bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2026–03–22
twelve papers selected by
William Grey, University of York



  1. Cell Rep Med. 2026 Mar 17. pii: S2666-3791(26)00103-5. [Epub ahead of print]7(3): 102686
      Eradicating leukemia stem cells (LSCs) and overcoming tyrosine kinase inhibitor (TKI) resistance is urgent for chronic myeloid leukemia (CML) treatment. We find that F-box protein 3 (FBXO3) is highly upregulated in CD34+ CML stem cells from TKI-resistant patients and identify it as an innovative CML-LSC marker via single-cell RNA sequencing (scRNA-seq). FBXO3 deficiency induces apoptosis and reduces proliferation of CML cell lines and LSCs in vitro and in vivo, with minimal effects on normal CD34+ hematopoietic stem cells (HSCs). Mechanistically, FBXO3 interacts with DUSP9 to promote its ubiquitination and activate the MAPK pathway, critical for CML cell activity. DUSP9 knockdown partially reverses FBXO3-deficiency-mediated LSC elimination. Furthermore, FBXO3 inhibitor monotherapy or combination with imatinib effectively eradicates CML-LSCs, overcomes TKI resistance, and spares normal hematopoiesis. Collectively, our findings highlight FBXO3's role in CML progression and support combining FBXO3 inhibitors with TKIs for durable LSC elimination.
    Keywords:  CML-LSCs; DUSP9; FBXO3; TKI resistance; chronic myeloid leukemia
    DOI:  https://doi.org/10.1016/j.xcrm.2026.102686
  2. Cell Death Differ. 2026 Mar 17.
      Histone methyltransferase SETD2 is recurrently mutated in hematopoietic malignancies. Our previous study showed that Setd2 deficiency impairs the self-renewal potential of murine hematopoietic stem cells (HSCs) and drives myelodysplastic syndrome (MDS)-like disorders. However, the precise oncogenic advantages conferred upon HSCs by Setd2 loss remain unclear. In this study, we found that Setd2 deficiency disrupted the fidelity of HSC lineage differentiation with preferential erythroid commitment and excessive macrophage priming, leading to ineffective erythropoiesis and the production of inflammatory embryonic-derived Kupffer cell (EmKC)-like cells. Notably, these EmKC-like cells exhibited HSC-independent self-renewal capability and remotely perturbed intramedullary hematopoiesis by inducing systemic inflammation. Furthermore, macrophage depletion effectively alleviated the inflammatory state and relieved MDS-like symptoms. Mechanistically, Setd2 loss leads to significant changes in DNA methylation and chromatin accessibility, resulting in the activation of Irf8. These findings suggest that the long-lived inflammatory cells may compensate for the HSC self-renewal defects, triggering systemic inflammation and driving hematopoietic malignant transformation. This paradigm provides a new understanding of hematopoietic malignancies with functional defects and exhaustion of HSCs.
    DOI:  https://doi.org/10.1038/s41418-026-01715-8
  3. bioRxiv. 2026 Mar 03. pii: 2026.03.02.708949. [Epub ahead of print]
      Though cancer cells' altered metabolism has been recognized for a century, the clinical success of metabolic targeting remains limited due to metabolic plasticity. Here, we use acute myeloid leukemia (AML) as a model to investigate this adaptability through combinatorial metabolic compound screening. Synthetic lethality emerged when AML cells were simultaneously treated with a glutaminase inhibitor and TOFA, a hypolipidemic agent. Sensitivity to this combination was also seen in primary patient samples and in other cancer types, while healthy hematopoietic progenitors were not affected. Unexpectedly, we discovered that TOFA acts through a non-canonical inhibition of protein S-acyltransferases. Protein S-acylation in AML cells specifically requires 16-to-18 carbon long fatty acids and is essential to maintain mitochondrial respiration upon glutaminolysis inhibition. Healthy cells in contrast have high intrinsic metabolic flexibility independent of S-acylation. Our results expose a unique mechanism of metabolic plasticity in cancer that could be targeted to enhance metabolic anti-cancer therapies.
    DOI:  https://doi.org/10.64898/2026.03.02.708949
  4. NPJ Syst Biol Appl. 2026 Mar 19. pii: 38. [Epub ahead of print]12(1):
      Acute myeloid leukemia (AML) is a hematologic malignancy originating in the bone marrow and often progressing to extramedullary sites. Despite advances in molecularly targeted therapies and hematopoietic stem cell transplantation, clinical outcomes remain poor. Tyrosine kinase inhibitors (TKIs) provide benefit to a subset of AML patients harboring FLT3-ITD mutations; however, relapse and resistance remain common. These therapeutic failures are driven by both intrinsic properties of leukemic stem cells (LSCs)-a quiescent, self-renewing population-and extrinsic cues from the tumor microenvironment. We previously demonstrated that arteriolar endothelial cells (ECs) produce miR-126, which is transferred to LSCs, promoting quiescence, treatment resistance, and niche retention. During disease progression, TNF-α secreted by expanding blasts suppresses EC miR-126 production. Following TKI administration, blast reduction lowers TNF-ɑ levels, restoring EC miR-126 production, and this miR-126 expression enables LSCs to re-enter quiescence-thereby escaping therapy and facilitating relapse. To explore this dynamic, we developed an agent-based computational model of the AML bone marrow microenvironment, parameterized with in vitro and in vivo data. The model captures vascular niche remodeling and feedback between leukemic populations and endothelial signaling. Simulations reveal that LSC protection mediated by miR-126 can be disrupted by combining TKIs with miRisten, a miR-126 inhibitor. When administered on a defined schedule, this combination dismantles the protective niche and enhances LSC eradication. These findings underscore the therapeutic potential of targeting microenvironmental feedback to overcome resistance and prevent AML relapse.
    DOI:  https://doi.org/10.1038/s41540-026-00675-6
  5. Exp Hematol. 2026 Mar 18. pii: S0301-472X(26)00052-4. [Epub ahead of print] 105419
      Cellular composition and spatial architecture of the bone marrow niche play a critical role in regulating both normal and malignant hematopoiesis. While flow cytometry enables rapid analysis of hematopoietic and niche cell composition, it requires single-cell dissociation, thereby disrupting the spatial context. In contrast, immunofluorescence imaging preserves tissue architecture but is limited in the number of markers that can be simultaneously detected. Recent advances in multiplex staining technologies now permit visualization of numerous antigens within a single tissue section, providing a more comprehensive view of the bone marrow microenvironment. Despite the central role of murine models in studying hematopoiesis, validated multiplex panels for analyzing murine bone marrow remain limited. This is particularly true for formalin-fixed, paraffin-embedded (FFPE) sections, where challenges such as high autofluorescence and tissue damage during antigen retrieval place substantial demands on tissue preparation. In this study, we optimized tissue preparation for staining murine FFPE bone marrow and developed an efficient multiplex immunohistochemistry panel for detecting hematopoietic stem cell-containing populations within their native niche architecture. Applying our panel to FFPE bone marrow sections from Jak2V617F mice revealed alterations in the megakaryocytic niche, demonstrating the utility of this approach for characterizing disease-associated spatial changes within the hematopoietic microenvironment.
    Keywords:  Bone marrow microenvironment; FFPE tissue; Hematopoietic stem and progenitor cells; Imaging-based analysis; JAK2V617F mouse model; Megakaryocytic niche; Multiplex Immunohistochemistry; Murine bone marrow; Spatial profiling
    DOI:  https://doi.org/10.1016/j.exphem.2026.105419
  6. Development. 2026 Mar 19. pii: dev.204726. [Epub ahead of print]
      Following specification in the dorsal aorta, hematopoietic stem and progenitor cells (HSPCs) proliferate in the HSPC niche, known as the caudal hematopoietic tissue (CHT) in zebrafish. Here we demonstrate that bmal1a, a core component of the circadian clock machinery, is expressed in CHT endothelial cells (ECs) and affects HSPCs in a non-cell autonomous manner. Using endothelial cell-specific dominant-negative Bmal1a zebrafish lines, we demonstrate a striking increase in HSPC numbers in the CHT, resulting from enhanced HSPC proliferation. RNA-sequencing of dominant-negative bmal1a ECs sorted from the CHT shows a downregulation of glud1a, resulting in increased glutamine levels in the CHT. This newly discovered bmal1a-glud1a-glutamine pathway fuels HSPC expansion. We demonstrate that this glutamine synthesis pathway controlling HSPC expansion is likely conserved in the mouse fetal liver (FL) niche, in which hepatocytes are the likely source of glutamine. Together, our data uncover a novel mechanism of HSPC homeostasis, in which EC BMAL1, expressed by the niche, controls the amount of bioavailable glutamine for HSPCs by regulating the expression of genes involved in glutamine synthesis.
    Keywords:  Endothelial cell; Expansion; Glutamine; HSPC; Mouse; Niche; Zebrafish
    DOI:  https://doi.org/10.1242/dev.204726
  7. Blood Neoplasia. 2026 May;3(2): 100195
      Multiple myeloma (MM) is a glutamine (Gln)-auxotroph and Gln-addicted cancer, with Gln synthetase (GS)-deficient MM cells avidly taking up extracellular Gln to sustain their metabolism. Thus, MM cells create a peculiar metabolic niche in the patients' bone marrow (BM), where low levels of Gln contribute to the osteolytic bone lesions by inhibiting the osteoblastic differentiation of mesenchymal stromal cells (MSCs). The effects of the altered MM metabolic niche on other BM cell populations remain to be clarified. We demonstrate here that MM cells secrete high amounts of glutamate through the exchange transporter SLC7A11/xCT. In turn, BM MSCs, but neither MM cells nor osteoblasts (OBs), actively take up extracellular glutamate through the transporter EAAT3 (SLC1A1), whose expression decreases during osteogenesis. GS-positive MSCs secrete Gln, a process boosted by extracellular glutamate in undifferentiated MSCs, but not in differentiated OBs. Coculture of MSCs with MM cells promotes the expression of the bidirectional transporter SNAT5 (SLC38A5), suggesting its involvement in Gln efflux. Consistently, MSCs, derived from either patients with MM or healthy donors, sustain MM growth in a low-Gln environment, an effect suppressed by the inhibition or silencing of glutamate uptake or Gln synthesis. In conclusion, a metabolic cycle occurs in MM BM microenvironment, where Gln-auxotroph MM cells extrude glutamate that is converted into Gln by MSC, sustaining in turn MM anabolism through Gln secretion. The inhibition of this metabolic trade-off impairs MM cell growth, thus highlighting novel potential, niche-oriented therapeutic targets.
    DOI:  https://doi.org/10.1016/j.bneo.2026.100195
  8. Leukemia. 2026 Mar 18.
      Despite extensive research and intensive use of chemotherapies in clinics, the 5-year overall survival of acute myeloid leukemia (AML) patients does not exceed 20%. The clonal expansion of leukemic blasts leads to modifications of the bone marrow physical properties, including increased extracellular matrix stiffening, upregulation of intramedullary pressure and reduction of the space available for cells. These biomechanical modifications are speculated to alter therapeutic response and cause treatment resistance. To address this, we herein focused on the role of mechanotransduction pathways in AML. Analysis of primary AML samples or cell lines revealed that BMPR1B and TAZ/TEAD but not YAP levels were higher after patient relapse or in cells resistant to cytarabine or venetoclax. In addition, highly confined resident mesenchymal stem cells expressed higher levels of BMP4, which in turn specifically activated AML-resistant cells. In these cells, TAZ expression was associated with improved adhesion to microenvironmental components and increased intrinsic deformability. Finally, using a 3D human bone marrow-like model, we showed that targeting BMPR1B or TAZ/TEAD in combination with cytarabine impaired persistence of AML primary cells within the AML niche. Future therapeutic approaches could involve BMPR1B and/or TAZ/TEAD targeting in the context of AML patients refractory to chemotherapy or after relapse.
    DOI:  https://doi.org/10.1038/s41375-026-02904-7
  9. Blood Adv. 2026 Mar 20. pii: bloodadvances.2025018279. [Epub ahead of print]
      Clonal hematopoiesis (CH), the clonal expansion of a hematopoietic stem cell (HSC) and its progeny driven by somatic mutations, has been associated with inferior survival outcomes amongst recipients of autologous stem cell transplants (ASCT). Leukocyte telomere length (LTL) has a complex but well-documented interaction with CH, but the impact of this interaction on stem cell transplantation (SCT) has not been adequately examined. We measured LTL in graft cell DNA from 452 patients undergoing ASCT for myeloma, for whom targeted DNA sequencing for CH driver gene mutations was available. We interrogated clinical and longitudinal large-scale laboratory data for these patients to understand the impact of graft LTL on progression-free (PFS) and overall survival (OS) post-transplantation, as well as blood count indices and their trajectories. In multivariate analyses, longer LTL was associated with increased PFS amongst patients without CH. However, this protective association was not seen in patients with CH. We also report that amongst patients with CH, longer LTL was associated with an increased red cell distribution width (RDW) prior to myeloablative chemotherapy and after ASCT. Collectively, these data reveal hitherto undescribed interactions between LTL, CH and ASCT outcomes.
    DOI:  https://doi.org/10.1182/bloodadvances.2025018279
  10. Nat Rev Mol Cell Biol. 2026 Mar 19.
      How proteins localize to specific compartments, function in coordination with other biomolecules and, ultimately, contribute to diverse cellular activities are crucial questions in cell biology. Complicating the answers to these questions are multilocalizing and multifunctional proteins, whose impact on the cell depends on both spatial and temporal contexts. Therefore, contextualizing protein functions based on their subcellular localization is necessary to fully understand cell behaviours. Recent advances in instrumentation and protein labelling techniques are rapidly increasing the availability of tools, technologies and applications that measure and control protein localization and compartment-specific function. In this Review, we first discuss microscopy, mass spectrometry-based correlation profiling and proximity labelling methods that assign localizations to proteins, ranging from cellular compartments to protein-protein interactions. We next examine the available tools for manipulating protein localization and measuring the effects of these manipulations, including localization tags and bifunctional molecules. For each technology, we assess the strengths and weaknesses that ultimately determine their usefulness. We conclude with an outlook on future technological advances in the field of spatial subcellular proteomics and their potential implications for cell biology and clinical applications.
    DOI:  https://doi.org/10.1038/s41580-026-00957-1
  11. Nat Commun. 2026 Mar 14.
      DIS3, a key nuclear RNA-degrading enzyme, is essential for immunoglobulin class switch recombination (CSR), promoting activation-induced cytidine deaminase (AID) activity on both DNA strands to induce double-strand DNA breaks. During somatic hypermutation, AID-dependent lesions predominantly occur on the non-template DNA strand. Dominant mutations impairing DIS3 exoribonucleolytic activity are common in multiple myeloma (MM), but their role in carcinogenesis remains unclear. Here we show, using a knock-in mouse model, that the clinically relevant DIS3 G766R variant causes chromosomal translocations in B-cells, characterized by aberrant AID activity signatures. The mice develop pristane-induced plasmacytomas, modeling early-stage MM. In clinical MM samples, DIS3 mutations correlate with IGH translocations and AID-driven lesions in driver genes. Mechanistically, mutated DIS3 accumulates on chromatin-bound RNA, particularly at aberrant AID target sites, promoting mutations on both DNA strands. This results in increased AID-dependent double-strand DNA breaks, fostering microhomology-mediated oncogenic rearrangements. Translocations occur specifically during CSR, which remains functionally intact. The DIS3 G766R mutation does not disrupt chromatin architecture in activated B cells but exploits spatial proximity to permanently juxtapose enhancers and proto-oncogenes, facilitating transformation. Thus, gain-of-function DIS3 mutations enhance AID promiscuity, driving IGH translocations and MM development without broadly affecting B-cell physiology.
    DOI:  https://doi.org/10.1038/s41467-026-70386-3