bims-ginsta Biomed News
on Genome instability
Issue of 2025–06–22
thirty-six papers selected by
Jinrong Hu, National University of Singapore



  1. Cell. 2025 Jun 11. pii: S0092-8674(25)00572-0. [Epub ahead of print]
      Metazoan life requires the coordinated activities of thousands of genes in spatially organized cell types. Understanding the basis of tissue function requires approaches to dissect the genetic control of diverse cellular and tissue phenotypes in vivo. Here, we present Perturb-Multimodal (Perturb-Multi), a paired imaging and sequencing method to construct large-scale, multimodal genotype-phenotype maps in tissues with pooled genetic perturbations. Using imaging, we identify perturbations in individual cells while simultaneously measuring their gene expression profiles and subcellular morphology. Using single-cell sequencing, we measure full transcriptomic responses to the same perturbations. We apply Perturb-Multi to study hundreds of genetic perturbations in the mouse liver. Our data suggest the genetic regulators and mechanisms underlying the dynamic control of hepatocyte zonation, the unfolded protein response, and steatosis. Perturb-Multi accelerates discoveries of the genetic basis of complex cell and tissue physiology and provides critical training data for emerging machine learning models of cellular function.
    Keywords:  RCA-MERFISH; hepatocyte stress response; in vivo pooled screening; lipid droplet accumulation; liver zonation; machine learning morphology; multimodal phenotyping; multiplexed RNA imaging; multiplexed protein imaging; scRNA-seq
    DOI:  https://doi.org/10.1016/j.cell.2025.05.022
  2. Mol Cell. 2025 Jun 19. pii: S1097-2765(25)00464-2. [Epub ahead of print]85(12): 2390-2408.e6
      Sirtuin enzymes are deeply associated with senescence and aging. Sirtuin proteins are tightly regulated, but how their levels are governed during aging and how they elicit tissue-specific cellular changes are unclear. Here, we demonstrate that SIRT7 undergoes proteasomal degradation during senescence via targeting by the E3 ligase TRIP12. We identified the transcription factor nuclear casein kinase and cyclin-dependent kinase substrate 1 (NUCKS1) as an interactor of SIRT7 and found NUCKS1 recruitment onto chromatin during senescence mediated by SIRT7 loss, correlating with increased NUCKS1 acetylation. NUCKS1 depletion delayed senescence, leading to reduced inflammatory gene expression associated with transcription factors RELA and CEBPβ. In Sirt7 knockout and aged mouse livers, NUCKS1 was bound at the promoters and enhancers of age-related genes, and these regulatory regions gained accessibility during aging. Overall, our results uncover NUCKS1 as an interactor of SIRT7 and indicate that proteasomal loss of SIRT7 during senescence and liver aging promotes NUCKS1 acetylation and chromatin binding to induce metabolic and inflammatory genes.
    Keywords:  NUCKS1; SIRT7; acetylation; aging; post-translation modification; protein regulation; senescence; sirtuins
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.025
  3. Nat Struct Mol Biol. 2025 Jun 13.
      Oocyte maturation is essential for both gametogenesis and early development, when large amounts of transcripts are produced without DNA replication. Histone variants, which can be incorporated at cis-regulatory elements in a replication-independent manner, are naturally suited for such regulation. However, their roles during mammalian oocyte maturation remain elusive. Here we show that oocyte-specific depletion of H2A.Z, an evolutionarily conserved histone variant, in female mice results in profound epigenetic and transcriptional alterations, impedes resumption of oocyte meiosis II and causes infertility. Mechanistically, H2A.Z in mouse oocytes is incorporated into chromatin at active promoters and putative enhancers. Interestingly, H2A.Z is depleted from CG-rich silenced promoters, including poised Polycomb target genes, in fully grown oocytes (FGOs), unlike what occurs in growing oocytes, early embryos and mouse embryonic stem cells. In FGOs, the presence of H2A.Z correlates with histone acetylation, except in regions marked by DNA methylation and H3K36me3. Depletion of H2A.Z leads to impaired activities of a subset of promoters and enhancers, correlated with defective gene expression. Consistent with a role in gene activation, H2A.Z in FGOs is widely acetylated at the promoters and enhancers. Together, our findings uncover an essential role of H2A.Z in mammalian oocyte maturation and female fertility.
    DOI:  https://doi.org/10.1038/s41594-025-01580-y
  4. Cell Metab. 2025 Jun 12. pii: S1550-4131(25)00266-9. [Epub ahead of print]
      Epidermal stem cells produce the skin's barrier that excludes pathogens and prevents dehydration. Hair follicle stem cells (HFSCs) are dedicated to bursts of hair regeneration, but upon injury, they can also reconstruct, and thereafter maintain, the overlying epidermis. How HFSCs balance these fate choices to restore physiologic function to damaged tissue remains poorly understood. Here, we uncover serine as an unconventional, non-essential amino acid that impacts this process. When dietary serine dips, endogenous biosynthesis in HFSCs fails to meet demands (and vice versa), slowing hair cycle entry. Serine deprivation also alters wound repair, further delaying hair regeneration while accelerating re-epithelialization kinetics. Mechanistically, we show that HFSCs sense each fitness challenge by triggering the integrated stress response, which acts as a rheostat of epidermal-HF identity. As stress levels rise, skin barrier restoration kinetics accelerate while hair growth is delayed. Our findings offer potential for dietary and pharmacological intervention to accelerate wound healing.
    Keywords:  dietary intervention; epidermal stem cells; fate selection; hair follicle stem cells; hair regrowth; integrated stress response; serine metabolism; tissue regeneration; tissue repair; wound healing
    DOI:  https://doi.org/10.1016/j.cmet.2025.05.010
  5. Nat Cell Biol. 2025 Jun;27(6): 959-971
      Mitotic spindles are dynamically intertwined with the cytoplasm they assemble in. How the physicochemical properties of the cytoplasm affect spindle architecture and size remains largely unknown. Using quantitative biochemistry in combination with adaptive feedback microscopy, we investigated mitotic cell and spindle morphology during neural differentiation of embryonic stem cells. While tubulin biochemistry and microtubule dynamics remained unchanged, spindles changed their scaling behaviour; in differentiating cells, spindles were considerably smaller than those in equally sized undifferentiated stem cells. Integrating quantitative phase imaging, biophysical perturbations and theory, we found that as cells differentiated, their cytoplasm became more dilute. The concomitant decrease in free tubulin activated CPAP (centrosomal P4.1-associated protein) to enhance the centrosomal nucleation capacity. As a consequence, in differentiating cells, microtubule mass shifted towards spindle poles at the expense of the spindle bulk, explaining the differentiation-associated switch in spindle architecture. This study shows that cell state-specific cytoplasmic density tunes mitotic spindle architecture. Thus, we reveal physical properties of the cytoplasm as a major determinant in organelle size control.
    DOI:  https://doi.org/10.1038/s41556-025-01678-x
  6. Nat Commun. 2025 Jun 17. 16(1): 5328
      Aneuploidy, or aberrant chromosomal content, disrupts cellular proteostasis through altered expression of numerous proteins. Aneuploid cells accumulate SQSTM1/p62-positive cytosolic bodies, exhibit impaired protein folding, and show altered proteasomal and lysosomal activity. Here, we employ p62 proximity- and affinity-based proteomics to elucidate p62 interactors in aneuploid cells and observe an enrichment of mitochondrial proteins. Increased protein aggregation and colocalization of p62 with both novel interactors and mitochondrial proteins is further confirmed by microscopy. Compared to parental diploids, aneuploid cells suffer from mitochondrial defects, including perinuclearly-clustered mitochondrial networks, elevated reactive oxygen species levels, reduced mitochondrial DNA abundance, and impaired protein import, leading to cytosolic accumulation of mitochondrial precursor proteins. Overexpression of heat shock proteins in aneuploid cells mitigates protein aggregation and decreases the colocalization of p62 with the mitochondrial protein TOMM20. Thus, proteotoxic stress caused by chromosome gains results in the sequestration of mitochondrial precursor proteins into cytosolic p62-bodies, thereby compromising mitochondrial function.
    DOI:  https://doi.org/10.1038/s41467-025-60857-4
  7. Proc Natl Acad Sci U S A. 2025 Jun 24. 122(25): e2309772122
      Circulating monocytes are recruited to the tumor microenvironment, where they can differentiate into macrophages that mediate tumor progression. To reach the tumor microenvironment, monocytes must first extravasate and migrate through the type-1 collagen rich stromal matrix. The viscoelastic stromal matrix around tumors not only stiffens relative to normal stromal matrix, but often exhibits enhanced viscous characteristics, as indicated by a higher loss tangent or faster stress relaxation rate. Here, we studied how changes in matrix stiffness and viscoelasticity impact the three-dimensional (3D) migration of monocytes through stromal-like matrices. Interpenetrating networks of type-1 collagen and alginate, which enable independent tunability of stiffness and stress relaxation over physiologically relevant ranges, were used as confining matrices for 3D culture of monocytes. Increased stiffness and faster stress relaxation independently enhanced the 3D migration of monocytes. Migrating monocytes have an ellipsoidal or rounded wedge-like morphology, reminiscent of amoeboid migration, with accumulation of actin at the trailing edge. Matrix adhesions were dispensable for monocyte migration in 3D, but migration did require actin polymerization and myosin contractility. Mechanistic studies indicate that actin polymerization at the leading edge generates protrusive forces that open a path for the monocytes to migrate through in the confining viscoelastic matrices. Taken together, our findings implicate matrix stiffness and stress relaxation as key mediators of monocyte migration and reveal how monocytes use pushing forces at the leading edge mediated by actin polymerization to generate migration paths in confining viscoelastic matrices.
    Keywords:  3D migration; monocytes; stromal matrix; viscoelasticity
    DOI:  https://doi.org/10.1073/pnas.2309772122
  8. Cell. 2025 Jun 12. pii: S0092-8674(25)00576-8. [Epub ahead of print]
      When a material enters the body, it is immediately attacked by hundreds of proteins, organized into complex networks of binding interactions and reactions. How do such complex systems interact with a material, "deciding" whether to attack? We focus on the complement system of ∼40 blood proteins that bind microbes, nanoparticles, and medical devices, initiating inflammation. We show a sharp threshold for complement activation upon varying a fundamental material parameter, the surface density of potential complement attachment points. This sharp threshold manifests at scales spanning single nanoparticles to macroscale pathologies, shown here for diverse engineered and living materials. Computational models show these behaviors arise from a minimal subnetwork of complement, manifesting percolation-type critical transitions in the complement response. This criticality switch explains the "decision" of a complex signaling network to interact with a material.
    Keywords:  biomaterials; complement; complexity science; host response; immunology; nanomedicine; systems biology
    DOI:  https://doi.org/10.1016/j.cell.2025.05.026
  9. Cell. 2025 Jun 13. pii: S0092-8674(25)00571-9. [Epub ahead of print]
      Aging is characterized by a deterioration of stem cell function, but the feasibility of replenishing these cells to counteract aging remains poorly defined. Our study addresses this gap by developing senescence (seno)-resistant human mesenchymal progenitor cells (SRCs), genetically fortified to enhance cellular resilience. In a 44-week trial, we intravenously delivered SRCs to aged macaques, noting a systemic reduction in aging indicators, such as cellular senescence, chronic inflammation, and tissue degeneration, without any detected adverse effects. Notably, SRC treatment enhanced brain architecture and cognitive function and alleviated the reproductive system decline. The restorative effects of SRCs are partly attributed to their exosomes, which combat cellular senescence. This study provides initial evidence that genetically modified human mesenchymal progenitors can slow primate aging, highlighting the therapeutic potential of regenerative approaches in combating age-related health decline.
    Keywords:  FOXO3; aging; biomarker; brain; gene editing; intervention; rejuvenation; reproductive system; senescence; stem cell
    DOI:  https://doi.org/10.1016/j.cell.2025.05.021
  10. Nat Struct Mol Biol. 2025 Jun 13.
      Mammalian oocytes establish a unique landscape of histone modifications, some of which are inherited by early embryos. How histone variants shape the maternal histone landscape remains unknown. Here we map histone H2A variants in mouse fully grown oocytes (FGOs) and find that H2A.Z forms broad domains across intergenic regions, along non-canonical H3K4me3 (ncH3K4me3). During oocyte growth, H2A.Z progressively transitions from an active promoter-rich, canonical distribution to a non-canonical broad distribution (ncH2A.Z). Depletion of H2A.Z in oocytes partially impairs ncH3K4me3 formation and causes severe defects in meiotic progression, which resemble Mll2-knockout oocytes. Conversely, depletion of ncH3K4me3 by Mll2 knockout also causes a reduction of ncH2A.Z in FGOs. Thus, our study suggests that ncH2A.Z and ncH3K4me3 reinforce each other to form functional oocytes.
    DOI:  https://doi.org/10.1038/s41594-025-01573-x
  11. Life Sci Alliance. 2025 Sep;pii: e202403082. [Epub ahead of print]8(9):
      Mitochondrial gene expression regulation is required for the biogenesis of oxidative phosphorylation (OXPHOS) complexes, yet the spatial organization of mitochondrial RNAs (mt-RNAs) remains unknown. Here, we investigated the spatial distribution of mt-RNAs during various cellular stresses using single-molecule RNA-FISH. We discovered that transcription inhibition leads to the formation of distinct RNA granules within mitochondria, which we term inhibition granules. These structures differ from canonical mitochondrial RNA granules and form in response to multiple transcription arrest conditions, including ethidium bromide treatment, specific inhibition or stalling of the mitochondrial RNA polymerase, and depletion of the SUV3 helicase. Inhibition granules appear to stabilize certain mt-mRNAs during prolonged transcription inhibition. This phenomenon coincides with an imbalance in OXPHOS complex expression, where mitochondrial-encoded transcripts decrease while nuclear-encoded subunits remain stable. We found that cells recover from transcription inhibition via resolving the granules, restarting transcription, and repopulating the mitochondrial network with mt-mRNAs within hours. We suggest that inhibition granules may act as a reservoir to help overcome OXPHOS imbalance during recovery from transcription arrest.
    DOI:  https://doi.org/10.26508/lsa.202403082
  12. Cell. 2025 Jun 12. pii: S0092-8674(25)00561-6. [Epub ahead of print]
      Developmental gene expression is regulated by the dynamic interplay of histone H3 lysine 4 (H3K4) and histone H3 lysine 27 (H3K27) methylation, yet the physiological roles of these epigenetic modifications remain incompletely understood. Here, we show that mice depleted for all forms of H3K4 methylation, using a dominant histone H3-lysine-4-to-methionine (H3K4M) mutation, succumb to a severe loss of all major blood cell types. H3K4M-expressing hematopoietic stem cells (HSCs) and committed progenitors are present at normal numbers, indicating that H3K4 methylation is dispensable for HSC maintenance and commitment but essential for progenitor cell maturation. Mechanistically, we reveal that H3K4 methylation opposes the deposition of repressive H3K27 methylation at differentiation-associated genes enriched for a bivalent (i.e., H3K4/H3K27-methylated) chromatin state in HSCs and progenitors. Indeed, by concomitantly suppressing H3K27 methylation in H3K4-methylation-depleted mice, we rescue the acute lethality, hematopoietic failure, and gene dysregulation. Our results provide functional evidence for the interaction between two crucial chromatin marks in mammalian tissue homeostasis.
    Keywords:  H3K27 methylation; H3K27M; H3K4 methylation; H3K4M; bivalent genes; differentiation; hematopoiesis; hematopoietic stem and progenitor cells; histone methylation; lysine-to-methionine mutation
    DOI:  https://doi.org/10.1016/j.cell.2025.05.011
  13. Cell Stem Cell. 2025 Jun 10. pii: S1934-5909(25)00192-4. [Epub ahead of print]
      Repair of muscle damage declines with age due to the accumulation of dysfunctional muscle stem cells (MuSCs). Here, we uncover that aged MuSCs have blunted prostaglandin E2 (PGE2)-EP4 receptor signaling, which causes precocious commitment and mitotic catastrophe. Treatment with PGE2 alters chromatin accessibility and overcomes the dysfunctional aged MuSC fate trajectory, increasing viability and triggering cell cycle re-entry. We employ neural network models to learn the complex logic of transcription factors driving the change in accessibility. After PGE2 treatment, we detect increased transcription factor binding at sites with CRE and E-box motifs and reduced binding at sites with AP1 motifs, overcoming the changes that occur with age. We find that short-term exposure of aged MuSCs to PGE2 augments their long-term regenerative capacity upon transplantation. Strikingly, PGE2 injections following myotoxin- or exercise-induced injury overcome the aged niche, leading to enhanced regenerative function of endogenous tissue-resident MuSCs and an increase in strength.
    Keywords:  Prostaglandin E2; aging; epigenetic remodeling; inflammaging; molecular memory; muscle stem cells; neural network analysis; regeneration; rejuvenation; sarcopenia
    DOI:  https://doi.org/10.1016/j.stem.2025.05.012
  14. Nat Commun. 2025 Jun 13. 16(1): 5290
      Mapping the spatial organization of DNA-level somatic copy number changes in tumors can provide insight to understanding higher-level molecular and cellular processes that drive pathogenesis. We describe an integrated framework of spatial transcriptomics, tumor/normal DNA sequencing, and bulk RNA sequencing to identify shared and distinct characteristics of an initial cohort of eleven gliomas of varied pathology and a replication cohort of six high-grade glioblastomas. We identify focally amplified extrachromosomal DNA (ecDNA) in four of the eleven initial gliomas, with subclonal tumor heterogeneity in two EGFR-amplified grade IV glioblastomas. In a TP53-mutated glioblastoma, we detect a subclone with EGFR amplification on ecDNA coupled to chromosome 17 loss of heterozygosity. To validate subclonal somatic aneuploidy and copy number alterations associated with ecDNA double minutes, we examine the replication cohort, identifying MDM2/MDM4 ecDNA subclones in two glioblastomas. The spatial heterogeneity of EGFR and p53 inactivation underscores the role of ecDNA in enabling rapid oncogene amplification and enhancing tumor adaptability under selective pressure.
    DOI:  https://doi.org/10.1038/s41467-025-59805-z
  15. Nat Commun. 2025 Jun 18. 16(1): 5333
      The eukaryotic replisome, which consists of the CDC45-MCM2-7-GINS (CMG) helicase, replicative polymerases, and several accessory factors, sometimes encounters proteinaceous obstacles that threaten genome integrity. These obstacles are targeted for removal or proteolysis by the E3 ubiquitin ligase TRAIP, which associates with the replisome. However, TRAIP must be carefully regulated to avoid inappropriate ubiquitylation and disassembly of the replisome. Here, we demonstrate that human cells lacking the de-ubiquitylating enzyme USP37 are hypersensitive to topoisomerase poisons and other replication stress-inducing agents. Furthermore, TRAIP loss rescues the hypersensitivity of USP37 knockout cells to topoisomerase inhibitors. In Xenopus egg extracts depleted of USP37, TRAIP promotes premature CMG ubiquitylation and disassembly when converging replisomes stall. Finally, guided by AlphaFold-Multimer, we discovered that binding to CDC45 mediates USP37's response to topological stress. We propose that USP37 protects genome stability by preventing TRAIP-dependent CMG unloading when replication stress impedes timely termination.
    DOI:  https://doi.org/10.1038/s41467-025-60139-z
  16. Nat Cell Biol. 2025 Jun;27(6): 1006-1020
      DNA double-strand breaks (DSB) are among the most deleterious forms of DNA damage and, if unresolved, result in DNA mutations and chromosomal aberrations that can cause disease, including cancer. Repair of DSBs by homologous recombination requires extensive nucleolytic digestion of DNA ends in a process known as DNA-end resection. In recent years, progress has been made in understanding how this process is initiated, but the later stages of this process-long-range DNA-end resection-are not well understood. Many questions remain in terms of how the DNA helicases and endonucleases that catalyse this process are regulated, a key step to avoiding spurious activity in the absence of breaks. The importance of DNA-end resection in human disease is highlighted by several human genetic syndromes that are caused by mutations or deficiencies in key proteins involved in this process. Here, using high-throughput microscopy coupled with a cDNA 'chromORFeome' library, we identified ZNF280A as an uncharacterized chromatin factor that is recruited to breaks and essential for DNA DSB repair. Lack of ZNF280A drives genomic instability and substantial sensitivity to DNA-damaging agents. Mechanistically, we demonstrate that ZNF280A promotes long-range DNA-end resection by facilitating the recruitment of the BLM-DNA2 helicase-nuclease complex to DNA DSB sites, enhancing efficiency of the enzymatic activity of this complex at DNA damage sites. ZNF280A is therefore essential for DNA-end resection and DNA repair by homologous recombination. Importantly, ZNF280A is hemizygously deleted in a human genetic condition, 22q11.2 distal deletion syndrome. Features of this condition include congenital heart disease, microcephaly, immune deficiency, developmental delay and cognitive deficits-features that are associated with other human syndromes caused by defects in genes involved in DNA repair. Remarkably, cells from individuals with a 22q11.2 distal deletion have defects in DNA-end resection and homologous recombination, resulting in increased incidence of genomic instability. These phenotypes are rescued by reintroduction of ZNF280A, providing evidence of defective DNA repair as a potential mechanistic explanation for several clinical features associated with this human condition.
    DOI:  https://doi.org/10.1038/s41556-025-01674-1
  17. Sci Adv. 2025 Jun 20. 11(25): eadu3741
      Cell behavior emerges from the intracellular distribution of properties such as protrusion, contractility, and adhesion. Thus, characteristic emergent rules of collective migration can arise from cell-cell contacts locally tweaking architecture, orchestrating self-regulation during development, wound healing, and cancer progression. The Drosophila testis-nascent-myotube system allows dissection of contact-dependent migration in vivo at high resolution. Here, we describe a role for the axon guidance factor Plexin A in collective cell migration: maintaining cell-cell interfaces at a precise point on the mesenchymal-to-epithelial continuum. This is crucial for testis myotubes to migrate as a continuous sheet, allowing normal sculpting-morphogenesis. Cells must maintain filopodial N-cadherin-based junctions and remain ECM-tethered near cell-cell contacts to spread while collectively moving. Our data further suggest Semaphorin 1b is a Plexin A antagonist, fine-tuning activation. This reveals a contact-dependent mechanism to maintain sheet integrity during migration, driving organ morphogenesis. This is relevant for mesenchymal organ sculpting in other migratory contexts such as angiogenesis.
    DOI:  https://doi.org/10.1126/sciadv.adu3741
  18. Cell. 2025 Jun 17. pii: S0092-8674(25)00577-X. [Epub ahead of print]
      Single-cell RNA sequencing has revolutionized our understanding of cellular diversity but remains constrained by scalability, high costs, and the destruction of cells during analysis. To overcome these challenges, we developed STAMP (single-cell transcriptomics analysis and multimodal profiling), a highly scalable approach for the profiling of single cells. By leveraging transcriptomics and proteomics imaging platforms, STAMP eliminates sequencing costs, enabling cost-efficient single-cell genomics of millions of cells. Immobilizing (stamping) cells in suspension onto imaging slides, STAMP supports multimodal (RNA, protein, and H&E) profiling, while retaining cellular structure and morphology. We demonstrate STAMP's versatility by profiling peripheral blood mononuclear cells, cell lines, and stem cells. We highlight the capability of STAMP to identify ultra-rare cell populations, simulate clinical applications, and show its utility for large-scale perturbation studies. In total, we present data for 10,962,092 high-quality cells/nuclei and 6,030,429,954 transcripts. STAMP makes high-resolution cellular profiling more accessible, scalable, and affordable.
    Keywords:  cell atlas; circulating tumor cells; genomics; imaging; multimodal; phenotyping; proteomics; single cell; stem cells; transcriptomics
    DOI:  https://doi.org/10.1016/j.cell.2025.05.027
  19. Curr Biol. 2025 Jun 16. pii: S0960-9822(25)00664-5. [Epub ahead of print]
      During development, tissues undergo morphogenesis to achieve their final form. This process relies on coordinated cell shape changes, which have predominantly been studied in one plane, at the apical (top) surface of developing tissues. However, tissues are three dimensional, often exhibiting deformations along multiple axes. To understand how morphogenesis is coordinated across tissue axes, we used the genetically amenable Drosophila retina, a curved, dome-shaped epithelium, as a model system. Using intravital imaging, we found that retinal curvature is induced early in development. Modeling early retinal development with a vertex model suggests that this curvature arises from differential planar growth between the apical and basal tissue surfaces. In addition, mechanical perturbation experiments revealed that inside-out fluid pressure plays a crucial role in promoting this curvature. Further combining computational modeling, genetic perturbations, and force-inference experiments, we demonstrate that uniform thickening of the curved retinal epithelium requires coordination of two key processes: growth, promoting cell elongation along the apical-basal axis of the tissue, and basal surface contraction. Remarkably, inhibiting basal surface contraction-both in silico and through genetic manipulations targeting the basal surface receptor integrin and non-muscle myosin-II-prevented cell elongation. We conclude that thickening of a curved epithelium, like the Drosophila retina, requires both integrin and non-muscle myosin-II to coordinate basal surface contraction and cell growth along the apical-basal axis of the tissue.
    Keywords:  Drosophila; cell growth; epithelial morphogenesis; integrins; non-muscle myosin II; vertex model
    DOI:  https://doi.org/10.1016/j.cub.2025.05.048
  20. Nat Aging. 2025 Jun 20.
      Cochlear aging causes substantial hearing impairment in older adults, yet primate-specific mechanisms remain poorly characterized. Our comprehensive analysis combining single-cell and histopathological profiling in aging Macaca fascicularis demonstrates progressive cochlear degeneration featuring accelerated sensory hair cell loss, senescent spiral ganglion neurons with elevated neuroinflammation, and marked stria vascularis atrophy. We discovered that downregulation of transmembrane transport proteins, particularly SLC35F1, serves as a critical biomarker of hair cell aging. Functional validation through Slc35f1 knockdown in adult mice successfully recapitulated key aspects of age-related hearing loss, including hair cell degeneration and auditory function decline. Notably, we showed that long-term metformin administration at clinically relevant doses effectively delays cochlear aging in primates. These findings provide fundamental insights into the cellular and molecular basis of primate cochlear aging while establishing a foundation for developing targeted interventions against age-related hearing loss.
    DOI:  https://doi.org/10.1038/s43587-025-00896-0
  21. EMBO J. 2025 Jun 16.
      The accumulation of mitochondrial precursor proteins in the cytosol due to mitochondrial dysfunction compromises cellular proteostasis and is a hallmark of diseases. Why non-imported precursors are toxic and how eukaryotic cells prevent their accumulation in the cytosol is still poorly understood. Using a proximity labeling-based assay to globally monitor the intramitochondrial location of proteins, we show that, upon mitochondrial dysfunction, many mitochondrial matrix proteins are sequestered in the intermembrane space (IMS); something we refer to as "mitochondrial triage of precursor proteins" (MitoTraP). MitoTraP is not simply the result of a general translocation block at the level of the inner membrane, but specifically directs a subgroup of matrix proteins into the IMS, many of which are constituents of the mitochondrial ribosome. Using the mitoribosomal protein Mrp17 (bS6m) as a model, we found that IMS sequestration prevents its mistargeting to the nucleus, potentially averting interference with assembly of cytosolic ribosomes. Thus, MitoTraP represents a novel, so far unknown mechanism of the eukaryotic quality control system that protects the cellular proteome against the toxic effects of non-imported mitochondrial precursor proteins.
    Keywords:  Intermembrane Space; Mitochondria; Nucleolus; Protein Targeting; Ribosome
    DOI:  https://doi.org/10.1038/s44318-025-00486-1
  22. Nat Cell Biol. 2025 Jun;27(6): 902-917
      The peroxidation of membrane phospholipids (PLs) is a hallmark of ferroptosis. The endoplasmic reticulum and mitochondria have been implicated in ferroptosis, but whether intracellular PL peroxidation ensues at their contact sites (endoplasmic reticulum-mitochondria contact sites, EMCSs) is unknown. Using super-resolution live imaging, we charted the spatiotemporal events triggered by ferroptosis at the interorganelle level. Here we show that EMCSs expand minutes after localized PL peroxides are formed and secondarily spread to mitochondria, promoting mitochondrial reactive oxygen species and fission. Oxidative lipidomics unravels that EMCSs host distinct proferroptotic polyunsaturated-PLs, including doubly proferroptotic polyunsaturated-acylated PLs, demonstrating their high propensity to undergo PL peroxidation. Endoplasmic reticulum-mitochondria untethering blunts PL peroxidation and ferroptosis, while EMCS stabilization enhances them. Consistently, distancing EMCSs protects the ferroptosis-susceptible triple-negative breast cancer subtype, harbouring high EMCS-related gene expression and basal PL peroxide levels. Conversely, in insensitive triple-negative breast cancer subtypes, bolstering EMCSs sensitizes them to ferroptosis. Our data unveil endoplasmic reticulum-mitochondria appositions as initial hubs of PL peroxide formation and posit that empowering EMCSs endorses ferroptosis in cancer cells.
    DOI:  https://doi.org/10.1038/s41556-025-01668-z
  23. Mol Cell. 2025 Jun 12. pii: S1097-2765(25)00468-X. [Epub ahead of print]
      Polycomb repressive complexes (PRCs) sustain regulatory T (Treg) cell identity through transcriptional silencing, yet their role in modulating Treg functional plasticity during immune adaptation remains unclear. Here, we identify KDM2B, a defining component of non-canonical PRC1.1, as a critical regulator for sustaining the proportion and immunosuppressive functions of active Treg (aTreg) cells without altering Treg abundance or identity. Mechanistically, PRC1.1 deposits H2AK119 monoubiquitylation (H2AK119ub1) at active promoters, enabling rather than repressing transcriptional activation of aTreg programs. Disruption of PRC1.1 via Kdm2b ablation or pharmacological inhibition with iBP, a selective inhibitor, reduces H2AK119ub1, blunts stimulus-dependent transcriptional activation, and suppresses Treg activation. Notably, Treg-specific Kdm2b deletion in melanoma-bearing mice enhances anti-tumor immunity and synergizes with anti-PD-L1 therapy. Therefore, our study underscores H2AK119ub1 as a dual-function epigenetic mark and PRC1.1 as a molecular rheostat fine-tuning Treg adaptability, establishing PRC1.1 as a therapeutic target to decouple immune suppression in cancer while preserving Treg homeostasis.
    Keywords:  H2AK119ub1; PRC; Polycomb; Treg; plasticity; tumor-infiltrated Treg
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.029
  24. Nature. 2025 Jun 18.
      Distant-acting enhancers are central to human development1. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease2. Here we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers that are active in the developing brain, heart, limb and face, we created over 1,700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-base-pair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modelling, we annotated critical nucleotides at the base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes in in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features that are required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.
    DOI:  https://doi.org/10.1038/s41586-025-09182-w
  25. J Clin Invest. 2025 Jun 16. pii: e186593. [Epub ahead of print]135(12):
      Myxomatous valve disease (MVD) is the most common form of cardiac valve disease in the developed world. A small fraction of MVD is syndromic and arises in association with matrix protein defects such as those in Marfan syndrome, but most MVD is acquired later in life through an undefined pathogenesis. The KLF2/4 transcription factors mediate endothelial fluid shear responses, including those required to create cardiac valves during embryonic development. Here we test the role of hemodynamic shear forces and downstream endothelial KLF2/4 in mature cardiac valves. We find that loss of hemodynamic forces in heterotopically transplanted hearts or genetic deletion of KLF2/4 in cardiac valve endothelium confers valve cell proliferation and matrix deposition associated with valve thickening, findings also observed in mice expressing the mutant fibrillin-1 protein known to cause human MVD. Transcriptomic and histologic analysis reveals increased monocyte recruitment and TGF-β signaling in both fibrillin-1-mutant valves and valves lacking hemodynamic forces or endothelial KLF2/4 function, but only loss of TGF-β/SMAD signaling rescued myxomatous changes. We observed reduced KLF2/4 expression and augmented SMAD signaling in human MVD. These studies identify hemodynamic activation of endothelial KLF2/4 as an environmental homeostatic regulator of cardiac valves and suggest that non-syndromic MVD may arise in association with disturbed blood flow across the aging valve.
    Keywords:  Cardiology; Cardiovascular disease; Endothelial cells; Vascular biology
    DOI:  https://doi.org/10.1172/JCI186593
  26. Cell Stem Cell. 2025 Jun 10. pii: S1934-5909(25)00193-6. [Epub ahead of print]
      The human airway lining consists of two physiologically distinct compartments: the surface airway epithelium (SAE) and the submucosal glands (SMGs). Despite their critical role, the SMGs have remained largely overlooked in airway in vitro modeling of respiratory inflammation and infection. In this study, we leverage long-term cultured organoids derived separately from SAE and SMGs to investigate their unique physiological characteristics. Single-cell RNA sequencing (scRNA-seq) analysis confirms that these organoid models accurately replicate the cellular heterogeneity inherent to each tissue type. Specifically, SMG organoids are enriched in MUC5B-producing mucous cells and also generate alpha-smooth muscle actin (αSMA)-expressing myoepithelial cells. ANPEP/CD13 specifically marks SMG secretory cells. Exposure to cytokines elicits distinct inflammatory transcriptomic responses in SMG secretory cells. Infection assays with human alpha-coronavirus 229E (HCoV-229E) reveal the selective vulnerability of CD13-positive secretory cells, triggering an unfolded protein response. These findings broaden the utility of airway organoids for modeling respiratory (patho-)physiology.
    Keywords:  ANPEP; CD13; MUC5B; airway inflammation; airway submucosal gland; coronavirus infection; human airway organoids; mucous cells
    DOI:  https://doi.org/10.1016/j.stem.2025.05.013
  27. Cell Commun Signal. 2025 Jun 14. 23(1): 283
      The nucleolus is the site of rDNA transcription and ribosome biogenesis. Alterations in nucleolar function and architecture correlate with drastic heterochromatin rearrangement and global changes in gene expression. However, the precise mechanism that connects nucleolar function to heterochromatin organization and transcription is yet unknown. Here, we report that the RNA polymerase II (RNA pol II) transactivator and chromatin condenser, Positive Coactivator 4 (PC4), is a bona fide nucleolar protein. PC4 showed dynamic nucleolar accumulation, which is critical for rDNA transcription. The lysine acetyltransferase, KAT5 (Tip60) acetylates PC4 at K35, which facilitates nucleolar release of PC4 and concomitated inhibition of rDNA transcription. By employing PC4 mutant, which is defective in nucleolar accumulation, we found that nucleolar PC4 is crucial for RNA pol I-mediated rDNA transcription. To validate this significant novel role of PC4, in the context of nucleolus organization and function, at the organismal level, we looked into B cell-specific conditional knockout of Sub1 encoding PC4 in mice, which revealed that indeed the rDNA transcription and protein synthesis in B cells are severely repressed in the absence of PC4. Furthermore, PC4 CKO B cells were associated with the loss of H3K9me3-marked heterochromatin foci but not global H3K9me3 levels. LC-MS/MS analysis of the H3K9me3 chromatin complexes revealed that most non-histone heterochromatin proteins were reduced or absent in the constitutive heterochromatin of PC4 CKO B cells. These findings establish PC4 as a critical functional component of nucleolus for rDNA transcription.
    Keywords:  B cells; Heterochromatin; KAT5; Lysine acetyltransferase; Nucleolus; Ribosomal DNA; Ribosome; TIP60
    DOI:  https://doi.org/10.1186/s12964-025-02238-4
  28. Curr Opin Cell Biol. 2025 Jun 12. pii: S0955-0674(25)00097-3. [Epub ahead of print]95 102559
      Upon engagement of E-cadherin or when mechanical force is applied, E-cadherin recruits cytoskeletal proteins and triggers various signal transduction cascades including PI3K, Src, Rho family GTPases, kinases, YAP/TAZ, AMPK, and other metabolic enzymes. These cascades modulate E-cadherin's stability, viscosity, and its connection to the actin cytoskeleton, thereby reinforcing cell-cell adhesion.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102559
  29. JACC Case Rep. 2025 Jun 11. pii: S2666-0849(25)00400-0. [Epub ahead of print]30(14): 103622
       BACKGROUND: Multiple studies demonstrate the cardiac regenerative capacity in neonatal mice in the first week of life. Although a similar regenerative window in the human neonatal hearts has not been defined clearly, existing evidence supports the concept of human neonatal cardiac regeneration.
    CASE SUMMARY: A neonate with a complex form of cyanotic tetralogy of Fallot demonstrated complete recovery of left ventricular function after an acute cardiac injury suffered on day of life 8.
    DISCUSSION: This case report adds to limited but intriguing observations that human neonatal hearts may possess the regenerative capacity observed in animal models and that that capacity may be prolonged by hypoxemia.
    TAKE-HOME MESSAGES: A human neonatal heart has shown complete functional recovery after an ischemic injury. Hypoxemia may have extended the regenerative window of the human neonatal myocardium.
    Keywords:  cardiac regeneration; congenital heart disease; hypoxemia; ischemia
    DOI:  https://doi.org/10.1016/j.jaccas.2025.103622
  30. Mol Cell. 2025 Jun 11. pii: S1097-2765(25)00469-1. [Epub ahead of print]
      The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome complex, revealing how established proteasomal components are repurposed to enable a unique form of proteolysis. While the proteasomal subunit PSMD2/Rpn1 binds to ubiquitinated or ubiquitin-like (Ubl) proteins, we discover that it also interacts with the midnolin nuclear localization sequence, elucidating how midnolin's activity is confined to the nucleus. Likewise, PSMD14/Rpn11, an enzyme that normally cleaves ubiquitin chains, surprisingly functions non-enzymatically as a receptor for the midnolin Ubl domain, positioning the substrate-binding Catch domain directly above the proteasomal entry site to guide substrates into the proteasome. Moreover, we demonstrate that midnolin downregulation is critical for the survival of myeloma cells by stabilizing the transcription factor substrate IRF4. Our findings uncover the mechanisms underlying the midnolin-proteasome pathway and midnolin downregulation as a driver of multiple myeloma.
    Keywords:  IRF4; PSMD14/Rpn11; PSMD2/Rpn1; midnolin; myeloma; proteasome; ubiquitin-independent
    DOI:  https://doi.org/10.1016/j.molcel.2025.05.030
  31. Sci Adv. 2025 Jun 20. 11(25): eadt8346
      The cellular networks that maintain genome stability encompass numerous pathways involved in all aspects of nucleic acid metabolism. Through bioinformatic analysis, we identified the Zinc Finger CCCH-Type Containing 4 protein (ZC3H4), a suppressor of noncoding RNA (ncRNA) production, as a pivotal player in this system. Experimentally, ZC3H4 deficiency led to increased DNA damage, abnormal mitosis, and cellular senescence. Biochemical analysis and super-resolution microscopy revealed that the loss of ZC3H4 increased replication stress (RS)-a major driver of genome instability-by inducing a hypertranscription state that promoted R loop formation and transcription-replication conflicts (TRCs), both of which drive RS. Further bioinformatic analysis demonstrated that ZC3H4 preferentially binds to genomic regions prone to TRCs and R loops, where it suppresses ncRNA bursts, functioning as part of the Restrictor complex. Our findings identify ZC3H4 as a crucial factor in maintaining genome integrity, strategically positioned at the critical intersection of DNA and RNA synthesis.
    DOI:  https://doi.org/10.1126/sciadv.adt8346
  32. Cell Rep. 2025 Jun 17. pii: S2211-1247(25)00614-X. [Epub ahead of print]44(6): 115843
      Discovering mechanisms of regeneration holds great promise for advancing regenerative medicine. Non-histone modifications by epigenetic factors participate in important biological processes. Through in vivo CRISPR screening combined with partial hepatectomy (PHx-CRISPR), we identified the histone H3K9 methyltransferase SETDB1 as an enhancer of regeneration. Loss of SETDB1 delays regeneration, and overexpressing SETDB1 accelerates liver regeneration across various liver injury models. SETDB1 promotes liver regeneration by positively regulating the expression of granulocyte colony-stimulating factor (CSF3) in hepatocytes. SETDB1 facilitates the expression of CSF3 in hepatocytes by methylating and activating AKT, establishing CSF3 as a critical downstream effector in the SETDB1-AKT liver regeneration pathway. Notably, increasing SETDB1 levels in humanized mouse liver suppresses drug-induced liver damage. Our findings reveal an unexpected role for non-histone modification by SETDB1 in regulating cytokine signaling during liver regeneration and offer insights into targeted therapies for regenerative medicine and tissue repair.
    Keywords:  Akt methylation; CP: Stem cell research; CSF3/CSF3r; PHx-CRISPR screening; SETDB1; Tyosinemia type I mice; acute liver injury; hepatectomy; liver regeneration; liver-humanized mouse; non-histone methylation
    DOI:  https://doi.org/10.1016/j.celrep.2025.115843
  33. Nat Rev Nephrol. 2025 Jun 19.
      Fibroblasts are a special type of interstitial cell that has an essential role in maintaining the structural framework of tissues and organs. In response to injury, fibroblasts are activated and produce large amounts of extracellular matrix proteins. Fibroblast activation has a crucial role in tissue repair and wound healing. However, uncontrolled and persistent activation of fibroblasts ultimately leads to fibrotic diseases of organs such as the kidney, liver, lung and heart. Activated fibroblasts predominantly originate from the local activation and expansion of resident fibroblasts and pericytes. A diverse array of extracellular cues, including soluble factors, extracellular vesicles, matricellular proteins and mechanical stiffness, induce fibroblast activation after tissue injury. Fibroblast activation primarily takes place in the fibrogenic niche, a unique tissue microenvironment in which fibroblasts interact with injured parenchymal cells, inflammatory cells and endothelial cells. The fates of activated fibroblasts, including apoptosis, senescence, dedifferentiation and lineage reprogramming, determine the outcome of tissue repair and organ fibrosis. Potential therapeutic strategies for fibrotic diseases include disrupting the formation of the fibrogenic niche, inhibiting fibroblast activation, promoting fibroblast depletion, accelerating fibrosis resolution or promoting tissue repair and regeneration.
    DOI:  https://doi.org/10.1038/s41581-025-00969-8
  34. Nat Struct Mol Biol. 2025 Jun 17.
      Lysosomes, central hydrolytic organelles, are regulated by ion flow, including calcium and protons, via transporters and channels to maintain an acidified lumen for hydrolytic activity. TRPML1, a lysosomal ion channel, effluxes cations upon activation, promoting rapid conjugation of ATG8 proteins to the lysosomal membrane in a process known as conjugation of ATG8 to single membranes (CASM). However, our understanding of how TRPML1 activation reorganizes the lysosomal proteome is poorly understood. Here, we identify DMXL1 as a key regulator of lysosomal homeostasis through quantitative proteomics of lysosomes during TRPML1 activation by the agonist MLSA5. DMXL1 is recruited to lysosomes and Salmonella-containing vacuoles, both in a CASM-dependent manner. As the mammalian ortholog of yeast Rav1, DMXL1 assembles with Rav2 ortholog ROGDI and WDR7, and associates with V0 and V1 subunits of the lysosomal V-ATPase. TRPML1 activation drives V1 subunit recruitment to lysosomes in a DMXL1- and DMXL2-dependent manner. DMXL1- and DMXL2-deficient cells display reduced V1-ATPase recruitment, increased lysosomal pH and diminished hydrolytic capacity. Using AlphaFold modeling supported by cross-linking proteomics, we identify interaction interfaces within the DMXL1-ROGDI-WDR7 complex, as well as an ATP6V1A binding interface in DMXL1, whose mutation affects interaction and function. Our findings suggest CASM-dependent DMXL1 recruitment, coupled with V-ATPase assembly, is critical for maintaining lumenal pH and lysosomal function in response to TRPML1 activation.
    DOI:  https://doi.org/10.1038/s41594-025-01581-x
  35. Nature. 2025 Jun 18.
      Brain organoids enable the mechanistic study of human brain development and provide opportunities to explore self-organization in unconstrained developmental systems1-3. Here we establish long-term, live light-sheet microscopy on unguided brain organoids generated from fluorescently labelled human induced pluripotent stem cells, which enables tracking of tissue morphology, cell behaviours and subcellular features over weeks of organoid development4. We provide a novel dual-channel, multi-mosaic and multi-protein labelling strategy combined with a computational demultiplexing approach to enable simultaneous quantification of distinct subcellular features during organoid development. We track actin, tubulin, plasma membrane, nucleus and nuclear envelope dynamics, and quantify cell morphometric and alignment changes during tissue-state transitions including neuroepithelial induction, maturation, lumenization and brain regionalization. On the basis of imaging and single-cell transcriptome modalities, we find that lumenal expansion and cell morphotype composition within the developing neuroepithelium are associated with modulation of gene expression programs involving extracellular matrix pathway regulators and mechanosensing. We show that an extrinsically provided matrix enhances lumen expansion as well as telencephalon formation, and unguided organoids grown in the absence of an extrinsic matrix have altered morphologies with increased neural crest and caudalized tissue identity. Matrix-induced regional guidance and lumen morphogenesis are linked to the WNT and Hippo (YAP1) signalling pathways, including spatially restricted induction of the WNT ligand secretion mediator (WLS) that marks the earliest emergence of non-telencephalic brain regions. Together, our work provides an inroad into studying human brain morphodynamics and supports a view that matrix-linked mechanosensing dynamics have a central role during brain regionalization.
    DOI:  https://doi.org/10.1038/s41586-025-09151-3
  36. Nat Cell Biol. 2025 Jun;27(6): 890-901
      Mitochondria are critical double-membraned organelles that act as biosynthetic and bioenergetic cellular factories, with the outer membrane providing an interface with the rest of the cell. Mitochondrial outer membrane proteins regulate a variety of processes, including metabolism, innate immunity and apoptosis. Although the biophysical and functional diversity of these proteins is highly documented, the mechanisms of their biogenesis and the integration of that into cellular homeostasis are just starting to take shape. Here, focusing on α-helical outer membrane proteins, we review recent insights into the mechanisms of synthesis and cytosolic chaperoning, insertion and assembly in the lipid bilayer, and quality control of unassembled or mislocalized transmembrane domains. We further discuss the role convergent evolution played in this process, comparing key biogenesis players from lower eukaryotes, including yeast and trypanosomes, with multicellular metazoan systems, and draw comparisons with the endoplasmic reticulum biogenesis system, in which membrane proteins face similar challenges.
    DOI:  https://doi.org/10.1038/s41556-025-01683-0