bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2026–08–09
fifteen papers selected by
William Grey, University of York



  1. Blood. 2026 Aug 06. pii: blood.2026034240. [Epub ahead of print]
      Ex vivo expansion of human hematopoietic stem cells (HSCs) holds promise for overcoming their limited availability, a major barrier to broader clinical application. Although recent advances in culture systems can increase HSC numbers, these conditions frequently impair self-renewal and induce myeloid bias, and the underlying molecular mechanisms remain poorly understood. Here, we performed single-cell multiome sequencing (scMultiome-seq) on human umbilical cord blood-derived CD34⁺ hematopoietic stem and progenitor cells to co-profile transcriptional and epigenetic adaptations within the same cells during ex vivo culture. Our analyses revealed reduced transcriptional and epigenetic HSC signatures, accompanied by markedly increased activity of myeloid-associated transcription factor motifs, providing molecular insight into the functional decline and myeloid bias of cultured HSCs. We further observed substantial functional heterogeneity among phenotypically defined HSCs following culture. To address these limitations, we established a niche-mimetic culture system that integrates intrinsic and extrinsic bone marrow regulatory cues, including pharmacologic inhibition of the m6A reader YTHDF2 using the small molecule Y13-27, a three-dimensional microenvironment, and N-cadherin-mediated adhesion. This condition (3D-NcadP-Y) robustly preserved long-term repopulating capacity. When combined with the self-renewal agonist UM729, the resulting platform (3D-NcadP-Y-UM) uniquely enabled the expansion of serially transplantable long-term HSCs with balanced multilineage potential. scMultiome-seq and cellular analyses demonstrated that this condition preserves transcriptional and epigenetic long-term HSC signatures, maintains multilineage-associated transcription factor motifs, and limits excessive cell-cycle activation. Together, these findings elucidate molecular mechanisms underlying culture-induced HSC dysfunction and establish a niche-mimetic strategy for expanding functional human long-term HSCs while preserving key features of stemness.
    DOI:  https://doi.org/10.1182/blood.2026034240
  2. Cytotherapy. 2026 Jun 05. pii: S1465-3249(26)00886-8. [Epub ahead of print]28(10): 102925
       BACKGROUND: Background: Hematopoietic stem/progenitor cell (HSPC) transplantation outcomes depend critically on the dose of functional stem cells delivered to patients, yet current ex vivo cell therapy manufacturing processes lack reliable methods to quantify therapeutic hematopoietic stem cells (HSCs) after in vitro culture. This gap poses significant clinical risks, as culture-induced changes may alter the cellular composition of therapeutic products. The challenge stems from two key limitations: (i) biological-conventional HSC markers to phenotypically characterize subpopulations such as CD38 become unreliable during culture, and (ii) technical-existing assays cannot distinguish between HSCs and phenotypically similar progenitors in manipulated products.
    AIM: To solve this problem, we compared an ITGA3- and CD49f-based identification strategy that bypasses culture-sensitive markers.
    METHODS: Through single-cell analysis of adult mobilized peripheral blood HSPCs cultured under clinical manufacturing conditions, we demonstrate that ITGA3+ cells better maintain stemness signatures (higher AVP/HLF expression) compared to CD49f+.
    RESULTS: Functional validation through xenotransplantation revealed superior engraftment and multilineage reconstitution with ITGA3+ HSCs.
    CONCLUSIONS: Our findings provide the first validated method to track functional HSCs during clinical manufacturing, addressing a fundamental quality control challenge in the field. This advance enables more accurate dosing for transplants and provides a critical tool for emerging gene-modified HSPC therapies where product characterization is paramount.
    Keywords:  Cellular therapy; gene therapy; hematopoietic stem cell; immunophenotype; manufacturing
    DOI:  https://doi.org/10.1016/j.jcyt.2026.102925
  3. Antioxid Redox Signal. 2026 Aug 05. 15230864261475098
       AIMS: Aging-related functional decline in hematopoietic stem cells (HSCs) is closely associated with mitochondrial dysfunction and impaired mitophagy. This study aimed to investigate whether targeted restoration of mitophagy via the myeloid cell leukemia 1 (MCL-1)/light chain 3A pathway could rejuvenate aged HSCs and improve their regenerative capacity.
    RESULTS: We identified MCL-1 as the most highly expressed mitophagy receptor in aged HSCs. Treatment with UMI-77, a selective MCL-1 agonist, significantly enhanced mitophagy, reduced mitochondrial mass, improved mitochondrial membrane potential, and reduced reactive oxygen species levels in aged HSCs both in vitro and in vivo. Single-cell RNA sequencing revealed that UMI-77 upregulated mitophagy-related genes (Sqstm1, Fundc1, Bnip3) and restored stemness signatures in long-term HSCs. Transplantation assays demonstrated that UMI-77-treated aged HSCs exhibited superior hematopoietic reconstitution capacity compared with those from control mice. However, this intervention also increased the proportion of myeloid-biased CD150high HSCs, a hallmark of aging.
    CONCLUSION: Targeted mitophagy restoration via MCL-1 activation improves mitochondrial fitness and stemness in aged HSCs but does not reverse myeloid bias. These findings highlight mitophagy enhancement as a viable therapeutic approach, while suggesting combinatorial strategies may be needed to fully restore lineage balance in aging hematopoiesis. Antioxid. Redox Signal. 00, 000-000.
    Keywords:  MCL-1; UMI-77; aging; hematopoietic stem cells; mitophagy
    DOI:  https://doi.org/10.1177/15230864261475098
  4. EMBO J. 2026 Aug 05.
      Progressive aging of bone marrow hematopoietic stem cells (HSCs) underlies clonal hematopoiesis and age-associated hematologic disorders. Defining early molecular events driving HSC functional decline is essential for rejuvenation strategies. Here, we identify P-selectin (Selp) as a surface marker that stratifies HSCs into conserved functional and transcriptional states during organismal aging in humans and mice. P-selectin expression increases early during aging and remains elevated in old HSCs. Selphigh-HSCs exhibit increased DNA damage and bias towards megakaryocytic/myeloid lineage fate, whereas Selplow-HSCs maintain metabolic integrity, enhanced antioxidant capacity, and reduced myeloid skewing. Transcriptomic analysis revealed that Selphigh-HSCs adopt megakaryocytic-primed, pro-inflammatory, and oxidative stress programs, while Selplow-HSCs retain lymphoid-associated and redox-balanced signatures consistent with a more preserved stem-cell state. Further ATAC-seq analysis demonstrates distinct chromatin landscapes with Selphigh-HSCs being enriched for inflammatory and platelet-related regulatory elements and CTCF motifs, but Selplow-HSCs displaying accessible ETS-driven networks linked to metabolic fitness and stem cell resilience. Together, these findings uncover conserved heterogeneity during blood stem cell aging and establish P-selectin as an early biomarker and potential therapeutic target to mitigate age-associated hematopoietic decline.
    DOI:  https://doi.org/10.1038/s44318-026-00887-w
  5. Blood Neoplasia. 2026 Aug;3(3): 100259
      Expression of RUNX1::RUNX1T1 (also known as RUNX1::ETO) is frequently observed in acute myeloid leukemia (AML) and has been shown to block myeloid development. Although several studies have shown RUNX1::RUNX1T1 transcriptional deregulation, the proteome in human hematopoietic stem and progenitor cells (HSPCs) is poorly characterized. Using mass spectrometry, we show that expression of RUNX1::RUNX1T1 in human HSPCs was linked to differential expression of 257 proteins, including CCAAT/enhancer-binding protein beta (C/EBPβ) downregulation. Consistent with this observation, although CEBPB mRNA is generally overexpressed in AML, patients with t(8;21) have comparatively low CEBPB expression. We show in human HSPCs that ectopic expression of C/EBPβ can promote proliferation of myeloid cells. Conversely, short hairpin RNA-mediated knockdown of C/EBPβ inhibited the growth of normal human myeloid cells; however, it promoted the growth of cells expressing RUNX1::RUNX1T1. C/EBPβ also influenced differentiation, with ectopic expression promoting monocyte development, whereas reduced expression favored granulocyte differentiation, which in turn suggests that C/EBPβ expression may act as a lineage discriminator for these myeloid cell types. In summary, our data reveal how RUNX1::RUNX1T1 drives deregulation of the HSPC proteome and suggest a mechanism by which RUNX1::RUNX1T1 expression contributes to leukemia development, including C/EBPβ, which itself affects normal myeloid development.
    DOI:  https://doi.org/10.1016/j.bneo.2026.100259
  6. Nat Cell Biol. 2026 Aug 06.
      Microenvironment remodelling impacts tumour growth and metastasis, but whether remodelling promotes pre-malignant clonal fitness remains unknown. Here, using single-cell RNA-sequencing of the bone-marrow microenvironment in a mouse model of DNMT3A-mutant clonal haematopoiesis (CH), we identify mesenchymal stromal cells (MSCs) in a molecular state of cellular senescence. Elevated bone-marrow MSC senescence is also observed in humans with CH driven by several common somatic mutations. MSC senescence is induced by mutant haematopoietic cells in a contact-independent manner through production of soluble factors including TNF-α and IL-6. These cytokines activate a Stat3-driven pathway that is necessary and sufficient for MSC senescence induction. Genetic or pharmacological depletion of senescent non-haematopoietic cells reduces the burden of CH and delays progression to myeloid neoplasia. Our findings show that microenvironment remodelling modifies pre-malignant clonal fitness and identifies disruption of the crosstalk between pre-malignant cells and their niche as a cancer prevention strategy.
    DOI:  https://doi.org/10.1038/s41556-026-02025-4
  7. Exp Hematol. 2026 Aug 07. pii: S0301-472X(26)00122-0. [Epub ahead of print] 105489
      Hematopoietic stem and progenitor cells (HSPCs) are characterized by the ability to proliferate, differentiate into multiple lineages, self-renew and repopulate the hematopoietic system. Development of functional assays enabling qualitative and quantitative measurements of these different features are cornerstones of the field. In this review, we summarize key approaches, from early transplantation and spleen colony-forming unit assays to in vitro clonogenic systems, long-term culture assays, xenotransplantation models, and single-cell platforms with historical perspectives and evaluation of their utilities as well as limitations. We emphasize the principles of functional definition of stem and progenitor cells and the discoveries of clonal origin and functional heterogeneity within phenotypically defined HSPC populations.
    DOI:  https://doi.org/10.1016/j.exphem.2026.105489
  8. Blood Sci. 2026 Sep;8(3): e00301
      Signal transducer and activator of transcription 3 (STAT3) is a pivotal oncogenic driver in multiple myeloma (MM), and its constitutive activation promotes malignant plasma cell proliferation, survival, and drug resistance in the bone marrow microenvironment. Despite therapeutic advances, MM remains incurable due to persistent STAT3-driven tumorigenesis and the resilience of MM stem cells. We investigated the therapeutic potential of napabucasin (BBI608), a novel STAT3 inhibitor, in MM. Our data demonstrated that BBI608 potently suppressed MM cell proliferation in vitro and in vivo, while significantly impairing the clonogenic potential and inducing robust apoptosis. Mechanistically, BBI608 exhibited dual efficacy by targeting bulk tumor cells and eradicating the stem-like compartment of MM cells, thereby addressing a critical therapeutic challenge. Moreover, we revealed that BBI608 triggered immunogenic cell death (ICD) via the activation of endoplasmic reticulum (ER) stress and the unfolded protein response (UPR), which subsequently enhanced T-cell-mediated anti-tumor immunity. Our findings highlight STAT3 inhibition as a promising strategy to simultaneously eradicate MM cells, target stem cell reservoirs, and harness anti-tumor immunity, providing a robust rationale for the clinical translation of BBI608 in MM therapy.
    Keywords:  Cancer stem cells; ICD; Napabucasin; STAT3
    DOI:  https://doi.org/10.1097/BS9.0000000000000301
  9. Cancer Res. 2026 Aug 03.
      Casein kinase 1⍺ (CK1⍺) is a multifunctional serine/threonine kinase, serving as an upstream regulator of the p53 pathway and a potential therapeutic target for acute myeloid leukemia (AML). Small-molecule degraders show preclinical promise in AML by selectively degrading target proteins. Here, we developed and evaluated PinA1, a molecular glue degrader targeting CK1⍺, in preclinical AML models. PinA1 preferentially degraded CK1⍺ at nanomolar concentrations, resulting in enhanced p53 expression, cell-cycle arrest, and apoptosis in TP53 wild-type AML cell lines but not in TP53 mutated cells. PinA1 also induced CK1⍺ degradation and p53-dependent apoptosis in primary AML cells with wild-type TP53. Notably, PinA1 had minimal effects on the viability of human peripheral blood and bone marrow mononuclear cells, including CD34+ cells, with limited activation of the p53 pathway. In both cell lines and primary AML cells, PinA1 enhanced apoptosis when combined with targeted agents, including FLT3, BCL-2, or MDM2 inhibitors. PinA1 demonstrated robust anti-leukemic efficacy as a monotherapy and exhibited synergistic effects when combined with targeted agents in xenografts derived from human AML cell lines and primary AML cells. In conclusion, PinA1 degrades CK1⍺, activates the p53 pathway, and induces cell-cycle arrest and apoptosis in TP53 wild-type AML cells. The robust anti-leukemic efficacy of PinA1, both as monotherapy and further in combination with targeted agents, along with its minimal toxicity to normal hematopoietic cells, underscores its potential for future clinical applications.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-25-3629
  10. Leukemia. 2026 Aug 03.
      Mature plasmacytoid dendritic cell proliferation associated with acute myeloid leukemia (pDC-AML) is a distinct entity with poor prognosis. Yet, the mechanisms underlying the immune evasion and aberrant pDC expansion remain poorly understood. We performed multi-omic profiling of 18 pDC-AML cases, along with 207 non-pDC-AML and 16 BPDCN cases as controls. Single-cell RNA-seq and proteomic analyses demonstrated that pDC-AML leukemia stem cells exhibited unfolded protein response activation, particularly the IRE1α-XBP1 axis, which preceded the acquisition of the pDC maturation program. Supporting this, pharmacological induction of endoplasmic reticulum stress in myeloid cells upregulated BCL11A, the master transcription factor in pDC differentiation, and induced a pDC immunophenotype (CD123+BDCA2+). Importantly, pDC-AML-derived pDCs exhibited functional impairment, including compromised antigen-presenting pathways and reduced interactions between pDCs and CD8+ T cells. scTCR-seq analysis revealed significantly restricted T-cell clonal expansion in the pDC-AML bone marrow microenvironment, which correlated with leukemic burden and reversed upon clinical remission. Notably, allogeneic hematopoietic stem cell transplantation (HSCT) significantly improved overall and progression-free survival, abrogating the prognostic disadvantage relative to non-pDC-AML. Collectively, these findings establish impaired anti-leukemia immunity as a hallmark of pDC-AML, support early HSCT as a clinical priority, and identify ER-stressed pDCs as a potential novel therapeutic target.
    DOI:  https://doi.org/10.1038/s41375-026-03080-4
  11. Nat Biomed Eng. 2026 Aug 05.
      In vivo genetic engineering of haematopoietic stem and progenitor cells (HSPCs) holds the potential to revolutionize the treatment landscape for numerous diseases. However, despite its transformative potential, it remains hindered by the difficulty in efficiently and specifically targeting quiescent human HSCs while maintaining their long-term functionality. Here, after screening 15 lipid nanoparticles (LNPs), we report an LNP that efficiently delivers reporter mRNA to human HSPCs both in ex vivo and in vivo settings when conjugated with the anti-CD34 antibody (CD34/LNPDP). Using CRISPR/Cas editing cargos, CD34/LNPDP achieves high editing efficiency in human HSPCs ex vivo. Intrafemoral administration of CD34/LNPDP in humanized mice results in efficient editing of the erythroid-specific BCL11A enhancer within human HSPCs, enabling the sustained long-term reactivation of fetal haemoglobin (HbF) expression in erythroid cells. In a humanized neutropaenia model harbouring an ELANE mutation, intrafemoral administration of CD34/LNPDP achieves robust editing, targeting exon 2 of ELANE in human HSPCs, partially restoring neutrophil development impairment under long-term observation. Collectively, CD34-targeted delivery enables in vivo HSPC modification without perturbing haematopoiesis, underscoring its suitability for clinical translation.
    DOI:  https://doi.org/10.1038/s41551-026-01765-w
  12. Front Oncol. 2026 ;16 1921345
      TP53 mutations are strongly associated with resistance to venetoclax in acute myeloid leukemia (AML) and represent a major challenge in current treatment strategies. Importantly, different TP53 mutants exhibit substantial functional heterogeneity, leading to distinct resistance phenotypes that are not adequately captured by conventional variant allele frequency (VAF)-based stratification. Emerging evidence suggests that TP53 mutations promote venetoclax resistance through multiple mechanisms, including apoptotic dysregulation, metabolic reprogramming, enhancement of leukemic stem cell properties, and epigenetic remodeling, with the relative contribution of each pathway varying among mutant types. This review systematically summarizes recent advances in the molecular mechanisms underlying TP53-mediated venetoclax resistance, with a particular focus on how mutant-specific functional differences shape therapeutic responses. Unlike previous broad reviews of TP53-mutated AML, this article specifically addresses venetoclax resistance as a clinically critical therapeutic challenge. We further discuss the limitations of current VAF-based classification systems and propose a practical framework that integrates mutant-specific resistance biology with precision therapeutic strategies.
    Keywords:  TP53 mutation; acute myeloid leukemia (AML); functional heterogeneity; leukemia stem cell (LSC); metabolic reprogramming; precision medicine; venetoclax resistance
    DOI:  https://doi.org/10.3389/fonc.2026.1921345
  13. Trends Biochem Sci. 2026 Aug 05. pii: S0968-0004(26)00214-8. [Epub ahead of print]
      The endoplasmic reticulum (ER) membrane is both the central site of cellular lipid synthesis and the platform on which ER-associated degradation (ERAD) selects membrane proteins for ubiquitination and proteasomal destruction. ERAD shapes ER lipid composition by degrading biosynthetic enzymes and regulators of lipid metabolism, while the lipid environment in turn modulates each step of the pathway. In this review, we apply biophysical concepts of membrane protein dynamics to explain how changes in membrane composition shift conformational equilibria and bias proteostatic fate. We distinguish three modes through which lipid information reaches ERAD: substrate-intrinsic sensing, adaptor-mediated coupling, and lipid sensitivity of the ubiquitination machinery itself. These perspectives reframe ERAD as a lipid-responsive pathway integrating membrane composition with selective protein turnover.
    Keywords:  marginal stability; membrane composition; membrane protein quality control; proteostasis; sterol regulation; ubiquitination
    DOI:  https://doi.org/10.1016/j.tibs.2026.07.006
  14. Hemasphere. 2026 Aug;10(8): e70424
      A streamlined, sensitive, and universal molecular method for MRD detection in pediatric AML remains an unmet clinical need. Here, we propose a novel approach based on tracking somatic non-coding passenger variants. Using whole-genome sequencing (WGS) of diagnostic bone marrow DNA, we identify patient-specific somatic passenger variants, which we term "leukemia-specific passenger variants" (LSPVs). Single-cell DNA proteogenomic analyses demonstrate that LSPVs are specific and robust markers of leukemic cells, present across the entire leukemic cell population. Moreover, we show that LSPVs are accurate markers of disease burden, stable from diagnosis to relapse. Importantly, LSPVs can be detected in all patients, suggesting the universal applicability of this approach. Leveraging these findings, we developed DAISY-MRD, a streamlined WGS-based MRD method that does not rely on the presence of specific trackable genetic aberrations and does not require tailored assay design, making it simple, efficient, and feasible in clinical settings.
    DOI:  https://doi.org/10.1002/hem3.70424
  15. Signal Transduct Target Ther. 2026 Aug 03. pii: 306. [Epub ahead of print]11(1):
      Cancer cells maintain chronically elevated levels of reactive oxygen species (ROS) while relying on robust antioxidant programs to preserve redox homeostasis and viability. Although therapeutic strategies that disrupt this balance to induce lethal oxidative stress and ferroptosis have emerged as promising anticancer approaches, the upstream signaling mechanisms that constrain ROS accumulation under physiologically relevant stress conditions remain incompletely understood. Here, we identify the stress-responsive kinases SMG1 and DNA-dependent protein kinase (DNA-PK) as functionally redundant regulators of redox homeostasis and ferroptosis resistance. Genetic or pharmacological inhibition of either kinase triggers ferroptotic cell death, accompanied by marked accumulation of total ROS, ferrous iron, and lipid hydroperoxides. Mechanistically, under mild oxidative stress, SMG1 and DNA-PK cooperatively phosphorylate the central antioxidant transcription factor NRF2 at serine 13 and serine 40, weakening its interaction with the negative regulator KEAP1 and promoting NRF2 accumulation and transcriptional activation. Transcriptomic profiling of de novo mRNAs revealed that inhibition of either kinase is sufficient to suppress NRF2-driven antioxidant gene expression. In contrast, excessive oxidative stress overrides this pro-survival pathway and redirects signaling toward anti-survival responses mediated by ATF4, ATM-CHK2, and JNK/p38 pathways. Collectively, these findings uncover a previously unrecognized SMG1/DNA-PK-NRF2 signaling axis that functions as a redox stress-intensity-dependent switch governing cell fate decisions between antioxidant adaptation and ferroptotic death. Targeting this axis may represent a promising therapeutic strategy for cancer treatment.
    DOI:  https://doi.org/10.1038/s41392-026-02892-1