bims-scepro Biomed News
on Stem cell proteostasis
Issue of 2026–10–04
29 papers selected by
William Grey, University of York



  1. Blood. 2026 Nov 04. pii: blood.2025030268. [Epub ahead of print]
      The ability to robustly expand transplantable hematopoietic stem cells (HSCs) ex vivo enables basic science and clinical therapies otherwise hindered by the scarcity of these self-renewing multipotent cells. Despite recent improvements in long-term ex vivo HSC expansion conditions, the molecular mechanisms required for successful ex vivo expansion of functional HSCs remain unknown. Here we characterized the ex vivo expansion potential of HSCs from mouse fetal liver, young bone marrow, and aged bone marrow at the functional and molecular levels. We find that Lin28b, the in vivo fetal-restricted gene, contributes to the mechanism of both fetal and adult ex vivo HSC expansion. The expression of Lin28b correlates with reconstitution potential, with higher levels observed in HSCs expanded from the fetal liver and young adults. By contrast, expanded aged HSCs fail to robustly express Lin28b and also fail to stably reconstitute the hematopoietic system following transplantation. Consistent with a functional role for this fetal program in ex vivo expanded HSCs, Lin28b-deficient HSCs display aging-associated molecular and functional features following ex vivo expansion cultures. Importantly, Lin28b overexpression during ex vivo expansion was sufficient to enhance reconstitution potential of aged HSCs. In summary, we identify Lin28b as an important regulator of functional HSC expansion ex vivo, suggesting novel opportunities for HSC rejuvenation and clinical applications.
    DOI:  https://doi.org/10.1182/blood.2025030268
  2. Aging Cell. 2026 Oct;25(10): e70656
      The functional decline of the hematopoietic system during aging affects organismal function and contributes to reduced healthspan. Quantifying hematopoietic aging holds great scientific and clinical relevance. Alterations in chromatin architecture are a well-established hallmark of aging that encode rich and informative signatures of the aging process, yet they remain largely unexplored as quantitative markers. Here, we present an interpretable deep learning approach based on convolutional neural networks, ChromAgeNet, that learns changes in the spatial features of chromatin architecture upon aging of hematopoietic stem cells (HSCs). We trained our algorithm on 3D microscope images of DAPI-stained HSC nuclei to discriminate between young and aged murine HSCs, achieving an AUROC of 0.77 ± 0.03. This approach outperforms classical machine learning models trained on handcrafted chromatin features from the same dataset. We then applied explainable artificial intelligence techniques, identifying chromatin entropy, peripheral heterochromatin, and chromatin condensates as predictive markers. As a proof of concept, we evaluated the potential of our model as a phenotypic screening tool for aged HSCs treated with epigenetic drugs to detect rejuvenation. Altogether, we demonstrate that changes in chromatin organization can be modeled via machine learning to predict age-associated chromatin states in the hematopoietic compartment. Our developed framework, ChromAgeNet, serves as an interpretable algorithm to unravel the intricate relationship between chromatin changes and stem cell aging, and advance high-throughput drug screening for rejuvenation therapies.
    Keywords:  age measurement; cellular aging; deep learning; hematopoietic stem cells; machine learning; nuclear architecture
    DOI:  https://doi.org/10.1111/acel.70656
  3. Leukemia. 2026 Sep 28.
      Acquired non-genetic resistance mechanisms to existing therapies contribute to poor outcomes for acute myeloid leukemia (AML) patients, and the inability to target leukemic stem cells (LSCs) can lead to relapse. To overcome these challenges, we tested whether LSCs have dependencies on PI3- kinase (PI3K). We found that LSCs are susceptible to isoform-selective targeting of PI3K and are particularly dependent on the p110 alpha isoform of PI3K. We discovered that PI3K inactivation leads to dynamic changes in EZH2/PRC2 function in leukemic cells, and we uncovered downregulation of EZH2 protein levels as an adaptive resistance mechanism in response to PI3K inhibition. We found that PI3K inhibition in AML cells can lead to compensatory upregulation of EZH1, and that EZH1 knockdown can sensitize AML cells to PI3K inhibition. We leveraged this resistance mechanism by combining a PI3K inhibitor with an EZH1/2 dual inhibitor, which successfully overcomes the acquired resistance and leads to sustained targeting of AML cells ex vivo and in murine AML and PDX models in vivo. This study identifies a promising novel therapeutic regimen for targeting LSCs in AML.
    DOI:  https://doi.org/10.1038/s41375-026-03145-4
  4. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753907. [Epub ahead of print]
      Hematopoietic stem and progenitor cells (HSPC) depend on interactions with nearby stromal cells to support their homeostatic functions and mount responses to perturbations. The murine bone marrow (BM) niche can be profiled using single-cell RNA sequencing (scRNA-seq), but there is considerable inconsistency in cell type identification, and uncertainty over how populations can be isolated prospectively by flow cytometry. Here, we produced new scRNA-seq reference datasets using purified populations of murine BM stromal cells, which we used to create a bespoke classifier for stromal cells. Our NicheScribe approach is consistent, accurate, and generalizable to query datasets irrespective of methods used for cell isolation. Moreover, consistent annotation permits comparative analyses of the same stromal cells across different bone types and perturbations like inflammation, neoplasia, and aging. Our work provides new tools for consistent cell type annotation in the murine BM niche and new insights for combined molecular and functional analyses.
    HIGHLIGHTS: New NicheScribe approach for annotation of stromal cells in scRNA-seq datasetsNicheScribe links molecular state to prospective isolation by flow cytometryDifferent bones have distinct complements of stromal cells LepR + mesenchymal stromal cells adopt diverse transcriptional programs upon stimulation.
    eTOC BLURB: Swann et al. develop a computational approach for consistent annotation of stromal cells in murine bone marrow niche, which is applicable to single-cell and spatial transcriptomics. They find that stromal cell frequencies vary in different bones, and that leptin receptor-expressing mesenchymal stromal cells exhibit diverse transcriptional responses to different perturbations.
    DOI:  https://doi.org/10.64898/2026.09.23.753907
  5. EMBO Rep. 2026 Sep 30.
      Greatwall kinase regulates mitotic progression by phosphorylating ENSA and ARPP19, thereby inhibiting PP2A-B55. Moreover, Greatwall has been implicated in oncogenesis, particularly in solid tumours, but the mechanisms by which Greatwall regulates the cell cycle in other malignancies remain unclear. Here, we show that Greatwall regulates cytokinesis and cell cycle progression in acute myeloid leukaemia (AML) cells through a pathway distinct from ENSA-PP2A-B55. AML cells require Greatwall expression and activity to proliferate, as revealed by pharmacological and systematic genetic perturbation experiments. Mechanistically, Greatwall inactivation or genetic depletion does not measurably affect the ENSA-PP2A-B55 pathway. Instead, loss of Greatwall function alters cytokinesis, and the phosphorylation of proteins involved in cytoskeletal organisation and cytokinesis, including MARK3, which we identify as a direct Greatwall substrate in AML cells. Together, these findings reveal that the Greatwall kinase signalling network is wired differently in leukemic cells, thus uncovering a novel mechanism of cell cycle regulation.
    DOI:  https://doi.org/10.1038/s44319-026-00955-6
  6. Nat Commun. 2026 09 01. pii: 10384. [Epub ahead of print]17(1):
      Mixed lineage leukemia (MLL) rearrangements drive approximately 10% of acute leukemias, including acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). Individuals with Fanconi anemia (FA), a hereditary DNA damage repair (DDR) disorder, are at markedly increased risk of AML, yet the interplay between FA deficiency and MLL-rearranged (MLL-r) leukemia remains unclear. Using murine models and human MLL-r leukemia cells, we show that the FA pathway suppresses leukemogenesis by limiting error-prone non-homologous end joining (NHEJ)-mediated genomic instability. Loss of FA components accelerates leukemia development, promotes leukemic stem cell expansion, and increases DNA damage through hyperactive NHEJ. Pharmacological NHEJ inhibition selectively impairs the survival of FA-deficient MLL-r leukemia cells, revealing a synthetic lethal vulnerability. Consistent with these findings, reduced FA pathway gene expression in patient samples correlates with poor prognosis and increased sensitivity to NHEJ inhibition. These findings identify NHEJ blockade as a promising targeted therapeutic strategy for high-risk MLL-r leukemia.
    DOI:  https://doi.org/10.1038/s41467-026-77335-0
  7. J Transl Res. 2026 ;3(1): 2660423
      Hematopoietic stem and progenitor cells (HSPCs) play a critical role in immune system regeneration and have therapeutic potential in hematological disorders and immunotherapy. However, gene editing in HSPCs remains challenging, particularly in murine HSPCs, limiting preclinical studies and translational advancements. Here, we present a CRISPR/Cas9 mRNA-based protocol for efficient gene editing of human CD34+ HSPCs and murine HSPCs. Using electroporation of Cas9 mRNA and sgRNAs, we achieved up to 80% gene knock-down in HSPCs while retaining cell viability. Edited murine HSPCs successfully reconstituted bone marrow in lethally irradiated mice, demonstrating functional engraftment. We also demonstrated that knocking-out IL-6R in murine HSPCs and CD34+ cells skewed myeloid differentiation toward less immunosuppressive phenotypes, and combining IL-6R-knock-out murine HSPCs with immune checkpoint inhibitors enhanced glioma treatment efficacy in preclinical models, showcasing the potential of this method to facilitate translation of cellular therapies. This method offers a scalable and cost-effective approach to genetic modification of HSPCs, supporting advancements in hematopoietic stem cell transplants (HSCTs) and next-generation immunotherapies. By streamlining gene editing for both preclinical and translational applications, this protocol has the potential to accelerate the development of personalised cellular therapies and improve clinical outcomes in oncology and immune-related disorders.
    Keywords:  CD34+ cells; CRISPR gene editing; Hematopoietic stem and progenitor cells (HSPCs); cell therapy and immunotherapy; translational research
    DOI:  https://doi.org/10.1080/29947448.2026.2660423
  8. bioRxiv. 2026 Sep 22. pii: 2026.09.21.753355. [Epub ahead of print]
      The citric acid cycle (TCA cycle) is the common terminal pathway for the oxidation of all nutrients. Citrate oxidation to oxaloacetate produces CO 2 , and citrate synthase (CS) uses nutrient-derived acetyl groups to regenerate citrate and fuel cycle turning. However, the essentiality of cycle fueling and turning in vivo remains unclear. Here, we use hematopoiesis, the most proliferative system in the body, as a model to show that, contrary to common assumptions, TCA cycle turning is dispensable for respiration, survival, and proliferation of stem and progenitor cells in vivo and its loss promotes stem cell function. Hematopoietic-specific Cs deletion in adult mice blocked citrate cycling without reducing the frequency of hematopoietic stem (HSC) and progenitor cells. HSCs and progenitor cells adapted to TCA cycle loss by markedly increasing nutrient consumption and biosynthesis. Disruption of cycle turning increased HSC regeneration, myeloid progenitor proliferation, and myelopoiesis in vivo. HSCs without a turning TCA cycle outcompeted wild-type HSCs within the same environment. The effect of CS deletion on HSC function was not phenocopied by genetic ablation of cytosolic citrate use and was rescued by ablation of glutamine use in biosynthesis. Therefore, TCA cycle turning restrains nutrient uptake, biosynthesis, cell proliferation, and stem cell function. These results suggest an explanation for the reduction in cycle activity observed in many normal proliferating cells and cancer cells.
    DOI:  https://doi.org/10.64898/2026.09.21.753355
  9. Cell Stem Cell. 2026 Oct 01. pii: S1934-5909(26)00316-4. [Epub ahead of print]33(10): 1578-1579
      Traditional ex vivo hematopoietic stem cell (HSC) gene therapy faces manufacturing challenges. A recent study1 in Nature Biomedical Engineering demonstrates that antibody-engineered lipid nanoparticles achieve efficient and durable in vivo editing of HSCs in humanized mice, offering a promising therapeutic strategy for genetic blood diseases.
    DOI:  https://doi.org/10.1016/j.stem.2026.08.015
  10. bioRxiv. 2026 Sep 07. pii: 2026.09.03.749278. [Epub ahead of print]
      Neutrophils' ability to rapidly and efficiently migrate through narrow pores in tissues is essential for host defense and is proposed to depend on their multilobulated and deformable nucleus. When during neutrophil differentiation does optimal migration and its proposed nuclear determinants emerge, and whether they are intrinsic to progenitors, is unclear in part because of the scarcity of tractable models of human neutrophils and their progenitors. Here, we optimized a CD34+ hematopoietic stem cell (HSC) to neutrophil differentiation pipeline to generate millions of mature neutrophils (HSC-neutrophils) that recapitulate the surface markers, proteome, ROS production and NETosis of primary human blood-derived neutrophils, better than the widely used HL60-derived neutrophils. Comparative proteomics across differentiation showed that HSC-neutrophils become translationally repressed while acquiring immune functions and actin-related processes. Quantitative microscopy and proteomics showed that nuclear multilobulation occurs at the granulocyte progenitors-early neutrophils transition and is accompanied by drastic remodeling of nuclear envelope composition (increasing LBR, decreasing lamin A/C, B1/B2 and NUPs). Single nuclear envelope proteins only weakly correlate with nuclear multilobularity suggesting that an ensemble envelope state, rather than any one protein, sets nuclear shape. Using microfabricated devices with constrictions, we show that migration speed increases the most in early neutrophils; that the capacity to cross nucleus-deforming pores is continuously enhanced during differentiation; and that early neutrophils recover the best from such migration. We show that while mature neutrophils most effectively cross pores, they remain impaired. Our work resolves three features of neutrophils migration - speed, deformation through constrictions, and recovery from deformation - and maps when each emerges, opening the door to future mechanistic and engineering studies for modulating neutrophil migration in tissue-like microenvironments.
    DOI:  https://doi.org/10.64898/2026.09.03.749278
  11. Exp Hematol. 2026 Oct 02. pii: S0301-472X(26)00573-4. [Epub ahead of print] 105940
      Aldehyde dehydrogenase 2 (ALDH2) is a key mitochondrial enzyme that detoxifies reactive aldehydes including formaldehyde, thereby mitigating their genotoxic effects. While ALDH2 deficiency exacerbates bone marrow (BM) failure in Fanconi anemia models, its role under exogenous genotoxic stress is less clear. In this study, we used Aldh2-/- mice to investigate how ALDH2 deficiency impacts hematopoiesis following treatment with busulfan (BSF), sublethal total body irradiation (TBI), or a combined (BSF+TBI) regimen. Under BSF or TBI monotherapy, Aldh2-/- mice exhibited moderate increases in DNA damage, measured by γH2AX expression in hematopoietic stem and progenitor cells (HSPCs), with a mild decline in BM cell engraftment, compared to Aldh2+/+ controls. However, BSF+TBI treatment triggered more severe HSPC DNA damage confirmed by concordant γH2AX and 53BP1 elevation, and a sharper decline in mature hematopoietic cells. Notably, this dual stress significantly upregulated DNA repair and metabolic adaptation genes, including Ccno, Pold4, Taf1c, Npr2, and Aldh18a1. These results suggest that BSF+TBI treatment drives advanced DNA damage and compensatory gene expression shifts in the absence of ALDH2. We conclude that the impact of ALDH2 deficiency on hematopoiesis is dependent on the severity of exogenous stress. TEASER ABSTRACT: The ALDH2 rs671 loss-of-function polymorphism is carried by 30-40% of East Asian individuals, yet its hematopoietic consequences under clinical genotoxic stress remain poorly understood. Using Aldh2-/- mice, we demonstrate that ALDH2 deficiency increases DNA damage in hematopoietic stem and progenitor cells (HSPCs) following busulfan (BSF) or total body irradiation (TBI) monotherapy, without altering mature hematopoietic cell populations or long-term repopulating capacity. However, combined BSF+TBI treatment unmasks a clear, stress-severity-dependent phenotype: Aldh2-/- mice exhibit significantly greater HSPC apoptosis and DNA damage confirmed by concordant γH2AX and 53BP1 elevation, and more severe peripheral blood cytopenias. Transcriptomic analysis reveals compensatory upregulation of DNA repair pathways and Aldh18a1, suggesting a metabolic adaptation to mitigate genotoxic burden. These findings establish ALDH2 deficiency as a latent hematopoietic risk factor with direct implications for personalizing conditioning regimens in ALDH2 rs671 carriers undergoing hematopoietic stem cell transplantation.
    Keywords:  Aldh2 deficiency; DNA damage; busulfan; hematopoiesis; irradiation
    DOI:  https://doi.org/10.1016/j.exphem.2026.105940
  12. Methods Mol Biol. 2026 Sep 30.
      Single-cell quantitative time-lapse microscopy is a valuable tool for directly observing the dynamic activities and decisions of individual stem cells within a population. Successful application of time-lapse microscopy requires automated segmentation of thousands of individual cells to track their features frame-by-frame over time. However, this can be challenging due to unpredictable cell movement, changes in cell shape, and mitotic activity. Such limitations are particularly notable in imaging approaches such as label-free phase-contrast microscopy, which is widely available and non-toxic for long-term time-lapse imaging. Our team has previously developed a deep-learning model and software, DeepSea, to overcome the challenges of single-cell phase-contrast microscopy through automation of segmentation and tracking. In this chapter, we present how to install and use DeepSea to segment and track individual cells in time-lapse phase-contrast images.
    Keywords:  Cell tracking; Deep-learning model; Phase-contrast microscopy; Single-cell segmentation; Time-lapse imaging
    DOI:  https://doi.org/10.1007/7651_2026_717
  13. Sci Transl Med. 2026 Sep 30. 18(869): eaec7031
      GATA2 (GATA binding protein 2) deficiency is a severe immunodeficiency caused by heterozygous variants in the gene encoding the transcription factor GATA2. Ex vivo gene editing of a patient's own CD34+ hematopoietic stem and progenitor cells (HSPCs) could provide curative treatment. However, current methods that rely on nuclease-dependent editing face considerable challenges, including off-target effects, genotoxicity, and reduced engraftment potential. Here, we report the development of an efficient gene editing therapy for GATA2 deficiency using prime editing with a favorable safety profile in terms of off-target effects and genotoxicity. We used prime editing to correct a GATA2 c.956_962del variant in patient-derived CD34+ HSPCs, reaching up to 70% prime editing efficiency and an increase in functional GATA2 alleles from 50 to 77%. We demonstrate that prime-edited patient HSPCs showed increased engraftment potential compared with untreated cells and detected limited on-target genotoxicity and no off-target editing at the top 20 predicted sites. Short prestimulation of CD34+ HSPCs supported efficient prime editing while preserving stemness, mitigating p53 activation, and increasing multilineage engraftment. We report PASSIGE (prime editing-assisted site-specific integrase gene editing) in CD34+ HSPCs, developing a more broadly applicable, double-strand break-independent complementary DNA insertion strategy with the potential to address a large proportion of alleles causing GATA2 deficiency. Together, our results demonstrate the preclinical development of prime editing-based therapies for GATA2 deficiency in CD34+ HSPCs.
    DOI:  https://doi.org/10.1126/scitranslmed.aec7031
  14. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753593. [Epub ahead of print]
      Germline mutations in the RNA helicase DDX41 are the most common genetic predisposition to myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), representing 5-7% of AML. Over 70% of patients acquire a somatic mutation at specific hotspots ( R525H/G530D ) in the helicase domain of DDX41 in trans , which is linked to disease progression. DDX41 has diverse cellular functions, including RNA splicing, ribosome biogenesis, R-loop resolution and inflammation. However, the mechanisms by which somatic DDX41 mutations drive MDS/AML pathogenesis are yet to be determined. Here, we systematically evaluated the function of pathogenic, missense germline and somatic DDX41 mutations. We report that DDX41 somatic mutations are gain of function alleles and fail to rescue AML cell growth, distinct from germline DDX41 mutations. DDX41 somatic mutations R525H and G530D drive widespread splicing changes in isogenic AML cell lines, consistent in genetically engineered murine bone marrow HSPCs and CD34 + cells from DDX41 -mutant MDS/AML patients. Mechanistically, DDX41-R525H exhibits increased RNA binding affinity compared to wildtype, with aberrantly spliced RNA targets overlapping with enriched binding. Strikingly, aberrant splicing of SEPTIN7 is enriched exclusively in CD34 + HSPCs of patients harboring both germline and somatic DDX41 mutations but absent in samples with germline mutation alone or lacking DDX41 mutations altogether. SEPTIN7 mis-splicing introduces a premature stop codon resulting in its downregulation at the protein level. SEPTIN7 is a known regulator of cytokinesis, HSC polarity and repopulation capacity. Our results identify a novel mis-spliced candidate, SEPTIN7, whose deregulation implicates a mechanism by which the DDX41 somatic mutations promote dysplastic hematopoiesis.
    DOI:  https://doi.org/10.64898/2026.09.23.753593
  15. Nat Immunol. 2026 Sep 30.
      Clonal hematopoiesis of indeterminate potential is associated with systemic inflammation and increased malignant risk in humans, yet understanding of how it reshapes the bone marrow (BM) microenvironment has been limited. Using single-cell transcriptomic profiling of freshly isolated BM samples, combined with histological and spatial transcriptomic analyses, we identified fibro-inflammatory remodeling as a hallmark of clonal hematopoiesis of indeterminate potential. Fibroblasts were markedly expanded and acquired cancer-associated fibroblast-like transcriptional states, while mesenchymal and vascular cells upregulated collagen production and extracellular matrix remodeling pathways. Spatial transcriptomics revealed discrete fiber-enriched regions populated by active and CXCL12+ fibroblasts, macrophages and lymphoid cells. These regions exhibited major enrichment of proinflammatory pathways, including transforming growth factor-beta and tumor necrosis factor signaling, identifying them as spatially confined inflammatory hubs within the BM. Collectively, these findings establish fibro-inflammatory BM remodeling as a defining feature of clonal hematopoiesis of indeterminate potential, linking it to prefibrotic stromal changes and niche reorganization that may facilitate progression to overt malignancy.
    DOI:  https://doi.org/10.1038/s41590-026-02668-3
  16. Blood. 2026 Sep 09. pii: blood.2026034085. [Epub ahead of print]
      Colony Stimulating Factor 3 Receptor (CSF3R) mutations are the molecular hallmark of chronic neutrophilic leukemia (CNL). A subset of these patients (~25%) have two mutations in CSF3R on the same allele. These "compound" CSF3R mutations include both an activating point mutation and a cytoplasmic truncating mutation. While compound mutations are prevalent, we have a limited understanding of their molecular characteristics. In this study, we interrogated the mechanisms driving the evolution of compound mutations. We found that CSF3R compound mutations induce a hyperproliferative leukemia compared to single mutations. Compound mutations also markedly enhance activation of STAT5 and ERK1/2 downstream of CSF3R. Utilizing a proteomics approach, we identified enrichment of MYC and mTOR pathways in compound mutant-cells. The most differentially expressed protein in this dataset was the kinase PIM1. We find that in CSF3R compound mutant-cells with high STAT activity there is increased transcription of PIM kinases. We further validated that PIM1 transcript levels are high in a human CSF3R mutant-cohort. High PIM levels drive stabilization of MYC protein, and the downstream activation of MYC-driven leukemogenic transcriptional programs. Indeed, inhibitors of PIM reverse MYC stabilization. Finally, we show promising therapeutic potential for PIM-inhibition in CSF3R mutant-disease using both human cell lines and CNL patient samples. Together, these findings uncover a novel and targetable vulnerability in CSF3R compound mutant-CNL, thus opening a new avenue of treatment for patients with this devastating disease.
    DOI:  https://doi.org/10.1182/blood.2026034085
  17. Blood Cancer Discov. 2026 Sep 30.
      Oncogenic RAS pathway mutations are associated with therapeutic resistance in acute myeloid leukemia, and identification of therapeutic vulnerabilities has been hindered by a lack of clinically relevant models and tractable ex vivo platforms. We utilize a bone marrow endothelial cell co-culture system to perform CRISPR screens on wild-type hematopoietic cells and isogenic leukemias with and without mutant Nras. We credentialed Elovl1, a very long chain fatty acid elongase, as a dependency in RAS pathway mutant leukemia using genetic and pharmacologic approaches. Metabolic and genetic studies in primary leukemias revealed that the fitness defect from Elovl1 loss reflects a mutant-specific dependency on de novo sphingolipid biosynthesis, specifically sphingomyelin production, as Sgms1 deletion phenocopies Elovl1 loss. Sphingomyelin-mediated generation of lipid rafts, key scaffolds for multiple signaling pathways, is essential to the survival of Nras-mutant AML cells. Our work leverages a new leukemia model to identify a targetable dependency in this treatment-refractory leukemia.
    DOI:  https://doi.org/10.1158/2643-3230.BCD-26-0274
  18. Philos Trans R Soc Lond B Biol Sci. 2026 Oct 01. pii: 20250279. [Epub ahead of print]381(1960):
      Protein homeostasis is often described as the capacity of cellular quality-control systems to maintain proteome function by favouring functional protein states. Yet many proteins can populate multiple states, including native conformations, liquid-like condensed assemblies, and aggregated states, reflecting the metastability of the proteome. As a framework for understanding how cells preserve proteome function under such conditions, we discuss protein rheostasis as the system that regulates thermodynamic driving forces and kinetic barriers to control the flux between alternative states over time. Framing proteome maintenance in terms of rheostatic control over the multiple states helps rationalize how ageing, stress, and mutations redistribute populations towards condensed and aggregated states by eroding kinetic buffering capacity, and it suggests therapeutic opportunities that restore control by tuning the transitions between metastable states. This article is part of the Theo Murphy meeting issue 'ProteostaSys: a systems view of proteostasis'.
    Keywords:  liquid–liquid phase separation; protein aggregation; protein homeostasis; protein misfolding
    DOI:  https://doi.org/10.1098/rstb.2025.0279
  19. STAR Protoc. 2026 Sep 26. pii: S2666-1667(26)00514-9. [Epub ahead of print]7(4): 104861
      Malignant cells under chemotherapy stress alter protein translation, necessitating sensitive methods to profile rare, surviving populations in vivo. We present a protocol for profiling low-input acute myeloid leukemia samples using an optimized ribosome profiling approach. We describe steps for lysing cell inputs, digesting unshielded RNA, enriching ribosome footprints, and gel-based size selection. We then detail procedures for constructing sequencing-ready libraries and using a computational pipeline to align and quantify both protected fragments and matching transcriptomes for reproducible translation analysis. For complete details on the use and execution of this protocol, please refer to Mayerhofer et al.1.
    Keywords:  Cancer; Cell Biology; Metabolism
    DOI:  https://doi.org/10.1016/j.xpro.2026.104861
  20. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753758. [Epub ahead of print]
      The endoplasmic reticulum (ER) is the primary site of eukaryotic membrane protein synthesis and quality control, which largely relies on ER-associated degradation (ERAD) to eliminate aberrant nascent proteins. In yeast, two ubiquitin ligases target proteins for ERAD based on aberrancies in substrate transmembrane (ERAD-M), lumenal (ERAD-L), or cytosolic (ERAD-C) domains. How an expanded repertoire of mammalian ERAD factors selects substrates across these classifications is unclear. Here, we show that the human ER-resident RNF185 ubiquitin ligase complex destabilizes a small but specific set of membrane proteins that span all three ERAD branches. Comparisons of three single-pass membrane proteins destabilized by RNF185 identify ERAD-M features in misoriented CHST10, ERAD-C features in unassembled SRPRB, and N-linked glycosylation-dependent ERAD-L features in ATP1B2. Our findings identify RNF185-destabilized membrane proteins with distinct aberrancies that collectively encompass all canonical ERAD substrate classifications and unexpectedly diverse quality control defects.
    DOI:  https://doi.org/10.64898/2026.09.23.753758
  21. bioRxiv. 2026 Sep 23. pii: 2026.09.19.752713. [Epub ahead of print]
      Communication between peroxisomes and mitochondria is essential for cellular metabolic homeostasis, yet how peroxisomal import stress impacts mitochondria function during aging and cellular senescence remains poorly defined. Using a genome-wide CRISPR screening in HEK293 cells under peroxisome import stress, we identified SCAF1 (SR-related CTD-associated factor 1) a known canonical nuclear pre-mRNA splicing factor, as an essential regulator of mitochondrial homeostasis. Under peroxisome stress SCAF1 undergoes proteolytic processing and translocates to the mitochondria, where its N-terminal region acts as an autonomous repressor module that blocks mitoribosomal subunit joining. Consequently, SCAF1 depletion accelerates subunit joining and elevates oxidative phosphorylation protein levels, whereas its overexpression in IMR90 fibroblast cells triggers robust cellular senescence characterized by increased senescence associated β gal staining. Together, our findings uncover a stress-responsive peroxisome-to-mitochondria signaling axis mediated by SCAF1 translocation. This pathway directly modulates mitoribosome assembly to maintain translational homeostasis, providing a precise molecular mechanism for how upstream peroxisomal decline drives downstream mitochondrial dysfunction and cellular senescence.
    DOI:  https://doi.org/10.64898/2026.09.19.752713
  22. Nat Struct Mol Biol. 2026 Sep 30.
      Protein phosphorylation orchestrates cellular signaling and controls most biological processes, with its dysregulation driving diseases, notably cancer. Comprehensive, high-throughput phosphoproteomics remains limited by detection sensitivity, data completeness and computational bottlenecks, especially in low-input settings. Here we present a comprehensive empirical human phosphoproteome resource, regrouping over 200,000 class I phosphosites across 33 diverse human cell lines. We demonstrate that this spectral library dramatically improves single-shot phosphoproteomics with 30-fold faster data processing compared with library-free approaches and enhances confidence in phosphosite localization even from minimal sample input. Integrating proteome and phosphoproteome data, we develop a combined kinase activity score (Cscore), revealing cell line- and cancer-specific signaling vulnerabilities, many correlating with drug sensitivity. This resource accelerates deep and reproducible phosphoproteomics, enables the systematic mapping of cellular signaling networks and may empower precision oncology by highlighting actionable kinase targets in diverse cell states.
    DOI:  https://doi.org/10.1038/s41594-026-01877-6
  23. bioRxiv. 2026 Sep 24. pii: 2026.09.23.753803. [Epub ahead of print]
      Dietary restriction (DR) protects against metabolic disease, extends lifespan, and is associated with remodeling of tissue reactive oxygen species (ROS). ROS control biological adaptation through reversible oxidation of protein cysteines, yet the targets of DR-initiated redox signaling are unknown. Here we generate OxiDR, a tissue-resolved atlas of the cysteine redox proteome that quantifies oxidation state under DR. Rather than oxidizing the proteome broadly, DR selectively targets a high-amplitude set of cysteines in a tissue-specific manner, allowing systematic classification of biological processes subject to DR-mediated redox regulation. Among the cysteines most highly oxidized upon DR is Cys19 of the core autophagy protein ATG5. We show oxidation of Cys19 is required for ATG5-mediated autophagosome formation and for autophagy triggered by nutrient restriction in human cells and mice. Reversible oxidation of this cysteine promotes ATG5 binding to ATG10, thus forming the ATG5-ATG12 conjugate that lipidates LC3B/ATG8 and matures the autophagosome. In mice, loss of this redox switch prevents effective initiation of autophagy upon nutrient restriction, resulting in gross tissue pathology and rapid onset of mortality. The autophagic response to nutrient restriction is thus gated by oxidation of a single cysteine.
    DOI:  https://doi.org/10.64898/2026.09.23.753803
  24. Nat Commun. 2026 Aug 26. pii: 10238. [Epub ahead of print]17(1):
      Peroxisomes are single-membrane-bound organelles essential for diverse metabolic reactions and cellular redox homeostasis, yet the contribution of ubiquitin-proteasome system to peroxisomal biology remains unclear. Here, we demonstrate that the AAA-ATPase complex comprising Cell Division Cycle48 (CDC48), Nuclear Protein Localization4 (NPL4) and Ubiquitin Fusion Degradation1 (UFD1) is indispensable for peroxisomal biogenesis and physiological function in Arabidopsis. We identify the peroxisomal membrane peroxin PEX22 as a direct substrate of the CDC48 complex and show that this complex promotes ubiquitin-dependent PEX22 turnover. Genetic analyses place CDC48 complex upstream of PEX22 in controlling peroxisomal biogenesis and activity. Moreover, H₂O₂‑triggered Cys271 oxidation represses CDC48 ATPase activity, stabilizing PEX22 via slowed degradation; nucleoredoxin NRX1 reduces oxidized CDC48 to recover its function. Consistently, transgenic plants harboring the redox-insensitive CDC48-C271S variant display accelerated PEX22 turnover and enhanced susceptibility to oxidative stress. Collectively, our findings establish the CDC48 complex as a putative H₂O₂ sensor that governs ubiquitin-mediated peroxisome-associated protein degradation (PexAD), enabling fine-tuning of peroxisomal performance in plant development and upon environmental stress.
    DOI:  https://doi.org/10.1038/s41467-026-77146-3
  25. Blood. 2026 Oct 01. pii: blood.2026033335. [Epub ahead of print]
      Although intensified chemotherapy regimens have improved survival of T-cell acute lymphoblastic leukemia (T-ALL) patients, treatment-related toxicities and poor outcomes following relapse highlight the need for alternative therapeutics. Our previous studies showed that leukemia-associated myeloid cells support T-ALL progression, suggesting myeloid cells or associated signals could serve as therapeutic targets. It remains unknown whether leukemia-associated myeloid cells support multiple molecular subtypes of T-ALL, and if so, whether subtype-specific mechanisms are involved. We demonstrate that tumor-associated myeloid cells support survival of both Early T-cell Progenitor (ETP)-like and non-ETP-like T-ALL subtypes from the LMO2 mouse model in vitro and in vivo. Transcriptional profiling and in vitro assays of mouse and human T-ALL reveal that myeloid cells support distinct T-ALL subtypes via different signaling pathways: IL6ST/STAT3 signaling supports ETP-like T-ALL, while growth factor receptor signaling supports non-ETP-like T-ALL. Notably, both subtypes require AKT activation for myeloid-mediated support, and acute myeloid depletion in vivo induces a common metabolic shift towards oxidative phosphorylation (OxPhos). These findings suggest that myeloid cells promote T-ALL survival via subtype-specific signals that converge on a common pathway regulating metabolism. The shared metabolic adaptation to myeloid cell loss suggests a compensatory mechanism enabling T-ALL persistence under stress. Consistent with this possibility, combining myeloid depletion with OxPhos inhibition reduces survival of mouse and patient T-ALL cells and prolongs leukemic mouse survival more than either single treatment. Our data highlight unique and shared mechanisms by which myeloid cells support T-ALL subtypes and implicate tumor-myeloid interactions and downstream metabolic reprogramming as promising therapeutic targets.
    DOI:  https://doi.org/10.1182/blood.2026033335
  26. EJHaem. 2026 Oct;7(5): e70419
      Umbilical cord blood transplantation is a viable source of stem cells due to accessibility and low incidence of chronic graft-versus-host disease despite human-leukocyte-antigen mismatching. Disadvantages of low stem cell dose in larger recipients include delayed immune reconstitution, graft rejection, and mortality. Successful transplants with ex-vivo expanded cords resulted in approval in malignant disorders and aplastic anemia. We report the first successful expanded cord transplantation in an adolescent with cerebral adrenoleukodystrophy who had no alternative donor/treatment options and required transplant emergently for neurologic preservation. This report highlights a mechanism for timely transplant in metabolic disorders, and preservation of functional advantages despite ex-vivo expansion. Trial Registration: The authors have confirmed clinical trial registration is not needed for this submission.
    Keywords:  case report; expanded cord blood; hematopoietic cell transplantation; metabolic disorders; umbilical cord blood transplantation; x‐linked adrenoleukodystrophy
    DOI:  https://doi.org/10.1002/jha2.70419
  27. Blood Adv. 2026 Sep 30. pii: bloodadvances.2026020173. [Epub ahead of print]
      Haplo-identical hematopoietic cell transplantation (haploHCT) is an integral treatment paradigm for patients with leukemia. While overall survival (OS) post-haploHCT has steadily improved, relapse-free survival (RFS) remains relatively stagnant. Upon the discovery of killer immunoglobulin-like receptors (KIRs) on natural killer (NK) cells and their cognate human leukocyte antigen (HLA) ligands, algorithms have been developed to enhance graft versus leukemia effects. However, these algorithms fail to yield consistent predictions in patient outcomes. We utilized a combination of in silico protein folding and interactions to determine KIR:HLA reactivity in conjunction with in vitro acoustic force microscopy to measure cell avidity (CA) as a readout for KIR signal strength. CA was determined using monoallelic HLA expressing K562 cell lines, monoallelic KIR Jurkat cells, and peripheral blood NK cells. We extended the CA results and performed standard cytotoxicity assays as well. We discovered that HLA-B*35 interacts with KIR2DS4. We applied the newly discovered interaction to predict outcomes for HCT patients. Stratifying patients based on their HLA-B*35 positivity and donor KIR2DS4 status, we delineated a correlation to survival (P=0.061) when donors only had full-length KIR2DS4. Patients who received a haploHCT and NK cell addback from donors with only full-length KIR2DS4 had a significantly improved RFS (P=0.001) and OS (P=0.016) compared to truncated (KIR1D) and full-length KIR2DS4 donors. This was independently validated in a diverse 10/10 HLA matched European cohort with RFS (P=0.0255) and OS (P=0.0388). Thus, the identified novel KIR2DS4:HLA-B*35 interaction axis predicts patient survival, in both haplo-identical and fully matched, HCT and highlights that our current understanding of the KIR:HLA interactome is incomplete and requires remapping for enhanced therapeutic applications.
    DOI:  https://doi.org/10.1182/bloodadvances.2026020173