exhaust HSCs when IL-10R signaling is intact. Jak2 V617F mutant HSCs resist the aging acceleration induced by blockade. Consistent with this resistance, IL-10R blocking antibody promotes Jak2 V617F clonal expansion and augments the myeloproliferative neoplasm phenotype. Together, these findings identify IL-10R signaling as a key coordinator of post inflammatory return to quiescence and suggest that modulating this axis could preserve HSCs and shape clonal hematopoiesis.
Summary: Wadley et al. show that IL-10 receptor signaling restrains inflammation-induced hematopoietic stem cell cycling and exhaustion; its blockade prolongs cycling, accelerates aging-related decline, and selectively favors Jak2 V617F mutant HSCs, establishing IL-10 signaling as a critical regulator of inflammatory HSC exhaustion and malignant clonal evolution.

DOI: https://doi.org/10.1101/2025.09.30.679613
Am J Hematol. 2025 Nov 22.

Effectiveness of Gilteritinib Beyond Second-Line Therapy in Relapsed/Refractory FLT3-Mutated Acute Myeloid Leukemia: A Real-World Multicenter Study of 171 Patients.

Matteo Molica, Gema Miralles, Richard Dillon, Mario Annunziata, Faisal Basheer, Juan M Bergua, Ferran Vall-Llovera Calmet, Victoria Campbell, Denis Cetin, Gaetano Cimino, Giulia Ciotti, Andrea Corbingi, Laura De Fazio, Hasim Atakan Erol, Vincenzo Federico, Cristina Gil, Yasa Mutlu Gulu, Amaia Balerdi Malcorra, Sabrina Mariani, Carla Mazzone, Antonino Mulè, Gerardo Musuraca, Anjum Khan, Mariana Norata, Jenny O'Nions, Fanny Erika Palumbo, Cristina Papayannidis, Anna Lina Piccioni, Maria Teresa Olave Rubio, Jackeline Sanchez-Tovar, Istemi Serin, Alessandra Serrao, Omur Gokmen Sevindik, Giuseppe Sucato, Marina Aurora Urbano, Calogero Vetro, Susana Vives, Marco Rossi, Maria Paola Martelli, Pau Montesinos, Jad Othman, Salvatore Perrone.

  Gilteritinib is a selective FLT3 inhibitor approved for the treatment of relapsed or refractory (R/R) FLT3-mutated acute myeloid leukemia (AML) following ≥ 1 prior line of therapy. However, data on its effectiveness in later-line settings is limited. We conducted a multicenter, retrospective study including 171 adult patients with R/R FLT3-mutated AML who received gilteritinib as third-line or beyond between August 2017 and March 2024 across centers in Italy, Spain, the United Kingdom, and Turkey. The primary endpoint was overall survival (OS). Secondary endpoints included overall response rate (ORR), composite complete remission (cCR), duration of response. Among the 171 patients, 84% carried FLT3-ITD mutations and 26% had received ≥ 3 prior lines of therapy. The cCR rate was 28%, and ORR was 47%. Patients who were younger and presented with relapsed (vs. refractory) disease had better outcomes. Prior exposure to venetoclax or allogeneic hematopoietic stem cell transplantation (HSCT) was associated with inferior response. Gilteritinib enabled HSCT in 12% of patients. Median OS was 7.1 months (95% CI, 5.9-10.1), and in Cox-regression analysis was significantly improved among responders and those who underwent HSCT (median OS: 21.5 months; 95% CI, 12.8-NR). Prior venetoclax exposure was associated with shorter survival (5.7 months; 95% CI, 5.1-8.8). On multivariate analysis, previous exposure to venetoclax and FLT3 inhibitors was the strongest predictor of reduced response rates. Despite heavy pretreatment, gilteritinib retained clinically relevant activity in later-line R/R FLT3-mutated AML. Its use beyond second-line may serve as a bridge to HSCT in selected patients. Resistance mechanisms, particularly following venetoclax, remain a therapeutic challenge. These data support the continued use of gilteritinib beyond second-line and highlight the need for prospective studies to optimize sequencing strategies.

Keywords:  AML; FLT3 mutation; gilteritinib; hematopoietic stem cell transplantation; real‐world evidence; third‐line therapy

DOI:  https://doi.org/10.1002/ajh.70142
Haematologica. 2025 Nov 20.

Clonal megakaryocyte dysplasia with normal blood values: a covert, thrombosisprone, early myeloproliferative neoplasm.

Giovanni Barosi, Vittorio Rosti, Rita Campanelli, Margherita Massa, Carlotta Abbà, Adriana Carolei, Paolo Catarsi, Alessandro Inzoli, Lorena Pergola, Tiziano Barbui, Caterina Tatarelli, Maria Chiara Finazzi, Annalisa Condorelli, Silvia Salmoiraghi, Alessandro Rambaldi, Andrea Gianatti, Valerio De Stefano, Anna Gallì, Martina Gandossini, Michela Bardelli, Robert Peter Gale, Luca Malcovati.

To improve our knowledge on the epidemiological, clinical and pathobiological profile of clonal megakaryocyte dysplasia with normal blood values (CMD-NBV), a BCR::ABLnegative myeloproliferative neoplasms (MPNs) clinical variant, we here report a series of 30 consecutive subjects with CMD-NBV. Sixteen subjects were men and the median age was 48 years (IQR, 39-53 years). A situation-driven diagnosis (70% of cases had the diagnosis triggered by an incidental or symptomatic venous or arterial thrombosis), high incidence of thrombotic events (6.5 events x 100 subject-years), and indolent disease (the 10-year CMD-NBV specific survival was 100%) were common. Nineteen subjects had a high BMI at diagnosis and 14 had ≥ 1 Charlson co-morbidities. In 21 the driver variant was JAK2V617F with a median variant allele frequency at diagnosis of 8.9% (IQR, 5.4- 18.4%). Six of 24 (25%) subjects with data on next generation sequencing (NGS) for myeloid neoplasm-related genes had ≥ 1 pathogenic somatic variant in ASXL1, TET2, DNMT3A or SRSF2, a frequency in the lower range of values of chronic MPNs. Twelve putative germline, non-pathogenic, missense variants in ASXL1, TET2, DNMT3A, RUNX1, CUX1, ABL1, NF1, KIT and CSF3R or 5' UTR in NF1 and 3' UTR in ASXL1 were detected in 10 of 24 (42%) subjects. These data further support identification of CMD-NBV as a distinct entity.

DOI: https://doi.org/10.3324/haematol.2025.288681
Leukemia. 2025 Nov 18.

Long read nanopore DNA sequencing with adaptive sampling to identify tyrosine kinase fusion genes.

Matthew Salmon, Nicole Naumann, Jenny Rinke, Manja Meggendorfer, Deepti Radia, Mark Pomfret, Thomas Ernst, Andreas Hochhaus, Andreas Reiter, William J Tapper, Helen White, Nicholas C P Cross.

Diverse haematological neoplasms are driven by tyrosine kinase (TK) fusion genes formed by recurrent or non-recurrent genomic rearrangements. The resulting chimeric proteins often present excellent targets for treatment with kinase inhibitors, and the fusion transcripts or genomic junctions can be used as specific targets for molecular monitoring. Whilst the TK genes involved are generally well characterised (e.g. ABL1, PDGFRA, FGFR1), the fusion partners are very diverse, presenting a challenge for detection and characterisation of these structural variants (SV) using current diagnostic methods. We assessed the ability of targeted nanopore sequencing using adaptive sampling to detect fusion genes in myeloid neoplasms. We sequenced genomic DNA from patients (n = 20) with a known or suspected TK gene fusion and identified rearrangements in 18 cases, including all cases with a known TK fusion, typical and atypical BCR::ABL1 rearrangements, an 843Kb deletion causing a FIP1L1::PDGFRA fusion, novel AGAP2::PDGFRB and NFIA::PDGFRB fusions, and a complex CCDC88C::PDGFRB rearrangement with multiple translocation events. The approach was fast (<72 h/sample from DNA to result), flexible with minimal hands-on laboratory time, and provided accurate, patient-specific characterisation of genomic breakpoints.

DOI: https://doi.org/10.1038/s41375-025-02801-5
Haematologica. 2025 Nov 20.

Decitabine plus all-trans retinoic acid versus decitabine monotherapy for myelodysplastic syndromes with excess blasts: a multicenter, randomized controlled trial.

Xinping Zhou, Yanjuan Lin, Yan Gao, Zheng Ge, Li Huang, Jin Zhang, Hai Cheng, Guifang Ouyang, Fanjun Meng, Yulu Tian, Yuemin Kuang, Fengping Zhou, Lixia Sheng, Weimei Jin, Gaixiang Xu, Liya Ma, Li Ye, Chen Mei, Jian Li, Jie Jin, Hongyan Tong.

Despite standard treatment with hypomethylating agents, the prognosis of patients with higher-risk myelodysplastic syndrome (MDS) remains poor. All-trans retinoic acid (ATRA) has demonstrated promising efficacy in unfit patients with acute myeloid leukemia. This multicenter controlled trial randomized (1:1) untreated patients with MDS with excess blasts (MDS-EB) to ATRA plus decitabine (ATRA at 25 mg/m2/day in 2 divided daily doses throughout the 28-day cycle plus decitabine at 20 mg/m2 on days 1-5) or decitabine alone (20 mg/m2 on days 1-5). The primary endpoint was the overall response rate within 4 treatment cycles. A total of 227 patients were randomized. Four patients who did not commence therapy were excluded from the modified intention-to-treat (mITT) analysis. The median patient age was 62 years (range: 19-81). The overall response rate was 78% (86/110) in the ATRA group versus 51% (58/113) in the decitabine group (odds ratio [OR] 3.40; 95% confidence interval [CI] 1.90-6.09; p.

DOI: https://doi.org/10.3324/haematol.2025.288526
J Clin Invest. 2025 Nov 18. pii: e171634. [Epub ahead of print]

Clonal hematopoiesis activates pro-calcific pathways in macrophages and promotes aortic valve stenosis.

Wesley T Abplanalp, Michael A Raddatz, Bianca Schuhmacher, Silvia Mas-Peiro, María A Zuriaga, Nuria Matesanz, José J Fuster, Yash Pershad, Caitlyn Vlasschaert, Alexander J Silver, Eric H Farber-Eger, Yaomin Xu, Quinn S Wells, Delara Shahidi, Sameen Fatima, Xiao Yang, Adwitiya Ap Boruah, Akshay Ware, Maximilian Merten, Moritz von Scheidt, David John, Mariana Shumliakivska, Marion Muhly-Reinholz, Mariuca Vasa-Nicotera, Stefan Guenter, Michael R Savona, Brian R Lindman, Stefanie Dimmeler, Alexander G Bick, Andreas M Zeiher.

  Clonal hematopoiesis due to TET2-driver mutations (CH) is associated with coronary heart disease and worse prognosis among patients with aortic valve stenosis (AVS). However, it is unknown what role CH plays in the pathogenesis of AVS. In a meta-analysis of All Of Us, BioVU, and the UK Biobank, patients with CHIP exhibited an increased risk of AVS, with a higher risk among patients with TET2 or ASXL1 mutations. Single-cell RNA-sequencing of immune cells from AVS patients harboring TET2 CH-driver mutations revealed monocytes with heightened pro-inflammatory signatures and increased expression of pro-calcific paracrine signaling factors, most notably Oncostatin M (OSM). Secreted factors from TET2-silenced macrophages increased in vitro calcium deposition by mesenchymal cells, which was ablated by OSM silencing. Atheroprone Ldlr-/- mice receiving CH-mimicking Tet2-/- bone marrow transplants displayed greater calcium deposition in aortic valves. Together, these results demonstrate that monocytes with CH promote aortic valve calcification, and that patients with CH are at increased risk of AVS.

Keywords:  Aging; Cardiology; Cardiovascular disease; Inflammation; Monocytes

DOI:  https://doi.org/10.1172/JCI171634
bioRxiv. 2025 Sep 29. pii: 2025.09.27.678113. [Epub ahead of print]

High-Dimensional Spatiotemporal Single-Cell and 3D Atlas of the Bone Marrow Microenvironment during Leukemic Progression.

Lanzhu Li, Isabelle Rottmann, Geoff Ivison, Huan Wei, Jan C Schroeder, Gina Dunkel, Yury Goltsev, Garry P Nolan, Aaron T Mayer, Borhan R Saeed, Bettina Weigelin, Christian M Schürch.

  The bone marrow microenvironment (BMME) is essential for hematopoiesis and immunity, yet spatiotemporal single-cell analysis during leukemogenesis remains challenging. We characterized the BMME in femurs from wild-type and chronic myeloid leukemia (CML) mice at 7, 14 and 21 days post-induction by highly multiplexed and 3D microscopy. Using a 54-marker CODEX panel, we profiled 2,033,725 cells in 55 tissue regions of interest and identified 41 cell types through unsupervised clustering and supervised annotation. During leukemic progression, we observed an expansion of myeloid and progenitor cell populations, increased PD-L1+ leukemic cells, the upregulation of PD-1 on CD4+ and CD8+ T cells, and a profound loss of B cells, plasma cells and bone cells. Advanced CML exhibited a striking expansion of immature, pericyte-deficient vasculature that disrupted vascular niches and impaired hematopoietic stem/progenitor cell positioning. Spatial mapping revealed leukemia-specific cellular neighborhoods enriched in PD-1+CD8+ T cells, suggesting localized immune cell exhaustion. Early-stage CML showed increaseds between plasmacytoid dendritic cells and megakaryocytes, whereas advanced CML featured heightened megakaryocyte emperipolesis of non-leukemic granulocytes. Megakaryocytes were morphologically irregular in CML mice and BM trephine biopsies from CML patients. Laser-capture microdissected megakaryocytes from newly diagnosed CML patients had reduced expression of cytoskeleton genes, which was reversed in advanced cases treated with tyrosine kinase inhibitors. 3D imaging revealed vascular disorganization and depleted megakaryocytes in the diaphysis, underscoring region-specific pathology. Together, this study provides a spatiotemporal single-cell atlas of the BMME during leukemic progression, showing how leukemic cells reprogram the niche to support their expansion and immune evasion.

Keywords:  3D light sheet microscopy; Bone marrow microenvironment; CODEX; Chronic myeloid leukemia; Immature vessels; Immunosuppressive; Leukemic progression; Megakaryocyte dysplasia; Vascularized bone marrow

DOI:  https://doi.org/10.1101/2025.09.27.678113
Nature. 2025 Nov 19.

Prime editing-installed suppressor tRNAs for disease-agnostic genome editing.

Sarah E Pierce, Steven Erwood, Keyede Oye, Meirui An, Nicholas Krasnow, Emily Zhang, Aditya Raguram, Davis Seelig, Mark J Osborn, David R Liu.

Precise genome-editing technologies such as base editing1,2 and prime editing3 can correct most pathogenic gene variants, but their widespread clinical application is impeded by the need to develop new therapeutic agents for each mutation. For diseases that are caused by premature stop codons, suppressor tRNAs (sup-tRNAs) offer a more general strategy. Existing approaches to use sup-tRNAs therapeutically, however, require lifelong administration4,5 or show modest potency, necessitating potentially toxic overexpression. Here we present prime editing-mediated readthrough of premature termination codons (PERT), a strategy to rescue nonsense mutations in a disease-agnostic manner by using prime editing to permanently convert a dispensable endogenous tRNA into an optimized sup-tRNA. Iterative screening of thousands of variants of all 418 human tRNAs identified tRNAs with the strongest sup-tRNA potential. We optimized prime editing agents to install an engineered sup-tRNA at a single genomic locus without overexpression and observed efficient readthrough of premature termination codons and protein rescue in human cell models of Batten disease, Tay-Sachs disease and cystic fibrosis. In vivo delivery of a single prime editor that converts an endogenous mouse tRNA into a sup-tRNA extensively rescued disease pathology in a model of Hurler syndrome. PERT did not induce detected readthrough of natural stop codons or cause significant transcriptomic or proteomic changes. Our findings suggest the potential of disease-agnostic therapeutic genome-editing approaches that require only a single composition of matter to treat diverse genetic diseases.

DOI: https://doi.org/10.1038/s41586-025-09732-2