bims-tremyl 2025-08-10 papers

bims-tremyl

Biomed News

on Therapy resistance biology in myeloid leukemia

Issue of 2025–08–10
29 papers selected by
Paolo Gallipoli, Barts Cancer Institute, Queen Mary University of London

Characteristics and prognostic implications of TP53 mutations in Chinese patients with myelodysplastic syndromes.
Overexpression of the signaling-coordinator GAB2 can play an important role in Acute Myeloid Leukemia progression.
Hypomethylating Agent and Venetoclax Combination Is a Safe and Effective Alternative to Intensive Chemotherapy in Older (≥ 70 Years) Patients With Newly Diagnosed Favorable Risk Acute Myeloid Leukemia.
Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models.
Young unrelated donors confer a survival advantage for patients with myeloid malignancies compared to older siblings.
Optimization of IRAK1/4/pan-FLT3 kinase inhibitors as treatments for acute myeloid leukemia.
A precision medicine approach to the myelodysplastic syndrome with isolated deletion 5q 50 years after its discovery.
The histone-methyltransferase DOT1L cooperates with LSD1 to control cell division in blast-phase MPN.
DDX41 resolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death.
Induction chemotherapy and molecular MRD influence outcomes in KMT2A-rearranged AML.
PPARγ-induced upregulation of fatty acid metabolism confers resistance to venetoclax and decitabine therapy in AML.
Impact of the addition of antithymocyte globulin to post-transplantation cyclophosphamide in haploidentical transplantation with peripheral blood compared to post-transplantation cyclophosphamide alone: A retrospective study on behalf of the Cellular Therapy and Immunobiology Working Party of the European Society for Blood and Marrow Transplantation.
Chromatin Perturbation Promotes Susceptibility to Hypomethylating Agents.
Neutrophil-to-Lymphocyte ratio as surrogate for JAK2V617F suppression and event-free survival in polycythemia vera.
Single-cell transcriptome profiling reveals blast cell heterogeneity and identifies novel therapeutic target IKZF2 in t(8;21) acute myeloid leukaemia.
Clonal haematopoiesis associates with distinct cytometric changes of red blood cells and platelets.
Midostaurin in daily clinical practice of patients with advanced systemic mastocytosis.
Synergistic potential of CDK4/6 inhibitors and ATRA in non-APL AML.
CBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice.
Jab1 promotes immune evasion and progression in acute myeloid leukemia models under oxidative stress.
Statins induce monocytic differentiation in acute myeloid leukemia cells through the KLF4/DPYSL2A axis.
Enlarged PML-nuclear bodies trigger conflicting cell cycle signal-mediated cytotoxicity in leukemia cells.
Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis.
Management of Anemia in Lower-Risk Myelodysplastic Syndromes/Neoplasms With Novel Agents.
Discovery of chromatin-based determinants of azacytidine and decitabine anti-cancer activity.
Plot twist: TET2 clones save the brain.
Association of the composition of the bone marrow tumor microenvironment in BCR::ABL1-negative myeloproliferative neoplasms with IFN-γ signaling and driver mutations.
Ultra-high-scale cytometry-based cellular interaction mapping.
Excised DNA circles from V(D)J recombination promote relapsed leukaemia.

Br J Haematol. 2025 Aug 04.

Characteristics and prognostic implications of TP53 mutations in Chinese patients with myelodysplastic syndromes.

Nanfang Huang, Chunkang Chang, Lingyun Wu, Qi He, Zheng Zhang, Xiao Li, Feng Xu.

  Tumour protein p53 (TP53) mutations occur frequently in myelodysplastic syndromes (MDS) and are associated with a high risk of treatment failure and adverse outcomes. In this study, we analysed 1219 patients with MDS, focusing on the clinical and molecular characteristics of those with TP53 mutations and investigating factors contributing to worse survival and disease progression. One hundred and fifteen (9.4%) patients carried TP53 alterations, of which 70.4% had biallelic and 29.6% had monoallelic alterations. Individuals with biallelic mutations showed elevated bone marrow (BM) blasts (p < 0.001), decreased platelet counts (p = 0.007) and higher the Revised International Prognostic Scoring System (IPSS-R) and Molecular International Prognostic Scoring System (IPSS-M) categories. The biallelic variants, complex karyotype, -7, del(7q) and higher BM blast were linked to worse survival and a higher risk of acute myeloid leukaemia (AML) transformation in TP53-mutated patients. SF3B1 mutations were protective factors for both end-points within TP53-mutated MDS. These characteristics are very similar to populations from the International Working Group for the Prognosis of MDS (IWG-PM) cohort. By performing longitudinal sequencing, we revealed the acquisition or clonal amplification of TP53 alterations during AML transformation. We also conducted repeated sequencing in patients who achieved complete remission (CR) and observed that TP53 mutations were undetectable in 10 of 12 patients. Our findings revealed the clinical significance of TP53 mutations in MDS and highlighted the importance of early detection and dynamic monitoring of TP53 during treatment.

Keywords:  TP53 mutations; allelic state; myelodysplastic syndromes; prognosis

DOI:  https://doi.org/10.1111/bjh.70078
J Clin Invest. 2025 Aug 07. pii: e195929. [Epub ahead of print]

Overexpression of the signaling-coordinator GAB2 can play an important role in Acute Myeloid Leukemia progression.

Michael H Kramer, Stephanie N Richardson, Yang Li, Tiankai Yin, Nichole M Helton, Daniel R George, Michelle Cai, Sai Mukund Ramakrishnan, Casey Ds Katerndahl, Christopher A Miller, Timothy J Ley.

  Mutations that initiate AML can cause clonal expansion without transformation ("clonal hematopoiesis"). Cooperating mutations, usually in signaling genes, are needed to cause overt disease, but these may require a specific "fitness state" to be tolerated. Here, we show that nearly all AMLs arising in a mouse model expressing two common AML initiating mutations (Dnmt3aR878H and Npm1cA) acquire a single copy amplification of chromosome 7, followed by activating mutations in signaling genes. We show that overexpression of a single gene on chromosome 7 (Gab2, which coordinates signaling pathways) is tolerated in the presence of the Npm1cA mutation, can accelerate the development of AML, and is important for survival of fully transformed AML cells. GAB2 is likewise overexpressed in many human AMLs with mutations in NPM1 and/or signaling genes, and also in Acute Promyelocytic Leukemia initiated by PML::RARA; the PML::RARA fusion protein may activate GAB2 by directly binding to its 5' flanking region. A similar pattern of GAB2 overexpression preceding mutations in signaling genes has been described in other human malignancies. GAB2 overexpression may represent an oncogene-driven adaptation that facilitates the action of signaling mutations, suggesting an important (and potentially targetable) "missing link" between the initiating and progression mutations associated with AML.

Keywords:  Genetics; Leukemias; Oncology

DOI:  https://doi.org/10.1172/JCI195929
Am J Hematol. 2025 Aug 07.

Hypomethylating Agent and Venetoclax Combination Is a Safe and Effective Alternative to Intensive Chemotherapy in Older (≥ 70 Years) Patients With Newly Diagnosed Favorable Risk Acute Myeloid Leukemia.

Somedeb Ball, Akriti G Jain, Najla Al Ali, Luis E Aguirre, Jan Philipp Bewersdorf, Andrew Kent, Ameera Rose, Alexander Hayden, Alexa Siddon, Jill Lykon, Ellen Madarang, David M Swoboda, Eric Padron, Kendra Sweet, David A Sallman, Jeffrey Lancet, Hetty E Carraway, Justin Watts, Amer Zeidan, Daniel A Pollyea, Rami S Komrokji.



Keywords:   NPM1 ; BCL2; complete remission; core binding factor; overall survival; venetoclax

DOI:  https://doi.org/10.1002/ajh.70031
Sci Transl Med. 2025 Aug 06. 17(810): eadn5400

Activation of a nongenetic AHR-ELMSAN1 axis optimizes BET-targeting therapy and suppresses leukemia stem cells in preclinical models.

Xinyue Zhou, Steven Moreira, Cecilia Restelli, Hong Wang, Soheil Jahangiri, Sajesan Aryal, Emily Tsao, Pengcheng Zhang, Mingming Niu, Harish Kumar, Zaldy Balde, Ana Vujovic, Lina Liu, Nicholas Wong, Andrea Arruda, Mark D Minden, Yang Zhou, Bhatia Ravi, Jun Qi, Chunliang Li, Kristin J Hope, Rui Lu.

Developing strategies to enhance the response to bromodomain and extraterminal domain (BET) inhibitors and effectively eradicate cancer stem cells would represent a major cancer treatment advance against leukemia. Through a functional CRISPR screen, we identified the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor, as a critical regulator of MYC expression and BET inhibitor sensitivity in human acute myeloid leukemia (AML). Constitutive or pharmacological activation of AHR repressed MYC and synergized with BET inhibitors to inhibit MYC transcription and suppress leukemia growth across diverse AML models. Mechanistically, AHR directly up-regulated a noncanonical target, ELMSAN1, a component of the MiDAC histone deacetylase complex, which promotes histone deacetylation at MYC regulatory elements. ELMSAN1 depletion led to up-regulation of MYC and impaired AHR signaling-induced BET inhibitor sensitization. In vivo, AHR agonists enhanced BET inhibitor efficacy in patient-derived xenografts and murine leukemia models, enabling the use of lower BET inhibitor doses while preserving therapeutic benefit and reducing toxicity. This combination suppressed leukemia stem cell (LSC) gene signatures and reduced LSC frequency, with minimal impact on normal hematopoietic stem and progenitor cells in both human cord blood xenografts and immunocompetent mouse models. Together, these findings uncover a MYC-repressive, nongenetic AHR-ELMSAN1 axis that enhances BET-targeting therapies and selectively impairs LSCs, providing a compelling rationale for clinical translation in AML and potentially other MYC-driven cancers.

DOI: https://doi.org/10.1126/scitranslmed.adn5400
Leukemia. 2025 Aug 06.

Young unrelated donors confer a survival advantage for patients with myeloid malignancies compared to older siblings.

German Cooperative Transplant Study Group

Donor age is one factor to optimize allogeneic hematopoietic cell transplantation (alloHCT). Therefore, we investigated whether young unrelated donors (UD) provide a benefit for older patients with myeloid malignancies compared to HLA-identical sibling donors (MSD). We performed a retrospective registry study on patients ≥50 years who received a first alloHCT between 2010 and 2020. We compared event-free survival (EFS) of patients who were transplanted from MSD aged ≥50 years versus UD aged ≤35 years who were HLA-compatible for HLA-A, -B, -C, and -DRB1. In total, we analyzed data from 3460 patients. With multivariable adjustment EFS (HR 0.86, p = 0.003), OS (HR 0.82, p < 0.001), and risk of relapse (HR 0.84, p = 0.018) were significantly better for HLA-compatible UD compared to MSD. No survival advantage was found, when UD with unfavorable sex or CMV constellation were compared to MSD with favorable constellations. In a meta-analysis on 9905 patients with myeloid malignancies, including ours, we found reduced risk of relapse (pooled HR 0.78, p = 0.006) and better EFS (pooled HR 0.89, p < 0.001) for young matched UD versus MSD. To select young HLA-compatible UD over older MSD may reduce relapse risk and improve survival for older patients with myeloid malignancies.

DOI: https://doi.org/10.1038/s41375-025-02724-1
Bioorg Med Chem Lett. 2025 Aug 01. pii: S0960-894X(25)00264-1. [Epub ahead of print] 130355

Optimization of IRAK1/4/pan-FLT3 kinase inhibitors as treatments for acute myeloid leukemia.

Patrick J Sutter, Morgan M Walker, Chris J Finocchio, Jian-Kang Jiang, Gregory J Tawa, Xiaohu Zhang, Xin Xu, Pranav Shah, Glenn Y Gomba, Daniel T Starczynowski, Craig J Thomas, Scott Hoyt.

  FLT3 kinase inhibitors have been advanced to the clinic as targeted treatments for acute myeloid leukemia (AML). These inhibitors can produce promising initial responses, but patients often relapse with treatment-resistant disease. A significant factor contributing to relapse involves adaptive signaling through an alternative pathway mediated by IRAK1 and IRAK4 kinases. Compounds that inhibit IRAK1/4 and FLT3 may thus provide superior efficacy relative to compounds that inhibit FLT3 only. We report the optimization of an imidazopyridine series of IRAK1/4/pan-FLT3 kinase inhibitors. Optimization efforts have produced key compound 31, which displays potent inhibition of IRAK1, IRAK4, and FLT3, potent activity in multiple AML tumor cell viability assays, and efficacy superior to that of approved FLT3 inhibitors in multiple mouse xenograft models of AML.

Keywords:  AML; FLT3; IRAK1; IRAK4; Kinase; Leukemia

DOI:  https://doi.org/10.1016/j.bmcl.2025.130355
Blood. 2025 Aug 04. pii: blood.2025028619. [Epub ahead of print]

A precision medicine approach to the myelodysplastic syndrome with isolated deletion 5q 50 years after its discovery.

Marco Roncador, Elsa Bernard, Robert P Hasserjian, Jacqueline Boultwood, Chiara Elena, Anna Galli, Carmelo Gurnari, Cristina Mecucci, Lucienne Michaux, Moshe Mittelman, Martina Sarchi, Erica Travaglino, Donal P McLornan, Seishi Ogawa, Elli Papaemmanuil, Eva S Hellstrom-Lindberg, Luca Malcovati, Mario Cazzola.

In 1974, Vanden Berghe et al described a distinct hematologic disorder associated with acquired, interstitial deletion of part of the long arm of chromosome 5. This condition is now classified as myelodysplastic syndrome (MDS) with isolated deletion 5q, or MDS-del(5q). The common deletion region 5q32-5q33 contains several genes and microRNAs whose expression levels are reduced in hematopoietic cells, consistent with the loss of one allele. Haploinsufficiency production of multiple gene transcripts, primarily involving CSNK1A1, RPS14, MIR145, and MIR146A, results in myelodysplastic hematopoiesis. Lenalidomide can selectively suppress the del(5q)-mutant clone by promoting proteasomal degradation of casein kinase 1A1 and inducing mutant stem cell failure. However, lenalidomide is not a curative treatment, as almost all patients relapse. Molecular profiling studies have significantly improved our understanding of MDS-del(5q). Only a minority of patients have interstitial deletion 5q as their sole genetic lesion, a condition that is associated with an indolent clinical course. Most patients have co-occurring somatic mutations in myeloid genes, including DNMT3A, TET2, ASXL1, SF3B1, TP53, RUNX1, and CSNK1A1. These comutations have independent effects on leukemic transformation and survival, so genomic profiling is required for implementing a precision management approach to MDS-del(5q) in a clinical setting. Accurate assessment of the TP53 allelic state is crucial for distinguishing MDS-del(5q) from TP53-mutant MDS, a myeloid malignancy characterized by TP53 multihit state and very aggressive clinical course. Genomic profiling is also critical for therapeutic decision making in patients with MDS-del(5q), particularly for assessing a patient's eligibility for allogeneic transplantation, which remains the only curative treatment.

DOI: https://doi.org/10.1182/blood.2025028619
Leukemia. 2025 Aug 08.

The histone-methyltransferase DOT1L cooperates with LSD1 to control cell division in blast-phase MPN.

Karl Kapahnke, Thomas Plenge, Tabea Klaus, Manoj K Gupta, Disha Anand, Tamer T Önder, Birgit Perner, Tina M Schnöder, Felicitas R Thol, Frederik Damm, Florian H Heidel, Florian Perner.

Persistence of JAK2-mutated clones that may undergo clonal evolution and malignant transformation remains a challenge in myeloproliferative neoplasms (MPN), Novel therapeutic approaches to attenuate clonal evolution and progression to blast-phase are therefore urgently needed. LSD1 (KDM1A) inhibitors reduce symptoms and clonal burden in MPN, but whether these compounds may be effective in advanced disease stages remained so far elusive. Using a chromatin-focused CRISPR-Cas9 screen, we identified the histone methyltransferase DOT1L as a synthetic lethal target under pharmacologic LSD1 inhibition. DOT1L knockout impaired cellular fitness, reduced proliferation, and prolonged survival in xenografts. Furthermore, genetic inactivation of DOT1L increased LSD1 inhibitor sensitivity up to 100-fold resulting in cell cycle arrest and apoptosis induction in TP53 mutant blast-phase MPN. Mechanistically, we have identified a novel, non-canonical function of DOT1L which co-occupied LSD1-bound enhancers and contributed to the repression of transcriptional programs independent of its enzymatic activity. DOT1L loss cooperated with LSD1 inhibitors to activate tumor suppressive programs, while pharmacologic inhibition of DOT1Ls catalytic activity failed to elicit comparable effects. These findings indicate that leveraging DOT1L targeting via protein degradation or RNA interference, rather than conventional enzymatic inhibition, could enhance the therapeutic efficacy of LSD1 inhibitors in blast-phase MPN.

DOI: https://doi.org/10.1038/s41375-025-02719-y
Nat Commun. 2025 Aug 05. 16(1): 7195

DDX41 resolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death.

Honghao Bi, Kehan Ren, Pan Wang, Ermin Li, Xu Han, Wen Wang, Jing Yang, Inci Aydemir, Kara Tao, Renee Ma, Lucy A Godley, Yan Liu, Vipul Shukla, Elizabeth T Bartom, Yuefeng Tang, Lionel Blanc, Madina Sukhanova, Peng Ji.

Deleterious germline DDX41 variants constitute the most common inherited predisposition disorder linked to myeloid neoplasms (MNs), yet their role in MNs remains unclear. Here we show that DDX41 is essential for erythropoiesis but dispensable for other hematopoietic lineages. Ddx41 knockout in early erythropoiesis is embryonically lethal, while knockout in late-stage terminal erythropoiesis allows mice to survive with normal blood counts. DDX41 deficiency induces a significant upregulation of G-quadruplexes (G4), which co-distribute with DDX41 on the erythroid genome. DDX41 directly binds to and resolves G4, which is significantly compromised in MN-associated DDX41 mutants. G4 accumulation induces erythroid genome instability, ribosomal defects, and p53 upregulation. However, p53 deficiency does not rescue the embryonic death of Ddx41 hematopoietic-specific knockout mice. In parallel, genome instability also activates the cGas-Sting pathway, impairing survival, as cGas deficiency rescues the lethality of hematopoietic-specific Ddx41 knockout mice. This is supported by data from a DDX41-mutated MN patient and human iPSC-derived bone marrow organoids. Our study establishes DDX41 as a G4 resolvase, essential for erythroid genome stability and suppressing the cGAS-STING pathway.

DOI: https://doi.org/10.1038/s41467-025-62307-7
Blood. 2025 Aug 06. pii: blood.2025029556. [Epub ahead of print]

Induction chemotherapy and molecular MRD influence outcomes in KMT2A-rearranged AML.

Jad Othman, Nicola Potter, Sylvie D Freeman, Nicholas McCarthy, Jelena Jovanovic, Manohursingh Runglall, Joanna Canham, Ian Thomas, Sean Johnson, Amanda Frances Gilkes, James Durrell Cavenagh, Panagiotis Kottaridis, David C Taussig, Claire Arnold, Claire Jane Hemmaway, Dominic Culligan, Ulrik Malthe Overgaard, Mike Dennis, Alan K Burnett, Nigel H Russell, Richard James Dillon.

We analyzed 217 patients with KMT2A-rearranged AML in two large sequential randomized trials. Those randomized to FLAG-Ida had markedly lower rates of relapse than other chemotherapy regimens. Molecular MRD assessment after cycle two was strongly prognostic for relapse and death. AML17 ISRCTN55675535 AML19 ISRCTN78449203.

DOI: https://doi.org/10.1182/blood.2025029556
Blood Neoplasia. 2025 Aug;2(3): 100121

PPARγ-induced upregulation of fatty acid metabolism confers resistance to venetoclax and decitabine therapy in AML.

Kotoko Yamatani, Tatsuro Watanabe, Kaori Saito, Abdullah Khasawneh, Abhishek Maiti, Zhihong Zeng, Kala Hayes, Shinya Kimura, Courtney D DiNardo, Xiaoping Su, Shuko Nojiri, Yasushi Okazaki, Michael Andreeff, Marina Konopleva, Yoko Tabe.

The combination of the B-cell lymphoma 2 (BCL2) inhibitor venetoclax (VEN) and the hypomethylating agent decitabine (DEC; VEN/DEC) constitutes a primary therapeutic strategy for treating older adults with acute myeloid leukemia (AML). However, a notable subset of patients exhibits resistance to VEN/DEC, demonstrating either no disease response or relapse after initial remission. This study aimed to elucidate the molecular mechanisms underlying this resistance through analyses of gene expression and DNA methylation profiles. We conducted comprehensive RNA sequencing analysis and DNA methylation profiling on AML samples from 35 patients undergoing VEN/DEC therapy. The RNA sequencing analysis revealed that several genes related to fatty acid metabolism were significantly upregulated in leukemia cells from patients who received VEN/DEC treatment and relapsed or failed to respond. Increased expression of peroxisome proliferator-activated receptor gamma (PPARG) occurred after treatment and correlated with decitabine-induced promoter hypomethylation. Subsequent in vitro validation demonstrated that decitabine treatment results in hypomethylation of the PPARG promoter, elevating PPARG levels and promoting a metabolic environment characterized by enhanced fatty acid oxidation pathways conducive to VEN/DEC resistance. Furthermore, pharmacological inhibition using either a PPARγ antagonist or a fatty acid oxidation inhibitor enhanced the sensitivity of resistant cells to VEN/DEC, underscoring the crucial role of PPARγ in the development of therapeutic resistance. These findings not only shed light on the metabolic adaptation that contributes to VEN/DEC resistance in AML but also identify PPARγ as a potential therapeutic target for overcoming such resistance, providing new opportunities to improve the efficacy of VEN/DEC-based therapy in AML.

DOI: https://doi.org/10.1016/j.bneo.2025.100121
Br J Haematol. 2025 Aug 07.

Impact of the addition of antithymocyte globulin to post-transplantation cyclophosphamide in haploidentical transplantation with peripheral blood compared to post-transplantation cyclophosphamide alone: A retrospective study on behalf of the Cellular Therapy and Immunobiology Working Party of the European Society for Blood and Marrow Transplantation.

Antoine Capes, Jarl E Mooyaart, Didier Blaise, Stefania Bramanti, Mi Kwon, Mohamad Mohty, Patrice Chevallier, Jan Vydra, Péter Reményi, Edouard Forcade, Lucía López Corral, Maija Itälä-Remes, Ali Bazarbachi, Enrico Derenzini, Jorinde D Hoogenboom, Jürgen Kuball, Giorgia Battipaglia, Florent Malard, Annalisa Ruggeri.

  In the setting of haploidentical haematopoietic cell transplantation (HCT), post-transplant cyclophosphamide (PTCy) has dramatically reduced the incidence of graft-versus-host disease (GVHD) and non-relapse mortality. To further reduce GVHD incidence, the addition of antithymocyte globulin (ATG) to PTCy was evaluated in retrospective and non-comparative prospective studies showing promising results. We conducted a large retrospective analysis of the European Society for Blood and Marrow Transplantation (EBMT) registry to evaluate this approach. We analysed haploHCT with peripheral blood stem cells performed for haematological malignancies between 2014 and 2021. GVHD prophylaxis included either PTCy alone or PTCy+ATG. Four thousand five hundred and nineteen patients were analysed in the PTCy only group versus 675 with PTCy+ATG. Median follow-up was 29.80 months. In univariate analysis, 2-year GVHD-free, relapse-free survival (GRFS), relapse-free survival (RFS), overall survival (OS), cumulative incidence of relapse, non-relapse mortality (NRM) and chronic GvHD (cGVHD) were, respectively: 40.5% versus 37.5% (p = 0.098), 50.9% versus. 45.8% (p = 0.015), 56.9% versus 52.5% (p = 0.01), 24.2% versus 28.1% (p = 0.032), 25% versus 26.1% (p = 0.49) and 28.4% versus 18.5% (p < 0.001). aGVHD did not differ. After multivariable adjustment, OS and RFS were lower in the PTCy+ATG group: HR = 1.18 (p = 0.037) and HR = 1.18 (p = 0.027) and patients receiving PTCy+ATG had less cGVHD: HR = 0.68 (p = 0.004). In that retrospective analysis, the addition of ATG to PTCy for GVHD prophylaxis in haploHCT was associated with a reduction of cGVHD but also a worse OS and RFS.

Keywords:  BMT; GVHD; cell therapy

DOI:  https://doi.org/10.1111/bjh.70050
bioRxiv. 2025 Jul 31. pii: 2025.07.28.666975. [Epub ahead of print]

Chromatin Perturbation Promotes Susceptibility to Hypomethylating Agents.

Constanze Schneider, Gabriela Alexe, Lucy A Merickel, Ashleigh Meyer, Michelle L Swift, Rodolfo B Serafim, Allen T Basanthakumar, Audrey Taillon, Silvi Salhotra, Fabio Boniolo, Sander Lambo, Yara Rodriguez, Björn Häupl, Rani E George, David E Root, Thomas Oellerich, Volker Hovestadt, Dipanjan Chowdhury, Kimberly Stegmaier.

Cancer-directed drugs are often clinically deployed without definitive understanding of their molecular mechanisms of action (MOA). Hypomethylating agents (HMAs), which result in the degradation of the DNA methyltransferase 1 (DNMT1), have been deployed for decades in the treatment of haematological malignancies 1,2 . The precise mechanism of action of these drugs, however, has been debated, rendering the design of rational combination therapies challenging. Here, we identified the deubiquitinating enzyme USP48 as a crucial regulator of posttranslational histone modification in the context of DNA demethylation. USP48 loss selectively enhances response to DNMT1 inhibition, leading to a rapid induction of cell death. We demonstrate that USP48 is localized at sites of DNA damage and deubiquitinates H2A variants and proteins important for DNA damage repair. Functionally, loss of USP48 triggers an increase in chromatin accessibility upon HMA treatment, rendering AML cells more susceptible to DNA damage. Our results support USP48 as a posttranslational histone modifier for chromatin stability and DNA damage in response to HMA-related DNA demethylation. These findings propose USP48 as a new target for combination therapy with HMAs for acute myeloid leukaemia (AML).

DOI: https://doi.org/10.1101/2025.07.28.666975
Blood Cancer J. 2025 Aug 06. 15(1): 132

Neutrophil-to-Lymphocyte ratio as surrogate for JAK2V617F suppression and event-free survival in polycythemia vera.

Tiziano Barbui, Arianna Ghirardi, Victoria Empson, Francesca Fenili, Giuseppe Gaetano Loscocco, Annalisa Condorelli, Alessandra Iurlo, Daniele Cattaneo, Elena Rossi, Valerio De Stefano, Paola Guglielmelli, Christoph Klade, Heinz Gisslinger, Alessandro Rambaldi, Joseph M Scandura, Alessandro Maria Vannucchi.

Chronic systemic inflammation is a key driver of polycythemia vera (PV) progression, but the immunomodulatory effects of current treatments remain poorly defined. The neutrophil-to-lymphocyte ratio (NLR) is an accessible biomarker of systemic inflammation proven in other contexts, but its role in monitoring PV disease activity has not been established. Using data from three of the largest PV clinical trials, we evaluated the effects of PV therapies on NLR and its relationship with molecular response and clinical outcomes. In 404 hematocrit-controlled patients from the ECLAP study, hydroxyurea (HU) failed to significantly lower NLR (p = 0.11) due to the parallel declines in ANC and ALC. Neither leukocyte counts nor NLR were significantly reduced by phlebotomy in ECLAP patients treated without cytoreductive therapy. In contrast, the Low-PV study showed that while phlebotomy tended to increase NLR, low-dose ropeginterferon alfa-2b (Ropeg) significantly reduced NLR (-18.2% and -36.3% in patients with low and high baseline NLR, respectively) by suppressing ANC rather than lymphocytes. NLR reduction correlated with the primary Low-PV endpoint (p = 0.021) and reduction of JAK2 variant allele frequency (VAF) [1]. The PROUD-PV/CONTINUATION-PV study confirmed the superior effect of Ropeg over HU, with a significantly greater NLR reduction at 60 months (-56.5% versus -33.6%, respectively, p = 0.019) in patients with high baseline NLR. Moreover, NLR reduction was associated with decreased JAK2V617F VAF (p < 0.0001) and improved event-free survival (p = 0.010). These findings identify NLR as a dynamic biomarker of treatment response and prognosis in PV and support its incorporation into routine monitoring.

DOI: https://doi.org/10.1038/s41408-025-01317-6
Br J Haematol. 2025 Aug 08.

Single-cell transcriptome profiling reveals blast cell heterogeneity and identifies novel therapeutic target IKZF2 in t(8;21) acute myeloid leukaemia.

Yu Liu, Wenbing Liu, Yihan Mei, Qianqian Huang, Xiaoyu Liu, Chengcai Guo, Manling Chen, Junli Mou, Shangshang Wang, Wanqing Xie, Zheng Tian, Kejing Tang, Haiyan Xing, Ying Wang, Hui Wei, Runxia Gu, Qing Rao, Min Wang, Shaowei Qiu, Jianxiang Wang.

  The t(8;21)(q22;q22) translocation is one of the most recurrent cytogenetic aberrations in acute myeloid leukaemia (AML). While most patients achieve complete remission, approximately 40% of them still relapse. Early identification and elimination of leukaemia clones with relapse potential could improve prognosis for t(8;21) AML patients. Here, through single-cell RNA sequencing, we characterized the intra-tumoral heterogeneity of t(8;21) AML and identified haematopoietic stem cell (HSC)-like subset as the most quiescent and primitive subgroup among all leukaemia cell populations. Further investigations revealed IKZF2 as the master regulator for HSC-like subset. Notably, IKZF2 was upregulated in t(8;21) AML compared with other AML subtypes and was specifically targeted by AML1-ETO. Using primary samples and mouse models, we verified the high enrichment of IKZF2 in primitive and quiescent leukaemic cells. Moreover, IKZF2 knockout hindered the accumulation of aberrant stem cells driven by AML1-ETO and promoted cellular differentiation both in vitro and in vivo. These facilitate a better understanding of the leukaemia cell heterogeneity in t(8;21) AML and unveil IKZF2 as a potential target for improving current treatment strategies.

Keywords:  HSC‐like subset; IKZF2; t(8;21) AML

DOI:  https://doi.org/10.1111/bjh.70077
Br J Haematol. 2025 Aug 03.

Clonal haematopoiesis associates with distinct cytometric changes of red blood cells and platelets.

J B Salzbrunn, I A van Zeventer, A O de Graaf, S Klatte, L J van Pelt, P Kamphuis, M G J M van Bergen, A G Dinmohamed, B A van der Reijden, J Linssen, J J Schuringa, J H Jansen, G Huls.

  Individuals with macrocytosis or a high RDW are at increased risk of developing haematological malignancies. The mechanisms that mediate this association remain unknown but may involve the presence of clonal haematopoiesis (CH). Here, we performed targeted next-generation sequencing on all individuals ≥60 years with macrocytosis (MCV >100 fL; n = 269) or high RDW (RDW ≥16%; n = 242) and 1:2 age- and sex-matched controls from the population-based Lifelines cohort. Macrocytosis is not associated with CH or peripheral blood count abnormalities. In contrast, individuals with a high RDW were associated with an increased number of mutated genes, larger clone sizes and a high prevalence of blood count abnormalities. Interestingly, individuals with a high RDW and CH display a uniform population of red blood cells in the distribution plots, despite not all cells carrying the respective mutation, suggesting an indirect effect of CH on the red blood cell population. While macrocytosis is not associated with CH in general, SF3B1 mutations associate with an elevated MCV. Individuals with a combination of TET2 and SRSF2 mutations show marked disturbances in platelet morphology. In conclusion, cytometric parameters of peripheral blood cells may serve as early indicators of dysplastic changes and are associated with distinct mutational patterns in CH.

Keywords:  acute leukaemia; clinical haematology; clonal evolution; clonal haematopoiesis; epidemiology; genetic analysis

DOI:  https://doi.org/10.1111/bjh.70031
Br J Haematol. 2025 Aug 08.

Midostaurin in daily clinical practice of patients with advanced systemic mastocytosis.

Johannes Lübke, Nicole Naumann, Timo Brand, Laurenz Steiner, Roland Repp, Georgia Metzgeroth, Alice Fabarius, Wolf-Karsten Hofmann, Deepti H Radia, Andreas Reiter, Juliana Schwaab.

  Midostaurin, a multikinase/KIT inhibitor, is approved for the treatment of advanced systemic mastocytosis (AdvSM). We evaluated dosing regimens, safety, efficacy and overall survival (OS) of 79 patients from the 'German Registry on Disorders of Eosinophils and Mast Cells'. Midostaurin was initiated at 200 and ≤150 mg daily in 63/79 (80%) and 16/79 (20%) and continued at month 12 in 44/63 (70%) and 10/16 (63%) patients respectively. Over a cumulative observation period of 146 patient-years, 96 adverse events (AE) led to dose adjustment, most commonly nausea/emesis (n = 22, 23%) and neutropenia (n = 8, 8%). Responses were achieved in 60% (modified Valent criteria), 29% (IWG-MRT-ECNM, International Working Group-Myeloproliferative Neoplasms Research and Treatment & ECNM criteria) and 13% (pure pathological response criteria) of patients. Within the first 12 months, achievement of a response was dose independent except for modified Valent criteria. The response duration (modified Valent/IWG-MRT-ECNM criteria) correlated with improved OS (p < 0.001). Midostaurin was ultimately stopped in patients due to lack of response/progression, death and AEs in 28 (39%), 5 (6%) and 13 (17%) patients respectively. Following midostaurin discontinuation, 7/41 (17%) patients experienced a discontinuation syndrome, which was effectively prevented in subsequent patients through dose tapering and corticosteroid bridging. In conclusion, midostaurin demonstrated a favourable safety profile and yielded durable responses in AdvSM patients across dosing regimens.

Keywords:  KIT inhibitor; advanced systemic mastocytosis; dosing profiles; efficacy; midostaurin; multikinase inhibitor; safety

DOI:  https://doi.org/10.1111/bjh.70065
Br J Haematol. 2025 Aug 04.

Synergistic potential of CDK4/6 inhibitors and ATRA in non-APL AML.

Rafał Skopek, Setenay Gupse Özcan, Paulina Chmiel, Stephanie Morgner, Jaqueline Schütt, Faezeh Ghazvini Zadegan, Clara Stanko, Małgorzata Palusińska, Karolina Maślińska-Gromadka, Yordan Sbirkov, Sven Stengel, Martin Fischer, Annamaria Brioli, Arthur Zelent, Łukasz Szymański, Tino Schenk.

  Acute myeloid leukaemia (AML) is a heterogeneous disease characterized by diverse genetic abnormalities. The standard of care remains to be chemotherapy and stem cell transplantation. In acute promyelocytic leukaemia (APL), differentiation therapy with all-trans retinoic acid (ATRA) has significantly improved outcomes. Despite this, the success of ATRA has yet to be transferred to non-APL AML. Exploring combinations to enhance the efficacy of ATRA in non-APL AML remains a key focus. To investigate the therapeutic effect of ATRA in combination with cyclin-dependent kinase 4/6 (CDK4/6) inhibitors in non-APL AML. Non-APL AML cell lines and primary patient samples were treated with ATRA and CDK4/6 inhibitors. Key outcomes included differentiation, proliferation, cell viability and colony-forming capacity. Combination synergy was evaluated, and gene expression analysis identified pathways associated with therapeutic effects. The combination demonstrated dose-dependent effects, enhancing differentiation and reducing proliferation, cell viability and colony-forming capacity. A synergistic effect was observed across AML cell lines. Gene expression profiling revealed the co-regulation of differentiation-associated genes, unveiling the mechanisms driving therapeutic synergy. Combination of CDK4/6 inhibitors with ATRA shows potential for differentiation-based AML treatment. This approach offers a promising avenue for improved outcomes in non-APL AML.

Keywords:  AML; ATRA; CDK4/6; CDK4i; acute myeloid leukaemia; non‐APL; palbociclib; ryuvidine; synergy

DOI:  https://doi.org/10.1111/bjh.70057
J Clin Invest. 2025 Aug 05. pii: e192923. [Epub ahead of print]

CBFβ-SMMHC-driven leukemogenesis requires enhanced RUNX1-DNA binding affinity in mice.

Tao Zhen, Yaqiang Cao, Tongyi Dou, Yun Chen, Guadalupe Lopez, Ana Catarina Menezes, Xufeng Wu, John Hammer, Jun Cheng, Lisa Garrett, Stacie Anderson, Martha Kirby, Stephen Wincovitch, Bayu Sisay, Abdel G Elkahloun, Di Wu, Lucio H Castilla, Wei Yang, Jiansen Jiang, Keji Zhao, Paul P Liu.

  The leukemia fusion gene CBFB-MYH11 requires RUNX1 for leukemogenesis, but the underlying mechanism is unclear. By in vitro studies, we found that CBFβ-SMMHC, the chimeric protein encoded by CBFB-MYH11, could enhance the binding affinity between RUNX1 and its target DNA. Increased RUNX1-DNA binding was also observed in myeloid progenitor cells from mice expressing CBFβ-SMMHC. Moreover, only CBFβ-SMMHC variants able to enhance the DNA binding affinity by RUNX1 could induce leukemia in mouse models. Marked transcriptomic changes, affecting genes associated with inflammatory response and target genes of CBFA2T3, were observed in mice expressing leukemogenic CBFβ-SMMHC variants. Finally, we show that CBFβ-SMMHC could not induce leukemia in mice with a Runx1-R188Q mutation, which reduces RUNX1 DNA binding but not affecting its interaction with CBFβ-SMMHC or its sequestration to cytoplasm by CBFβ-SMMHC. Our data suggest that, in addition to binding RUNX1 to regulate gene expression, enhancing RUNX1 binding affinity to its target DNA is an important mechanism by which CBFβ-SMMHC contributes to leukemogenesis, highlighting RUNX1-DNA interaction as a potential therapeutic target in inv(16) AML.

Keywords:  Genetics; Hematology; Leukemias; Mouse models; Transcriptomics

DOI:  https://doi.org/10.1172/JCI192923
J Clin Invest. 2025 Aug 05. pii: e183761. [Epub ahead of print]

Jab1 promotes immune evasion and progression in acute myeloid leukemia models under oxidative stress.

Nan Zhang, Qian Wang, Guopeng Chen, Li Liu, Zhiying Wang, Linlu Ma, Yuxing Liang, Jinxian Wu, Xinqi Li, Xiaoyan Liu, Fuling Zhou.

  Acute myeloid leukemia (AML) is the most common hematological malignancy. Leukemia stem cells exhibit high levels of oxidative stress, with reactive oxygen species (ROS) being the primary products of this stress, inducing the expression of Jab1. Previous studies have demonstrated that Jab1, as a transcriptional coactivator of c-JUN, promotes the malignant progression of AML under oxidative stress. However, its role in immune evasion is still under investigation. Here, we observed that knocking out Jab1 reduced the expression of immune checkpoints in vivo, effectively overcame the immune evasion of AML. Interestingly, the deletion of Jab1 had no impact on the maturation of normal hematopoietic cells in mice. Mechanistically, Jab1 directly activated IGF2BP3 by driving the transcription factor c-JUN, consequently modulated the m6A modification of LILRB4 mRNA and promoted immune evasion in AML. Finally, CSN5i-3 effectively disrupted the signaling pathway mediated by Jab1, thereby restoring cellular immune surveillance and halting the progression of AML. Thus, our results highlight the functional role of Jab1 in supporting AML survival and support the development of targeted therapeutic strategies.

Keywords:  Cancer gene therapy; Cell biology; Hematology; Leukemias; Signal transduction

DOI:  https://doi.org/10.1172/JCI183761
FEBS Open Bio. 2025 Aug 08.

Statins induce monocytic differentiation in acute myeloid leukemia cells through the KLF4/DPYSL2A axis.

Mina Noura, Kota Shoji, Michidai Nobe, Moe Ishikawa, Miu Tanaka, Akiko Okayama, Souichi Adachi, Hidemasa Matsuo.

  Acute myeloid leukemia (AML) is a bone marrow malignancy characterized by arrested early-stage hematopoietic precursor development. Differentiation therapy, which induces terminal differentiation of immature leukemic cells, is less toxic than standard intensive chemotherapy and a promising treatment strategy for AML. Despite the success of all-trans retinoic acid and arsenic trioxide in treating acute promyelocytic leukemia (APL), effective differentiation therapy for non-APL AML has not been established. We previously demonstrated that dihydropyrimidinase-like 2A (DPYSL2A) is crucial for the monocytic differentiation of AML cells. In this study, analysis using the Comparative Toxicogenomics Database identified statins, which are well-known cholesterol-lowering drugs, as potential compounds that upregulate DPYSL2A expression in a Krüppel-like factor 4 (KLF4)-dependent manner. Most of the tested statins promoted the monocytic differentiation of non-APL AML cells, leading to rapid apoptosis. The statin-induced effects were reversed by mevalonate (MVA) supplementation, indicating dependence on MVA pathway inhibition. Furthermore, the inhibition of protein farnesylation, a downstream process of the MVA pathway, mimicked the statin-induced effects, suggesting that farnesylation suppression is essential for statin-induced KLF4/DPYSL2A expression and monocytic differentiation. These findings may help develop more effective differentiation therapies for patients with non-APL AML.

Keywords:  DPYSL2A; KLF4; leukemia; statins cell differentiation

DOI:  https://doi.org/10.1002/2211-5463.70104
Cell Death Dis. 2025 Aug 02. 16(1): 586

Enlarged PML-nuclear bodies trigger conflicting cell cycle signal-mediated cytotoxicity in leukemia cells.

Tomohisa Baba, Soichiro Kumamoto, Yuta Moriguchi, Soji Morishita, Atsushi Hirao, Yoshikazu Johmura.

Accumulating evidence suggests that mitogenic signaling during cell cycle arrest can lead to severe cytotoxic outcomes, such as senescence, though the underlying mechanisms remain poorly understood. Here, we explored the link between cell cycle dynamics and the formation of PML-nuclear bodies (PML-NBs), intranuclear structures known to mediate cellular stress responses. Our findings demonstrate that PML-NBs increase their number during interphase arrest. Moreover, the activation of mitogenic ERK signaling by all-trans retinoic acid (ATRA) during CDK4/6 inhibitor-induced cell cycle arrest synergistically enhances the formation of larger PML-NBs by associating with SUMO. This enlargement, triggered by the simultaneous engagement of opposing cell cycle signals, leads to potent cytotoxicity accompanied by either terminal differentiation or apoptosis, depending on the cell type, across multiple acute myeloid leukemia (AML) cell lines. Importantly, in an AML mouse model, this combination treatment significantly improved therapeutic efficacy with minimal effects on normal hematopoiesis. Our results introduce conflicting cell cycle signal-induced cytotoxicity as a promising therapeutic strategy for AML.

DOI: https://doi.org/10.1038/s41419-025-07911-7
bioRxiv. 2025 Aug 01. pii: 2025.08.01.668217. [Epub ahead of print]

Dynamics of Ribosomal RNA Transcription and Abundance in Normal and Leukemic Hematopoiesis.

Eleanor I Sams, Victoria K Feist, Erin M Gray, Subin S George, Charles Antony, Jill A Henrich, Julia Wald, Margaret C Dunagin, Zhengyi Wang, Noa Erlitzki, Arjun Raj, Robert A J Signer, Vikram R Paralkar.

Transcription of ribosomal RNAs (rRNAs) from rDNA repeats is the first step of ribosome biogenesis, accounting for a major portion of all cellular transcription. Often regarded as a housekeeping process, its cell-type-specific regulation in complex organ systems is largely neglected. We used rRNA FISH-Flow to profile nascent and mature rRNA levels in detail across mouse hematopoiesis, and observed that rRNA abundance is a cell-type-specific property, largely uncoupled from cell cycling or protein synthesis rates. Absolute quantification of rRNA molecules unexpectedly revealed that 28S rRNA is in excess in all cell types, most prominently in the normal myeloid lineage. In acute myeloid leukemia (AML), leukemic progenitors showed notably higher nascent and mature rRNA levels than matched normal counterparts. Across contexts of hematopoiesis, broad trends in rRNA transcription paralleled changes in accessibility but not methylation of rDNA repeats. Collectively, our work provides a detailed map of the complex dynamics of rRNAs within and between normal and leukemic hematopoiesis.

DOI: https://doi.org/10.1101/2025.08.01.668217
JCO Oncol Pract. 2025 Aug 05. OP2400910

Management of Anemia in Lower-Risk Myelodysplastic Syndromes/Neoplasms With Novel Agents.

Fieke W Hoff, Stephen S Chung, Amer M Zeidan, Yazan F Madanat.

Myelodysplastic syndromes (MDS) are a heterogeneous group of diseases that are prognostically stratified into lower-risk (LR-MDS) and higher-risk MDS on the basis of the International Prognostic Scoring System (eg, IPSS, revised IPSS, and molecular IPSS). Anemia is a hallmark of MDS and can lead to worsening of preexisting comorbidities, long-term RBC transfusion dependence, and profound fatigue. Although RBC transfusion support provides rapid relief of anemia-associated symptoms, it also carries a risk of iron overload and alloimmunization, and is associated with a decreased quality of life. Thus, many clinical trials and treatment strategies for LR-MDS focus on RBC transfusion independence (RBC-TI) as a primary end point. In this review, we discuss the updated treatment paradigm for anemia in LR-MDS. Novel insights in the pathogenesis of MDS and results from positive phase III clinical trials in LR-MDS have led to a growing number of therapeutic options (eg, luspatercept and imetelstat). Imetelstat was recently added as a new agent for patients who are refractory/resistant or ineligible for erythropoiesis-stimulating agent treatment on the basis of the randomized phase III IMerge trial, showing that imetelstat led to the primary end point of RBC-TI for ≥8 weeks in 40% of patients compared with 15% in patients receiving placebo. However, future clinical trials are needed to investigate the optimal sequencing of different agents and the potential of improving efficacy using combination of therapeutic strategies in LR-MDS.

DOI: https://doi.org/10.1200/OP-24-00910
bioRxiv. 2025 Aug 01. pii: 2025.07.29.664810. [Epub ahead of print]

Discovery of chromatin-based determinants of azacytidine and decitabine anti-cancer activity.

Rishi V Puram, Qiangzong Yin, YuhJong Liu, Justine C Rutter, Daniel Bondeson, Maria C Saberi, Lisa Miller, Michael Du, Khanh Nguyen, Donovan L Batzli, Hilina B Woldemichael, Christian Taeger, Anna Goldstein, Ming Y Chu, Qi Guo, D R Mani, Michael Naumann, Melissa M Ronan, Matthew G Rees, Blanche C Ip, Mustafa Kocak, Mikolaj Slabicki, John G Doench, Jennifer A Roth, Steven A Carr, Namrata D Udeshi, Jingyi Wu, Todd R Golub.

The DNA-incorporating nucleoside analogs azacytidine (AZA) and decitabine (DEC) have clinical efficacy in blood cancers, yet the precise mechanism by which these agents kill cancer cells has remained unresolved -- specifically, whether their anti-tumor activity arises from conventional DNA damage or DNA hypomethylation via DNA methyltransferase 1 (DNMT1) inhibition. This incomplete mechanistic understanding has limited their broader therapeutic application, particularly in solid tumors, where early clinical trials showed limited efficacy. Here, through the assessment of drug sensitivity in over 600 human cancer models and comparison to a non-DNA-damaging DNMT1 inhibitor (GSK-3685032), we establish DNA hypomethylation, rather than DNA damage, as the primary killing mechanism of AZA and DEC across diverse cancer types. In further support of an epigenetic killing mechanism, CRISPR drug modifier screens identified a core set of chromatin regulators, most notably the histone deubiquitinase USP48, as AZA and DEC protective factors. We show that USP48 is recruited to newly hypomethylated CpG islands and deubiquitinates non-canonical histones, establishing USP48 as a key molecular link between the two components of epigenetic gene regulation: DNA methylation and chromatin modification. Furthermore, loss of USP48, which occurs naturally through biallelic deletions in human cancers, sensitized both hematologic and solid tumors to DNMT1 inhibition in vitro and in vivo. Our findings elucidate the epigenetic mechanism of action of AZA and DEC and identify a homeostatic link between DNA methylation and chromatin state, revealing new therapeutic opportunities for DNMT1 inhibitors in solid tumors.

DOI: https://doi.org/10.1101/2025.07.29.664810
Cell Stem Cell. 2025 Aug 07. pii: S1934-5909(25)00258-9. [Epub ahead of print]32(8): 1187-1189

Plot twist: TET2 clones save the brain.

Maria A Telpoukhovskaia, Jennifer J Trowbridge.

While clonal hematopoiesis (CH) is associated with protection from Alzheimer's disease (AD), a limited understanding of the mechanisms by which this occurs has been a barrier to therapeutic intervention. In a new study, Matatall et al.1 discover protective mechanisms by which TET2-mutant, but not DNMT3A-mutant, CH impacts dementia pathology and cognition.

DOI: https://doi.org/10.1016/j.stem.2025.07.001
Leukemia. 2025 Aug 05.

Association of the composition of the bone marrow tumor microenvironment in BCR::ABL1-negative myeloproliferative neoplasms with IFN-γ signaling and driver mutations.

Marcus Bauer, Christoforos Vaxevanis, Nadja Jaekel, Hubert Hackl, Andreas Wilfer, Clara Zoellig, Monika Haemmerle, Carsten Müller-Tidow, Haifa Kathrin Al-Ali, Barbara Seliger, Claudia Wickenhauser.

Constitutive JAK/STAT pathway activation is crucial in the pathogenesis of BCR::ABL1-negative myeloproliferative neoplasms (MPN), but has not yet been linked to interferon (IFN)-γ signaling and tumor microenvironment. Human JAK2 V617F-mutated cell lines, 265 bone marrow biopsies (BMB) of two MPN cohorts, and 50 non-neoplastic BMB, revealed an intrinsic activation of IFN-γ signaling, which was confirmed by public RNA expression data. In vitro analysis of JAK2-mutated cell lines showed an activation of IFN-γ signaling pathway in the absence of IFN-γ in the cell supernatants. In addition, a heterogeneous, but increased expression of IFN-γ signaling components was found in BMB of JAK2-mutated samples with the highest expression in lymphocytes and monocytes, accompanied by increased tumor infiltrating lymphocytes (TIL). Unsupervised clustering identified a prognostic favorable cluster in both patient cohorts characterized by augmented IFN-γ signaling and TILs. This cluster was enriched with JAK2-mutated, JAK-inhibition naive MPN, mainly essential thrombocythemia and polycythemia vera with mild bone marrow fibrosis. Moreover, in silico data confirmed the link between JAK2 mutations and increased IFN-γ signaling. Multivariate Cox regression revealed TILs to be the strongest prognostic marker. In conclusion, JAK2-mutated MPN exhibit an intrinsic activation of IFN-γ signaling associated with changes in the BM TME and patients' outcome. Constitutive activation of the Janus kinases and signal transducer and activator of transcription (JAK/STAT) signaling pathway mainly mediated by mutations in the JAK2, CALR and MPL genes in pluripotent hematopoietic stem cells (HSC) is crucial for the pathogenesis of BCR::ABL1-negative myeloproliferative neoplasms (MPN). Despite the activation of JAK/STAT signaling and its influence on the proliferation of malignant cells is well studied in patient samples and JAK2- and CALR-mutated cell systems, there exists limited information about the link between interferon (IFN)-γ signaling and bone marrow (BM) environment alterations. Therefore, two human JAK2 V617F-mutated cell lines, 265 bone marrow biopsies (BMB) of MPN patients, separated in two independent cohorts, both with known clinical parameters, such as driver mutations, treatment and survival, 50 non-neoplastic BMB and five publicly available bulk and single cell RNA expression data sets of MPN samples with known JAK2 or CALR mutation status were analyzed regarding (i) the role of IFN-γ signaling, (ii) its interrelation with the composition of the local BM tumor microenvironment (TME), (iii) the expression of immune response relevant molecules and (iv) their impact on patients' survival. Created in BioRender. Bauer, M. (2025) https://BioRender.com/h133y7w .

DOI: https://doi.org/10.1038/s41375-025-02706-3
Nat Methods. 2025 Aug 07.

Ultra-high-scale cytometry-based cellular interaction mapping.

Dominik Vonficht, Lea Jopp-Saile, Schayan Yousefian, Viktoria Flore, Inés Simó Vesperinas, Ruth Teuber, Bogdan Avanesyan, Yanjiang Luo, Caroline Röthemeier, Florian Grünschläger, Mirian Fernandez-Vaquero, Vincent Fregona, Diana Ordoñez-Rueda, Laura K Schmalbrock, Luca Deininger, Angelo Jovin Yamachui Sitcheu, Zuguang Gu, Maja C Funk, Ralf Mikut, Mathias Heikenwälder, Angelika Eggert, Arend von Stackelberg, Sebastian Kobold, Jan Krönke, Ulrich Keller, Andreas Trumpp, Ahmed N Hegazy, Cornelia Eckert, Daniel Hübschmann, Simon Haas.

Cellular interactions are of fundamental importance, orchestrating organismal development, tissue homeostasis and immunity. Recently, powerful methods that use single-cell genomic technologies to dissect physically interacting cells have been developed. However, these approaches are characterized by low cellular throughput, long processing times and high costs and are typically restricted to predefined cell types. Here we introduce Interact-omics, a cytometry-based framework to accurately map cellular landscapes and cellular interactions across all immune cell types at ultra-high resolution and scale. We demonstrate the utility of our approach to study kinetics, mode of action and personalized response prediction of immunotherapies, and organism-wide shifts in cellular composition and cellular interaction dynamics following infection in vivo. Our scalable framework can be applied a posteriori to existing cytometry datasets or incorporated into newly designed cytometry-based studies to map cellular interactions with a broad range of applications from fundamental biology to applied biomedicine.

DOI: https://doi.org/10.1038/s41592-025-02744-w
Nature. 2025 Aug 06.

Excised DNA circles from V(D)J recombination promote relapsed leukaemia.

Zeqian Gao, James N F Scott, Matthew P Edwards, Dylan Casey, Xiaoling Wang, Andrew D Gillen, Sarra Ryan, Lisa J Russell, Anthony V Moorman, Ruth de Tute, Catherine Cargo, Anthony M Ford, David R Westhead, Joan Boyes.

Extrachromosomal DNA amplification is associated with poor cancer prognoses1. Large numbers of excised signal circles (ESCs) are produced as by-products of antigen receptor rearrangement during V(D)J recombination2,3. However, current dogma states that ESCs are progressively lost through cell division4. Here we show that ESCs replicate and persist through many cell generations and share many properties in common with circular extrachromosomal DNAs. Increased ESC copy numbers at diagnosis of B cell precursor acute lymphoblastic leukaemia were highly correlated with subsequent relapse. By taking advantage of the matching recombination footprint that is formed upon the generation of each ESC, we measured ESC persistence and replication and found increased ESC replication in patients who later relapsed. This increased replication is controlled by cell-intrinsic factors and corresponds to increased expression of DNA replication- and repair-associated genes. Consistent with high ESC levels having a role in disease progression, the number of mutations typical of those caused by the V(D)J recombinase-ESC complex was significantly increased at diagnosis in patients who later relapsed. The number of such mutations in genes associated with relapse increased between diagnosis and relapse, and corresponded to clonal expansion of cells with high ESC copy numbers. These data demonstrate that the by-product of V(D)J recombination, when increased in abundance, potently associates with the V(D)J recombinase to cause adverse disease outcomes.

DOI: https://doi.org/10.1038/s41586-025-09372-6