bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2025–04–27
eighteen papers selected by
William Grey, University of York



  1. Exp Hematol. 2025 Apr 22. pii: S0301-472X(25)00081-5. [Epub ahead of print] 104790
      CD34+ human hematopoietic stem and progenitor cells (HSPCs) and primary patient-derived leukemia cells are important tools for basic and translational research. Their limited availability demands additional expansion ex vivo in many cases. The use of either cytokine cocktails or co-cultures with mesenchymal stromal cells (MSCs) has advanced cell expansion but combinations of both have not been addressed extensively so far. Here, we present a novel approach to generate human cytokine-expressing MSCs (ceMSCs) via genetic engineering. Co-culture with ceMSCs and their culture supernatant led to an efficient expansion and maintenance of functional CD34+CD45RA-CD90+CD201+CD49c+ HSCs ex vivo. Similarly, ceMSCs and their culture supernatant support the growth of cytokine-dependent leukemic cell lines in vitro, and improved the survival, maintenance, and expansion of patient-derived acute myeloid leukemia (AML) cells, a cell population very challenging to be cultured ex vivo. ceMSCs even surpass the support provided by wild-type MSCs or external cytokines alone. Therefore, ceMSCs offer a cost-effective, straightforward alternative to traditional cytokine supplementation, enhancing the feasibility of ex vivo studies on healthy and leukemic stem and progenitor cells, including therapeutic drug testing and mechanistic investigations.
    DOI:  https://doi.org/10.1016/j.exphem.2025.104790
  2. Blood. 2025 Apr 21. pii: blood.2024027872. [Epub ahead of print]
      Hematopoietic stem cells (HSCs) are heterogeneous, and the quality of HSCs - that is, 'transplantability' - is a key determinant for posttransplant hematopoietic reconstitution. However, molecular modalities of high-potency HSCs with superior transplantability still remain poorly understood. Here, we conducted large-scale single-clone serial-transplant experiments and tracked descendant cells of 288 HSC clones to quantify their intrinsic capability for hematopoietic reconstitution. Using integrated single-cell transcriptional, immunophenotypical, and Bayesian dynamic analyses, we uncovered three classes of HSC clones - 'Super', 'Flash', and 'Trickle' - that had higher output in the 1st generation but exhibited markedly different behavior in later generations. The 'Super'-class HSC clones comprised 4% of the HSCs and manifested persistent superior transplantability and balanced myeloid/lymphoid lineage outputs across generations in serial transplants. The 'Super'-class HSCs had a unique molecular signature, including low expression of CD27, that was distinct from previously known 'Classical HSC' signatures. Validation experiments indicated that CD27- HSCs had superior transplantability compared to CD27+ HSCs. Our study asserted an operational definition for 'Super' transplantability of HSCs, defined its molecular program, and suggested new directions for enriching high-potency HSCs in grafts.
    DOI:  https://doi.org/10.1182/blood.2024027872
  3. Cell Regen. 2025 Apr 22. 14(1): 15
      The fetal liver is the primary site for the expansion of hematopoietic stem and progenitor cells (HSPCs) during fetal hematopoiesis. However, the spatial organization of different hematopoietic progenitor populations within the fetal liver remains poorly characterized. In this study, we utilized SeekSpace, a high-resolution single-nucleus spatial transcriptomics platform, to map the spatial distribution of hematopoietic stem cells and multipotent progenitor cells (HSC/MPPs) and downstream restricted progenitors (RPs) in relation to other hematopoietic and stromal cell populations in the fetal liver at embryonic day 13.5. Using SeekSpace, we constructed a detailed single-cell spatial transcriptomic atlas of fetal liver hematopoiesis, revealing that both HSC/MPPs and many RPs undergo active expansion in the fetal liver, a process distinct from their behavior in adult bone marrow. Proximity analysis and in situ imaging demonstrated that HSC/MPPs expansion occurs in close association with macrophages and endothelial cells throughout the fetal liver, supported by signaling pathways involving IGF and collagen. In contrast, RPs exhibited no specific spatial proximity to other cell populations during their expansion. Collectively, this study provides a comprehensive resource for understanding the spatial and molecular mechanisms underlying HSC/MPPs and RP expansion during fetal liver hematopoiesis.
    Keywords:  Fetal liver; Hematopoiesis; Hematopoietic stem and progenitor cells; Niche; Spatial transcriptomic
    DOI:  https://doi.org/10.1186/s13619-025-00234-0
  4. Hemasphere. 2025 Apr;9(4): e70118
      Targeting metabolism represents a promising approach to eradicate leukemic stem cells (LSCs) that are considered critical drivers of relapse in acute myeloid leukemia (AML). In this study, we demonstrate that the phosphatidic acid phosphatase LPIN1, which regulates the synthesis of diacylglycerol, the key substrate for triacylglycerol, and phospholipid production, is crucial for the function of healthy and leukemic hematopoietic stem and progenitor cells (HSPC and LSC). LPIN1 mRNA was highly expressed in the CD34+ compartment of primary human AML samples. LPIN1 suppression inhibited the proliferation of primary leukemic cells and normal HSPCs in vitro and in xenotransplantation assays. Lipidomics analyses revealed a reduction of phosphatidylcholine (PC) and phosphatidylethanolamine and an upregulation of sphingomyelin upon LPIN1 depletion. Distinct phospholipid composition was associated with genetic AML groups, and targeting PC production by choline kinase inhibitors showed strong anti-leukemic activity. In summary, our data establish a regulatory role of LPIN1 in HSPC and LSC function and provide novel insights into the role of glycerophospholipid homeostasis in stemness and differentiation.
    DOI:  https://doi.org/10.1002/hem3.70118
  5. STAR Protoc. 2025 Apr 17. pii: S2666-1667(25)00184-4. [Epub ahead of print]6(2): 103778
      Hematopoietic stem cells (HSCs) maintain their self-renewal capacity in an autocrine manner through hematopoietic stem and progenitor cell (HSPC)-derived extracellular vesicles (EVs). Here, we present a protocol for the isolation and characterization of EVs from HSPCs starting from an in vivo murine model. We describe steps for murine bone marrow isolation, HSPC staining and sorting, HSPC-derived EV isolation, size and concentration characterization, and EV visualization and marker description. For complete details on the use and execution of this protocol, please refer to Bonora et al.1.
    Keywords:  Cell Biology; Cell isolation; Flow Cytometry; Metabolism; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2025.103778
  6. Nat Biotechnol. 2025 Apr 23.
      Immunotherapies for acute myeloid leukemia (AML) and other cancers are limited by a lack of tumor-specific targets. Here we discover that RNA-binding proteins and glycosylated RNAs (glycoRNAs) form precisely organized nanodomains on cancer cell surfaces. We characterize nucleophosmin (NPM1) as an abundant cell surface protein (csNPM1) on a variety of tumor types. With a focus on AML, we observe csNPM1 on blasts and leukemic stem cells but not on normal hematopoietic stem cells. We develop a monoclonal antibody to target csNPM1, which exhibits robust anti-tumor activity in multiple syngeneic and xenograft models of AML, including patient-derived xenografts, without observable toxicity. We find that csNPM1 is expressed in a mutation-agnostic manner on primary AML cells and may therefore offer a general strategy for detecting and treating AML. Surface profiling and in vivo work also demonstrate csNPM1 as a target on solid tumors. Our data suggest that csNPM1 and its neighboring glycoRNA-cell surface RNA-binding protein (csRBP) clusters may serve as an alternative antigen class for therapeutic targeting or cell identification.
    DOI:  https://doi.org/10.1038/s41587-025-02648-2
  7. Hemasphere. 2025 Apr;9(4): e70120
      Hematopoiesis develops in the bone marrow (BM) where multiple interactions regulate the differentiation and preservation of hematopoietic stem and progenitor cells (HSPCs). Immune-deficient murine models have enabled the analysis of molecular and cellular regulation of human HSPCs, but the physiology of these models is questioned as human hematopoietic cells develop in xenogenic microenvironments. In this study, we thoroughly characterized a humanized (h) in vivo BM model, developed from fetal (F/) and post-natal (P-N/) mesenchymal stromal cell (MSC) differentiation (called hOssicles [hOss]), in which human hematopoietic cells are generated following the transplantation of CD34+ cells. Serial isolation and transplant experiments of hMSCs and HSPCs from hOss revealed the dynamic nature of these hBM niches. hOss modified human hematopoietic development by modulating myeloid/lymphoid cell production and HSPC levels, with no major transcriptional changes in HSPCs at the single-cell level. Clonal tracking using genetic barcodes highlighted hematopoietic cell cross-talks between the endogenous murine BM and hOss and differences in clonal myeloid/multipotent cell production between F/hOss and P-N/hOss, uncovering ontogeny-related impact of the BM on human hematopoietic cell production.
    DOI:  https://doi.org/10.1002/hem3.70120
  8. Nat Nanotechnol. 2025 Apr 23.
      Under stress conditions, such as ex vivo culture, chemotherapy, irradiation and infection, haematopoietic stem cells (HSCs) actively divide to maintain blood cell production. This process leads to production of reactive oxygen species (ROS) that causes HSC exhaustion and haematopoietic failure. Here we show that ferumoxytol (FMT; Feraheme), a Food and Drug Administration-approved nanodrug, is a powerful ROS scavenger capable of relieving ROS in stressed HSCs, facilitating their post-injury regeneration. Mechanistically, the catalase-like activity of FMT reduces intracellular levels of H2O2 and diminishes H2O2-induced cytotoxicity. Moreover, FMT maintains long-term regenerative capacity of transplanted HSCs in pre-conditioned leukaemic mice and shows potential to effectively eliminate leukaemia in vivo while preserving HSCs. Our study highlights FMT as a powerful clinical tool to promote haematopoietic cell recovery in patients undergoing stress-generating treatments.
    DOI:  https://doi.org/10.1038/s41565-025-01907-2
  9. Blood. 2025 Apr 21. pii: blood.2024026936. [Epub ahead of print]
      Recent studies indicate the human lympho-myeloid restriction process to be a different and more heterogeneous one than historically inferred. Here we describe the development of bulk and clonal culture systems that efficiently support early B-lymphoid differentiation and its use to elucidate the biological and molecular changes that accompany their initial restriction from subsets of CD34+ human cord blood cells with lympho-myeloid-limited potential. Analyses of these changes revealed that the acquisition of B-lymphoid- and neutrophil/monocyte (NM)-restricted properties are accompanied by a concomitantly accelerated and lineage-shared cell cycling activity and loss of self-renewal potential. Single-cell transcriptome analysis identified reduced expression of multiple self-renewal-associated genes and an accompanying heterogeneous activation of lineage-regulatory modules during the production of B, NM and dendritic cell precursors. By applying a novel culture system that supports early human lymphoid differentiation, we uncover a shared mechanism of proliferation control, along with persistent biological and transcriptional heterogeneity in cells undergoing B and NM lineage restriction.
    DOI:  https://doi.org/10.1182/blood.2024026936
  10. Leukemia. 2025 Apr 23.
      Hematopoietic cells and lymphocytes arise from a common stem cell for both lineages. This explains why similar signaling networks regulate the development and biological functions of these cells. One crucial regulatory mechanism involves interactions with soluble mediators of innate immunity, including activated elements of the complement cascade (ComC). For many years, ComC proteins were thought to be synthesized only in the liver and released into blood to be activated by one of the three proteolytic cascades. The regulatory effects of activated components of ComC on hematopoietic stem progenitor cells (HSPCs) and mature hematopoietic cells have been well demonstrated in the past. However, recent data indicate that complement proteins are also expressed in several cell types, including lymphocytes and innate immune cells. This intracellular complement network has been named the "complosome." Recent evidence from our group shows that the complosome is also expressed in HSPCs and plays an important yet underappreciated role in the expansion, trafficking, and metabolism of these cells. We propose that the complosome, like its role in lymphocytes, is necessary for the optimal function of mitochondria in hematopoietic cells, including HSPCs. This opens a new area for investigation and potential pharmacological intervention into the complosome network in normal and malignant hematopoiesis.
    DOI:  https://doi.org/10.1038/s41375-025-02613-7
  11. Cell Death Dis. 2025 Apr 23. 16(1): 331
      Acute myeloid leukemia (AML) is an aggressive hematological malignancy. Patients with wild-type FLT3 relapsed or refractory (R/R) AML face significant therapeutic challenges due to the persistent lack of effective treatments. A comprehensive understanding of the mechanisms underlying chemotherapy resistance is needed to the development of effective treatment strategies. Therefore, we investigated the molecular mechanisms underlying cytarabine (Ara-C) resistance and daunorubicin (DNR) tolerance in Ara-C-resistant RHI-1 cells derived from the wild-type FLT3 AML cell line SHI-1. Quantitative analysis of intracellular drug concentrations, proteomics, and phosphoproteomics showed that DNR resistance in Ara-C-resistant RHI-1 cells is driven by metabolic remodeling toward mitochondrial metabolism, upregulation of DNA repair pathways, and enhanced reactive oxygen species (ROS) detoxification rather than reduced drug uptake. Moreover, targeting these compensatory mechanisms, particularly the OXPHOS complex I proteins, significantly improved the efficacy of both Ara-C and DNR. Conclusively, these findings highlight mitochondrial metabolism and DNA repair as critical factors in chemotherapy resistance and offer valuable insights into potential therapeutic targets for enhancing treatment outcomes in patients with wild-type FLT3 R/R AML.
    DOI:  https://doi.org/10.1038/s41419-025-07653-6
  12. Nature. 2025 Apr 23.
      Clonal haematopoiesis of indeterminate potential (CHIP) involves the gradual expansion of mutant pre-leukaemic haematopoietic cells, which increases with age and confers a risk for multiple diseases, including leukaemia and immune-related conditions1. Although the absolute risk of leukaemic transformation in individuals with CHIP is very low, the strongest predictor of progression is the accumulation of mutant haematopoietic cells2. Despite the known associations between CHIP and increased all-cause mortality, our understanding of environmental and regulatory factors that underlie this process during ageing remains rudimentary. Here we show that intestinal alterations, which can occur with age, lead to systemic dissemination of a microbial metabolite that promotes pre-leukaemic cell expansion. Specifically, ADP-D-glycero-β-D-manno-heptose (ADP-heptose), a biosynthetic bi-product specific to Gram-negative bacteria3-5, is uniquely found in the circulation of older individuals and favours the expansion of pre-leukaemic cells. ADP-heptose is also associated with increased inflammation and cardiovascular risk in CHIP. Mechanistically, ADP-heptose binds to its receptor, ALPK1, triggering transcriptional reprogramming and NF-κB activation that endows pre-leukaemic cells with a competitive advantage due to excessive clonal proliferation. Collectively, we identify that the accumulation of ADP-heptose represents a direct link between ageing and expansion of rare pre-leukaemic cells, suggesting that the ADP-heptose-ALPK1 axis is a promising therapeutic target to prevent progression of CHIP to overt leukaemia and immune-related conditions.
    DOI:  https://doi.org/10.1038/s41586-025-08938-8
  13. Leukemia. 2025 Apr 22.
      The risk of progression of monoclonal gammopathy of undetermined significance (MGUS) to multiple myeloma (MM) increases with advancing age, suggesting that progression may be influenced by age-related changes within the bone marrow (BM) microenvironment. We hypothesise that senescent mesenchymal stromal cells (MSCs), which accumulate in the BM with age, may contribute to MGUS progression to MM. Here, we show that, like BM MSCs from aged non-cancer controls, BM MSCs from both MM and MGUS patients exhibit a senescent phenotype characterised by enlarged, flattened morphology, increased β-galactosidase activity and CDKN2A expression, and decreased proliferation rate compared with BM MSCs from healthy young individuals. While coculture with BM MSCs suppresses the proliferative capacity of MM cell lines in vitro, induction of senescence via irradiation or replicative exhaustion in healthy MSCs relieves this suppression, compared with non-senescent MSCs. This may, in part, be attributable to upregulated expression of the BMP antagonist Gremlin1 in senescent MSCs, which facillitates MM cell proliferation. Notably, the risk of progression to MM was significantly elevated in MGUS patients with increased MSC senescence. Collectively, our data provide evidence that age-related accumulation of senescent MSCs may be a driver of MGUS to MM progression.
    DOI:  https://doi.org/10.1038/s41375-025-02621-7
  14. Cell Death Dis. 2025 Apr 22. 16(1): 327
      FMS-like tyrosine kinase 3-internal tandem duplication (FLT3/ITD) is a common driver mutation that presents with a high leukemic burden and its impact on metabolic homeostasis remains to be further investigated. Here, we revealed that the oncogenic activation of FLT3/ITD induced upregulation of target genes of sterol regulatory element-binding proteins (SREBPs) in vivo and in acute myeloid leukemia patients. Quizartinib is a second-generation FLT3 inhibitor that selectively inhibits the activating FLT3 mutations. We demonstrated the critical role of SREBP1 degradation in conferring the response of FLT3/ITD cells to quizartinib. Mechanistically, quizartinib facilitated degradation of the precursor form of SREBP1 via the FLT3/AKT/GSK3 axis and reduced protein levels of its target gene fatty acid synthase (FASN). Lipidomics analysis by Liquid Chromatography Mass Spectrometry (LC-MS) demonstrated that inhibition of FLT3 altered global levels of phospholipids including reduction of cardiolipin, leading to subsequent loss of mitochondrial membrane potential. Pharmacological inhibition of SREBP1 or FASN sensitized FLT3/ITD leukemia cells to quizartinib. Quizartinib combined with SREBP inhibitor fatostatin or FASN inhibitor orlistat provided substantial therapeutic benefit over monotherapies in the murine FLT3/ITD leukemia model. Our results indicated the mechanistic link between FLT3/ITD and SREBP degradation and suggested the combination therapy via targeting FLT3/SREBP/FASN axis.
    DOI:  https://doi.org/10.1038/s41419-025-07661-6
  15. Nat Commun. 2025 Apr 23. 16(1): 3804
      Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative disorder that predominantly affects infants and young children. Hematopoietic stem cell transplantation (HSCT) is standard of care, but post-HSCT relapse is common, highlighting the need for innovative therapies. While adoptive immunotherapy with chimeric antigen receptor (CAR) T cells has improved outcomes for patients with advanced lymphoid malignancies, it has not been comprehensively evaluated in JMML. In the present study, we use bulk and single-cell RNA sequencing, mass spectrometry, and flow cytometry to identify overexpression of CLL-1 (encoded by CLEC12A) on the cell surface of cells from patients with JMML. We develop immunotherapy with CLL-1 CAR T cells (CLL1CART) for preclinical testing and report in vitro and in vivo anti-leukemia activity. Notably, CLL1CART reduce the number of leukemic stem cells and serial transplantability in vivo. These preclinical data support the development and clinical investigation of CLL-1-targeting immunotherapy in children with relapsed/refractory JMML.
    DOI:  https://doi.org/10.1038/s41467-025-59040-6
  16. J Hematol Oncol. 2025 Apr 23. 18(1): 47
      Extramedullary disease (EMD) in multiple myeloma (MM) represents a significant clinical challenge, with a limited understanding of the spatial architecture and its pathobiological impact. To address this unmet need, we examined 10 matched samples from bone marrow (BM) and cognate EMD sites. This investigation provides critical insights into the distinct features of EMD, offering potential avenues for more effective diagnosis and targeted therapies. To this aim, we employed MACSima™ Imaging Cyclic Staining (MICS) to unveil distinct biomarker expression profiles as companion diagnostics for a personalized therapeutic approach for MM. We observed elevated BCL-2 levels in EMD plasma cells (p < 0.0001), indicating the potential of BCL-2 inhibitors to target anti-apoptotic pathways in select cases. The higher expression of EZH2 in EMD compared to BM (p < 0.0001) highlights its role in sustaining aggressive tumor phenotypes and supports the use of epigenetic-targeting agents in key situations. In contrast, CD3 + T-cell distance was significantly higher in EMD, reflecting impaired immune surveillance (p < 0.0001). Across the cohort, our analysis revealed significant differences between BM and EMD regarding the expression and spatial organization of key markers. CD38 expression was markedly reduced in EMD plasma cells (p < 0.0001). These findings underscore profound biological heterogeneity in MM and its BM emancipated disease phenotype, emphasizing dysfunctional apoptosis, immune evasion and resistance to CD38-targeting therapies in EMD, conceivably informing future validations. By integrating high-dimensional data, this study provides insights into potential druggable vulnerabilities for crafted interventions, particularly challenging in EMD cases.
    Keywords:  Extramedullary disease; MACSima™ imaging system; MICS technology; Multiple myeloma
    DOI:  https://doi.org/10.1186/s13045-025-01699-x
  17. Autophagy. 2025 Apr 25. 1-3
      Mitophagy, selective degradation of dysfunctional mitochondria by the autophagy-lysosome pathway, is critical for maintaining cellular homeostasis. In recent years, significant progress has been made in understanding how PINK1 (PTEN-induced kinase 1)-mediated phosphorylation and the E3 ubiquitin (Ub) ligase (PRKN/parkin)-mediated ubiquitination form a positive feedforward loop in control of mitophagy. Nevertheless, a fundamental question remains: How is PINK1 transcriptionally modulated under mitochondrial stress to finely support mitophagy? Recently, we unveiled a novel mechanism in control of PINK1 transcription by SMAD3 (SMAD family member 3), an essential component of the TGFB/TGFβ (transforming growth factor beta)-SMAD signaling pathway. Upon mitochondrial depolarization, SMAD3 is activated through PINK1-mediated phosphorylation of SMAD3 at serine 423/425 independent of canonical TGFB signaling. More importantly, the SMAD3-PINK1 regulatory axis appears to functionally provide a pro-survival mechanism against mitochondrial stress. Therefore, PINK1 and SMAD3 constitute a newly discovered positive feedforward loop to regulate mitophagy, highlighting the need for further exploring the crosstalk between TGFB-SMAD signaling and mitophagy.
    Keywords:  Mitophagy; PINK1; SMAD3; phosphorylation; transcription
    DOI:  https://doi.org/10.1080/15548627.2025.2496364