bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2025–09–28
twelve papers selected by
William Grey, University of York
  1. A Rare Hematopoietic Stem Cell-Derived Megakaryocyte Progenitor Accumulates via Enhanced Survival and Contributes to Exacerbated Thrombopoiesis Upon Aging.
  2. CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias.
  3. FLT3L-based drug conjugate effectively targets chemoresistant leukemia stem cells in acute myeloid leukemia.
  4. Fusion Gene Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia.
  5. Nuclear rupture in confined cell migration triggers nuclear actin polymerization to limit chromatin leakage.
  6. DEGRONOPEDIA: A practical guide to identifying and targeting protein degrons.
  7. Omacetaxine and venetoclax in relapsed/refractory acute myeloid leukemia or myelodysplastic syndrome with mutant RUNX1.
  8. Ubiquitination-activated TAB-TAK1-IKK-NF-κB axis modulates gene expression for cell survival in the lysosomal damage response.
  9. New molecular targets in acute leukemias: cytoskeletal regulatory proteins.
  10. High-throughput proteome integral solubility alteration assay for low cell input using One-Tip.
  11. Design of facilitated dissociation enables timing of cytokine signalling.
  12. Modelling Actin-Microtubule Crosstalk , in Migrating Cells.
  1. Aging Cell. 2025 Sep 23. e70221
    A Rare Hematopoietic Stem Cell-Derived Megakaryocyte Progenitor Accumulates via Enhanced Survival and Contributes to Exacerbated Thrombopoiesis Upon Aging.
    Bryce A Manso, Paloma Medina, Stephanie Smith-Berdan, Alessandra Rodriguez Y Baena, Elmira Bachinsky, Lydia Mok, Angela Deguzman, Sarah Beth Avila, Connor Van Voorhis, Saran Chattopadhyaya, Marcel G E Rommel, Jenna Myers, Vanessa D Jönsson, E Camilla Forsberg.
      Distinct routes of cellular production from hematopoietic stem cells (HSCs) have defined our current view of hematopoiesis. Recently, we and others have challenged classical views of platelet generation, demonstrating that megakaryocyte progenitors (MkPs) and ultimately platelets can be specified via an alternate and additive route of HSC-direct specification specifically during aging. This "shortcut" pathway generates hyperactive platelets likely to contribute to age-related platelet-mediated morbidities. Here, we used single-cell RNA/CITEseq to demonstrate that these age-unique, noncanonical (nc)MkPs can be prospectively defined and experimentally isolated from wild-type mice. Surprisingly, this revealed that a rare population of ncMkPs also exists in young mice. Young and aged ncMkPs are functionally distinct from each other and from their canonical (c)MkP counterparts, with aged ncMkPs paradoxically and uniquely exhibiting enhanced survival and platelet generation capacity. We further demonstrate that aged HSCs generate significantly more ncMkPs than their younger counterparts, yet this is accomplished without strict clonal restriction. Together, these findings reveal significant phenotypic, functional, and aging-dependent heterogeneity among the MkP pool and uncover unique features of megakaryopoiesis throughout life, potentially offering cellular and molecular targets for the mitigation of age-related adverse thrombotic events.
    Keywords:  aging; blood platelets; hematopoiesis; hematopoietic stem cells; megakaryocyte progenitor cells
    DOI:  https://doi.org/10.1111/acel.70221
  2. Blood. 2025 Sep 24. pii: blood.2025028954. [Epub ahead of print]
    CEBPA repression by MECOM blocks differentiation to drive aggressive leukemias.
    Travis Fleming, Mateusz Antoszewski, Sander Lambo, Michael Gundry, Riccardo Piussi, Lara Wahlster, Sanjana B Shah, Fiona Reed, Kevin Dong, Joao A Paulo, Steven Gygi, Claudia A Mimoso, Seth Goldman, Karen Adelman, Jennifer A Perry, Yana Pikman, Kimberly Stegmaier, Maria N Barrachina, Kellie R Machlus, Volker Hovestadt, Andrea Arruda, Mark D Minden, Richard A Voit, Vijay G Sankaran.
      Acute myeloid leukemias (AMLs) have an overall poor prognosis with many high-risk cases co-opting stem-cell gene regulatory programs, yet the mechanisms through which this occurs remain poorly understood. Increased expression of the stem-cell transcription factor, MECOM, underlies one key driver mechanism in largely incurable AMLs. How MECOM results in such aggressive AML phenotypes remains unknown. To address existing experimental limitations, we engineered and applied targeted protein degradation with functional genomic readouts to demonstrate that MECOM promotes malignant stem-cell-like states by directly repressing pro-differentiation gene regulatory programs. Remarkably and unexpectedly, a single node in this network, a MECOM-bound cis-regulatory element located 42 kb downstream of the myeloid differentiation regulator CEBPA is both necessary and sufficient for maintaining MECOM-driven leukemias. Importantly, targeted activation of this regulatory element promotes differentiation of these aggressive AMLs and reduces leukemia burden in vivo. These findings suggest a broadly applicable approach for functionally dissecting oncogenic gene regulatory networks to inform improved therapeutic strategies.
    DOI:  https://doi.org/10.1182/blood.2025028954
  3. Cell Rep Med. 2025 Sep 19. pii: S2666-3791(25)00438-0. [Epub ahead of print] 102365
    FLT3L-based drug conjugate effectively targets chemoresistant leukemia stem cells in acute myeloid leukemia.
    Dengyang Zhang, Yao Guo, Zhiyong Peng, Yan Xiao, Zhiguang Chang, Liuting Yu, Yuming Zhao, Qi Zhang, Lingling Ma, Shuping Li, Chi-Kong Li, Kam Tong Leung, Zhizhuang Joe Zhao, Chun Chen, Yun Chen.
      Acute myeloid leukemia (AML) is a heterogeneous malignancy with poor prognosis due to relapse and chemotherapy resistance. FLT3 mutations promote AML and predict adverse outcomes. As most AML cells express FLT3, it represents a promising therapeutic target. In this study, we develop FL-Fc-DM1, a FLT3-targeted conjugate linking FLT3 ligand-Fc to DM1. FL-Fc-DM1 demonstrates potent anti-leukemic activity in vitro, ex vivo, and in both cell line- and patient-derived xenograft models. Notably, it effectively targets cytarabine-resistant AML cells by promoting cell cycle entry and inducing apoptosis. FL-Fc-DM1 also significantly reduces functional leukemia stem cell frequency, as demonstrated by limiting dilution transplantation assays. The therapeutic efficacy can be further strengthened by BH3 mimetics. Importantly, toxicity assessments in a humanized mouse model show limited impact on normal human hematopoiesis at therapeutic doses. Our findings suggest that FL-Fc-DM1 is a promising candidate for AML treatment, even for cell cycle-arrested or slow-cycling chemo-resistant AML cells.
    Keywords:  AML; DM1; FLT3; FLT3L; cell cycle; chemotherapy resistance; ligand-drug conjugate
    DOI:  https://doi.org/10.1016/j.xcrm.2025.102365
  4. Blood. 2025 Sep 24. pii: blood.2025028988. [Epub ahead of print]
    Fusion Gene Depletion Eliminates Stemness and Induces Bidirectional Differentiation of Acute Myeloid Leukemia.
    Polina K Derevyanko, Laura E Swart, L Daniel Mata Casimiro, Anita van Oort, Manisha Du Plessis, Luca van den Brink, Minoo Ashtiani, C Michel Zwaan, Anja Krippner-Heidenreich, Constanze Bonifer, Ray Michel Schiffelers, Josef Josef Vormoor, Sophie Kellaway, Olaf Heidenreich.
      Chromosomal rearrangements that generate novel fusion genes are a hallmark of acute myeloid leukemia (AML). Depletion experiments in cell line models have suggested that their continued expression is required for maintaining their leukemic phenotype and that fusion genes therefore represent ideal cancer-specific therapeutic targets. However, to which extent this result holds true for the different stages of hematopoietic development in primary cells and whether therapeutic agents can be efficiently delivered to those cells is still unclear. In this study, we demonstrate that primary AML cells harboring the chromosomal translocation t(8;21) are critically dependent on the corresponding fusion gene, RUNX1::RUNX1T1, to suppress differentiation and maintain stemness. Silencing RUNX1::RUNX1T1 expression using siRNA-loaded lipid nanoparticles induces substantial changes in chromatin accessibility, thereby redirecting the leukemia-associated transcriptional network towards a myeloid differentiation program. Single-cell analyses reveal that this transcriptional reprogramming is associated with the depletion of immature stem and progenitor-like cell populations, accompanied by an expansion of granulocytic and eosinophilic/mast cell-like populations with impaired self-renewal capacity. These findings underscore the essential role of RUNX1::RUNX1T1 in sustaining AML and highlight the therapeutic potential of targeting fusion gene expression in primary AML cells.
    DOI:  https://doi.org/10.1182/blood.2025028988
  5. EMBO J. 2025 Sep 22.
    Nuclear rupture in confined cell migration triggers nuclear actin polymerization to limit chromatin leakage.
    Christos Kamaras, Dennis Frank, Hong Wang, Friedel Drepper, Pitter F Huesgen, Robert Grosse.
      Upon cell migration in confined space, such as during cancer metastasis, mechanical forces from the extracellular matrix act onto the nucleus leading to nuclear envelope (NE) rupture, chromatin leakage and genomic instability. Here we found that during confined migration, NE rupture triggers dynamic nuclear F-actin formation dependent on the formins DIAPH1 and DIAPH3. We show that DIAPH3 dynamically and transiently relocates to the nucleus upon NE rupture. Interfering with DIAPH1/3 or with nuclear actin polymerization resulted in nuclear instability during confined migration. Notably, nuclear formin activity or actin assembly limit NE rupture-induced chromatin leakage. Similarly, silencing of Ataxia Telangiectasia and Rad3-related protein (ATR) reduced NE rupture-triggered nuclear F-actin assembly and increased chromatin leakage. Consistent with this, ATR promotes the phosphorylation of DIAPH3 at S1072 adjacent to its autoregulatory domain to promote nuclear actin polymerization. Using atomic force microscopy, we found that nuclear actin assembly or nuclear DIAPH3 activity promotes nuclear stiffness in an ATR-dependent manner. Thus, our study identifies an ATR-formin module that regulates nuclear mechanical properties through induction of intranuclear actin scaffolding.
    Keywords:  Cancer Cell Invasion; Nuclear Actin; Nuclear Mechanics
    DOI:  https://doi.org/10.1038/s44318-025-00566-2
  6. Methods Enzymol. 2025 ;pii: S0076-6879(25)00222-8. [Epub ahead of print]719 67-94
    DEGRONOPEDIA: A practical guide to identifying and targeting protein degrons.
    Natalia A Szulc, Wojciech Pokrzywa.
      Degrons are recognition motifs mediating substrate binding to E3 ubiquitin ligases within the ubiquitin-proteasome system, driving protein ubiquitination and degradation. These motifs, located at protein N- and C-termini or within internal regions, are essential for maintaining proteostasis. Effective degradation relies on a tripartite architecture: a degron motif, a ubiquitination site, and a proteasomal unwinding seed. This chapter introduces DEGRONOPEDIA, a web server for identifying and predicting degrons across eukaryotic proteomes. It integrates machine learning, solvent accessibility modeling, and proteolysis simulations to analyze degrons in sequential and structural contexts. We provide detailed guidance on its workflow and applications, highlighting its role in studying terminal and internal degrons.
    Keywords:  Degron; E3 ligase; Protein degradation; Protein stability; Protein turnover; SLIMs; Ubiquitin-proteasome system
    DOI:  https://doi.org/10.1016/bs.mie.2025.06.014
  7. Blood Neoplasia. 2025 Nov;2(4): 100145
    Omacetaxine and venetoclax in relapsed/refractory acute myeloid leukemia or myelodysplastic syndrome with mutant RUNX1.
    Courtney D DiNardo, Wei-Ying Jen, Guillermo Montalban-Bravo, Xuemei Wang, Sanam Loghavi, Sravanthi Lavu, Nicholas J Short, Kelly Chien, Ghayas C Issa, Naveen Pemmaraju, Musa Yilmaz, Michael Andreeff, Gautam Borthakur, Tapan M Kadia, Naval G Daver, Guillermo Garcia-Manero, Christopher P Mill, Xiaoping Su, Warren Fiskus, Kapil N Bhalla.
      Mutations in RUNX1 (RUNX1 mut) occur in 10% to 20% of patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and are associated with poor outcomes to standard therapy. Omacetaxine mepesuccinate (OM), a semisynthetic analog of homoharringtonine, has been shown to be lethal to RUNX1 mut AML cells in vitro through reduction of MCL1 and BCL-XL, and synergizes with venetoclax (VEN) in RUNX1 mut AML models. We investigated the safety and efficacy of OM + VEN in relapsed/refractory RUNX1 mut MDS/AML in a Bayesian Optimal Interval design. VEN 400 mg daily from days 1 to 14 and OM 1.25 mg/m2 twice daily from days 2 to 4 was selected as the recommended phase 2 dose. Twenty-four patients were treated, 22 with AML and 2 with MDS with excess blasts. There were no dose-limiting toxicities or episodes of tumor lysis syndrome. The most common grade ≥3 toxicity was infection. There were no responses in our heavily pretreated cohort of patients with AML. Both patients with MDS achieved composite complete remission and transitioned to allogeneic stem cell transplant. Treatment-induced downregulation in gene expression in the β-catenin and hedgehog signaling pathway genes were identified in peripheral blood mononuclear cells from patients who responded. As compared to nonresponders, samples from responders also exhibited reduced antiapoptotic and increased proapoptotic protein expression. OM can synergize with VEN to promote loss of viability of myeloid cells. Clinical responses were seen exclusively in patients with MDS, which suggests that dose optimization or combination with cytoreductive agents may be necessary for eliciting clinical activity in AML. This trial was registered at www.ClinicalTrials.gov as #NCT04874194.
    DOI:  https://doi.org/10.1016/j.bneo.2025.100145
  8. Elife. 2025 Sep 24. pii: RP106901. [Epub ahead of print]14
    Ubiquitination-activated TAB-TAK1-IKK-NF-κB axis modulates gene expression for cell survival in the lysosomal damage response.
    Akinori Endo, Chikage Takahashi, Naoko Ishibashi, Yasumasa Nishito, Koji Yamano, Keiji Tanaka, Yukiko Yoshida.
      The lysosomal damage response is important for the maintenance of cellular homeostasis in human cells. Although the mechanisms underlying the repair and autophagic elimination of damaged lysosomes have been elucidated, the early signal transduction pathways and genes induced in response to lysosomal damage remain elusive. We performed transcriptome and proteome analyses and found that the TAB-TAK1-IKK-NF-κB axis is activated by K63-linked ubiquitin chains that accumulate on damaged lysosomes. This activates the expression of various transcription factors and cytokines that promote anti-apoptosis and intercellular signaling. The findings highlight the crucial role of ubiquitin-regulated signal transduction and gene expression in cell survival and cell-cell communication in response to lysosomal damage. The results suggest that the ubiquitin system is not only involved in the removal of damaged lysosomes by lysophagy, but also functions in the activation of cellular signaling for cell survival.
    Keywords:  NF-κB; TAB; TAK1; cell biology; human; lysosomal damage response; ubiquitin
    DOI:  https://doi.org/10.7554/eLife.106901
  9. Biochem Soc Trans. 2025 Sep 22. pii: BST20253017. [Epub ahead of print]
    New molecular targets in acute leukemias: cytoskeletal regulatory proteins.
    João Agostinho Machado-Neto, Hugo Passos Vicari, Jean Carlos Lipreri da Silva, Keli Lima, James Murphy.
      Acute leukemias are hematological malignancies characterized by the uncontrolled proliferation of immature bone marrow cells, disrupting normal hematopoiesis. These diseases, classified into acute lymphoblastic leukemia and acute myeloid leukemia (AML), often result from acquired genetic alterations that drive deregulated cell growth and inhibit differentiation. The cytoskeleton has emerged as a promising therapeutic target due to its pivotal role in cellular processes such as adhesion, motility, and division. Among its components, stathmin 1 (STMN1) and ezrin (EZR) stand out for their significant involvement in the pathogenesis and progression of acute leukemias. STMN1, a regulator of microtubule dynamics, is associated with chromosomal instability and leukemic cell proliferation, and is frequently overexpressed in these malignancies. Anti-microtubule agents, such as paclitaxel, eribulin, and cyclopenta[b]indole derivatives have demonstrated the ability to inhibit STMN1 by inducing its phosphorylation at regulatory sites, thereby impairing cell viability and promoting apoptosis. EZR, a membrane-actin linker protein, plays a critical role in cell signaling and tumor survival. Its overexpression has been correlated with poor prognosis in AML. Pharmacological inhibitors like NSC305787 have shown efficacy in reducing cell viability, modulating key pathways such as PI3K (phosphatidylinositol-3-kinase)/AKT (AKT serine-threonine protein)/mTOR (mammalian target of rapamycin), and enhancing the activity of standard chemotherapeutics, thereby supporting their potential use in combination therapies. This review aims to explore the roles of STMN1 and EZR in the pathogenesis of acute leukemias, assessing their potential as therapeutic targets. The goal is to synthesize recent evidence to guide the development of more effective inhibitors, focusing on overcoming therapeutic resistance and tailoring treatments to individual profiles.
    Keywords:  acute leukemias; cytoskeleton; ezrin; stathmin 1; therapeutic targets
    DOI:  https://doi.org/10.1042/BST20253017
  10. Commun Chem. 2025 Sep 26. 8(1): 282
    High-throughput proteome integral solubility alteration assay for low cell input using One-Tip.
    Maico Lechner, Pierre Sabatier, Jesper V Olsen.
      Mass spectrometry-based versions of the cellular thermal shift assay (CETSA), like proteome integral solubility alteration (PISA), enable simultaneous monitoring of thousands of proteins for drug-target engagement. These methods are constrained in throughput and scalability, while the sample requirement limits the applicability to widely available material. Here, we combine PISA with the One-Tip method to simplify and streamline sample preparation. Using the mass spectrometry-compatible n-Dodecyl-β-D-Maltoside (DDM) non-ionic detergent for cell lysis in PISA sample preparation enables direct transfer to One-Tip with decreasing cell requirements down to 200 cells per µL. One-Tip provides similar depth and higher reproducibility, with lower material and solvent usage and a faster proteolytic digestion compared to a conventional sample cleaning and digestion protocol, making it a cost-effective, fast, and user-friendly option. To demonstrate its scalability, we applied One-Tip-PISA in a 96-well plate format, profiling a kinase inhibitor panel, allowing cell treatment to injection within 12 h, enhancing workflow efficiency and accessibility for a wide range of laboratories.
    DOI:  https://doi.org/10.1038/s42004-025-01670-4
  11. Nature. 2025 Sep 24.
    Design of facilitated dissociation enables timing of cytokine signalling.
    Adam J Broerman, Christoph Pollmann, Yang Zhao, Mauriz A Lichtenstein, Mark D Jackson, Maxx H Tessmer, Won Hee Ryu, Masato Ogishi, Mohamad H Abedi, Danny D Sahtoe, Aza Allen, Alex Kang, Joshmyn De La Cruz, Evans Brackenbrough, Banumathi Sankaran, Asim K Bera, Daniel M Zuckerman, Stefan Stoll, K Christopher Garcia, Florian Praetorius, Jacob Piehler, David Baker.
      Protein design has focused on the design of ground states, ensuring that they are sufficiently low energy to be highly populated1. Designing the kinetics and dynamics of a system requires, in addition, the design of excited states that are traversed in transitions from one low-lying state to another2,3. This is a challenging task because such states must be sufficiently strained to be poorly populated, but not so strained that they are not populated at all, and because protein design methods have focused on generating near-ideal structures4-7. Here we describe a general approach for designing systems that use an induced-fit power stroke8 to generate a structurally frustrated9 and strained excited state, allosterically driving protein complex dissociation. X-ray crystallography, double electron-electron resonance spectroscopy and kinetic binding measurements show that incorporating excited states enables the design of effector-induced increases in dissociation rates as high as 5,700-fold. We highlight the power of this approach by designing rapid biosensors, kinetically controlled circuits and cytokine mimics that can be dissociated from their receptors within seconds, enabling dissection of the temporal dynamics of interleukin-2 signalling.
    DOI:  https://doi.org/10.1038/s41586-025-09549-z
  12. Biophys J. 2025 Sep 23. pii: S0006-3495(25)00609-5. [Epub ahead of print]
    Modelling Actin-Microtubule Crosstalk , in Migrating Cells.
    Pinaki Nayak, Anil Kumar Dasanna, Raja Paul, Heiko Rieger.
      Actin-Microtubule crosstalk regulates the polarity and morphology of migrating cells and encompasses mechanical interactions, mediated by crosslinkers, molecular motors, and cytoskeletal regulators. Recent experiments indicate that local microtubule depolymerization promotes local actomyosin retraction, whereas local microtubule polymerization promotes local actin polymerization. Based on these observations, we develop a computational whole-cell model involving dynamic microtubules interacting mechanically and chemically with an active cell boundary. Specifically, the tips of microtubules send signals for local expansion or contraction to the active cell boundary, depending on whether they are in the growth or shrink phase. A rich, self-organized, dynamic behavior emerges, characterized by the repositioning of the microtubule-organizing center relative to the nucleus and the direction of migration. This also includes a variety of migration patterns, cell morphologies, and complex responses to obstacles in microfluidic and obstacle park environments. We demonstrate that microtubule length and numbers have a significant impact on these features, highlighting the need for new experimental investigations. Thus, the model provides a unified framework that explains a wide range of experimental observations and setups where actin-microtubule crosstalk plays a crucial role.
    DOI:  https://doi.org/10.1016/j.bpj.2025.09.029
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