bims-tremyl 2025-12-28 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2025–12–28
24 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

A European survey on allogeneic haematopoietic cell transplantation for myelofibrosis on behalf of the Chronic Malignancies Working Party of the EBMT: focus on 'real world' experience of JAK inhibitors, splenomegaly management and novel agents in the transplant algorithm.
Donor age and type in allogeneic haematopoietic stem cell transplantation: Strong effect in MDS, limited in AML.
Isolated KRAS and NRAS mutations in adults with monocytosis and/or cytopenia(s).
The impact of DNMT3A mutation on survival of AML patients receiving allotransplant in first remission depends on the karyotype and co-occurring mutations.
IFNγ signaling drives resistance to FLT3 inhibition in acute myeloid leukemia.
Targeting dysregulated epigenetic and transcription factor networks in KMT2A-rearranged AML using iPSC models.
Functional Equivalence of Gamma- and X-Ray Irradiation for Long-Term Hematopoietic and AML Transplant Outcomes in Mice.
How to drug a leukemic stem cell: deciphering heterogeneity for better specificity.
Impact of germline CHEK2 pathogenic variants on the risk of Acute Myeloid Leukemia and Myelodysplastic syndrome.
Leukemia-driven expansion of type 3 innate lymphoid cell facilitates a pro-tumoral microenvironment in acute myeloid leukemia.
Protocol for isolation of lipid droplets and mitochondria from acute myeloid leukemia cells for lipidomic analysis.
Romaciclib, a CDK8/CDK19 inhibitor, can overcome venetoclax resistance through a combinatorial strategy.
The PINNACLE study: A multicentre phase II trial of nilotinib in combination with pegylated interferon-α2b in newly diagnosed chronic phase chronic myeloid leukaemia.
Common clonal haematopoiesis driver mutations have disparate effects on macrophage cytokines, clonal expansion and atherogenesis.
Low-input proteomics identifies vWF as a negative regulator of Tet2 mutant hematopoietic stem cell expansion.
A microgel bone marrow model of mesenchymal stem cell paracrine signaling supporting hematopoietic stem cell retention.
The aryl hydrocarbon receptor is associated with monocytic AML and innate immune resistance reversible with an AHR inhibitor.
Interlaboratory cross validation of acute myeloid leukemia fusion genes and mutational targets detected by PCR: Performance of PETHEMA central laboratories.
Intestinal low-abundant bacteria drive MyD88/Trif-dependent CD8+ T cell exhaustion in chronic myeloid leukemia.
Whole exome sequencing and single-cell DNA sequencing for assessment of clonal heterogeneity and evolution in acute myeloid leukemia.
Correlates of organ damage in patients with advanced systemic mastocytosis enrolled in clinical trials of avapritinib.
Juvenile myelomonocytic leukemia stem cells are sensitive to NK cell-mediated lysis and express targetable antigens.
Improvements in Real-World Survival in the Setting of a Recent Paradigm Shift in Acute Myeloid Leukemia Treatment.
Thromboinflammation is associated with high thrombotic risk in patients with newly diagnosed myeloproliferative neoplasms.

Bone Marrow Transplant. 2025 Dec 24.

A European survey on allogeneic haematopoietic cell transplantation for myelofibrosis on behalf of the Chronic Malignancies Working Party of the EBMT: focus on 'real world' experience of JAK inhibitors, splenomegaly management and novel agents in the transplant algorithm.

Alexandros Rampotas, Jose Maria Aspa-Cilleruelo, Linda Koster, Daniele Avenoso, Jakob Passweg, Elisa Sala, Marie Robin, Anders Eivind Myhre, Moniek de Witte, Erfan Nur, Patrice Chevallier, Thomas Schroeder, Micha Srour, Patrizia Chiusolo, Urpu Salmenniemi, Mareike Verbeek, Maria Chiara Finazzi, Cristina Castilla-Llorente, Marie Therese Rubio, Patryk Sobieralski, Katja Sockel, Ahmad Alabdulkarim, Joanna Drozd-Sokolowska, Kavita Raj, Giorgia Battipaglia, Tomasz Czerw, Nicola Polverelli, Juan Carlos Hernández-Boluda, Donal P McLornan.

Allogeneic haematopoietic cell transplantation (allo-HCT) remains the only potentially curative option for patients with myelofibrosis (MF), yet the integration of JAK inhibitors (JAKi) and novel agents into transplant pathways has created increasing complexity. To capture current real-world practice, the EBMT Chronic Malignancies Working Party conducted a survey of 19 high-volume European centres performing MF allo-HCT. Most centres (68%) routinely initiated JAKi, primarily ruxolitinib, in transplant-eligible patients prior to conditioning, with goals of splenomegaly reduction and symptom control. Management of ruxolitinib intolerance or resistance was heterogeneous, with strategies including switching to alternative JAKi, proceeding directly to allo-HCT, or enroling in clinical trials. Peri-transplant approaches also varied: over half of centres continued ruxolitinib throughout conditioning, while others employed tapering or abrupt discontinuation. Experience with newer JAKi and investigational therapies was limited. Post-transplant, most centres did not routinely reintroduce JAKi, although some used them for relapse or GVHD mitigation. Notably, many centres reported transplant delays due to prolonged medical therapy, with adverse consequences including disease progression. These findings highlight significant heterogeneity in practice, which is likely to increase as more novel agents are integrated in treatment algorithms. Harmonised, multidisciplinary guidelines to optimise timing and outcomes for MF patients eligible for allo-HCT are needed.

DOI: https://doi.org/10.1038/s41409-025-02780-2
Br J Haematol. 2025 Dec 24.

Donor age and type in allogeneic haematopoietic stem cell transplantation: Strong effect in MDS, limited in AML.

Dong Hyun Kim, Sin Young Park, Hyunsoo Cho, Ja Min Byun, Dong-Yeop Shin, Youngil Koh, Inho Kim, Sung-Soo Yoon, Junshik Hong.

  Donor age is an important factor influencing outcomes after allogeneic haematopoietic stem cell transplantation (allo-HSCT), but its relevance across donor types and distinct disease biology in acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) remains unclear. We analysed 320 patients with AML/MDS who underwent first allo-HSCT between 2016 and 2024. Donors were categorized as matched or mismatched and further stratified as young (<35 years) or old (≥35 years). Matched donors achieved superior survival compared with mismatched donors, while outcomes with young mismatched donors were intermediate and old mismatched donors were inferior driven by high non-relapse mortality. This effect was most evident in MDS, where young mismatched donors achieved survival similar to matched donors, while old mismatched donors were associated with inferior overall survival (hazard ratio [HR] 2.66) and relapse-free survival (HR 2.45). By contrast, in AML, survival did not differ by donor age; instead, disease biology dominated prognosis, with marrow blasts and European LeukemiaNet (ELN) risk strongly predicting outcomes. In conclusion, donor age interacts with donor type to shape allo-HSCT outcomes, with a marked impact in MDS but limited effect in AML. These findings suggest that old mismatched donors should be avoided in MDS and underscore the importance of disease-specific considerations in donor selection.

Keywords:  acute myeloid leukaemia; allogeneic haematopoietic stem cell transplantation; donor age; donor type; myelodysplastic syndrome

DOI:  https://doi.org/10.1111/bjh.70303
Haematologica. 2025 Dec 24.

Isolated KRAS and NRAS mutations in adults with monocytosis and/or cytopenia(s).

Sa A Wang, Chi Young Ok, Harrison K Tsai, Naima Loayza, Parnaz Daneshpajouhnejad, Neha Seth, Miguel D Cantu, Adam Bagg, Wayne Tam, Olga Weinberg, Paul D Barone, Julia T Geyer, Coleman R Lindsley, Guillermo Montalban-Bravo, Cody R Simon, Daniel A Arber, Carlos E Bueso-Ramos, Eric D Hsi, Kathryn Foucar, Attilio Orazi, Mrinal M Patnaik, Robert P Hasserjian, Kaaren K Reichard.

NRAS and KRAS mutations, commonly identified alongside ancestral co-mutations, are generally regarded as pathogenic in adults presenting with monocytosis and/or cytopenia(s). However, their significance in isolation is not well defined. We studied a multi-institutional cohort of 52 patients with isolated RAS mutations and found that 26 (50%) did not meet diagnostic criteria for a myeloid neoplasm. Compared to typical chronic myelomonocytic leukemia (CMML)/myelodysplastic syndrome (MDS), these patients exhibited distinctive clinical features, including a younger age (65 years; range, 29-92), female predominance (60%), frequent immune-related disorders (39%), and splenomegaly (65%). Mutations predominantly involved KRAS (92%), with 87% affecting codons G12 or G13, and typically occurred at high variantallele- frequency (39.0%; range, 2.6-53.0). In three flow-sorted samples, KRAS/NRAS mutations were detected not only in granulocytes and monocytes but also in lymphocytes, reminiscent of pediatric RASopathies. A subset of patients (7/26, 27%) progressed to myeloid malignancy, with acquisition of additional genetic alterations or the development of dysplasia. These findings challenge the assumption that isolated RAS mutations are sufficient to diagnose myeloid neoplasms. Instead, some cases may reflect adult-onset RASopathies or early clonal proliferations with distinct biological behavior. Recognition of such cases warrants refinement of diagnostic criteria and may influence therapeutic decision-making.

DOI: https://doi.org/10.3324/haematol.2025.288906
Bone Marrow Transplant. 2025 Dec 23.

The impact of DNMT3A mutation on survival of AML patients receiving allotransplant in first remission depends on the karyotype and co-occurring mutations.

Iman Abou Dalle, Jacques-Emmanuel Galimard, Xavier Poire, Jaime Sanz, Anne Huynh, Nicolaus Kröger, Eva Maria Wagner-Drouet, David Burns, Matthias Eder, Bruno Lioure, Depei Wu, Jiri Mayer, Kristina Carlson, Matthias Stelljes, Matthew Collin, Mahmoud Aljurf, Arnon Nagler, Jordi Esteve, Fabio Ciceri, Ali Bazarbachi, Mohamad Mohty.

Mutations in the DNMT3A gene are not yet classified as a distinct prognostic group in the latest European Leukemia Net (ELN) 2022 genetic risk classification of AML. We analyzed 1888 adult AML patients with ELN 2022 intermediate- or poor-risk cytogenetics who received their first allo-transplant in first complete remission between 2015 and 2022. Among patients with cytogenetically normal AML, the triple-positive mutation group (DNMT3A, NPM1, and FLT3-ITD) was the most frequent (n = 340, 29%), while DNMT3A co-occurrence with either FLT3 or NPM1 mutations alone was less common (4% and 9%, respectively). Patients with DNMT3A mutations were less likely to have a secondary AML (14% versus 24%, p < 0.001). DNMT3A mutations negatively affected post-transplant leukemia-free survival (LFS) in patients with normal karyotype and NPM1 mutation without FLT3-ITD (2-year LFS: 70% versus 90%, hazard ratio [HR]: 3.3, p = 0.006), and increased relapse incidence (RI) in FLT3-ITD and wild-type NPM1 subgroup (2-year RI: 30% versus 18%, HR: 2.32, p = 0.03). Notably, patients with normal karyotype and triple-positive mutation exhibited excellent 2-year LFS and OS (61% and 70%), indicating that allo-transplant overcomes the dismal outcome of this group. The impact of DNMT3A mutations on post-transplant outcomes in AML patients in first remission varies based on karyotype and co-mutations.

DOI: https://doi.org/10.1038/s41409-025-02765-1
iScience. 2025 Dec 19. 28(12): 114079

IFNγ signaling drives resistance to FLT3 inhibition in acute myeloid leukemia.

Abraheem Khouqeer, Justin Cartailler, Christina Kim, Kirsten M Dickerson, Chad R Potts, Anna E Gilbert, Robert S Welner, P Brent Ferrell.

  Resistance to targeted therapies remains a major challenge in acute myeloid leukemia (AML). In FLT3-internal tandem duplication (FLT3-ITD) AML, FLT3 inhibitors such as quizartinib improve outcomes, but resistance limits long-term efficacy. While genetic resistance mechanisms are well characterized, the role of the bone marrow microenvironment remains unclear. We investigated how a pro-inflammatory microenvironment influences FLT3 inhibitor resistance and identified IFNγ as a key driver. IFNγ signaling activates STAT1, which in turn upregulates AXL, allowing leukemia cells to survive despite FLT3 inhibition. Knockdown, genomic degron tagging, and overexpression cell models confirmed STAT1 and AXL roles as mediators of resistance. Finally, analysis of IFNγ signaling and resistance in patient-derived AML blasts revealed variable sensitivity, suggesting the presence of additional compensatory mechanisms. These findings reveal IFNγ signaling as a mechanism of resistance, highlighting a potential therapeutic vulnerability in FLT3-mutated AML.

Keywords:  cancer; cell biology; immunology; microenvironment

DOI:  https://doi.org/10.1016/j.isci.2025.114079
Blood Neoplasia. 2026 Feb;3(1): 100172

Targeting dysregulated epigenetic and transcription factor networks in KMT2A-rearranged AML using iPSC models.

Anna Palau, Jonas Thier, Aonghus Naughton, Andrew Tae-Jun Kwon, David Cabrerizo Granados, Sophia Hofmann, Bogumił Kaczkowski, Xiangfu Zhong, Sören Lehmann, Erik Arner, Vanessa Lundin, Andreas Lennartsson.

KMT2A chromosomal rearrangements (KMT2A-r) are frequent in pediatric acute myeloid leukemia (AML) and are associated with poor prognosis. The KMT2A gene encodes a histone lysine methyltransferase responsible for maintaining active chromatin marks (H3K4me3) at gene promoters and enhancers. KMT2A-r lead to the formation of oncogenic KMT2A fusion proteins with over 70 potential partners, disrupting normal hematopoiesis and driving leukemogenesis. Among these, KMT2A::MLLT3, a fusion of KMT2A and MLLT3, is one of the most prevalent in AML. Disruption of the epigenome is a hallmark of AML, with recurrent abnormalities in epigenetic regulators. These alterations often occur early as disease-initiating events, making epigenetic-targeted therapeutics a promising avenue for treatment. Induced pluripotent stem cells (iPSCs) have emerged as faithful models of human AML pathogenesis, recapitulating the underlying genomic lesions and epigenetic profiles. We investigated transcriptional regulation of hematopoietic development using iPSCs derived from a patient with AML with the KMT2A::MLLT3 rearrangement. Our analysis identified key transcriptional activators and repressors that contribute to the altered regulatory landscape in KMT2A::MLLT3 AML. Further analysis of chromatin immunoprecipitation sequencing data indicated that a significant subset of genes, whose expression was downregulated in AML iPSC-derived hematopoietic stem and progenitor cells (AML-HSPCs), were direct targets of Polycomb Repressive Complex 2 (PRC2). Treatment with the dual EZH1/2 inhibitor UNC1999 and 5-azacytidine reactivated these PRC2 target genes, specifically in AML-HSPCs, toward normal gene expression patterns. These findings suggest that targeting Polycomb repression offers a promising epigenetic strategy for improving outcomes in KMT2A-rearranged AML.

DOI: https://doi.org/10.1016/j.bneo.2025.100172
bioRxiv. 2025 Dec 17. pii: 2025.12.15.694472. [Epub ahead of print]

Functional Equivalence of Gamma- and X-Ray Irradiation for Long-Term Hematopoietic and AML Transplant Outcomes in Mice.

Shawn David, Griffin J Nye, Ewelina Bolcun-Filas, Jennifer J Trowbridge, Kira A Young.

Total-body irradiation (TBI) is routinely used for myeloablation prior to mouse hematopoietic cell transplant. Widespread transition from 137 Cs γ -irradiators to X-ray systems has raised questions about whether these modalities yield equivalent biological outcomes. Although prior studies compared γ and X-ray irradiation in healthy syngeneic transplants, their performance in reciprocal congenic models and in primary acute myeloid leukemia (AML) transplant remains unclear. Here, we systematically evaluated γ and X-ray irradiation across dose and dose-rate conditions, and tested dose equivalents in CD45.1/CD45.2 reciprocal transplants and in AML transplant models. While each modality exhibited distinct early effects, both ultimately supported comparable long-term donor chimerism in congenic transplants and equivalent AML engraftment, leukemic burden, and disease progression. These findings indicate that, with proper dose calibration, X-ray irradiation is a functionally effective alternative to γ -irradiation for normal and malignant transplant studies.

DOI: https://doi.org/10.64898/2025.12.15.694472
Blood Neoplasia. 2025 Nov;2(4): 100146

How to drug a leukemic stem cell: deciphering heterogeneity for better specificity.

Alice Worker, Nicholas Jinks, Peter Woodmancy, Claire Seedhouse, Sophie G Kellaway.

Blood cancers, such as acute myeloid leukemia (AML), are becoming increasingly common due to an aging population but remain challenging to treat. Relapse is the most important singular cause of treatment failure in AML, and up to half of patients relapse after chemotherapy or bone marrow transplantation. Relapse in AML is primarily due to a population of quiescent leukemic stem cells (LSCs) that shelter in the bone marrow. Chemotherapy hits actively proliferating AML blasts, but LSCs escape and can later re-enter the cell cycle to regenerate the leukemia. LSCs resemble hematopoietic stem cells, but variable and unique differences may allow for LSC-specific treatment. In this review, we summarize the unique biology of LSCs, considering both global and subtype-specific traits. We describe how heterogeneity, both between different AML subtypes and within the LSC compartment, has impaired efforts to find drug targets so far and how this is being resolved with technological advances such as single-cell sequencing. We elucidate which aspects of LSC biology determine possibilities for targeted treatment and the progress so far made toward therapies to prevent or treat relapse.

DOI: https://doi.org/10.1016/j.bneo.2025.100146
Cancer Epidemiol Biomarkers Prev. 2025 Dec 23.

Impact of germline CHEK2 pathogenic variants on the risk of Acute Myeloid Leukemia and Myelodysplastic syndrome.

Fei Yang, Nicola Long, Jonathan C Savage, Jose Solis-Ruiz, Yu Li, Angela C Holt, Kevin Foley, Zhenzhen Zhang, Jeffrey W Tyner, Richard D Press, Ujwal Shinde, Anupriya Agarwal.

BACKGROUND: Pathogenic germline variants in CHEK2 are associated with a moderately increased risk of several solid tumors; however, their contribution to myeloid malignancies remains poorly defined.
METHODS: We analyzed germline CHEK2 variants in 1,035 patients with acute myeloid leukemia (AML) and 283 with myelodysplastic syndromes (MDS). Pathogenic (P) and likely pathogenic (LP) variants were identified, and their frequency, type, and clinical context were evaluated, including family and personal cancer histories.
RESULTS: P/LP CHEK2 variants were found in 1.74% of AML and 1.77% of MDS cases. While founder mutations such as c.1100delC and p.I157T were present, most were rare missense variants with a population allele frequency below 0.001. These variants were significantly enriched in AML and MDS, even after adjusting for ethnicity. Notably, 39% of AML patients with P/LP CHEK2 variants had a history of solid tumors or hematologic malignancies. Family history of cancer was also frequent, with 21% reporting hematologic and 57% reporting solid tumors.
CONCLUSIONS: Our findings support an expanded role for germline CHEK2 variants in predisposing individuals to myeloid neoplasms, in addition to their association with solid tumor risk.
IMPACT: Given the emerging evidence linking CHEK2 to clonal hematopoiesis, these results underscore the need for prospective studies to refine risk assessment, inform genetic counseling, and guide surveillance strategies. These results suggest that clinical guidelines may consider monitoring clonal hematopoiesis in CHEK2 carriers and weighing in risk and benefit when considering CHEK2 carriers as stem cell transplant donors.

DOI: https://doi.org/10.1158/1055-9965.EPI-25-1074
Leukemia. 2025 Dec 22.

Leukemia-driven expansion of type 3 innate lymphoid cell facilitates a pro-tumoral microenvironment in acute myeloid leukemia.

Thanh Thanh T Dinh, Matthew R Lordo, Amy Y Zhang, Chinmayee Goda, Nikolas Shilo, Ekaterina Altynova, Michael Ruesch, Parker Kronen, Megan Broughton, Erin Jeremy, Victoria L Sellers, Xiaoli Zhang, Karilyn T Larkin, Patrick L Collins, Adrienne M Dorrance, Aharon G Freud, Christopher C Oakes, Bethany L Mundy-Bosse.

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy with poor overall survival. Understanding how dysregulated immunity contributes to the development and progression of AML is an active area of investigation. Prior work has demonstrated functional defects in natural killer (NK) cells; however, the role of non-NK innate lymphoid cells (ILCs) in AML is incompletely understood. Conventional ILC3s are non-cytotoxic and regulate mucosal immunity through cytokine secretion. In this study, we discovered an expansion of ILC3s in both a murine model of AML and in AML patients. The transcription factor, aryl hydrocarbon receptor (AHR) is required for ILC3 development and function, and AML blasts have been shown to secrete AHR ligands. Modeling studies demonstrated ILC3 expansion was mediated by AHR activation in ILC precursors. ILC3s developed in leukemic settings had increased cytokine production, and co-culture of ILC3s significantly increased AML colony formation, which was mediated by ILC3-derived TNFα and GM-CSF. Furthermore, co-transfer of ILC3s with AML led to more rapid disease progression in vivo and human ILC3 frequency was associated with adverse risk stratification in AML patients. These data support a model in which AML promotes ILC3 expansion and function via an AHR-dependent mechanism to aid AML growth and survival.

DOI: https://doi.org/10.1038/s41375-025-02829-7
STAR Protoc. 2025 Dec 15. pii: S2666-1667(25)00663-X. [Epub ahead of print]6(4): 104257

Protocol for isolation of lipid droplets and mitochondria from acute myeloid leukemia cells for lipidomic analysis.

Ran Zhao, Liang Zhang, Shuxin Dong, Kazuharu Kamachi, Saurabh Kumar Gupta, Hiroki Akiyama, Jalen Nguyen, G Lavender Hackman, Michael Andreeff, Alessia Lodi, Jo Ishizawa.

  Lipid droplets (LDs) are dynamic organelles critical for lipid and energy homeostasis. LD dysregulation is implicated in various diseases, including acute myeloid leukemia (AML), which exhibits aberrant lipid metabolism and chemoresistance. Here, we describe an effective protocol for the co-isolation of LDs and mitochondria from lipid-deficient cell types, e.g., AML cells. We detail procedures for the isolation, quality verification, and results from mass spectrometry-based lipidomic analysis. This protocol enables the functional study of organellar lipidomic regulation in AML.

Keywords:  cancer; cell biology; cell isolation; cell separation/fractionation; mass cytometry

DOI:  https://doi.org/10.1016/j.xpro.2025.104257
bioRxiv. 2025 Dec 18. pii: 2025.12.16.693978. [Epub ahead of print]

Romaciclib, a CDK8/CDK19 inhibitor, can overcome venetoclax resistance through a combinatorial strategy.

Urszula Pakulska, Marta Obacz, Jerzy Woźnicki, Katarzyna Wiklik, Samarpana Chakraborty, Marta Micek, Vakul Mohanty, Diego Coelho, Elżbieta Adamczyk, Aniela Gołas, Adrianna Moszyńska, Hui Zhang, Magdalena Cybulska-Lubak, Ewelina Kaniuga, Zuzanna Sadowska-Markiewicz, Marina Konopleva, Michał Mikula, Przemysław Juszczyński, Aditi Shastri, Natalia Baran, Tomasz Rzymski, Milena Mazan.

The combination of venetoclax (VEN) and hypomethylating agents (HMA) is the standard of care in acute myeloid leukemia (AML) for elderly patients unfit for intensive chemotherapy. Despite its clinical success, most patients eventually relapse, creating an urgent need for effective therapeutic alternatives. In this study, we aimed to evaluate the potential of romaciclib, a first-in-class CDK8/CDK19 inhibitor, in combination with VEN to overcome stroma-mediated and primary/acquired VEN-resistance. We assessed the efficacy of RVU120+VEN combination in both sensitive and resistant AML cell lines and primary patient-derived models. Our finding demonstrated that romaciclib synergizes with VEN in AML cell lines and in 8 out of 11 patient-derived cell samples. The proteomic and functional studies demonstrated that combination induced apoptosis through caspase-dependent cleavage of MCL-1. In vivo studies confirmed the efficacy of RVU120+VEN, showing eradication of leukemic cells and bone marrow recovery. Importantly, the combination effectively overcame both stroma-mediated and transcriptionally dependent VEN-resistance. Mechanistic studies, focusing on transcriptomic analyses, identified key resistance-associated pathways, including IL6/JAK/STAT3, TGF-β, PI3K/AKT/MTOR, and inflammatory signaling, being suppressed by combination treatment. Furthermore, an in vivo study using a VEN-resistant patient-derived xenograft (PDX) model confirmed the efficacy of the combination, demonstrating a significant reduction in leukemia burden and a decreased proportion of leukemia initiating cells (LIC) following treatment. These findings prove the highly synergistic mechanism of action of RVU120+VEN combination and the potential to overcome primary/acquired VEN resistance in relapse/refractory AML disease. Altogether, the presented results support ongoing clinical studies evaluating romaciclib and VEN in VEN/HMA-refractory patients ( NCT06191263 ) and provide a basis for future exploration as a frontline therapy in VEN-naïve patients.

DOI: https://doi.org/10.64898/2025.12.16.693978
Br J Haematol. 2025 Dec 22.

The PINNACLE study: A multicentre phase II trial of nilotinib in combination with pegylated interferon-α2b in newly diagnosed chronic phase chronic myeloid leukaemia.

Australasian Leukaemia and Lymphoma Group

  We evaluated the tolerability and efficacy of pegylated interferon alfa-2B (peg-IFNα; PegIntron, MSD) combined with nilotinib in the Australasian Leukaemia and Lymphoma Group CML11 (Pinnacle) study. This phase II study started patients on nilotinib 300 mg twice daily. Subcutaneous peg-IFNα was added at 30-50 50 μg/week from 3 months until 24 months as tolerated. Sixty patients were enrolled with a median age of 48.5 years (range 19-72); 45% were female. With a median follow-up of 60 months, 40 patients (67%) remain on study. The proportion of patients who received ≥50% and ≥85% of their assigned peg-IFNα doses were 58% and 35% respectively. Common reasons for peg-IFNα discontinuation were mood disturbance (5), thyroid disease (4) and myalgia (4). The cumulative incidence of Major Molecular Response (MMR, BCR::ABL1≤0.1%) was 87% by 12 months; Molecular Response 4.5 (MR4.5, BCR::ABL1≤0.0032%) incidence at 24 and 60 months was 55% and 82% respectively. Thirty-seven patients (62%) had MR4.5 for >24 months, 14 of whom attempted treatment-free remission (TFR); 13 remained in TFR at a median follow-up of 32 months. CML11 demonstrated that peg-IFNα with nilotinib leads to high rates of molecular response, with tolerability similar to prior studies. Trial registration ANZCTRN12612000851864.

Keywords:  chronic myeloid leukaemia; clinical trial; deep molecular response; interferon; nilotinib

DOI:  https://doi.org/10.1111/bjh.70276
JCI Insight. 2025 Dec 23. pii: e200334. [Epub ahead of print]

Common clonal haematopoiesis driver mutations have disparate effects on macrophage cytokines, clonal expansion and atherogenesis.

Paul R Carter, Lauren Kitt, Amanda Rodgers, Nichola Figg, Ang Zhou, Chengrui Zhu, Ziyang Wang, Peter Libby, Stephen Burgess, George S Vassiliou, Murray Ch Clarke.

  Clonal haematopoiesis of indeterminate potential (CHIP) is the expansion of blood stem cells and progeny after somatic mutation. CHIP associates with increased cardiovascular disease (CVD) with inflammation from macrophages a proposed common effector. However, mouse CHIP studies are discordant for clonal expansion and inflammation. Similarly, directionality of association between CHIP and CVD remains debated. We investigated effects of three CHIP mutations on macrophage cytokines, clonal expansion and atherosclerosis in parallel. We find that Tet2 and Dnmt3a mutations increase cytokines and inflammasome activation in Tet2 but decrease in Dnmt3a. However, Jak2 mutant macrophages produced equivalent cytokine as wild-type. In mice, Tet2 mutants clonally expanded, but Dnmt3a and Jak2 mutants didn't. Expansion was unaffected by systemic inflammation, while hyperlipidemia expanded Tet2-/- cells, but not mono-allelic mutants. Similarly, human Mendelian randomisation showed no effect of serum cytokines or CVD on CHIP risk. Experimental atherosclerosis was increased in females with Tet2 and males with Jak2, but unchanged with Dnmt3a mutations. Together, common CHIP mutations have disparate effects on macrophage cytokines and clonal expansion, and sex-dependent effects on atherogenesis, suggesting a common mechanism across CHIP is unlikely. Thus, CHIP mutations differ in pathophysiology and clinical sequalae across sexes and should be treated as different entities.

Keywords:  Atherosclerosis; Cytokines; Immunology; Inflammation; Macrophages; Vascular biology

DOI:  https://doi.org/10.1172/jci.insight.200334
Cell Rep. 2025 Dec 24. pii: S2211-1247(25)01542-6. [Epub ahead of print]45(1): 116770

Low-input proteomics identifies vWF as a negative regulator of Tet2 mutant hematopoietic stem cell expansion.

Maria Jassinskaja, Daniel Bode, Monika Gonka, Theodoros I Roumeliotis, Alexander J Hogg, Juan A Rubio Lara, Ellie Bennett, Joanna Milek, Samuel Elberfeld, Bart Theeuwes, M S Vijayabaskar, Lilia Cabrera Cosme, James Lok Chi Che, Sandy MacDonald, Sophia Ahmed, Benjamin A Hall, Grace Vasey, Helena Kooi, Miriam Belmonte, Mairi S Shepherd, William J Brackenbury, Iwo Kucinski, Satoshi Yamazaki, Andrew N Holding, Alyssa H Cull, Nicola K Wilson, Berthold Göttgens, Jyoti Choudhary, David G Kent.

  Despite rapid advances in mapping genetic drivers and gene expression changes in hematopoietic stem cells (HSCs), few studies exist at the protein level. We perform a deep, multi-omics characterization (epigenome, transcriptome, and proteome) of HSCs in a mouse model carrying a loss-of-function mutation in Tet2, a driver of increased self-renewal in blood cancers. Using state-of-the-art, multiplexed, low-input mass spectrometry (MS)-based proteomics, we profile TET2-deficient (Tet2-/-) HSCs, revealing previously unrecognized molecular processes that define the pre-leukemic HSC molecular landscape. Specifically, we obtain more accurate stratification of wild-type and Tet2-/- HSCs than transcriptomic approaches and identify extracellular matrix (ECM) molecules as being dysregulated upon TET2 loss. HSC expansion assays using ECM-functionalized hydrogels confirm a selective effect on the expansion of Tet2-mutant HSCs. Taken together, our study represents a comprehensive molecular characterization of Tet2-mutant HSCs and identifies a previously unanticipated role of ECM molecules in regulating self-renewal of disease-driving HSCs.

Keywords:  CP: stem cell research; TET2; biophysics; extracellular matrix; hematopoietic stem cell; multi-omics; physical biology; proteomics; self-renewal; single cell biology

DOI:  https://doi.org/10.1016/j.celrep.2025.116770
bioRxiv. 2025 Dec 09. pii: 2025.12.05.692616. [Epub ahead of print]

A microgel bone marrow model of mesenchymal stem cell paracrine signaling supporting hematopoietic stem cell retention.

Gunnar B Thompson, Kaila M Kuo, Andrés J García, Brendan A C Harley.

Hematopoietic stem cells (HSCs) housed within the bone marrow give rise to the full complement of blood and immune cells. Methods to expand HSCs ex vivo have traditionally relied on two-dimensional or liquid culture, but hydrogel approaches have been hypothesized to provide three-dimensional bone marrow-associated biophysical and biomolecular signals that may improve HSC expansion and maintenance ex vivo . Here, we describe a granular biomaterial approach to create a multicellular model of the bone marrow. By seeding HSCs amongst mesenchymal stromal cell (MSC)-laden hydrogel microspheres (microgels), we establish paracrine-mediated interactions between HSCs and hydrogel encapsulated MSCs. We provide support for the importance of microgel encapsulation for the emergence of niche-favorable MSC transcriptional profiles. We identify a common cell culture media that accommodates MSC activity while avoiding the use of serum that typically induces differentiation of HSCs. We observe an MSC-density-dependent increase in maintenance of long-term repopulating HSCs in granular co-culture, and we identify significant depletion of long-term repopulating HSCs when both HSCs and MSCs are interstitially seeded in the granular matrix. Together, these findings establish a granular hydrogel co-culture model to examine the influence of MSC-HSC interactions on maintenance and expansion of HSCs in a defined three-dimensional engineered tissue.

DOI: https://doi.org/10.64898/2025.12.05.692616
Front Immunol. 2025 ;16 1554166

The aryl hydrocarbon receptor is associated with monocytic AML and innate immune resistance reversible with an AHR inhibitor.

Jennifer N Saultz, Daniel Bottomly, Faith Burns, Kaelan Byrd, Yoko Kosaka, Bernhard Alber, Daniel Chandra, Stephen E Kurtz, Guang Fan, Andy Kaempf, Nicola Long, Marta Sanchez-Martin, Lei Wang, Karen McGovern, Dan S Kaufman, Shannon K McWeeney, Brian J Druker, Jeffrey W Tyner, Evan F Lind.

   Background: Acute myeloid leukemia (AML) is characterized by a complex interplay between genomic alterations, aberrant hematopoiesis, and immune evasion. The aryl hydrocarbon receptor (AHR) pathway is a critical player in this phenomenon determining the fate of stem cell differentiation as well as dictating immune cell development and function. Despite this critical connection, little is known about how AHR regulates the immune microenvironment in AML.
Methods: We performed a retrospective study examining the pre-treatment effect of immune cell numbers (T and NK cells) in the bone marrow and their impact on overall survival in AML patients undergoing 7+3 induction chemotherapy. Utilizing flow cytometry and both bulk and single-cell RNA sequencing of AML patient samples, we characterized the immune signature of blast cells and the influence of AHR on the immune microenvironment. Lastly, we performed functional studies to determine impact of pharmacological and genomic AHR inhibition on NK cell function.
Results: Higher bone marrow NK cell percentage in ND-AML correlated with poorer OS and expression of HLA-E on leukemic blasts. AHR upregulation was associated with HLA-E expression on blasts and an innate immune resistant signature defined by upregulation of key cytokine pathways, interferon gamma (IFN-g) pathway, and MHC class I/II as well as impaired NK cell profiles. High AHR expression in AML was associated with monocytic maturation and discrepant MHC class I/II profiles. Pre-treatment of blasts with an AHR inhibitor (AHRi) prior to NK cell killing assay downregulated key checkpoint molecules, including HLA-E, and key IFN-g signaling transcription factors (STAT1, IRF1) and led to enhanced NK cell killing among multiple FAB subsets in AML.
Conclusion: The data support targeting the AHR pathway as a dual tumor intrinsic and immune targeting therapeutic strategy for AML, particularly in combination with NK cellular therapy.

Keywords:  AML; AhR; NK cells; immunotherapy; leukemia

DOI:  https://doi.org/10.3389/fimmu.2025.1554166
Leuk Res. 2025 Dec 19. pii: S0145-2126(25)00639-3. [Epub ahead of print]160 108149

Interlaboratory cross validation of acute myeloid leukemia fusion genes and mutational targets detected by PCR: Performance of PETHEMA central laboratories.

PETHEMA group

  The rapid and accurate laboratory identification of targetable therapeutic genes, together with the implementation of measurable residual disease (MRD) based decision is essential for optimal clinical management in acute myeloid leukemia (AML). The PETHEMA (Programa Español de Tratamientos en Hematología) cooperative group comprises nine laboratories that perform centralized molecular studies by conventional PCR and Real-time quantitative PCR (RT-qPCR) for AML patients. With the aim to validate laboratories performances, we conducted three rounds of interlaboratory cross validation (ICV) for the quantification of CBFB::MYH11, RUNX1::RUNX1T1 and NPM1 and one round to determine the mutational status of NPM1, FLT3 (ITD and TKD2) IDH1 and IDH2. For RT-qPCR a total of 19 samples were tested and only 3 (15.8 %) failed to achieve 100 % concordance, corresponding to samples with low target gene mean ratios (ICV1-S4, ICV2-S1, ICV2-S6). For mutation detection in a total of 227 returned results, concordance rate ranged from 95 % to 100 %. FLT3-ITD and NPM1 mutation detection had 100 % concordant results. One false negative was reported for IDH2- R140 mutation and 4 false positives were detected: 2 FLT3-TKD2 and 2 IDH1-R132, likely reflecting differences in assay sensitivity. Overall, the results were highly satisfactory, particularly regarding MRD assessment, and highlighted key points for improvement, especially in baseline detection of FLT3-TKD2 and IDH1 mutations. This study represents the first collaborative initiative to evaluate performance of AML molecular targets within a laboratory network and underscores the importance of regular exercises to monitor performance, identify and resolve technical or interpretive discrepancies to ultimately ensure accurate clinical decision-making.

Keywords:  Acute Myeloid Leukemia; Interlaboratory validation; MRD; Molecular

DOI:  https://doi.org/10.1016/j.leukres.2025.108149
Cell Rep. 2025 Dec 23. pii: S2211-1247(25)01525-6. [Epub ahead of print]45(1): 116753

Intestinal low-abundant bacteria drive MyD88/Trif-dependent CD8+ T cell exhaustion in chronic myeloid leukemia.

Francesca Ronchi, Magdalena Hinterbrandner, Viviana Rubino, Michaela Römmele, Tanja Chiorazzo, Catherine Mooser, Stephanie C Ganal-Vonarburg, Kathy D McCoy, Ravi Bhatia, Andrew J Macpherson, Adrian F Ochsenbein, Carsten Riether.

  Leukemia stem cells (LSCs) resist therapy and immune elimination, but the basis of their escape from cytotoxic T cell (CTL) attack is unclear. Here, we show that specific low-abundance gut commensals of the genera Sutterella and Bilophila suppress anti-leukemic immunity in chronic myeloid leukemia (CML). Germ-free and specific opportunistic pathogen-free mice were protected from CML progression, whereas colonization with Sutterella strains-but not other bacteria-restored disease. In specific pathogen-free CML mice, higher Sutterella prevalence correlated with MyD88/Trif-dependent CTL exhaustion, marked by upregulation of exhaustion markers, reduced interferon-γ and granzyme B production, impaired ex vivo LSC killing, and transcriptomic signatures of exhaustion. These results establish a direct link between the gut microbiota and immune regulation of LSCs, identifying Sutterella species as critical modulators of CTL dysfunction and CML progression. This work highlights microbial influences on cancer immunity and suggests potential therapeutic avenues.

Keywords:  CML; CP: Immunology; CP: Microbiology; LSC; Sutterella; T cell exhaustion; gut microbiota; immune escape

DOI:  https://doi.org/10.1016/j.celrep.2025.116753
Comput Struct Biotechnol J. 2025 ;27 5549-5560

Whole exome sequencing and single-cell DNA sequencing for assessment of clonal heterogeneity and evolution in acute myeloid leukemia.

Sadiksha Adhikari, Samuli Eldfors, Esa Pitkänen, Markus Vähä-Koskela, Caroline A Heckman.

   Background: Acute myeloid leukemia (AML) progresses by the accumulation of somatic mutations and clonal expansion of pre-leukemic cells. Patients may respond to initial therapy, but often relapse, underscoring an evolving disease. Next generation sequencing technologies are being applied to AML for risk stratification and monitoring treatment response. We aimed to evaluate the efficiency of whole exome sequencing (WES) and single-cell DNA sequencing (scDNA-seq) for determining clonal heterogeneity and evolution in AML induced by treatment, assessing strengths and limitations of each technology.
Methods: We conducted WES and scDNA-seq on samples from 6 patients with AML, including sequential samples from four patients. We identified somatic variants, clonal composition and phylogeny using both technologies and compared the results.
Results: WES detected more variants and clones due to broader coverage, while scDNA-seq provided clonality results for targeted genes revealing zygosity and rare clones. Both techniques missed clinically important variants, posing challenges for clinical application. However, they identified similar founding clones and strong correlation of variant allele frequencies and clonal prevalences.
Conclusions: As both technologies can overlook variants, multiple technologies should be utilized to understand clonality in heterogeneous diseases such as AML. Careful scDNA-seq target panel planning, utilizing knowledge obtained from bulk sequencing, can offer more information on clonal heterogeneity. One limitation of our study is the small sample size which may limit the generalizability of the conclusions.

Keywords:  Acute myeloid leukemia; Clonal heterogeneity; Single-cell DNA sequencing; Whole exome sequencing

DOI:  https://doi.org/10.1016/j.csbj.2025.11.066
Blood Neoplasia. 2025 Nov;2(4): 100127

Correlates of organ damage in patients with advanced systemic mastocytosis enrolled in clinical trials of avapritinib.

Emily C Liang, Cecelia Perkins, Rong Lu, Hongliang Shi, Saša Dimitrijević, Justin Abuel, Cheryl Langford, Parveen Abidi, Lenn Fechter, William Shomali, Jason Gotlib.

Organ damage in patients with advanced systemic mastocytosis (AdvSM) at the time of enrollment in clinical trials of KIT inhibitors has not been well characterized. We describe the spectrum and clinicopathologic correlates of organ damage as defined by World Health Organization (WHO) and modified International Working Group-Myeloproliferative Neoplasms Research and Treatment and European Competence Network on Mastocytosis (mIWG) criteria among patients with AdvSM enrolled in the phase 1 and 2 trials of the KIT D816V inhibitor avapritinib (n = 174; systemic mastocytosis [SM] with an associated hematologic neoplasm [SM-AHN], 68%; aggressive SM and mast cell leukemia [MCL], both 16%). Notably, 47% of patients received previous midostaurin. Patients with SM-AHN had the highest absolute monocyte and eosinophil counts, whereas those with MCL had the highest serum tryptase level, bone marrow (BM) mast cell burden, and spleen/liver volumes. Treatment-naïve patients were more likely to fulfill WHO and mIWG criteria for hepatic organ damage. The presence of tier 1 SRSF2, ASXL1, and/or RUNX1 mutations was associated with older age, shorter interval between diagnosis and enrollment, and fewer number of previous therapies, including midostaurin. AdvSM subtype, the presence and number of additional comutated genes beyond KIT D816V, BM mast cell burden, and KIT D816V variant allele fraction were associated with the presence and/or number of WHO/mIWG organ damage findings. Our study provides a snapshot of the correlates of organ damage in patients enrolled in clinical trials of avapritinib and identifies a key association between molecular profile and burden of organ damage.

DOI: https://doi.org/10.1016/j.bneo.2025.100127
Blood Neoplasia. 2025 Nov;2(4): 100135

Juvenile myelomonocytic leukemia stem cells are sensitive to NK cell-mediated lysis and express targetable antigens.

Shannalee Martinez, Vladimir V Senyukov, Suheyla Hasgur, Arianexys Aquino-López, Peter D Emanuel, Y Lucy Liu, Elliot Stieglitz, Gregory Behbehani, Amanda R Campbell, Dean A Lee.

Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative neoplasm for which hematopoietic stem cell transplantation is the only curative treatment. Innovative therapies are needed to address high rates of morbidity, treatment-related mortality, and relapse. Monoclonal antibodies and adoptive cell transfer of natural killer (NK) cells or T cells are approved or being investigated for other myeloid leukemias; however, their activity against JMML warrants further investigation. In this study, we hypothesized that NK cells may effectively target JMML tumor cells. Mass cytometry was used to evaluate the expression of NK cell-activating and -inhibitory ligands and candidate target antigens on the monocytic and stem cell subsets of JMML. Monocytes from healthy donors and monocytic subsets of JMML were similar in NK cell ligand expression, and JMML monocytes were resistant to NK cell cytotoxicity in vitro. However, NK cells effectively controlled proliferation of JMML colony-forming cells. CD34+CD38- JMML stem cells express a broad repertoire of NK cell ligands similar to that of acute myeloid leukemia stem cells; and CD33, CD44, and CD47 were expressed by both CD34+CD38- stem cells and CD34+CD38+ progenitors in JMML. This suggests that JMML may be responsive to NK cell-mediated activity, and that targeting CD33, CD44, or CD47 may facilitate eradication of JMML.

DOI: https://doi.org/10.1016/j.bneo.2025.100135
Eur J Haematol. 2025 Dec 23.

Improvements in Real-World Survival in the Setting of a Recent Paradigm Shift in Acute Myeloid Leukemia Treatment.

Thuy N Ho, Patrick Willard, Graeme F Murray, Li Liu, Nolan Wages, Hyun Lee, Keri R Maher.

  Therapeutic options for newly diagnosed (ND) acute myeloid leukemia (AML) have increased in recent years, leading to a shift in the treatment paradigm from conventional, intensive chemotherapy toward targeted and less intensive therapy. Since 2017, there has been a surge in FDA approvals for novel therapies, including small molecule inhibitors and new combinations of chemotherapy and targeted drugs. It is unclear what effect these changes have had on overall survival in the real-world clinical setting over time. We retrospectively analyzed 501 patients with ND AML treated at an urban academic cancer center from 2015 to 2022 with respect to survival rates and treatment regimen utilization trends over time, in the context of AML risk category and whether allogeneic stem cell transplantation (HSCT) occurred. Among European LeukemiaNet 2022 intermediate risk ND AML patients who did not undergo HSCT, overall survival and relapse-free survival improved significantly in the early versus later cohort (2015-2018 vs. 2019-2022, respectively). These gains were not observed in the adverse-risk subgroup, where outcomes remain unchanged. First-line use of hypomethylating agent-based therapies increased seven-fold, while reliance on chemotherapy alone decreased by half. These findings highlight a meaningful shift in treatment patterns associated with improved outcomes overall, but an ongoing lack of progress in the highest-risk subgroups.

Keywords:  acute myeloid leukemia; induction chemotherapy; molecular targeted therapy; survival analysis

DOI:  https://doi.org/10.1111/ejh.70087
Leukemia. 2025 Dec 23.

Thromboinflammation is associated with high thrombotic risk in patients with newly diagnosed myeloproliferative neoplasms.

French Intergroup of Myeloproliferative Neoplasms (FIM)

Thrombotic risk assessment is crucial in newly diagnosed essential thrombocythemia (ET) and polycythemia vera (PV) patients to guide cytoreductive therapy. We assessed whether thromboinflammation biomarkers would be good candidates to improve thrombosis risk stratification. We prospectively enrolled 394 newly diagnosed, cytoreductive therapy-naïve, ET and PV patients. We measured seven plasma biomarkers of neutrophil, monocyte, platelet, and endothelial activation, including NET markers, and evaluated their association with thrombosis risk scores at diagnosis. Multivariable analysis in the whole MPN cohort showed elevated calprotectin and tissue factor levels in high-risk versus low-risk patients using the conventional two-tiered score. This was also observed in ET patients only, but not in PV patients. Patients with a JAK2V617F allele burden >20% showed higher levels of three markers, including calprotectin, supporting its role in immunothrombosis. In PV patients, calprotectin correlated with the Venous Thrombosis Score (VETS), and five markers were elevated in those with prior venous thrombosis. Lastly, aspirin use was associated with lower H3Cit levels in patients with normal platelet counts, confirming its beneficial effect on NET formation. This is the largest study to date linking thromboinflammation markers to thrombotic risk in MPN patients and identifying potential biomarkers for future thrombosis risk scores.

DOI: https://doi.org/10.1038/s41375-025-02836-8