bims-scepro 2025-11-23 papers

bims-scepro

Biomed News

on Stem cell proteostasis

Issue of 2025–11–23
24 papers selected by
William Grey, University of York

Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells.
Functional and molecular analyses reveal impaired HSPCs in Multiple Myeloma patients post-induction.
DNMT3A R882H Is Not Required for Disease Maintenance in Primary Human AML, but Is Associated With Increased Leukemia Stem Cell Frequency.
An inflammatory T-cell-stromal axis contributes to hematopoietic stem/progenitor cell failure and clonal evolution in human myelodysplastic syndrome.
Oncogenic activation of EVC/EVC2 defines a therapeutically targetable subset of acute myeloid leukemia.
MAFB regulates hematopoietic stem cell proliferation and maintenance.
Impaired IL-10 Receptor Signaling Leads to Inflammation Induced Exhaustion in Hematopoietic Stem Cells.
In Vitro Lymphoid Differentiation of Human Hematopoietic Progenitor Cells from Co-cultures in Hypoxia.
Endothelial protein C receptor CD201 is a better marker than SCA1 to identify mouse long-term reconstituting hematopoietic stem cells following septic challenge.
Exploring MSC and HSPC interactions: new frontiers in hematopoiesis and transplant medicine.
Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.
Harnessing DNA barcoding to enhance and sustain polyclonality in gene-edited hematopoietic stem cells.
Fancl-mutant mice reveal central role of monoubiquitination in Fanconi anemia and a model for therapeutic gene editing.
Inflammatory stromal and T cells mediate human bone marrow niche remodeling in clonal hematopoiesis and myelodysplasia.
Macro-scale, scaffold-assisted model of the human bone marrow endosteal niche using hiPSC-vascularized osteoblastic organoids.
Gene Expression Imaging in Hematopoiesis.
Circular single stranded DNA potentiates non-viral gene insertion in hematopoietic stem and progenitor cells.
High-Dimensional Spatiotemporal Single-Cell and 3D Atlas of the Bone Marrow Microenvironment during Leukemic Progression.
Targeting the origins of multiple myeloma along hematopoietic stem cell lymphoid lineage differentiation.
Catalytic Inhibition of p300 Preferentially Targets IRF4 Oncogenic Activity and Tumor Growth in Multiple Myeloma.
DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development.
Precision prediction of venetoclax-azacitidine treatment efficacy in acute myeloid leukemia via integrative drug screening and machine learning.
Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.
Increased substrate stiffness disrupts nuclear-cytoskeletal mechanical coupling in senescent cells.

Nat Cell Biol. 2025 Nov 18.

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

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

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

DOI: https://doi.org/10.1038/s41556-025-01814-7
Stem Cells Transl Med. 2025 Nov 14. pii: szaf061. [Epub ahead of print]14(11):

Functional and molecular analyses reveal impaired HSPCs in Multiple Myeloma patients post-induction.

Thanh Mai Baumhardt, Amanda Amoah, Markus Hoenicka, Andreas Liebold, Vadim Sakk, Karin Soller, Angelika Vollmer, Miriam Kull, Jan Kronke, Jan-Philipp Mallm, Hartmut Geiger, Medhanie Mulaw.

  High-dose chemotherapy and consecutive autologous stem cell transplantation (ASCT) remain the backbone of treatment for transplant-eligible patients of Multiple Myeloma (MM). However, patients are still at high risk of relapse or treatment-related complications. Hence, by understanding the function of hematopoietic stem and progenitor cells (HSPCs) from MM patients in more detail, transplant outcomes in MM patients might be further improved. We combine in our study functional analyses of the potential of HSPCs from newly diagnosed (NDMM) and chemotherapy treated MM patients in a xenotransplant model system with in depth single cells sequencing analysis to provide novel data that might inform clinical routine to improve the outcome of ASCT in MM. Our data demonstrate that (i) HSPCs from treated MM patients are indeed significantly impaired in their overall reconstitution potential and provide a reduced level of B-cells in comparison to HSPCs from age-matched healthy donors and NDMM patients. (ii) We further demonstrate that CD34+ HSPCs acquire a high-risk MM expression profile signature upon induction treatment, which likely adds to the risk of relapse. This high-risk MM expression profile signature relies within CD34+ HSPCs primarily in granulocyte/macrophage progenitors (GMPs), megakaryocyte Erythroid Progenitors (MEPs) and monocytes, while hematopoietic stem cells (HSCs) stay unaffected by transcriptional changes. These data suggest that the elimination of myeloid progenitors and more mature monocytes (likely by purification for HSCs) in HSPCs harvests from treated MM patients for subsequent ASCT might improve transplant outcomes by avoiding re-infusion of cells with a dysregulated and disease-linked transcriptional program.

Keywords:  autologous stem cell transplantation; hematopoietic stem cells; multiple myeloma; single cells sequencing; xenotransplant model

DOI:  https://doi.org/10.1093/stcltm/szaf061
Cancer Discov. 2025 Nov 20.

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

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

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

DOI: https://doi.org/10.1158/2159-8290.CD-24-1604
Nat Commun. 2025 Nov 18. 16(1): 10041

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

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

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

DOI: https://doi.org/10.1038/s41467-025-65802-z
Leukemia. 2025 Nov 17.

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

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

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

DOI: https://doi.org/10.1038/s41375-025-02803-3
Sci Rep. 2025 Nov 18. 15(1): 40592

MAFB regulates hematopoietic stem cell proliferation and maintenance.

Saki Asano, Ching-Wei Liao, Yurina Matsunaga, Hyojung Jeon, Kyoko Sawaguchi, Keigo Asano, Manabu Kusakabe, Zeynab Javanfekr Shahri, Natalia Gogoleva, Tomomasa Yokomizo, Satoru Takahashi, Michito Hamada.

  MAFB, a transcription factor of the large Maf family, is expressed in both fetal liver (FL) and bone marrow (BM) hematopoietic stem cells (HSCs). However, its stage-specific roles remain elusive. Here, we reveal that MAFB plays distinct roles in FL and BM HSCs. Using Mafb-deficient and Mafb-GFP knock-in mouse models, we demonstrate that Mafb deletion enhances proliferation, cell cycle entry, and myeloid differentiation of FL HSCs, leading to enhanced chimerism rate in transplantation assays. However, Mafb-deficient BM HSCs exhibit impaired long-term reconstitution and progressive exhaustion, supported by serial transplantation and reduced colony-forming capacity. HSCs from Mafbf/f::Tie2-Cre mouse (Mafb cKO) further revealed a significant decline in long-term HSC (LT-HSC) populations and multilineage differentiation potential. Together, our findings suggest a stage-dependent role of MAFB as a regulator of HSC proliferation during fetal development and a critical factor for HSC maintenance during adulthood, providing insights into the stage-specific regulation of HSC function linked to cell cycle control and long-term repopulation capacity.

Keywords:  Cell cycle regulation; Hematopoietic stem cells (HSCs); MAFB; Self-renewal; Stem cell exhaustion

DOI:  https://doi.org/10.1038/s41598-025-24389-7
bioRxiv. 2025 Oct 02. pii: 2025.09.30.679613. [Epub ahead of print]

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

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

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

DOI: https://doi.org/10.1101/2025.09.30.679613
Methods Mol Biol. 2026 ;2990 221-230

In Vitro Lymphoid Differentiation of Human Hematopoietic Progenitor Cells from Co-cultures in Hypoxia.

Françoise Pflumio, Rima Haddad.

  Understanding the identity of cells from which lymphoid differentiation occurs can be addressed using specific cell assays. Ex vivo conditions have been established based on co-culture systems between human hematopoietic stem/progenitor cells or early lymphoid progenitors and stromal cells. These systems provide a functional approach to carefully assess cell potential at both qualitative and quantitative levels. This chapter describes a two-step co-culture system for isolated hematopoietic stem/progenitor cells, using a murine bone marrow stromal cell line (MS-5), a hypoxic environment (3.5% O2), defined lymphoid medium and cytokine conditions, and limiting dilution settings. This setup enables a robust characterization of the intrinsic lymphoid potential of progenitor cells, closely mimicking physiological condition. Importantly, this approach can be instrumental in investigating how intrinsic or microenvironmental alterations in early hematopoiesis contribute to immune dysregulation and the development of autoimmune diseases.

Keywords:  Co-cultures; Human CD34+ hemato-lymphoid progenitors; Hypoxia; In vitro lymphoid differentiation; Limiting dilution assays; MS-5 stromal cells; Umbilical cord blood

DOI:  https://doi.org/10.1007/978-1-0716-4997-8_16
Exp Hematol. 2025 Nov 19. pii: S0301-472X(25)00615-0. [Epub ahead of print] 105326

Endothelial protein C receptor CD201 is a better marker than SCA1 to identify mouse long-term reconstituting hematopoietic stem cells following septic challenge.

Kavita Bisht, Valérie Barbier, Svetlana Shatunova, Ingrid G Winkler, Jean-Pierre Lévesque.

  Stem cell antigen-1 (SCA1) is widely used to identify mouse hematopoietic stem cells (HSC) and multipotent progenitors (MPP) among lineage-negative KIT+ (LK) cells. However, SCA1 is expressed only in a few inbred mouse strains and becomes strongly upregulated on LK cells following in vivo challenge with interferons, lipopolysaccharide (LPS) or pathogens leading to incorrect analysis of HSC function subsets and delineation of HSC, MPP and lineage-restricted progenitor subsets. Endothelial protein C receptor CD201can be used as an alternative marker for mouse and even human HSC. However, whether CD201 expression changes following infectious challenge is unknown. Unlike SCA1, CD201 expression did not change on mouse LK cells in response to LPS in vivo. Long-term competitive transplantations with CD201+, CD201- or SCA1+ LK cells showed that most reconstituting HSCs are within the LK CD201+ population after LPS challenge. However long-term competitive repopulation potential of LK SCA1+ cells from LPS-treated mice was much more severely reduced than that of LK CD201+ cells from the same LPS-treated donors suggesting that the LK SCA1+ population in challenged donors becomes contaminated with CD201- progenitors devoid of long-term repopulation potential. Based on CD201 gating strategy, we re-assessed the effect of LPS on HSC and MPP cycling and mobilization, and their dependency on MY88 and TRIF adaptors. In conclusion, CD201 enables a more accurate analysis of mouse HSC and MPP subsets in all inbred strains in septic conditions or steady-state.

Keywords:  EPCR; Hematopoietic stem cell marker; Inflammation; MYD88; TRIF; lipopolysaccharide, SCA-1, CD201

DOI:  https://doi.org/10.1016/j.exphem.2025.105326
Stem Cell Res Ther. 2025 Nov 17. 16(1): 640

Exploring MSC and HSPC interactions: new frontiers in hematopoiesis and transplant medicine.

Sevanthy Suresh, Vigneshwaran Venkatesan, Saravanabhavan Thangavel, Srujan Marepally.

  Mesenchymal stromal cells (MSCs) play a critical role in supporting hematopoietic stem and progenitor cells (HSPCs) within the bone marrow (BM) niche by providing a specialized extracellular matrix and essential signaling cues. Through the secretion of key ECM proteins and cell adhesion molecules, MSCs regulate HSPC proliferation, differentiation, homing, retention, and maintain their quiescence necessary for effective hematopoiesis. Understanding the intricate dynamics between MSCs and HSPCs in the BM is essential for advancing HSPC-based therapies. Targeting niche components, such as ECM proteins and CAMs, can enable HSPC expansion and engraftment, benefiting hematopoietic stem cell transplantation and gene therapy outcomes. In this review, we provide an overview of the niche components involved in MSCs-HSPCs interactions and its co-culture in improving the therapeutic outcomes, discuss existing challenges and propose possible solutions.

Keywords:  Bone marrow niche; Bone marrow transplantations; Extracellular matrix; Gene editing; Gene therapy; Hematopoietic stem and progenitor cells (HSPCs); Mesenchymal stromal cells (MSCs)

DOI:  https://doi.org/10.1186/s13287-025-04753-0
Cell. 2025 Nov 19. pii: S0092-8674(25)01233-4. [Epub ahead of print]

Inhibition of heme biosynthesis triggers cuproptosis in acute myeloid leukemia.

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

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

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

DOI:  https://doi.org/10.1016/j.cell.2025.10.028
Mol Ther Methods Clin Dev. 2025 Dec 11. 33(4): 101615

Harnessing DNA barcoding to enhance and sustain polyclonality in gene-edited hematopoietic stem cells.

Isabel Ojeda-Perez, Andrés Bustos, Sridhar Selvaraj, Sara Fañanas-Baquero, Omaira Alberquilla-Fernandez, Luis-Javier Serrano, Jose Bonafont, Aida Garcia-Torralba, Raul Torres-Ruiz, Sandra Rodriguez-Perales, Valeri Lang, Cesar Trigueros, Rafael Mayo-Garcia, Oscar Quintana-Bustamante, Matthew Porteus, Rebeca Sánchez-Dominguez, Jose-Carlos Segovia.

  A challenge in gene editing for hematopoietic stem and progenitor cells (HSPCs) is achieving efficient editing while preserving long-term engraftment and clonal diversity. Tracking edited clones with high resolution is essential to understand the impact of editing on hematopoiesis. We developed a barcoded AAV6 donor template (BC-AAV) to precisely monitor the fate of edited HSPCs following transplantation. Our findings reveal that, despite initial barcode diversity in vitro, human hematopoiesis generated by edited HSPCs transplanted in immunodeficient mice is driven by a limited number of dominant clones. The engraftment of gene-edited cells follows an oligo/polyclonal pattern, indicating that editing does not alter clonal dynamics in this model. Using BC-AAV, we optimized a gene editing protocol for correcting the PKLR gene, responsible for pyruvate kinase deficiency, a rare disorder that causes severe anemia due to red blood energy imbalance. We implemented key improvements. GMP-grade StemSpan AOF medium and StemRegenin-1 increased clonal diversity while maintaining hematopoietic potential. NHEJ inhibitor AZD-7648, significantly boosted editing efficiency in vitro, and a shorter transduction period enhanced engraftment and clonal balance without compromising editing outcomes. This refined strategy for gene editing in human HSPCs optimizes both efficiency and long-term polyclonal dynamics and has important implications for clinical applications.

Keywords:  Adenoassociated viral vector; CRISPR-Cas9; DNA Barcode; Gene editing; HSC clones; Knock-in

DOI:  https://doi.org/10.1016/j.omtm.2025.101615
Blood Adv. 2025 Nov 19. pii: bloodadvances.2025017217. [Epub ahead of print]

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

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

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

DOI: https://doi.org/10.1182/bloodadvances.2025017217
Nat Commun. 2025 Nov 18. 16(1): 10042

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

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

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

DOI: https://doi.org/10.1038/s41467-025-65803-y
Cell Stem Cell. 2025 Nov 18. pii: S1934-5909(25)00377-7. [Epub ahead of print]

Macro-scale, scaffold-assisted model of the human bone marrow endosteal niche using hiPSC-vascularized osteoblastic organoids.

Qing Li, Marina T Nikolova, Gangyu Zhang, Igor Cervenka, Federica Valigi, Dominik Burri, Evelia Plantier, Andrea Mazzoleni, Anaïs Lamouline, Juerg Schwaller, Barbara Treutlein, Ivan Martin, Andrés García-García.

  Endosteal bone marrow (BM) niches are crucial to sustain non-steady-state hematopoiesis but are challenging to be modeled in their cellular and molecular complexity in standardized, human settings. We report a developmentally guided approach to generate a macro-scale organotypic model of BM endosteal niches (engineered vascularized osteoblastic niche [eVON]) based on human induced pluripotent stem cells and porous hydroxyapatite scaffolds. The eVON contains long-lasting vascular networks covered by pericytes and neural fibers within an osteogenic matrix. Key niche signals (CXCL12, KITLG, and vascular endothelial growth factor A [VEGFA]) are expressed in human-specific patterns. The system supports hematopoiesis in vitro and preserves hematopoietic stem and progenitor cell (HSPC) multilineage repopulation capacity in vivo. eVON perturbations at cellular (removing vasculature) and molecular (deregulating VEGF-A and CXCL12 signaling) levels enabled the investigation of the contribution of endosteal vasculature to myelopoiesis. The eVON faithfully captures phenotypic, structural, and functional features of human endosteal BM, enabling the study of pathophysiological interactions with hematopoietic cells.

Keywords:  3D model; bone marrow; endosteal; hiPSC; human hematopoiesis; organoids; vascularized osteoblastic niche

DOI:  https://doi.org/10.1016/j.stem.2025.10.009
J Mol Biol. 2025 Nov 14. pii: S0022-2836(25)00611-4. [Epub ahead of print] 169545

Gene Expression Imaging in Hematopoiesis.

Justin C Wheat, Robert A Coleman, Ulrich Steidl.

  Hematopoiesis, or the process of blood production, has long served as a prototype for stem cell biology research owing to the relative ease of obtaining blood as well as functional testing in vitro and in vivo (through stem cell transplantation). One central question in the field over the last century is how the various forms and phenotypes of blood cells arise from a common pool of hematopoietic stem cells. Key to that exercise have been in depth studies into how the genes required for cell differentiation are expressed and regulated. Paramount to these efforts have been single cell analysis techniques, which have helped resolve heterogeneity at multiple levels of hematopoietic regulation. Recently, as major advances in the fields of quantitative microscopy and systems biology have revolutionized modern molecular biology, the hematopoietic research community has begun to employ these techniques, leading to significant advances in our understanding of blood production. In this review, we discuss the historical role imaging has played in developing heuristics in the field of hematopoiesis research and, importantly, discuss the exciting areas being explored with novel and innovative technologies. Finally, we close with a discussion of the main challenges that will face the field going forward.

Keywords:  Gene expression; Transcription; cell fate; imaging; single-molecule resolution

DOI:  https://doi.org/10.1016/j.jmb.2025.169545
Nat Commun. 2025 Nov 19. 16(1): 10125

Circular single stranded DNA potentiates non-viral gene insertion in hematopoietic stem and progenitor cells.

Gil Letort, Aymeric Duclert, Diane Le Clerre, Isabelle Chion-Sotinel, Roger Salvatori, Emilie Dessez, Margaux Sevin, Marco Rotondi, Cosimo Ducani, Philippe Duchateau, Julien Valton.

Over the past decade, non-viral DNA template delivery has been used with engineered nucleases to target single-stranded DNA sequences in hematopoietic stem and progenitor cells. While effective for gene therapy, this method is limited to short DNA donor templates, restricting its applications to gene corrections. To expand its scope, we developed an editing process using kilobase-long circular single-stranded DNA donor templates and TALEN technology. Our results show that the CssDNA editing process achieves high gene insertion frequency in HSPCs. Compared to AAV-edited HSPCs, CssDNA-edited HSPCs show a higher propensity to engraft and maintain gene edits in a female NCG murine model. This positive outcome is partly due to higher levels of primitive edited HSPCs, a more quiescent metabolic state, and elevated expression of bone marrow niche adhesion markers. Our findings highlight the strong potential of CssDNA as a universal, scalable and efficient non-viral DNA template for gene therapy applications.

DOI: https://doi.org/10.1038/s41467-025-66318-2
bioRxiv. 2025 Sep 29. pii: 2025.09.27.678113. [Epub ahead of print]

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

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

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

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

DOI:  https://doi.org/10.1101/2025.09.27.678113
Sci Transl Med. 2025 Nov 19. 17(825): eadu0114

Targeting the origins of multiple myeloma along hematopoietic stem cell lymphoid lineage differentiation.

Jiaojiao Guo, Yaru Li, Zhiling Yan, Qing Li, Zhenhao Liu, Zhengjiang Li, Ruiqi Zhou, Nihan He, Yinghong Zhu, Xiaoshuang Wang, Xun Chen, Yi Qiu, Liang Zhao, Fangming Shi, Yanjuan He, Sha Hao, Jia Yu, Lu Xie, Jiaxi Zhou, Jian Li, Gang An, Xiangling Feng, Wei Jia, Xiaochen Bo, Kailin Xu, Tao Cheng, Hebing Chen, Wen Zhou.

The initiation and progression of multiple myeloma (MM) are intricate processes, and a critical challenge lies in understanding the mechanisms of malignant transformation in MM-initiating cells (MICs) and their driver genes. In this study, we used single-cell sequencing and genetic tracer analysis at each developmental stage, from hematopoietic stem cells to lymphoid lineage differentiation, to identify abnormal differentiation stages in patients with MM. We found that chromosome 1q amplification (1qAmp) originated from a specific subgroup of B cells, whereas chromosome 17p deletion occurred at the plasma cell stage. 1qAmp was present in CD24-FCRL5+ B cell subgroups and initiated B cell transformation into malignant plasma cells by enhancing B cell proliferation and promoting plasma cell differentiation in vitro and in vivo. FCRL5 facilitated B cell differentiation into malignant plasma cells through its interaction with the IRF4/SPI1 complex. The use of targeted FCRL5 CAR T cells in patients with relapsed or refractory MM (RRMM) showed promising safety and efficacy. Together, our work identified genetic events linked to the initiation and malignant transformation of MM along the B cell lineage. These findings form the foundation for identifying potential therapeutic strategies for patients with RRMM by targeting MICs and their driving oncogenes.

DOI: https://doi.org/10.1126/scitranslmed.adu0114
Cancer Res. 2025 Nov 17.

Catalytic Inhibition of p300 Preferentially Targets IRF4 Oncogenic Activity and Tumor Growth in Multiple Myeloma.

W Frank Lenoir, Michael R McKeown, Giulia Giorgetti, Marek J Kobylarz, Tamara D Hopkins, Wayne L Glore, Michelle G Shum, Yaretzi Calderón, Jessica Encinas Mayoral, Luis A Carvajal, Kameron R Mori, Jun Li, Hua Gao, Yupeng Zheng, Zhihua Ma, Nikolaus D Obholzer, Minyun Zhou, Benjamin W Trotter, Christopher J Dinsmore, Nikhil C Munshi, Charles Y Lin, Mariateresa Fulciniti, Peter B Rahl.

The oncogenic transcription factor (TF) IRF4 is a currently undrugged universal multiple myeloma (MM) dependency. Using transcriptional regulatory network (TRN) mapping, an unbiased multi-omic target ID approach, we identified the coactivator lysine acetyltransferase (KAT) p300 as a key IRF4 partner. Validation of this preferential relationship through quantitative interactome mapping revealed that IRF4 was the most abundant MM specific dependency and more closely complexed with p300 than other TFs, such as IKZF1/IKZF3. Development of optimized p300 lysine acetyltransferase (KAT) inhibitors enabled inhibition of IRF4 activity and MM proliferation ex vivo and in vivo. p300/CBP KAT inhibition preferentially targeted MM cells over normal cells, specifically modulating the MM transcriptome, and the p300 KAT inhibitors more completely inhibited IRF4 activity at lower levels compared to existing p300/CBP bromodomain inhibitors. Furthermore, combining p300/CBP KAT inhibition and therapeutics with orthogonal mechanisms targeting transcription in MM elicited synergistic anti-tumor effects. Together, these data motivate the ongoing clinical development of p300/CBP KAT inhibition in MM.

DOI: https://doi.org/10.1158/0008-5472.CAN-25-3440
Commun Biol. 2025 Nov 19. 8(1): 1612

DNA methyltransferase Dnmt3ba-mediated epigenetic modulation of Integrin signaling is essential for hematopoietic stem and progenitor cell development.

Kang Ai, Yue Wu, Guixian Liang, Haotian Kong, Xuening Yang, Na Li, Ziting Liu, Yijie Dong, Junjie Xu, Li Zhang, Xiuli Chen, Yuanyuan Fu, Lu Wang, Lei Li.

In vertebrate embryonic development, hematopoietic stem and progenitor cells (HSPCs) originate from a subset of arterial endothelial cells in the ventral wall of the dorsal aorta through endothelial-to-hematopoietic transition (EHT). Despite extensive research efforts, gaps persist in understanding the establishment of HSPC development. In this study, we demonstrate that DNA methyltransferase 3ba (Dnmt3ba), highly expressed in the hemogenic endothelial cells (HECs), plays a crucial role in regulating HEC survival in zebrafish. Dnmt3ba deficiency leads to hypomethylation at the itgα3b and itgα7 loci, diminishing the expression of these Integrins and downstream Akt signaling and Mdm2 phosphorylation, while concurrently triggering HEC apoptosis by upregulation of P53 activity. Manipulation of DNMT3B in an iPSC-derived human hematopoietic differentiation system indicates functional conservation. Collectively, our findings unveil an epigenetic mechanism governed by Dnmt3ba, orchestrating HEC survival through epigenetic modulation of Integrin signaling.

DOI: https://doi.org/10.1038/s42003-025-09003-w
Cell Rep Med. 2025 Nov 19. pii: S2666-3791(25)00534-8. [Epub ahead of print] 102461

Precision prediction of venetoclax-azacitidine treatment efficacy in acute myeloid leukemia via integrative drug screening and machine learning.

Peng Jin, Dan Wang, Jie Shen, Qiqi Jin, Hao Zhang, Xiaxin Liu, Mengke He, Wen Jin, Yixuan Li, Fangyi Dong, Fengbo Jin, Yanli Yang, Ruiji Zheng, Shaoyuan Wang, Jianxin Guo, Shuangyue Li, Debin Liu, Zhiling Yan, Chenghao Jin, Bing Xu, Weiming Guo, Hongming Zhu, Yunxiang Zhang, Zhen Jin, Kankan Wang.

  Venetoclax-azacitidine (VEN/AZA) has transformed acute myeloid leukemia (AML) therapy, yet reliable predictors of response remain lacking. We employ a multidisciplinary strategy combining ex vivo drug sensitivity testing, transcriptomic profiling, functional assays, and clinical data to identify determinants of VEN/AZA response. Core genes consistently associated with responsiveness are validated through CRISPR-Cas9 screening, with silencing of BCL2L1 and PINK1 preferentially enhancing drug sensitivity. Building on these insights, we develop and validate an eight-gene random forest model (RF8) that achieves high accuracy across four independent cohorts (n = 498). RF8 distills the downstream effects of genetic alterations to assist in predicting treatment response and outperforms existing genetic mutation-based signatures. Moreover, RF8 scores show a nearly monotonic relationship with clinical response probabilities and survival outcomes, enabling precise patient stratification. These findings demonstrate the feasibility of integrating transcriptomic and drug-response data to guide VEN/AZA therapy, representing an advance toward personalized therapeutic strategies.

Keywords:  acute myeloid leukemia; ex vivo drug sensitivity testing; machine learning; random forest model; treatment response prediction; venetoclax-azacitidine

DOI:  https://doi.org/10.1016/j.xcrm.2025.102461
Nat Commun. 2025 Nov 21. 16(1): 10276

Benchmarking informatics workflows for data-independent acquisition single-cell proteomics.

Jianwei Wang, Yi Huang, Fanghua Lu, Qinqin Xu, Zhuo Yang, Yirong Jiang, Shaowen Shi, Jianzhang Pan, Yi Yang, Qun Fang.

Recent years have seen a rise of single-cell proteomics by data-independent acquisition mass spectrometry (DIA MS). While diverse data analysis strategies have been reported in literature, their impact on the outcome of single-cell proteomic experiments has been rarely investigated. Here, we present a framework for benchmarking data analysis strategies for DIA-based single-cell proteomics. This framework provides a comprehensive comparison of popular DIA data analysis software tools and searching strategies, as well as a systematic evaluation of method combinations in subsequent informatic workflow, including sparsity reduction, missing value imputation, normalization, batch effect correction, and differential expression analysis. Benchmarking on simulated single-cell samples consisting of mixed proteomes and real single-cell samples with a spike-in scheme, recommendations are provided for the data analysis for DIA-based single-cell proteomics.

DOI: https://doi.org/10.1038/s41467-025-65174-4
Mater Today Bio. 2025 Dec;35 102472

Increased substrate stiffness disrupts nuclear-cytoskeletal mechanical coupling in senescent cells.

Mina Sohrabi Molina, Erik Brauer, Rebecca Günther, Stephanie Diederich, Ansgar Petersen.

  The physical coupling between the nucleus and the cytoskeleton is essential for the mechanobiological adaptation of cells to mechanical cues presented by the surrounding extracellular matrix (ECM). Although aging is known to influence both cellular and ECM mechanical properties, it remains poorly understood how cellular senescence, a hallmark of aging, affects cellular mechano-adaptation. Here, we use substrate stiffness as a mechano-modulatory cue across three distinct models of senescence and demonstrate that senescent fibroblasts are limited in their capacity to integrate mechanical signals of increasing stiffness. The senescent nucleus undergoes progressive actin-mediated deformation and flattening as substrate stiffness increases, until a mechanical threshold is reached that provokes a decoupling of the nucleus from the cytoskeleton. This mechanical disengagement of the nucleus on stiff substrates is accompanied by a loss of cytoskeletal organization, abnormal focal adhesion (FA) maturation, and nuclear softening. We further suggest that the loss of nuclear compression is linked to changes in the nuclear localization of the key mechanosensitive transcriptional regulator Yes-associated protein (YAP). Our findings reveal a fundamental biophysical limitation in the mechano-adaptive response of senescent cells to high-stiffness environments, conditions typically associated with advanced tissue maturation and pathological scarring, which may underlie altered nuclear mechanotransduction and contribute to their specific role in both physiological and pathological contexts.

Keywords:  Mechano-adaptation; Nuclear mechano-adaptation; Nuclear-cytoskeletal coupling; Senescence; Substrate stiffness

DOI:  https://doi.org/10.1016/j.mtbio.2025.102472