bims-scepro 2025-05-25 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2025–05–25
thirty-one papers selected by
William Grey, University of York

Lactate dehydrogenase A-coupled NAD+ regeneration is critical for acute myeloid leukemia cell survival.
Microwells as Minimalistic Niches to Study Heterotypic Interactions of Stromal and Hematopoietic Stem Cells.
Aberrant engagement of P-selectin drives hematopoietic stem cell aging in mice.
KK2845, a PBD dimer-containing antibody-drug conjugate targeting TIM-3-expressing AML.
The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status.
Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.
IL-33/ST2 signaling in ILC2s drives exhaustion and myeloid skewing of HSCs in response to hematopoietic stress and aging.
Mitochondrial fission factor drives an actionable metabolic vulnerability in multiple myeloma.
Periosteal skeletal stem cells can migrate into the bone marrow and support hematopoiesis after injury.
Leukaemia Stem Cells and Their Normal Stem Cell Counterparts Are Morphologically Distinguishable by Artificial Intelligence.
Multimodal spatial proteomic profiling in acute myeloid leukemia.
Stem cell therapies in the clinic.
Endogenous Hydrogen Sulphide Promotes the Ex Vivo Expansion of Haematopoietic Stem Cells by Regulating the Activation of the JAK2/STAT3 Pathway.
High-throughput single-cell density measurements enable dynamic profiling of immune cell and drug response from patient samples.
Clonal tracing with somatic epimutations reveals dynamics of blood ageing.
Comprehensive evaluation of phosphoproteomic-based kinase activity inference.
Mapping of Functional Metabolic Phenotypes in Acute Myeloid Leukemia.
Genomic landscape of multiple myeloma and its precursor conditions.
METTL13 is essential for the survival of acute myeloid leukemia cells by regulating MYC.
Translational control of leukemic metabolism and disease progression.
Protocol for high-quality RNA sequencing, cell surface protein analysis, and genotyping in single cells using TARGET-seq.
Deconvoluting clonal and cellular architecture in IDH-mutant acute myeloid leukemia.
Genetic and Phenotypic correlates of clinical outcomes with Venetoclax in Acute Myeloid Leukemia: The GEN-PHEN-VEN study.
Cholinergic regulation of thymocyte negative selection.
Visfatin promotes multiple myeloma cell proliferation and inhibits apoptosis by inducing IL-6 production via NF-κB pathways.
Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal.
CREBBP inactivation sensitizes B cell acute lymphoblastic leukemia to ferroptotic cell death upon BCL2 inhibition.
Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration.
Targeting lipid metabolism in acute myeloid leukemia: biological insights and therapeutic opportunities.
Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations.
A Revised Prognostic Model for Patients with Acute Myeloid Leukemia and First Relapse.

Cancer Metab. 2025 May 19. 13(1): 22

Lactate dehydrogenase A-coupled NAD+ regeneration is critical for acute myeloid leukemia cell survival.

Ayşegül Erdem, Séléna Kaye, Francesco Caligiore, Manuel Johanns, Fleur Leguay, Jan Jacob Schuringa, Keisuke Ito, Guido Bommer, Nick van Gastel.

   BACKGROUND: Enhanced glycolysis plays a pivotal role in fueling the aberrant proliferation, survival and therapy resistance of acute myeloid leukemia (AML) cells. Here, we aimed to elucidate the extent of glycolysis dependence in AML by focusing on the role of lactate dehydrogenase A (LDHA), a key glycolytic enzyme converting pyruvate to lactate coupled with the recycling of NAD+.
METHODS: We compared the glycolytic activity of primary AML patient samples to protein levels of metabolic enzymes involved in central carbon metabolism including glycolysis, glutaminolysis and the tricarboxylic acid cycle. To evaluate the therapeutic potential of targeting glycolysis in AML, we treated AML primary patient samples and cell lines with pharmacological inhibitors of LDHA and monitored cell viability. Glycolytic activity and mitochondrial oxygen consumption were analyzed in AML patient samples and cell lines post-LDHA inhibition. Perturbations in global metabolite levels and redox balance upon LDHA inhibition in AML cells were determined by mass spectrometry, and ROS levels were measured by flow cytometry.
RESULTS: Among metabolic enzymes, we found that LDHA protein levels had the strongest positive correlation with glycolysis in AML patient cells. Blocking LDHA activity resulted in a strong growth inhibition and cell death induction in AML cell lines and primary patient samples, while healthy hematopoietic stem and progenitor cells remained unaffected. Investigation of the underlying mechanisms showed that LDHA inhibition reduces glycolytic activity, lowers levels of glycolytic intermediates, decreases the cellular NAD+ pool, boosts OXPHOS activity and increases ROS levels. This increase in ROS levels was however not linked to the observed AML cell death. Instead, we found that LDHA is essential to maintain a correct NAD+/NADH ratio in AML cells. Continuous intracellular NAD+ supplementation via overexpression of water-forming NADH oxidase from Lactobacillus brevis in AML cells effectively increased viable cell counts and prevented cell death upon LDHA inhibition.
CONCLUSIONS: Collectively, our results demonstrate that AML cells critically depend on LDHA to maintain an adequate NAD+/NADH balance in support of their abnormal glycolytic activity and biosynthetic demands, which cannot be compensated for by other cellular NAD+ recycling systems. These findings also highlight LDHA inhibition as a promising metabolic strategy to eradicate leukemic cells.

Keywords:  Acute myeloid leukemia; Cancer metabolism; Glycolysis; Lactate dehydrogenase A; NAD+ ; Redox balance

DOI:  https://doi.org/10.1186/s40170-025-00392-4
Methods Mol Biol. 2025 May 22.

Microwells as Minimalistic Niches to Study Heterotypic Interactions of Stromal and Hematopoietic Stem Cells.

Adrian Candelas, Thomas Bessy, Benoit Vianay, Manuel Théry, Stephane Brunet.

  Hematopoietic stem and progenitor cells (HSPCs) can migrate and reside within the bone marrow in distinct microenvironments or niches. The niches organize around specific stromal cells, such as endothelial cells at the capillary or sinusoid walls, and osteoblasts along the bone matrix. Within each niche, a specific combination of external cues, including secreted and diffusible factors, cell-matrix, and cell-cell interactions, controls HSPCs behavior and fate. Deciphering the interplay between HSPCs and stromal cells of the niches is challenging: in vivo, it is hindered by the opacity of the bone matrix; in vitro, classical co-culture models only poorly recapitulate essential features of the physiological niches. The difficulty is moreover amplified by the exceptional migration capacity of HSPCs.In this chapter, we present a method to overcome these limitations by producing arrays of microwells designed to mimic bone marrow niches in a functional manner. These "microniches" promote a long-term interaction between the HSPC and a stromal cell of interest. We describe their microfabrication based on a maskless photolithography method allowing the production of arrays of microwells with reproducible volume and geometry, and the iterative improvement of the geometric design of the wells. We describe the loading and culture of stromal cells with HSPCs. We discuss the potentiality of microwells, in basic and applied research, as a platform to investigate molecular mechanisms involved in direct cell-cell interactions and local effects of diffusible factors, for any adherent and non-adherent cells of interest.

Keywords:  Hematopoietic stem and progenitor cells; High-resolution imaging; Hydrogel; Live imaging; Microfabrication artificial biomimetic niche; Microwell; Stem cell niche

DOI:  https://doi.org/10.1007/7651_2025_628
Nat Aging. 2025 May 23.

Aberrant engagement of P-selectin drives hematopoietic stem cell aging in mice.

Daozheng Yang, Natalia Skinder, Yun-Ruei Kao, Jiahao Chen, Victor Thiruthuvanathan, Arthur Flohr Svendsen, Chi Zhang, Bertien Dethmers-Ausema, Ellen Weersing, Maria Maryanovich, Britta Will, Gerald de Haan.

During aging, hematopoietic stem cell (HSC) function progressively declines which can lead to reduced blood cell production and regeneration. This work uncovered that cell surface presentation of P-selectin (CD62P, encoded by Selp) increases in a large fraction of aging HSCs driven by a proinflammatory milieu in mice. Notably, expression of P-selectin molecularly and functionally dichotomized the aging HSC pool; stem cells presenting with highly abundant P-selectin were hallmarked by aging-associated gene expression programs and reduced repopulation capacity upon regenerative stress. Ectopic expression of Selp in young HSCs was sufficient to impair long-term reconstitution potential and impair erythropoiesis. Mechanistically, we uncovered that P-selectin receptor activation by its primary ligand, P-selectin glycoprotein ligand-1, suppressed aging-associated gene expression, and, reversely, lack of P-selectin signaling led to HSC premature aging. Collectively, our study uncovered a functional role of P-selectin engagement in regulating HSC regeneration and driving stem cell aging when perturbed.

DOI: https://doi.org/10.1038/s43587-025-00880-8
Leukemia. 2025 May 22.

KK2845, a PBD dimer-containing antibody-drug conjugate targeting TIM-3-expressing AML.

Jian Zou, Haruka Kinosada, Shin-Ichiro Takayanagi, Toshihiko Ishii, Toru Amano, Kaito Nihira, Shohei Kanie, Maiko Adachi, Harunobu Tahara, Teppei Sakoda, Yoshikane Kikushige, Koichi Akashi, Hidetaka Satou.

Acute myeloid leukemia (AML) is a common hematopoietic malignancy with high recurrence rates, and there is an urgent need for new therapeutic agents. T-cell immunoglobulin mucin-3 (TIM-3) is expressed on the surface of both LSCs and blasts in most AML patients, but not in normal hematopoietic stem cells (HSCs). We have developed KK2845, an antibody drug conjugate (ADC) that consists of an anti-TIM-3 fully human IgG1 antibody, a valine-alanine linker and a highly potent DNA cross-linking pyrrolobenzodiazepine (PBD) dimer SG3199. KK2845 exhibited potent cytotoxicity against AML cells both in vitro and in vivo. The cytotoxicity against AML cells was almost comparable between KK2845 and CD33-ADC, an anti-CD33 antibody conjugated with PBD dimer that has shown high remission rates in clinical studies. In addition to the cytotoxicity depending on PBD dimer, KK2845 also showed potent antibody-dependent cell cytotoxicity (ADCC) activity against AML cells. KK2845 showed less cytotoxicity against human normal bone marrow cells than CD33-ADC. The pharmacokinetics of KK2845 in cynomolgus monkey after intravenous infusion demonstrated a favorable profile. Taken together, these data suggest that KK2845 could be a novel ADC therapeutic in AML.

DOI: https://doi.org/10.1038/s41375-025-02642-2
Blood Adv. 2025 May 22. pii: bloodadvances.2024015627. [Epub ahead of print]

The SAMD1 transcription factor coordinates hematopoietic lineage differentiation and H3K4 methylation status.

Meg A Schaefer, Samantha L Gomez, Venkatasai Rahul Dogiparthi, Yichao J Zhou, Pooja Roy, Suhita J Ray, Linda Chee, Sandipan Brahma, Robert Liefke, Kyle J Hewitt.

Cell progenitor to progeny transitions depend on precise transcriptional mechanisms to adjust gene expression. The sterile alpha motif-containing 1 protein (SAMD1) regulates a shift in transcriptional activity during embryonic stem cell exit from pluripotency. SAMD1 interacts with and facilitates the activity of the histone H3 lysine demethylating enzyme LSD1. SAMD1 is expressed throughout many biological systems, but its role in hematopoiesis is unknown. In human and mouse hematopoietic stem/progenitor cells, we tested the role of SAMD1 in hematopoiesis and erythropoiesis using loss-of-function approaches. SAMD1 promoted expression of critical drivers of hematopoiesis, including the GATA2 transcription factor, while opposing erythroid programs. Loss of SAMD1 in ex vivo differentiating cells increased erythroid and megakaryocyte differentiation and altered the landscape of histone H3K4 methylation genome-wide. Cohorts of SAMD1-repressed genes are linked to erythropoietic activities. SAMD1 expression promoted ERK signaling via SCF/Kit stimulation in progenitor populations. In erythroid precursor cells, SAMD1 co-occupies chromatin with LSD1 and GATA factors. Whereas SAMD1 downregulates H3K4me2 levels genome-wide, contributing to gene repression, SAMD1 also elevates transcription at select sites. To test Samd1 function in hematopoiesis, we performed competitive transplant experiments in mice. Samd1 knockdown hematopoietic stem cells (HSCs) contributed more to peripheral blood mononuclear cells versus control HSCs. Our results establish SAMD1 as a coordinator of H3K4 methylation and stem/progenitor activity in hematopoiesis and erythropoiesis.

DOI: https://doi.org/10.1182/bloodadvances.2024015627
Nat Commun. 2025 May 19. 16(1): 4656

Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12.

Selina Troester, Thomas Eder, Nadja Wukowits, Martin Piontek, Pablo Fernández-Pernas, Johannes Schmoellerl, Ben Haladik, Gabriele Manhart, Melanie Allram, Margarita Maurer-Granofszky, Nastassja Scheidegger, Karin Nebral, Giulio Superti-Furga, Roland Meisel, Beat Bornhauser, Peter Valent, Michael N Dworzak, Johannes Zuber, Kaan Boztug, Florian Grebien.

Nucleoporin 98 (NUP98) fusion oncoproteins are strong drivers of pediatric acute myeloid leukemia (AML) with poor prognosis. Here we show that NUP98 fusion-expressing AML harbors an epigenetic signature that is characterized by increased accessibility of hematopoietic stem cell genes and enrichment of activating histone marks. We employ an AML model for ligand-induced degradation of the NUP98::KDM5A fusion oncoprotein to identify epigenetic programs and transcriptional targets that are directly regulated by NUP98::KDM5A through CUT&Tag and nascent RNA-seq. Orthogonal genome-wide CRISPR/Cas9 screening identifies 12 direct NUP98::KDM5A target genes, which are essential for AML cell growth. Among these, we validate cyclin-dependent kinase 12 (CDK12) as a druggable vulnerability in NUP98::KDM5A-expressing AML. In line with its role in the transcription of DNA damage repair genes, small-molecule-mediated CDK12 inactivation causes increased DNA damage, leading to AML cell death. Altogether, we show that NUP98::KDM5A directly regulates a core set of essential target genes and reveal CDK12 as an actionable vulnerability in AML with oncogenic NUP98 fusions.

DOI: https://doi.org/10.1038/s41467-025-59930-9
iScience. 2025 May 16. 28(5): 112378

IL-33/ST2 signaling in ILC2s drives exhaustion and myeloid skewing of HSCs in response to hematopoietic stress and aging.

Pascal Naef, Carla A Jaeger-Ruckstuhl, Noah Schnüriger, Stefan Forster, Inês Monteiro, Daniel Brigger, Alexander Eggel, Kai Kessenbrock, Carsten Riether, Adrian F Ochsenbein.

  Inflammatory cues affect hematopoietic stem cell (HSC) homeostasis and drive proliferation and myeloid skewing of HSCs. The HSC niche in the bone marrow (BM) is populated by a variety of stromal and immune cells that sense and respond to cellular stress. We investigated how BM-resident type 2 innate lymphoid cells (ILC2s) regulate HSC homeostasis and differentiation in steady state, during aging, and after genotoxic stress. We documented that PDGFR-α+sca-1+ mesenchymal stromal cells in the BM produced interleukin (IL)-33 with elevated levels after irradiation and during aging. IL-33/ST2 signaling in BM-resident ILC2s activated MAPK/NF-κB/JAK-STAT signaling and induced cytokine secretion. IL-6 and granulocyte-macrophage colony-stimulating factor (GM-CSF), secreted by ILC2s, promoted HSCs to proliferate and differentiate into the myeloid lineage. Taken together, we identified that IL-33 produced by MSCs induced ILC2s to secrete myeloid differentiation factors leading to myeloid-skewed HSCs with reduced self-renewal during aging.

Keywords:  Cell biology; Immune response

DOI:  https://doi.org/10.1016/j.isci.2025.112378
Haematologica. 2025 May 22.

Mitochondrial fission factor drives an actionable metabolic vulnerability in multiple myeloma.

Maria Eugenia Gallo Cantafio, Ilenia Valentino, Roberta Torcasio, Ludovica Ganino, Claudia Veneziano, Pierpaolo Murfone, Maria Mesuraca, Ida Perrotta, Federico Tallarigo, Valter Agosti, Carmela De Marco, Teresa Pasqua, Cesarina Giallongo, Anna Rita Cappello, Marco Fiorillo, Massimo Gentile, Daniele Tibullo, Giuseppe Viglietto, Antonino Neri, Nicola Amodio.

Proliferating multiple myeloma (MM) cells in the bone marrow fluctuate across various metabolic states to resist cancer treatments. Herein, we investigate how mitochondrial dynamics, which controls mitochondrial fitness via coordinated fission and fusion events, shapes MM cell metabolism impacting growth, survival and drug sensitivity. We identify MFF (Mitochondrial Fission Factor), a pivotal driver of mitochondrial fragmentation, as being highly expressed in MM plasma cells bearing cytogenetic abnormalities predicting poor clinical outcome. In preclinical models, MFF selective inhibition via multiple RNAbased strategies (shRNAs, siRNAs or LNA gapmeR ASOs) reduces MM cell growth both in vitro and in vivo, enabling adaptive metabolic responses consistent with the induction of glycolysis and the inhibition of lactate-mediated OXPHOS. We also demonstrate that lactate supplementation, as well as clinically relevant drugs promoting lactate accumulation, such as AZD3965 and Syrosingopine, trigger MFF-dependent metabolic changes, enhancing the sensitivity of MM cells to strategies targeting mitochondrial fission. Finally, we highlight a novel lactate-MFF axis involved in proteasome inhibitor resistance, and show that combining AZD3965 or Syrosingopine with bortezomib results in synergistic anti-MM activity along with MFF down-regulation. Collectively, these data point to MFF-dependent mitochondrial fragmentation as a key metabolic hallmark of MM, providing a framework for the development of novel therapeutic strategies targeting mitochondrial dynamics and harnessing the metabolic plasticity of malignant plasma cells.

DOI: https://doi.org/10.3324/haematol.2025.287526
Elife. 2025 May 22. pii: RP101714. [Epub ahead of print]13

Periosteal skeletal stem cells can migrate into the bone marrow and support hematopoiesis after injury.

Tony Marchand, Kemi E Akinnola, Shoichiro Takeishi, Maria Maryanovich, Sandra Pinho, Julien Saint-Vanne, Alexander Birbrair, Thierry Lamy, Karin Tarte, Paul Frenette, Kira Gritsman.

  Skeletal stem cells (SSCs) have been isolated from various tissues, including periosteum and bone marrow, where they exhibit key functions in bone biology and hematopoiesis, respectively. The role of periosteal SSCs (P-SSCs) in bone regeneration and healing has been extensively studied, but their ability to contribute to the bone marrow stroma is still under debate. In the present study, we characterized a mouse whole bone transplantation model that mimics the initial bone marrow necrosis and fatty infiltration seen after injury. Using this model and a lineage tracing approach, we observed the migration of P-SSCs into the bone marrow after transplantation. Once in the bone marrow, P-SSCs are phenotypically and functionally reprogrammed into bone marrow mesenchymal stem cells (BM-MSCs) that express high levels of hematopoietic stem cell niche factors such as Cxcl12 and Kitl. In addition, using ex vivo and in vivo approaches, we found that P-SSCs are more resistant to acute stress than BM-MSCs. These results highlight the plasticity of P-SSCs and their potential role in bone marrow regeneration after bone marrow injury.

Keywords:  cell biology; mouse; niche; periosteum; regeneration

DOI:  https://doi.org/10.7554/eLife.101714
J Cell Mol Med. 2025 May;29(10): e70564

Leukaemia Stem Cells and Their Normal Stem Cell Counterparts Are Morphologically Distinguishable by Artificial Intelligence.

Dongguang Li, Ngoc DeSouza, Kathy Nguyen, Shaoguang Li.

  Leukaemia stem cells (LSCs) are a rare population among the bulk of leukaemia cells and are responsible for disease initiation, progression/relapse and insensitivity to therapies in numerous haematologic malignancies. Identification of LSCs and monitoring of their quantity before, during, and after treatments will provide a guidance for choosing a correct treatment and assessing therapy response and disease prognosis, but such a method is still lacking simply because there are no distinct morphological features recognisable for distinguishing LSCs from normal stem cell counterparts. Using artificial intelligence (AI) deep learning and polycythemia vera (PV) as a disease model (a type of human myeloproliferative neoplasms derived from a haematopoietic stem cell harbouring the JAK2V617F oncogene), we combine 19 convolutional neural networks as a whole to build AI models for analysing single-cell images, allowing for distinguishing between LSCs from JAK2V617F knock-in mice and normal stem counterparts from healthy mice with a high accuracy (> 99%). We prove the concept that LSCs possess unique morphological features compared to their normal stem cell counterparts, and AI, but not microscopic visualisation by pathologists, can extract and identify these features. In addition, we show that LSCs and other cell lineages in PV mice are also distinguishable by AI. Our study opens up a potential AI morphology field for identifying various primitive leukaemia cells, especially including LSCs, to help assess therapy responses and disease prognosis in the future.

Keywords:  artificial intelligence; leukaemia stem cells; morphology

DOI:  https://doi.org/10.1111/jcmm.70564
NPJ Precis Oncol. 2025 May 20. 9(1): 148

Multimodal spatial proteomic profiling in acute myeloid leukemia.

Christopher P Ly, Ivo Veletic, Christopher D Pacheco, Enes Dasdemir, Fatima Z Jelloul, Sammy Ferri-Borgogno, Akshay V Basi, Javier A Gomez, Jessica L Root, Patrick K Reville, Sonali Jindal, Sreyashi Basu, Padmanee Sharma, Andres E Quesada, Carlos Bueso-Ramos, Taghi Manshouri, Branko Cuglievan, Miriam Garcia, Jared K Burks, Hussein A Abbas.

Acute myeloid leukemia (AML) resides in an immune-rich microenvironment, yet, immune-based therapies have faltered in eliciting durable responses. Bridging this paradox requires a comprehensive understanding of leukemic interactions within the bone marrow microenvironment. We optimized a high-throughput tissue-microarray-based pipeline for high-plex spatial immunofluorescence and mass cytometry imaging on a single slide, capturing immune, tumor, and structural components. Using unbiased clustering on the spatial K function, we unveiled the presence of tertiary lymphoid-like aggregates in bone marrow, which we validated using spatial transcriptomics and an independent proteomics approach. We then found validated TLS signatures predictive of outcomes in AML using an integrated public 480-patient transcriptomic dataset. By harnessing high-plex spatial proteomics, we open the possibility of discovering novel structures and interactions that underpin leukemic immune response. Further, our study's methodologies and resources can be adapted for other bone marrow diseases where decalcification and autofluorescence present challenges.

DOI: https://doi.org/10.1038/s41698-025-00897-7
Bioeng Transl Med. 2025 May;10(3): e70000

Stem cell therapies in the clinic.

Shrinivas Acharya, Suyog Shaha, Michael Griffith Bibbey, Malini Mukherji, Zongmin Zhao, Samir Mitragotri.

  Stem cell therapies have emerged as a transformative approach in modern medicine, with the potential to address and possibly cure a broad spectrum of diseases. These therapies utilize living stem cells that can perform complex biological functions not replicable by traditional drugs. Stem cell therapies have an expanding therapeutic landscape, with several products already approved and numerous clinical trials underway. Among the various stem cell types, hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs) are most widely studied. In this review, we provide a detailed analysis of the current clinical landscape of stem cell therapies. We review 27 stem cell products that have received regulatory approvals and discuss 800 ongoing clinical trials, with a focus on HSCs and MSCs. We also discuss the critical challenges to be addressed to facilitate the clinical translation of stem cell therapies.

Keywords:  HSC; MSC; cell; cell therapy; clinical translation; clinical trials; iPSC; stem cell

DOI:  https://doi.org/10.1002/btm2.70000
Immunology. 2025 May 22.

Endogenous Hydrogen Sulphide Promotes the Ex Vivo Expansion of Haematopoietic Stem Cells by Regulating the Activation of the JAK2/STAT3 Pathway.

Zhiyuan Qiu, Hui Liu, Rongxuan Cao, Shan Wang, Junjun Wang, Wenjun Xu, Rui Zhang, Baohong Wang, Xiaoting Zhang, Qianpeng Li.

  Haematopoietic stem cell transplantation (HSCT) is one of the key strategies for treating various haematologic malignancies. Although there are haematopoietic stem cells (HSCs) in umbilical cord blood (UCB), the number is limited. Thus, the purpose of this work was to investigate if endogenous hydrogen sulphide (H2S) could encourage the ex vivo expansion of HSCs produced from UCB (UCB-HSCs). The CD34+ and CD34+CD38- cells were enriched and separated by immunomagnetic beads. UCB-HSCs were treated with overexpression plasmids of β-synthase (CBS), cystathionine γ-lyase (CSE), 3-mercaptopyruvate sulphurtransferase (MPST) and/or stimulated with AG490 (JAK2/STAT3 inhibitor) for 4, 7 or 10 days, respectively. The content of H2S in cells was detected using its assay kit. The proportion and quantity of CD34+, CD34+CD38- and CXCR4+CD34+ cells as well as the ALDH1A1+CD34+ cells in CD34+ cells were detected by flow cytometry. qPCR was used to detect the expression of CD34, CXCR4 and ALDH1A1 in CD34+ cells. Western blot was used to detect the activation of the JAK2/STAT3 pathway in CD34+ cells. The results showed that endogenous H2S enhanced the ex vivo expansion of CD34+ and CD34+CD38- cells, upregulated the expression of CXCR4 and ALDH1A1 during ex vivo expansion of HSCs, and promoted the JAK2/STAT3 pathway in CD34+ cells. However, the aforementioned effects of endogenous H2S were partially reversed by AG490. In conclusion, endogenous H2S promotes the activation of the JAK2/STAT3 pathway to facilitate the ex vivo expansion of UCB-HSCs.

Keywords:  JAK2/STAT3 pathway; ex vivo expansion; haematopoietic stem cells; hydrogen sulphide; umbilical cord blood

DOI:  https://doi.org/10.1111/imm.13935
Nat Biomed Eng. 2025 May 20.

High-throughput single-cell density measurements enable dynamic profiling of immune cell and drug response from patient samples.

Weida Wu, Sarah H Ishamuddin, Thomas W Quinn, Smitha Yerrum, Ye Zhang, Lydie L Debaize, Pei-Lun Kao, Sarah Marie Duquette, Mark A Murakami, Morvarid Mohseni, Kin-Hoe Chow, Teemu P Miettinen, Keith L Ligon, Scott R Manalis.

Cell density, the ratio of cell mass to volume, is an indicator of molecular crowding and a fundamental determinant of cell state and function. However, existing density measurements lack the precision or throughput to quantify subtle differences in cell states, particularly in primary samples. Here we present an approach for measuring the density of 30,000 single cells per hour by integrating fluorescence exclusion microscopy with a suspended microchannel resonator. This approach achieves a precision of 0.03% (0.0003 g ml-1) for cells larger than 12 μm in diameter. In human lymphocytes, we discover that cell density and its variation decrease as cells transition from quiescence to a proliferative state, suggesting that the level of molecular crowding decreases and becomes more regulated upon entry into the cell cycle. Using a pancreatic cancer patient-derived xenograft model, we find that the ex vivo density response of primary tumour cells to drug treatment can predict the in vivo tumour growth response. Our method reveals unexpected behaviour in molecular crowding during cell state transitions and suggests density as a biomarker for functional precision medicine.

DOI: https://doi.org/10.1038/s41551-025-01408-6
Nature. 2025 May 21.

Clonal tracing with somatic epimutations reveals dynamics of blood ageing.

Michael Scherer, Indranil Singh, Martina Maria Braun, Chelsea Szu-Tu, Pedro Sanchez Sanchez, Dominik Lindenhofer, Niels Asger Jakobsen, Verena Körber, Michael Kardorff, Lena Nitsch, Pauline Kautz, Julia Rühle, Agostina Bianchi, Luca Cozzuto, Robert Frömel, Sergi Beneyto-Calabuig, Caleb Lareau, Ansuman T Satpathy, Renée Beekman, Lars M Steinmetz, Simon Raffel, Leif S Ludwig, Paresh Vyas, Alejo Rodriguez-Fraticelli, Lars Velten.

Current approaches used to track stem cell clones through differentiation require genetic engineering1,2 or rely on sparse somatic DNA variants3,4, which limits their wide application. Here we discover that DNA methylation of a subset of CpG sites reflects cellular differentiation, whereas another subset undergoes stochastic epimutations and can serve as digital barcodes of clonal identity. We demonstrate that targeted single-cell profiling of DNA methylation5 at single-CpG resolution can accurately extract both layers of information. To that end, we develop EPI-Clone, a method for transgene-free lineage tracing at scale. Applied to mouse and human haematopoiesis, we capture hundreds of clonal differentiation trajectories across tens of individuals and 230,358 single cells. In mouse ageing, we demonstrate that myeloid bias and low output of old haematopoietic stem cells6 are restricted to a small number of expanded clones, whereas many functionally young-like clones persist in old age. In human ageing, clones with and without known driver mutations of clonal haematopoieis7 are part of a spectrum of age-related clonal expansions that display similar lineage biases. EPI-Clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.

DOI: https://doi.org/10.1038/s41586-025-09041-8
Nat Commun. 2025 May 22. 16(1): 4771

Comprehensive evaluation of phosphoproteomic-based kinase activity inference.

Sophia Müller-Dott, Eric J Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M Yaron-Barir, Sara R Savage, Martin Garrido-Rodriguez, Jared L Johnson, Alessandro Lussana, Evangelia Petsalaki, Jonathan T Lei, Aurelien Dugourd, Karsten Krug, Lewis C Cantley, D R Mani, Bing Zhang, Julio Saez-Rodriguez.

Kinases regulate cellular processes and are essential for understanding cellular function and disease. To investigate the regulatory state of a kinase, numerous methods have been developed to infer kinase activities from phosphoproteomics data using kinase-substrate libraries. However, few phosphorylation sites can be attributed to an upstream kinase in these libraries, limiting the scope of kinase activity inference. Moreover, inferred activities vary across methods, necessitating evaluation for accurate interpretation. Here, we present benchmarKIN, an R package enabling comprehensive evaluation of kinase activity inference methods. Alongside classical perturbation experiments, benchmarKIN introduces a tumor-based benchmarking approach utilizing multi-omics data to identify highly active or inactive kinases. We used benchmarKIN to evaluate kinase-substrate libraries, inference algorithms and the potential of adding predicted kinase-substrate interactions to overcome the coverage limitations. Our evaluation shows most computational methods perform similarly, but the choice of library impacts the inferred activities with a combination of manually curated libraries demonstrating superior performance in recapitulating kinase activities. Additionally, in the tumor-based evaluation, adding predicted targets from NetworKIN further boosts the performance. We then demonstrate how kinase activity inference aids characterize kinase inhibitor responses in cell lines. Overall, benchmarKIN helps researchers to select reliable methods for identifying deregulated kinases.

DOI: https://doi.org/10.1038/s41467-025-59779-y
Cancer Med. 2025 May;14(10): e70950

Mapping of Functional Metabolic Phenotypes in Acute Myeloid Leukemia.

Sissel Dyrstad, Kimberley Joanne Hatfield, Endre Stigen, Marte Karen Brattås, Karl Johan Tronstad, Håkon Reikvam.

   BACKGROUND: Acute myeloid leukemia (AML) is an aggressive hematologic malignancy with a poor prognosis, particularly in older patients. AML is highly heterogeneous, influenced by various chromosomal, genetic, and epigenetic alterations.
METHODS: This study investigated the metabolic profiles of primary AML cells from 46 patients, focusing on mitochondrial respiration and glycolysis. We hypothesized that the metabolic profiles would reflect distinct disease characteristics. Using Seahorse technology, we measured the oxygen consumption rate (OCR) for mitochondrial respiration and the extracellular acidification rate (ECAR) for glycolysis.
RESULTS: Our results showed significant variability in metabolic activity, with some samples relying more on glycolysis than mitochondrial respiration. Mature AML cells (FAB M4/M5, CD34 negative) exhibited increased rates of both mitochondrial respiration and glycolysis, indicating distinct metabolic adaptations. Higher glycolytic activity was observed in patients with adverse cytogenetic abnormalities. However, no clear associations were found between metabolic profiles and mutations in FLT3 or NPM1.
CONCLUSION: These findings highlight the role of metabolic variability in AML and suggest that targeting specific metabolic pathways could offer therapeutic opportunities, particularly for subgroups like FAB M4/M5 with unique metabolic features. Further studies are needed to refine these therapeutic strategies for clinical application.

Keywords:  acute myeloid leukemias; glycolysis; metabolic phenotypes; metabolism

DOI:  https://doi.org/10.1002/cam4.70950
Nat Genet. 2025 May 21.

Genomic landscape of multiple myeloma and its precursor conditions.

Jean-Baptiste Alberge, Ankit K Dutta, Andrea Poletti, Tim H H Coorens, Elizabeth D Lightbody, Rosa Toenges, Xavi Loinaz, Sofia Wallin, Andrew Dunford, Oliver Priebe, Johnathan Dagan, Cody J Boehner, Erica Horowitz, Nang K Su, Hadley Barr, Laura Hevenor, Katherine Towle, Rashmika Beesam, Jenna B Beckwith, Jacqueline Perry, David M Cordas Dos Santos, Luca Bertamini, Patricia T Greipp, Kirsten Kübler, Peter F Arndt, Carolina Terragna, Elena Zamagni, Eileen M Boyle, Kwee Yong, Gareth Morgan, Brian A Walker, Meletios Athanasios Dimopoulos, Efstathios Kastritis, Julian Hess, Romanos Sklavenitis-Pistofidis, Chip Stewart, Gad Getz, Irene M Ghobrial.

Reliable strategies to capture patients at risk of progression from precursor stages of multiple myeloma (MM) to overt disease are still missing. We assembled a comprehensive collection of MM genomic data comprising 1,030 patients (218 with precursor conditions) that we used to identify recurrent coding and non-coding candidate drivers as well as significant hotspots of structural variation. We used those drivers to define and validate a simple 'MM-like' score, which we could use to place patients' tumors on a gradual axis of progression toward active disease. Our MM precursor genomic map provides insights into the time of initiation and cell-of-origin of the disease, order of acquisition of genomic alterations and mutational processes found across the stages of transformation. Taken together, we highlight here the potential of genome sequencing to better inform risk assessment and monitoring of MM precursor conditions.

DOI: https://doi.org/10.1038/s41588-025-02196-0
Cell Death Discov. 2025 May 17. 11(1): 240

METTL13 is essential for the survival of acute myeloid leukemia cells by regulating MYC.

Kui Zhao, Hanyue Zhang, Shuoting Wang, Yuhang Zhou, Zhishuai Zhang, Baoqiang Kang, Huaisong Lin, Yanqi Zhang, Jiaming Gu, Carla Pantoja, Lingling Liu, Yi He, Guangjin Pan, Yongli Shan, Bing Long.

Recently, some methyltransferase-like (METTL) proteins have been found to play crucial roles in the development of acute myeloid leukemia (AML) through mediating RNA modifications, such as METTL3/14/16 mediated N6-methyladenosine (m6A) and METTL1 mediated N7-methylguanosine (m7G). However, the roles of other METTL proteins in AML progression remain unknown. Here, we examined the expression levels of all METTL members in AML samples and showed that METTL13 was increased in AML and positively correlated with poor prognosis. Moreover, METTL13 deficiency impaired AML cell proliferation capability in vitro, improved the survival of AML cell line xenograft immune-deficient mice, and reduced tumor infiltration in vivo. Mechanistically, MYC was downregulated after METTL13 knockdown and forced expression of MYC rescued the cell proliferation defect in METTL13-deficient AML cells. Our findings uncover the critical role of METTL13 in the survival of AML cells and identify MYC as a potential downstream target of METTL13. This work highlights METTL13 as a promising candidate target for AML therapy.

DOI: https://doi.org/10.1038/s41420-025-02512-x
Trends Cell Biol. 2025 May 22. pii: S0962-8924(25)00108-4. [Epub ahead of print]

Translational control of leukemic metabolism and disease progression.

François E Mercier, Victor Gife, Raquel Aloyz, Laura Hulea.

  Acute myeloid leukemia (AML) is an aggressive hematological cancer with a 70% five-year mortality rate. Relapse occurs in approximately half of adults treated with intensive chemotherapy, while responses to targeted therapies are short-lasting. Frequent mutations in signaling pathways, such as FLT3 tyrosine kinase and RAS, lead to dysregulated mammalian target of rapamycin complex 1 (mTORC1)and mitogen-activated protein kinase (MAPK) signaling, increased protein synthesis, enhanced mitochondrial fitness, and metabolic adaptations that drive leukemic cell proliferation and survival. Here, emerging evidence supporting the unique role of eukaryotic initiation factor 4F as a key driver of the expression of proteins regulating leukemic cell metabolism and survival and the potential therapeutic benefit of targeting this pathway pharmacologically in AML are discussed.

Keywords:  BCL2; FLT3; eIF4F; leukemic stem cells; mTORC1; metabolism

DOI:  https://doi.org/10.1016/j.tcb.2025.04.006
STAR Protoc. 2025 May 21. pii: S2666-1667(25)00238-2. [Epub ahead of print]6(2): 103832

Protocol for high-quality RNA sequencing, cell surface protein analysis, and genotyping in single cells using TARGET-seq.

N Asger Jakobsen, Sven Turkalj, Paresh Vyas.

  Studying the consequences of somatic mutations in pre-malignant and cancerous tissues is challenging due to noise in single-cell transcriptome data and difficulty in identifying the clonal identity of single cells. We optimized TARGET-seq to develop TARGET-seq+, which combines RNA sequencing (RNA-seq), the analysis of cell surface protein expression, and genotyping in single cells with improved sensitivity. We describe the steps for cell isolation, the preparation of single-cell RNA-seq (scRNA-seq) and genotyping libraries, and sequencing. We also provide guidance on the analysis of single-cell genotyping, transcriptome pre-processing, and data integration. For complete details on the use and execution of this protocol, please refer to Jakobsen et al.1.

Keywords:  Flow Cytometry; Gene Expression; Genomics; Molecular Biology; RNA-seq; Sequencing; Single Cell; Stem Cells

DOI:  https://doi.org/10.1016/j.xpro.2025.103832
Cell Stem Cell. 2025 May 21. pii: S1934-5909(25)00179-1. [Epub ahead of print]

Deconvoluting clonal and cellular architecture in IDH-mutant acute myeloid leukemia.

Maria Sirenko, Soobeom Lee, Zhengxi Sun, Ronan Chaligne, Sanam Loghavi, Georgios Asimomitis, Charlotte K Brierley, Elsa Bernard, Sheng F Cai, Robert M Myers, Bettina Nadorp, Junya Sango, Morgan Lallo, Max F Levine, Dylan Domenico, Juan E Arango Ossa, Juan S Medina-Martinez, Kamal Menghrajani, Audrey Lasry, Alice S Mims, Helee Desai, Andrea Laganson, Chris Famulare, Minal Patel, Gerard Lozanski, Kelly L Bolton, Aaron D Viny, Mikhail Roshal, Ross L Levine, Eirini P Papapetrou, Eytan M Stein, Dan A Landau, Ann-Kathrin Eisfeld, Iannis Aifantis, Elli Papaemmanuil.

  Isocitrate dehydrogenase 1/2 (IDH) mutations are early initiating events in acute myeloid leukemia (AML). The complex clonal architecture and cellular heterogeneity in IDH-mutant AML underlies the heterogeneous clinical presentation and outcomes. Integrating single-cell genotyping and transcriptomics, we demonstrate a stem-like and inflammatory phenotype of IDH-mutant AML and identify clone-specific programs associated with NPM1, NRAS, and SRSF2 co-mutations. Furthermore, these clones had distinct responses to treatment with combination IDH inhibitors and chemotherapy, including elimination, reconstitution of myeloid differentiation, or retention within progenitor populations. At relapse after IDH inhibitor monotherapy, we identify upregulated stemness, inflammation, mitochondrial metabolism, and anti-apoptotic factors, as well as downregulated major histocompatibility complex (MHC) class II antigen presentation. At the pre-leukemic stage, we observe upregulation of IDH2-associated pathways, including inflammation. We deliver a detailed phenotyping of IDH-mutant AML and a framework for dissecting contributions of recurrently mutated genes in AML at diagnosis and following therapy, with implications for precision medicine.

Keywords:  IDH inhibitors; IDH1/2 mutations; acute myeloid leukemia; cellular hierarchy; clonal architecture; clonal evolution; relapse; single-cell transcriptomics; targeted therapy; treatment resistance

DOI:  https://doi.org/10.1016/j.stem.2025.04.012
Blood Cancer Discov. 2025 May 21.

Genetic and Phenotypic correlates of clinical outcomes with Venetoclax in Acute Myeloid Leukemia: The GEN-PHEN-VEN study.

Curtis A Lachowiez, Mael Heiblig, Gaspar Aspas Requena, Emmanuelle Tavernier-Tardy, Fangyan Dai, Amenech B Ashango, Daniel T Peters, Jacob Fang, Andy Kaempf, Nicola Long, Christopher A Eide, Stephen E Kurtz, Wei Xie, Anupriya Agarwal, Aishwarya Sahasrabudhe, Christine M McMahon, Maria L Amaya, Gabrielle Meyers, Arpita Gandhi, Jessica Leonard, Brandon Hayes-Lattin, Richard T Maziarz, Elie Traer, Rachel J Cook, Ronan Swords, Theodore P Braun, Jennifer N Saultz, Ashley M Eckel, Michael R Loken, Joshua F Zeidner, Jeffrey W Tyner, Daniel A Pollyea.

Resistance to venetoclax-based therapy in acute myeloid leukemia (AML) includes genetic (i.e., mutations in N/KRAS, FLT3-ITD, TP53) and phenotypic (i.e., monocytic differentiation) features. Whether monocytic differentiation contributes to clinical venetoclax resistance secondary to a genetic bias remains unknown. This multimodal, multicenter, international analysis inclusive of 678 patients comprehensively characterized the prognostic role of monocytic differentiation in AML patients treated with hypomethylating agents combined with venetoclax. AML genetics and monocytic differentiation (HR: 1.89, 95% CI: 1.35-2.66, p < 0.001) in NPM1 wild-type cases correlated with an increased risk of death. Clustering of centralized quantitative multiparameter flow cytometry data, evaluation of RNA sequencing-derived AML maturation stage, and single-cell proteogenomics linked driver mutations with AML phenotype and anti-apoptotic gene expression. This comprehensive analysis of AML genetics, phenotype, and anti-apoptotic protein expression highlights the complementary role these factors impart following venetoclax-based therapy.

DOI: https://doi.org/10.1158/2643-3230.BCD-24-0256
Nat Immunol. 2025 May 21.

Cholinergic regulation of thymocyte negative selection.

Shaofeng Liu, Chunxing Zheng, Robert Nechanitzky, Ping Luo, Parameswaran Ramachandran, Dat Nguyen, Andrew J Elia, Soode Moghadas Jafari, Rhoda Law, Bryan E Snow, Andrew C Wakeham, Thorsten Berger, Hui Chen, Kyle T Gill, Ryan Mcwilliam, Jerome Fortin, Nastaran Fazel Modares, Mary E Saunders, Kiichi Murakami, Yangmin Qiu, Zhiwei You, Mahmood Mohtashami, Hai Qi, Pamela S Ohashi, Juan Carlos Zúñiga-Pflücker, Tak W Mak.

The immune and nervous systems use a common chemical language for communication, namely, the cholinergic signaling involving acetylcholine (ACh) and its receptors (AChRs). Whether and how this language also regulates the development of the immune system is poorly understood. Here, we show that mouse CD4+CD8+ double-positive thymocytes express high levels of α9 nicotinic AChR (nAChR) and that this receptor controls thymic negative selection. α9 nAChR-deficient mice show an altered T cell receptor (TCR) repertoire and reduced CD4+ and CD8+ T cells in a mixed bone marrow chimera setting. α9 nAChR-mediated signaling regulates TCR strength and thymocyte survival. Thymic tuft cells, B cells and some T cells express choline acetyltransferase and are potential ACh sources, with ACh derived from T cells having the most important role. Furthermore, α9 nAChR deficiency during thymocyte development contributes to the altered development of autoimmune diseases in mice. Our results thus reveal a mechanism controlling immune cell development that involves cholinergic signaling.

DOI: https://doi.org/10.1038/s41590-025-02152-4
Discov Oncol. 2025 May 20. 16(1): 826

Visfatin promotes multiple myeloma cell proliferation and inhibits apoptosis by inducing IL-6 production via NF-κB pathways.

Wenting Tie, Tao Ma, Jia Liu, Zhigang Yi, Hao Xiong, Jun Bai, Yanhong Li, Lijuan Li, Liansheng Zhang.

   BACKGROUND: Multiple myeloma (MM) is the second most prevalent hematological malignancy that results in the proliferation of malignant plasma cells and the overproduction of monoclonal immunoglobulin. Visfatin plays an important role in the regulation of apoptosis, oxidative stress, and inflammation; however, to this date, the role of visfatin in multiple myeloma is unclear.
OBJECTIVE: To explore the role of visfatin in multiple myeloma and find new targets for MM treatment.
METHODS: In this study, expression of visfatin in bone marrow was detected by ELISA. The diagnostic value of visfatin was determined by receiver operating characteristic (ROC) curve analysis. After the quality control by performing western blot to confirm the knockdown of visfatin in two MM cell lines, the phenotype (proliferation and apoptosis) of visfatin in MM was determined by carrying out in vitro experiments, including CCK8, flow cytometry, and western blot. Several cytokines were determined by real-time PCR, followed by in vivo experiments and immunohistochemical assays. IκB, NF-κbp65, and phosphorylation were determined by western blot.
RESULTS: We found that visfatin level increased in the bone marrow of MM patients compared to controls. ROC curve analysis result showed that bone marrow visfatin was able to distinguish MM patients from controls. In vitro and in vivo, visfatin promotes MM cell proliferation. The production of IL-6 was attenuated by visfatin knockdown. Furthermore, we showed that visfatin could activate IL-6 production via the NF-κB signaling pathway.
CONCLUSIONS: In MM, visfatin promotes tumor progression by upregulating IL-6 production, which may be a novel therapeutic target for the treatment of MM patients.

Keywords:  Apoptosis; Interleukin-6; Multiple myeloma; Nuclear factor kappa-B; Visfatin

DOI:  https://doi.org/10.1007/s12672-025-02682-1
Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2426644122

Macrophages release neuraminidase and cleaved calreticulin for programmed cell removal.

Allison Banuelos, Michelle Baez, Allison Zhang, Leyla Yılmaz, William Kasberg, Regan Volk, Nardin Georgeos, Elle Koren-Sedova, Uyen Le, Andrew T Burden, Kristopher D Marjon, Jennifer Lippincott-Schwartz, Balyn W Zaro, Irving L Weissman.

  Calreticulin (CALR) is primarily an endoplasmic reticulum chaperone protein that also plays a key role in facilitating programmed cell removal (PrCR) by acting as an "eat-me" signal for macrophages, directing their recognition and engulfment of dying, diseased, or unwanted cells. Recent findings have demonstrated that macrophages can transfer their own CALR onto exposed asialoglycans on target cells, marking them for PrCR. Despite the critical role CALR plays in this process, the molecular mechanisms behind its secretion by macrophages and the formation of binding sites on target cells remain unclear. Our findings show that CALR undergoes C-terminal cleavage upon secretion, producing a truncated form that functions as the active eat-me signal detectable on target cells. We identify cathepsins as potential proteases involved in this cleavage process. Furthermore, we demonstrate that macrophages release neuraminidases, which modify the surface of target cells and facilitate CALR binding. These insights reveal a coordinated mechanism through which lipopolysaccharide (LPS)-activated macrophages regulate CALR cleavage and neuraminidase activity to mark target cells for PrCR. How they recognize the cells to be targeted remains unknown.

Keywords:  calreticulin; cancer; macrophages; phagocytosis

DOI:  https://doi.org/10.1073/pnas.2426644122
Nat Commun. 2025 May 20. 16(1): 4274

CREBBP inactivation sensitizes B cell acute lymphoblastic leukemia to ferroptotic cell death upon BCL2 inhibition.

Alicia Garcia-Gimenez, Jonathan E Ditcham, Dhoyazan M A Azazi, George Giotopoulos, Ryan Asby, Eshwar Meduri, Jaana Bagri, Nathalie Sakakini, Cecile K Lopez, Nisha Narayan, Tumas Beinortas, Shuchi Agrawal-Singh, Kent Fung, David O'Connor, Marc R Mansour, Husam B R Alabed, Benjamin Jenkins, Albert Koulman, Michael P Murphy, Sarah J Horton, Brian J P Huntly, Simon E Richardson.

B-cell acute lymphoblastic leukemia (B-ALL) is a leading cause of death in childhood and outcomes in adults remain dismal. There is therefore an urgent clinical need for therapies that target the highest risk cases. Mutations in the histone acetyltransferase CREBBP confer high-risk and increased chemoresistance in ALL. Performing a targeted drug-screen in isogenic human cell lines, we identify a number of small molecules that specifically target CREBBP-mutated B-ALL, the most potent being the BCL2-inhibitor Venetoclax. Of note, this acts through a non-canonical mechanism resulting in ferroptotic rather than apoptotic cell death. CREBBP-mutated cell lines show differences in cell-cycle, metabolism, lipid composition and response to oxidative stress, predisposing them to ferroptosis, which are further dysregulated upon acquisition of Venetoclax resistance. Lastly, small-molecule inhibition of CREBBP pharmacocopies CREBBP-mutation, sensitizing B-ALL cells, regardless of genotype, to Venetoclax-induced ferroptosis in-vitro and in-vivo, providing a promising drug combination for broader clinical translation in B-ALL.

DOI: https://doi.org/10.1038/s41467-025-59531-6
Nat Commun. 2025 May 22. 16(1): 4753

Expanding the landscape of aging via orbitrap astral mass spectrometry and tandem mass tag integration.

Gregory R Keele, Yue Dou, Seth P Kodikara, Erin D Jeffery, Dina L Bai, Erik Hultenius, Zichen Gao, Joao A Paulo, Steven P Gygi, Xiao Tian, Tian Zhang.

Aging results in a progressive decline in physiological function due to the deterioration of essential biological processes. While proteomics offers insights into aging mechanisms, prior studies are limited in proteome coverage and lifespan range. To address this, we integrate the Orbitrap Astral Mass Spectrometer with the multiplex tandem mass tag (TMT) technology to profile the proteomes of cortex, hippocampus, striatum and kidney in the C57BL/6JN mice, quantifying 8,954 to 9,376 proteins per tissue (12,749 total). Samples spanned both sexes and three age groups (3, 12, and 20 months), representing early to late adulthood. To improve TMT quantitation accuracy, we develop a peptide-spectrum match-based filtering strategy that leverages resolution and signal-to-noise thresholds. Our analysis uncovers distinct tissue-specific patterns of protein abundance, with age and sex differences in the kidney and primarily age-related changes in brain tissues. We also identify both linear and non-linear proteomic trajectories with age, revealing complex protein dynamics over the adult lifespan. Integrating our findings with early developmental proteomic data from brain tissues highlights further divergent age-related trajectories, particularly in synaptic proteins. This study provides a robust data analysis workflow for Orbitrap Astral-based TMT analysis and expands the proteomic understanding of aging across tissues, ages, and sexes.

DOI: https://doi.org/10.1038/s41467-025-60022-x
Leukemia. 2025 May 22.

Targeting lipid metabolism in acute myeloid leukemia: biological insights and therapeutic opportunities.

Vilma Dembitz, Sophie C James, Paolo Gallipoli.

Metabolic rewiring is a hallmark of malignant transformation in leukemic cells and the potential offered by its therapeutic targeting has garnered significant attention. The development of clinically relevant metabolic targeted therapies in acute myeloid leukemia (AML) has mostly focused on targeting mitochondrial energy production, but progress has been hampered by generalized toxicities. An alternative strategy is to shift the focus from targeting energy production to targeting more specialized metabolic functions, such as energy storage, the regulation of oxidative stress and availability of cofactors needed for the function of specific metabolic reactions. Lipid metabolism plays a role in many of these metabolic functions and its importance in AML maintenance and response to therapy is being increasingly recognized but needs to be adequately interpreted in the context of its interaction with the microenvironment, particularly the adipose niche. In this review, we provide an overview of our current understanding of AML cellular metabolic dependencies on fatty acid and lipid metabolism and discuss their relevance in the context of functional interactions with adipocytes. We highlight unresolved questions about how to best target lipid metabolism and suggest approaches needed to fully understand the interplay between malignant cells and their niche in the context of metabolic dependencies.

DOI: https://doi.org/10.1038/s41375-025-02645-z
Nat Cardiovasc Res. 2025 May 23.

Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations.

Marle Kraft, Hans Schoofs, Milena Petkova, Jorge Andrade, Ana Rita Grosso, Rui Benedito, An-Katrien De Roo, Laurence M Boon, Miikka Vikkula, Friedrich G Kapp, René Hägerling, Michael Potente, Taija Mäkinen.

Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3Kα-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3Kα activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.

DOI: https://doi.org/10.1038/s44161-025-00655-9
Blood Adv. 2025 May 22. pii: bloodadvances.2025015797. [Epub ahead of print]

A Revised Prognostic Model for Patients with Acute Myeloid Leukemia and First Relapse.

Niek G Van Der Maas, Dimitri A Breems, Clara P W Klerk, Thomas Pabst, Patrycja Gradowska, Abin Thomas, Bart J Biemond, Jürgen Kuball, Catharina H M J van Elssen, Otto J Visser, Marie-Christiane Madeleine Vekemans, Carlos Graux, Johan A Maertens, Steven Knapper, Mike Dennis, Sylvie D Freeman, Ian Thomas, Berna H Beverloo, Gerwin A Huls, Charles Craddock, Peter J M Valk, Paresh Vyas, Nigel H Russell, Gert J Ossenkoppele, Bob Löwenberg, Jan J Cornelissen, Jurjen Versluis.

Most patients with acute myeloid leukemia (AML) may obtain remission upon induction chemotherapy, but relapse is frequent and associated with poor survival. Previous prognostic models for outcomes after relapse lacked analysis of comprehensive molecular data. A validated prognostic model integrating clinical, cytogenetic, and molecular variables may support treatment decisions. We studied 943 AML patients who relapsed after first-line intensive induction treatment in a development cohort (HOVON-SAKK). A random survival forest algorithm was used to evaluate the association of clinical parameters, cytogenetic abnormalities, and molecular variables at diagnosis with overall survival (OS). Relapsing patients (n=377) who were enrolled in the NCRI-AML18 trial were used for model validation. In the development cohort, the median age at relapse was 58 years, and patients were classified as 2022 ELN favorable (22%), intermediate (31%), and adverse (48%) risk. One-third underwent allogeneic transplantation in first complete remission. Variable selection yielded nine variables significantly associated with 1-year OS, including relapse-free interval, age, white blood cell count, mutated TP53, FLT3-ITD, core-binding factor abnormalities, t(v;11q23)/KMT2A-rearranged and complex/monosomal karyotype, which were assigned points according to their estimated hazard ratios. Three prognostic groups were defined with distinct 1-year OS in both development (favorable: 51±3%, intermediate: 29±3% and poor: 14±2%, respectively) and validation cohorts (51±4%, 26±5% and 14±3%, respectively). Independent validation confirmed the improved accuracy in predicting outcomes for AML patients in first relapse. The revised AML relapse model improved on previous classification systems for prognostication of outcomes after first AML relapse. It provides stratification which might support tailoring second line treatment.

DOI: https://doi.org/10.1182/bloodadvances.2025015797