bims-ginsta Biomed News
on Genome instability
Issue of 2025–12–14
34 papers selected by
Jinrong Hu, National University of Singapore



  1. Nat Commun. 2025 Dec 12.
      The final step of oocyte growth, which reorganizes chromatin from the non-surrounded nucleolus (NSN) to the surrounded nucleolus (SN) configuration is essential for embryonic development after meiotic maturation and fertilization. The underlying mechanisms remain unknown. We identify RNA polymerase II (RNAPII) degradation as the key driver of this process. Inhibitors that trigger RNAPII degradation, but not nucleoside-based transcription inhibitors, induce NSN-to-SN transition in oocytes. By establishing miniTrim-Away for nuclear proteins and using segregase and proteasome inhibitors, we demonstrate that RNAPII degradation is necessary and sufficient for NSN-to-SN transition. Further experiments reveal that RNAPII degradation results in a global collapsing force and a local attractive force required for the transition to SN configuration. Finally, embryos derived from NSN oocytes have aberrant RNAPII levels and localization, and are defective in maternal-to-zygotic transition. Our study elucidates the mechanistic framework of oocyte chromatin reorganization and presents a strategy for inducing fully grown oocyte nuclei.
    DOI:  https://doi.org/10.1038/s41467-025-67476-z
  2. Elife. 2025 Dec 08. pii: RP101140. [Epub ahead of print]13
      The first lineage allocation in mouse and human embryos separates the inner cell mass (ICM) from the outer trophectoderm (TE). This symmetry-breaking event is executed through polarization of cells at the 8 cell stage and subsequent asymmetric divisions, generating polar (TE) and apolar (ICM) cells. Here, we show that mouse embryo polarization is unexpectedly asynchronous. Cells polarizing at the early and late 8 cell stage have distinct molecular and morphological properties that direct their following lineage specification, with early polarizing cells being biased towards producing the TE lineage. More recent studies have also implicated heterogeneities between cells prior to the 8 cell stage in the first lineage allocation: cells exhibiting reduced methyltransferase CARM1 activity at the 4 cell stage are predisposed towards the TE fate. Here, we demonstrate that reduced CARM1 activity and upregulation of its substrate BAF155 promote early polarization and TE specification. These findings provide a link between asymmetries at the 4 cell stage and polarization at the 8 cell stage, mechanisms of the first lineage allocation that had been considered separate.
    Keywords:  cell fate; developmental biology; mouse; mouse embryo development; polarity; preimplantation development
    DOI:  https://doi.org/10.7554/eLife.101140
  3. Res Sq. 2025 Dec 01. pii: rs.3.rs-7923379. [Epub ahead of print]
      How embryos adapt their internal cellular machinery to reductions in cell size during development remains a fundamental question in cell biology 1-11 . Here, we use high-resolution lattice light-sheet fluorescence microscopy and automated image analysis to quantify lineage-resolved mitotic spindle and chromosome segregation dynamics from the 2- to 64-cell stages in Caenorhabditis elegans embryos. While spindle length scales with cell size across both wild-type and size-perturbed embryos, chromosome segregation dynamics remain largely invariant, suggesting that distinct mechanisms govern these mitotic processes. Combining femtosecond laser ablation 12,13 with large-scale electron tomography 14 , we find that central spindle microtubules mediate chromosome segregation dynamics and remain uncoupled from cell size across all stages of early development. In contrast, spindle elongation is driven by cortically anchored motor proteins and astral microtubules, rendering it sensitive to cell size 12,13,15-17 . Incorporating these experimental results into an extended stoichiometric model for both the spindle and chromosomes, we find that allowing only cell size and microtubule catastrophe rates to vary reproduces elongation dynamics across development. The same model also accounts for centrosome separation and pronuclear positioning in the one-cell C. elegans embryo 18 , spindle-length scaling across nematode species spanning ~100 million years of divergence 17 , and spindle rotation in human cells 19 . Thus, a unified stoichiometric framework provides a predictive, mechanistic account of spindle and nuclear dynamics across scales and species.
    DOI:  https://doi.org/10.21203/rs.3.rs-7923379/v1
  4. Nat Commun. 2025 Dec 06.
      Cadherin-based junctions establish dynamically regulated adhesion between cells to coordinate tissue integrity and morphogenetic movements. Adhesion strength can be modulated by the organization of individual cadherin complexes into lateral clusters. Here, we identify a clustering mechanism of the cadherin complex established by its core component β-catenin. We show that the disordered termini of β-catenin drive the formation of condensates that incorporate other components of the cadherin complex in vitro. Using β-catenin mutants with hampered condensation, we demonstrate that β-catenin condensation nucleates the formation of submicron cadherin/catenin clusters that further develop into stable sites of adhesion. Furthermore, we show that β-catenin-dependent clustering ensures the efficient formation of de novo cell-cell adhesions. Our data thus indicate a role for β-catenin condensates in the supramolecular organization of the cadherin complex, and reveal that the function of β-catenin in the cadherin complex extends beyond connecting cadherin to α-catenin and the actin cytoskeleton.
    DOI:  https://doi.org/10.1038/s41467-025-66984-2
  5. Mol Cell. 2025 Dec 09. pii: S1097-2765(25)00932-3. [Epub ahead of print]
      Controlling mRNA translation is critical for proper protein production. Although translation initiation and elongation regulations are becoming increasingly clear, whether and how translation termination is monitored remains poorly understood. Using an acute protein degradation system coupled with phenotypic rescue via ectopic expression, here we show that the impaired translation termination reaction leads to the rapid activation of GCN2, resulting in eIF2α phosphorylation and inhibition of translation initiation, which occurs prior to ribosome collisions. Ribosome profiling analyses reveal that GCN2 monitors terminating ribosomes and prevents ribosome collisions and translation readthrough when translation termination is compromised. This rapid activation of GCN2 by compromised translation termination occurs in both stem and somatic cells and in mouse and human cells. These results suggest a conserved surveillance mechanism for translation termination.
    Keywords:  GCN2; dTAG; eIF2α phosphorylation; eRF1; terminating ribosome; translation termination
    DOI:  https://doi.org/10.1016/j.molcel.2025.11.015
  6. Cell. 2025 Dec 08. pii: S0092-8674(25)01308-X. [Epub ahead of print]
      Conventional hydrogel-based bioprinting methods often suffer from insufficient cell densities, which may limit crucial cell-cell interactions and impair overall tissue functions. Here, we present an approach that modifies cell membranes with acrylate bonds, allowing living cells at physiological densities (up to ∼109 cells mL-1) to serve directly as bioinks, demonstrating photoactivated bioprinting through digital light processing using purely cellular bioinks. Our cell-dense bioinks (CLINKs) rapidly produce tissue constructs that closely mimic native tissues, characterized by strong structural relevancy and robust functionality. The high cellularity and living nature of CLINKs enable the creation of advanced biological models such as connected neural circuits and rhythmically contracting mini-hearts derived entirely from stem cells, effectively capturing essential native-like behaviors. Implants created through this method showcase the capacity to integrate with the host, thereby promoting regeneration. Our CLINK technology holds substantial promise in tissue biofabrication, opening alternative avenues for biomedical applications.
    Keywords:  3D bioprinting; cardiac tissues; cardiomyocytes; cell-dense; digital light processing; liver tissues; neural cells; neural circuits; scaffold-free; skin regeneration
    DOI:  https://doi.org/10.1016/j.cell.2025.11.012
  7. J Cell Biol. 2026 Jan 05. pii: e202507117. [Epub ahead of print]225(1):
      As cells contract and reshape to enable tissue morphogenesis, their own internal structures can constrain these behaviors. In the Drosophila germband, the uncrowding of nuclei away from an initially common plane is required for efficient cell intercalation and extension. Here, we find that a centrosomally derived microtubule network transitions into non-centrosomal arrays that are deeply embedded in nuclei before shifting towards the apical cortex as GBE progresses. Disrupting ncMT function by compromising CLASP or Patronin function leads to failures in nuclear dispersion and results in MT networks dominated by centrosomal arrays. CLASP disruption also causes a marked detachment of MTs from nuclei, severely affecting nuclear orientation and dispersion. Our results also reveal a fundamental antagonism between ncMT and centrosomal networks-an observation corroborated in γ-tubulin embryos. Lastly, EB1 disruption blocks the apical shift of ncMTs, leading to dispersion defects. Overall, our findings reveal that nuclear repositioning during epithelial remodeling depends on a centrosome-to-ncMT transition requiring CLASP, EB1, and Patronin function.
    DOI:  https://doi.org/10.1083/jcb.202507117
  8. Nat Commun. 2025 Dec 10.
      Pioneer transcription factors (TF) bind nucleosome-embedded DNA motifs to activate new regulatory elements and promote differentiation. However, the complexity, binding dependencies and temporal effects of their action remain unclear. Here, we dissect how ectopic induction of the pioneer TF GATA6 triggers Primitive Endoderm (PrE) differentiation from pluripotent cells. We show that transient GATA6 binding exploits accessible regions to decommission enhancers and promote pluripotency gene silencing. Simultaneously, GATA6 targets closed chromatin and initiates extensive remodeling culminating in the establishment of fragile nucleosomes flanked by ordered nucleosome arrays and increased accessibility. This is enhanced by rapidly expressed PrE TFs (SOX17) and by pluripotency TFs repurposed for differentiation (OCT4/SOX2). Accordingly, depletion of OCT4 during GATA6 induction decreases Gata6 expression, alters GATA6 and SOX17 binding and impairs differentiation. Therefore, pioneer TFs orchestrate complex regulatory networks involving many if not all available pioneer TFs, including those required to support the original identity of differentiating cells.
    DOI:  https://doi.org/10.1038/s41467-025-67308-0
  9. Nat Cardiovasc Res. 2025 Dec 11.
      The mitochondrial membrane potential (ΔΨm) drives oxidative phosphorylation and alterations contribute to cardiac pathologies, but real-time assessment of ΔΨm has not been possible. Here we describe noninvasive measurements using mitochondrial heme bL and bH absorbances, which rapidly respond to ΔΨm. Multi-wavelength absorbance spectroscopy enabled their continuous monitoring in isolated mitochondria and the perfused heart. Calibration of heme b absorbance in isolated mitochondria revealed that reduced heme bL relative to total reduced heme b (fbL = bL/(bL + bH)) exhibits a sigmoidal relationship with ΔΨm. Extrapolating this relationship to the heart enabled estimation of ΔΨm as 166 ± 18 mV (n = 25, mean ± s.d.). We used this approach to assess how ΔΨm changes during ischemia-reperfusion injury, an unknown limiting the understanding of ischemia-reperfusion injury. In perfused hearts, ΔΨm declined during ischemia and rapidly reestablished upon reperfusion, supported by oxidation of the succinate accumulated during ischemia. These findings expand our understanding of ischemia-reperfusion injury.
    DOI:  https://doi.org/10.1038/s44161-025-00752-9
  10. bioRxiv. 2025 Dec 03. pii: 2025.11.03.686286. [Epub ahead of print]
      To acquire the capacity for multi-lineage differentiation, pluripotent stem cells must undergo a transition from naïve pluripotency to lineage competency. This transition requires epithelialization and changes in nuclear architecture. We sought to determine whether the cell and tissue mechanics intrinsic to epithelialization drive pluripotency progression and subsequent lineage commitment to neuroectodermal fate. We demonstrate that naïve mouse embryonic stem cells (mESCs) undergoing early differentiation in vitro recapitulate features of epithelialization in the peri-implantation epiblast, specifically apical constriction. We further demonstrate that cell contractility during apical constriction induces a distinct nuclear mechanoresponse, notably enrichment of emerin at the outer nuclear membrane, nuclear envelope localization of SUN2, and the global loss of H3K9me3 heterochromatin which is compensated by H3K27me3. Importantly, these nuclear phenotypes and subsequent neuroectodermal lineage priming require myosin II-mediated contractility, an intact LINC complex, and emerin. We demonstrate that LINC-dependent mechanotransduction through emerin regulates H3K27me3 occupancy on the key early neuroectodermal transcription factor gene, Sox1, implicating a mechanical switch in chromatin mediation of neuroectodermal lineage competence. These results indicate that epithelialization-induced nuclear mechanotransduction poises a critical lineage gene for subsequent expression.
    DOI:  https://doi.org/10.1101/2025.11.03.686286
  11. Nat Commun. 2025 Dec 12.
      Nuclear envelope (NE) rupture is a hallmark of cancer cells, and persistent NE damage drives genome instability and inflammation. NE repair relies on activation of the endosomal sorting complex required for transport (ESCRT)-III repair machinery by the LEMD2-CHMP7 compartmentalization sensor, but little is known beyond these core factors. Here, we use convergent proximity proteomics to inventorise proteins mobilized to the NE upon assembly of LEMD2-CHMP7 and activation of ESCRT-III. Within this NE repairome, we identify LRRC59 as a critical regulator of LEMD2 accumulation at NE ruptures. We find that LRRC59, together with the nuclear transporters KPNB1 and XPO1, restricts the assembly of LEMD2-CHMP7 complexes to the site of rupture. Disruption of this regulatory axis escalates LEMD2-CHMP7 spreading across the NE, driving torsional DNA damage in ruptured nuclei and micronuclei. Thus, our work identifies a central regulatory layer of NE repair centered on LRRC59 and KPNB1. We propose that altered LRRC59 levels and deregulated nuclear transport coordinately compromise NE repair, driving genome instability and cancer development.
    DOI:  https://doi.org/10.1038/s41467-025-65994-4
  12. Nat Cell Biol. 2025 Dec 09.
      Cytosolic phospholipase A2 (cPLA2) controls some of the most powerful inflammatory lipids in vertebrates by releasing their metabolic precursor, arachidonic acid, from the inner nuclear membrane (INM). Ca2+ and INM tension (TINM) are thought to govern the interactions and activity of cPLA2 at the INM. However, as compensatory membrane flow from the contiguous endoplasmic reticulum (ER) may prevent TINM, the conditions permitting nuclear membrane mechanotransduction by cPLA2 or other mediators remain unclear. To test whether the ER buffers TINM, we created the genetically encoded, Ca²⁺-insensitive TINM biosensor amphipathic lipid-packing domain inside the nucleus (ALPIN). Confocal time-lapse imaging of ALPIN- or cPLA2-INM interactions, along with ER morphology, nuclear shape/volume and cell lysis revealed a link between TINM and disrupted ER-nuclear membrane contiguity in osmotically or ferroptotically stressed mammalian cells and at zebrafish wound margins in vivo. By combining ALPIN imaging with Ca2+-induced ER disruption, we reveal the causality of this correlation, which suggests that compensatory membrane flow from the ER buffers TINM without preventing it. Besides consolidating the biomechanical basis of cPLA2 activation by nuclear deformation, our results identify cell stress- and cell death-induced ER disruption as an additional nuclear membrane mechanotransduction trigger.
    DOI:  https://doi.org/10.1038/s41556-025-01820-9
  13. Nat Cell Biol. 2025 Dec 12.
      Macrophages are known to engulf small membrane fragments, or trogocytose, target cells and pathogens, rather than fully phagocytose them. However, little is known about what causes macrophages to choose trogocytosis versus phagocytosis. Here we report that cortical tension of target cells is a key regulator of macrophage trogocytosis. At low tension, macrophages will preferentially trogocytose antibody-opsonized cells, while at high tension, they tend towards phagocytosis. Using model vesicles, we demonstrate that macrophages will rapidly switch from trogocytosis to phagocytosis when membrane tension is increased. Stiffening the cortex of target cells also biases macrophages to phagocytose them, a trend that can be countered by increasing antibody surface density and is captured in a mechanical model of trogocytosis. This work suggests that the target cell, rather than the macrophage, determines whether phagocytosis or trogocytosis occurs, and that macrophages do not require a distinct molecular pathway for trogocytosis.
    DOI:  https://doi.org/10.1038/s41556-025-01807-6
  14. Nat Commun. 2025 Dec 08. 16(1): 10855
      Chromatin bridges experience significant tension due to spindle fiber pulling and cell migration. Uncontrolled breakage of chromatin bridges by actomyosin contractile forces leads to detrimental consequences. The existence of specialized mechanisms that process chromatin bridges to prevent catastrophic rupture remains uncertain. Here, we uncover a unique property of ANKLE1, a midbody-tethered endonuclease implicated in chromatin bridge processing, in sensing and responding to DNA tension and supercoiling during cell division. Using single-molecule analyses, we found that ANKLE1 specifically cuts supercoiled or mechanically stretched DNA. At higher stretching forces, ANKLE1 cleaves both strands of negatively supercoiled DNA, mirroring conditions in which stretched chromatin bridges lose histones to expose negatively supercoiled DNA. These findings show that ANKLE1 acts as a DNA tension sensor that resolves stretched chromatin bridges. Our study highlights the significance of mechanical forces in DNA bridge processing, enhances our understanding of how cells preserve genome integrity during cell division.
    DOI:  https://doi.org/10.1038/s41467-025-65905-7
  15. Nat Genet. 2025 Dec 11.
      Copy number alterations (CNAs) are hallmarks of cancer, yet investigation of their oncogenic role has been hindered by technical limitations and missing model systems. Here we generated a genome-wide DNA methylation and CNA atlas of 106 genetic mouse models across 31 pediatric tumor types, including 18 new models for pediatric glioma. We demonstrated their epigenetic resemblance to human disease counterparts and identified entity-specific patterns of immune infiltration. We discovered that mouse tumors harbor highly recurrent CNA signatures that occur distinctly based on the tumor subgroup and driving oncogene and showed that these CNAs share syntenic regions with the matching human tumor types, thereby revealing a conserved but previously underappreciated role in subgroup-specific tumorigenesis that can be analyzed using the presented models. Our study provides insights into globally available mouse models for pediatric solid cancers and enables access to functional CNA interrogation, with the potential to unlock new translational targets in pediatric cancers.
    DOI:  https://doi.org/10.1038/s41588-025-02419-4
  16. Nat Commun. 2025 Dec 12.
      Migrating cells dynamically adapt their morphogenetic programs in response to microenvironmental changes, requiring coordinated spatiotemporal integration of mechanical and biochemical signals. The plasma membrane, through membrane tension and actin dynamics modulation, is essential for cell motility. Caveolae, small plasma membrane invaginations, act as mechanosensors to buffer tension changes under mechanical stress. Recent evidence suggests a role for caveolae in cell migration. Here, we demonstrate that breast cancer cells exhibit a front-rear asymmetry in caveolae and caveolin-1 scaffolds, which is regulated by membrane tension and is crucial for persistent migration and cell directionality. RhoA-driven cell contraction relies on the spatiotemporally coordinated assembly of caveolae and recruitment of RhoA-GEFs at the cell rear. These results are supported by a physical model establishing a feedback loop between local membrane tension and contractility, through caveolae formation and disruption. Our findings underscore the importance of caveolae mechanosensing in regulating RhoA activation and guiding cell migration.
    DOI:  https://doi.org/10.1038/s41467-025-67090-z
  17. Nat Commun. 2025 Dec 07.
      Mutations in the global transcriptional activator EP300/KAT3B are being reported in aggressive malignancies. However, the mechanistic contribution of EP300 dysregulation to cancer is currently unknown. While EP300 has been implicated in regulating cell cycle and DNA replication, the role of EP300 in maintaining replication fork integrity has not been studied. Here, using EP300-mutated adult T-cell leukemia/lymphoma cells and an EP300-selective degrader, we reveal that EP300 loss leads to pronounced dysregulations in DNA replication dynamics and persistent genomic instability. Aberrant DNA replication in EP300-mutated cells is characterized by elevated replication origin firing due to replisome pausing. EP300 deficiency results in a prominent defect in fork protection resulting in the accumulation of single-stranded DNA gaps. Importantly, we find that the loss of EP300 results in decreased expression of BRCA2 protein leading to sensitivity to treatments that are cytotoxic to BRCA-deficient cancers. Overall, we demonstrate that EP300-mutated cells recapitulate features of BRCA-deficient cancers.
    DOI:  https://doi.org/10.1038/s41467-025-67171-z
  18. Science. 2025 Dec 11. 390(6778): 1156-1163
      Genome instability, including chromothripsis, is a hallmark of cancer. Cancer cells frequently contain micronuclei-small, nucleus-like structures formed by chromosome missegregation-that are susceptible to rupture, exposing chromatin to cytoplasmic nucleases. Through an unbiased, imaging-based small interfering RNA screen that targeted all 204 known and putative human nucleases, we identified a previously uncharacterized cytoplasmic endonuclease, NEDD4-binding protein 2 (N4BP2), that enters ruptured micronuclei and initiates DNA damage, leading to chromosome fragmentation. N4BP2 promoted genome rearrangements (including chromothripsis), formation of extrachromosomal DNA (ecDNA) in drug-induced gene amplification, tumorigenesis, and tumor cell proliferation in an induced model of human high-grade glioma. Analysis of more than 10,000 human cancer genomes revealed elevated N4BP2 expression to be predictive of chromothripsis and copy number amplifications, including ecDNA.
    DOI:  https://doi.org/10.1126/science.ado0977
  19. J Cell Biol. 2026 Jan 05. pii: e202503075. [Epub ahead of print]225(1):
      Unconventional protein secretion (UcPS) exports diverse signal peptide-lacking cargoes, yet its cargo selectivity remains poorly understood. Here, we identify TMED proteins as key regulators of vesicle-dependent UcPS, mediating selective cargo release via translocation into secretory carriers. TMED proteins act as translocators, facilitating cargo passage across lipid bilayers with assistance from HSP90 chaperones and partial cargo unfolding. Selectivity arises during translocation, where TMED cytoplasmic tails bind specific cargoes. The ER-Golgi intermediate compartment (ERGIC) is essential for TMED-mediated translocation and release. TMED homo-oligomerization enhances translocation, while hetero-tetramerization inhibits it. ERGIC localization promotes homo-oligomerization, which is further stabilized by cargo binding, forming a feed-forward mechanism to enhance translocation. These findings establish TMED proteins as central regulators of cargo diversity in UcPS, with their oligomerization and subcellular localization modulating translocation efficiency.
    DOI:  https://doi.org/10.1083/jcb.202503075
  20. Cell Rep. 2025 Dec 10. pii: S2211-1247(25)01426-3. [Epub ahead of print]44(12): 116654
      During peri-implantation development, the pluripotent tissue of the early embryo undergoes profound cellular and biochemical reprogramming. These transformations are essential for subsequent development, yet how they are coordinated with the preservation of genome integrity remains poorly understood. Here, we uncover a telomere length checkpoint that is elicited by metabolic remodeling as mouse embryonic stem cells (ESCs) transition from the naive to formative pluripotent state. We show that the exit of naive pluripotency is marked by accelerated mitochondrial respiration and de novo lipogenesis, fueling lipid droplet accumulation required for tissue remodeling. Unexpectedly, these acute metabolic shifts trigger transient telomere shortening and activate ZSCAN4, a pluripotency-associated regulator of telomeres, followed by telomere re-elongation as cells adopt a more glycolytic metabolic profile. Our findings reveal a feedback mechanism in which metabolism-induced telomere stress engages ZSCAN4 as a protective response, thereby linking metabolic state to telomere homeostasis during early developmental progression.
    Keywords:  3D spheroids; ALT pathway; CP: stem cell research; ZSCAN4; cell state transitions; early mouse development; embryonic stem cells; lipid droplets; metabolism; pluripotency; telomeres
    DOI:  https://doi.org/10.1016/j.celrep.2025.116654
  21. Nucleic Acids Res. 2025 Nov 26. pii: gkaf1255. [Epub ahead of print]53(22):
      While compelling genetic evidence supports the role of enhancers in regulating promoter activity even over large genomic distances, it remains unclear to what extent physical proximity to promoters is required. To address this, we combined fluorescence in situ hybridization (FISH) with super-resolution microscopy and Tri-C to examine enhancer-promoter (E-P) distances and regulatory element clustering at regulated loci (Nanog, Dppa3, Dnmt3a, Sox2, Prdm14) during the transition from naive to primed pluripotency in mouse embryonic stem cells. Despite transcriptional changes of several orders of magnitude, most genes show no major alterations in median E-P distances or in the probability of multiway contacts across states. However, Tri-C reveals a weak enrichment of multiway contacts at Nanog in naive cells, where it is highly expressed. Because transcription often occurs in transient bursts within a subset of cells, we combined RNA and DNA FISH to identify active alleles. For Nanog and Dppa3, reduced E-P distances correlate with transcriptional activity. Together, these findings support models in which transcription is associated with transient E-P proximity and suggest that multiway contact formation among regulatory elements may contribute to gene regulation.
    DOI:  https://doi.org/10.1093/nar/gkaf1255
  22. PLoS Genet. 2025 Dec;21(12): e1011964
      Recent studies have linked compound heterozygous mutations in ASNA1 to progressive dilated cardiomyopathy and early infantile mortality in humans. However, the specific role of ASNA1 in cardiomyocytes and the molecular mechanisms underlying ASNA1-related cardiomyopathy remain poorly understood. Tail-anchored (TA) proteins, characterized by a single C-terminal transmembrane domain (TMD), require post-translational targeting to intracellular membranes, a process primarily mediated by the evolutionarily conserved Guided Entry of Tail-anchored proteins (GET) pathway in yeast and the Transmembrane Recognition Complex (TRC) pathway in mammals. ASNA1 (also known as TRC40 or GET3) serves as the central ATP-dependent chaperone delivering TA proteins to the endoplasmic reticulum (ER) membrane. To address ASNA1's role in the heart, we generated constitutive and inducible cardiomyocyte-specific Asna1 knockout mouse models. Constitutive Asna1 deletion during embryogenesis caused perinatal lethality with marked ventricular myocardial thinning by embryonic day 16.5, whereas inducible deletion in adult cardiomyocytes led to rapid ventricular dilation, impaired cardiac function, pathological remodeling, and early mortality. Mechanistically, ASNA1 deficiency destabilized the pre-targeting complex and reduced the expression of multiple TA protein substrates, impairing membrane trafficking and protein transport. Transcriptomic analyses revealed compensatory upregulation of genes involved in protein trafficking and Golgi-to-ER transport, reflecting maladaptive responses to disrupted vesicular transport. Collectively, our findings identify ASNA1 as a critical regulator of TA protein stability and vesicular trafficking in cardiomyocytes, whose loss disrupts cardiac proteostasis and contributes to the cardiomyopathy pathogenesis. Our work provides mechanistic insights into ASNA1-related cardiac disease and highlights potential therapeutic targets.
    DOI:  https://doi.org/10.1371/journal.pgen.1011964
  23. Cell Stem Cell. 2025 Dec 11. pii: S1934-5909(25)00410-2. [Epub ahead of print]
      The sympathetic ganglia are essential components of the nervous system that regulate various aspects of involuntary body functions. Recapitulating sympathetic ganglion development with three-dimensional (3D) organoids is challenging and has not been achieved. Here, we report a method to differentiate human pluripotent stem cells into 3D neural organoids that resemble peripheral sympathetic ganglia, producing both neurons and glial cells of the ganglia in a self-organized manner. We developed an organoid system to construct functional connections between the sympathetic ganglia and one of their peripheral targets, the heart, by fusing human sympathetic ganglion organoids (hSGOs) and heart-forming organoids. Notably, this system enables the evaluation of signaling controls (i.e., nerve growth factor [NGF] signaling) on human sympathetic-to-cardiac innervation and reveals the reciprocal impacts between the sympathetic and cardiac lineages during their co-development. Our study provides a physiologically relevant platform for understanding the development of human sympathetic ganglia, their crosstalk with peripheral targets, and related diseases.
    Keywords:  assembloids; hPSCs; heart; organoids; sympathetic ganglion
    DOI:  https://doi.org/10.1016/j.stem.2025.11.003
  24. Cell Genom. 2025 Dec 11. pii: S2666-979X(25)00357-X. [Epub ahead of print] 101101
      Large-scale single-cell atlases have revealed many aging- and disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular analyses. To address this, we developed EnrichSci-a scalable, microfluidics-free platform that combines hybridization chain reaction RNA fluorescence in situ hybridization (FISH) with combinatorial indexing to profile single-nucleus transcriptomes of target cell types with full gene-body coverage. Applied to oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.
    Keywords:  brain aging; cell type targeted; combinatorial indexing; exon dynamics; hybridization chain reaction; isoform switching; oligodendrocytes; single-cell RNA sequencing; splicing; transcriptome dynamics
    DOI:  https://doi.org/10.1016/j.xgen.2025.101101
  25. Nat Commun. 2025 Dec 09. 16(1): 11040
      DNA replication is tightly regulated to occur once per cell cycle, with the MCM2-7 helicase loaded onto replication origins only during G1-phase. In higher eukaryotes, geminin negatively regulates this process during S-, G2- and M-phases by binding the essential licensing factor CDT1. Although geminin's function is crucial for genomic stability, its inhibitory mechanism remains elusive. Here, we utilise a fully reconstituted human DNA replication licensing assay to dissect geminin's role. AlphaFold modelling provides structural insights into an N-terminal CDT1-binding helix of geminin, which proves essential for inhibition. Structural docking of the CDT1-geminin complex into the ORC-CDC6-CDT1-MCM2-7 (OCCM) assembly shows that geminin's long coiled-coil domain sterically clashes with the MCM2 C-terminus, rather than directly blocking CDT1 binding to ORC-CDC6-MCM2-7. Shortening the coiled-coil preserves geminin dimerisation and CDT1 binding but abolishes inhibition, confirming its mechanistic role. Surprisingly, geminin is not able to fully inhibit DNA licensing. However, CDK1/2-cyclin A can partially inhibit DNA licensing and, in conjunction with geminin, result in a complete block. These findings uncover geminin's steric inhibitory mechanism and suggest that a dual CDK-geminin axis controls human DNA replication.
    DOI:  https://doi.org/10.1038/s41467-025-67073-0
  26. Nat Commun. 2025 Dec 10.
      Transcription factors regulate gene expression by binding specific DNA motifs, yet only a fraction of putative sites is occupied in vivo. Intrinsically disordered regions have emerged as key contributors to promoter selectivity, but the underlying mechanisms remain incompletely understood. Here, we use single-molecule optical tweezers to dissect how disordered regions influence DNA binding by Msn2, a yeast stress-response regulator. We show that these regions power a search mechanism, facilitating initial non-specific association with DNA and promoting one-dimensional scanning toward target motifs, supported by charge-mediated interactions. Remarkably, this mechanism displays sequence sensitivity, with promoter-derived sequences enhancing both initial binding and scanning rates, demonstrating that Msn2-DNA interactions alone are sufficient to confer promoter selectivity in the absence of chromatin or cofactors. Our findings provide direct mechanistic evidence for how intrinsically disordered regions tune transcription factor search dynamics for Msn2 and expand sequence recognition beyond canonical motifs, supporting promoter selectivity in complex genomic contexts.
    DOI:  https://doi.org/10.1038/s41467-025-67217-2
  27. Nat Methods. 2025 Dec 08.
      During development, cells differentiate through a hierarchy of increasingly restricted cell types, a process that is summarized by a cell differentiation map. Recent technologies profile lineages and cell types at scale, but existing methods to infer cell differentiation maps from these data rely on heuristic models with restrictive assumptions about the developmental process. Here we introduce a quantitative framework to evaluate cell differentiation maps and develop an algorithm, called Carta, that infers an optimal differentiation map from single-cell lineage tracing data. The key insight in Carta is to balance the tradeoff between the complexity of the map and the number of unobserved cell type transitions on the lineage tree. We show that, in models of mammalian trunk development and mouse hematopoiesis, Carta identifies important features of development that are not revealed by other methods, including convergent differentiation of cell types, progenitor differentiation dynamics and new intermediate progenitors.
    DOI:  https://doi.org/10.1038/s41592-025-02903-z
  28. Nat Commun. 2025 Dec 11.
      The type I interferon response is inactive during early mammalian development and becomes functional only after gastrulation. As a result, the totipotent and pluripotent embryonic stages remain susceptible to pathogens, including viruses. Here, we demonstrate that pluripotent mouse embryonic stem cells suppress the RIG-I-like receptor sensing pathway by silencing the expression of the double stranded RNA sensor MDA5. This silencing is necessary to avoid the recognition of double stranded RNAs of endogenous origin, which accumulate in mouse embryonic stem cells. Reintroducing MDA5 results in recognition of these endogenous double stranded RNAs and triggers the activation of the IFN response through IRF3. The production of interferon alters the differentiation ability of mouse embryonic stem cells, and affects the pluripotency gene expression programme, as shown by epigenetic, transcriptomic and proteomic analyses. Further, we show that zebrafish also repress MDA5 expression in early development and lack early-stage interferon activation, and that inducing double-stranded RNA-mediated signalling at this stage results in developmental defects. Altogether, we conclude that silencing the RIG-I-like receptor pathway during early development is important in preventing aberrant immune recognition of endogenous double stranded RNAs, safeguarding normal development.
    DOI:  https://doi.org/10.1038/s41467-025-66352-0
  29. Nat Commun. 2025 Dec 12.
      Mechanical forces are essential for organ function, but excessive or dysregulated forces can promote pathologic conditions. In asthma, bronchoconstriction narrows the airway, compressing the airway epithelium and activating mechanotransduction, yet key regulators of mechanotransduction remain unclear. Here we show that Hic-5, a focal adhesion adaptor, is a key regulator of epithelial mechanotransduction. In human airway epithelial cells at air-liquid interface exposed to mechanical compression that mimics bronchoconstriction, we find that compression induces Hic-5 expression in airway basal cells. We further validated these in vitro findings by reanalyzing single-cell RNA-seq data from patients with asthma undergoing bronchoconstriction after allergen challenge, which revealed increased Hic-5 expression in airway basal cells. Hic-5 knockdown in human airway epithelial cells markedly attenuates mechanoresponses to compression, including stress fiber formation, differential gene expression, and increased secretion of endothelin-1 (ET-1). Through secretion of ET-1, a potent bronchoconstrictor, Hic-5 drives epithelial mechanotransduction and promotes a feed-forward cycle of bronchoconstriction, thereby highlighting dysregulated mechanical forces as active drivers of human disease.
    DOI:  https://doi.org/10.1038/s41467-025-67210-9
  30. Nature. 2025 Dec 10.
      Microfold (M) cells are rare intestinal epithelial cells that reside in the follicle-associated epithelium of Peyer's patches1. M cells transport luminal antigens to submucosal antigen-presenting cells2,3. These insights primarily derive from transmission electron microscopy and studies using genetically modified mice2-4. Here we establish an intestinal organoid model to study human M cells and reconstruct the differentiation trajectory of M cells through transcriptome profiling. The results indicate that as well as facilitating luminal antigen transport, human M cells also directly present antigens via the class II major histocompatibility complex (MHC-II). Notably, the related enterocytes only express MHC-II in chronic inflammatory states and do not express typical dendritic cell markers. Human M cells physiologically express a gene profile that resembles that of dendritic cells. Similar to dendritic cells, M cell development is induced by RANKL and CSF2 and requires the transcription factors SPIB and RUNX2. HLA-DQ2.5 M cells process and present gluten antigen as demonstrated in organoid-T cell co-culture assays. These findings suggest that M cells may have a central role in coeliac disease.
    DOI:  https://doi.org/10.1038/s41586-025-09829-8
  31. Nat Commun. 2025 Dec 12. 16(1): 11085
      During mitosis, near-spherical chromosomes reconfigure into rod-like structures to ensure their accurate segregation to daughter cells. We explore here, the interplay between the nonequilibrium activity of molecular motors in determining the chromosomal organization in mitosis and its characteristic symmetry-breaking events. We present a hybrid motorized chromosome model that highlights the distinct roles of condensin I and II in shaping mitotic chromosomes. Guided by experimental observations, the simulations suggest that condensin II facilitates large-scale scaffold formation, while condensin I is paramount in local helical loop arrangement. Together, these two distinct grappling motors establish the hierarchical helical structure characteristic of mitotic chromosomes, which exhibit striking local and, sometimes global, chirality and contribute to the robust mechanical properties of mitotic chromosomes. Accompanying the emergence of rigidity, the model provides mechanisms of forming defects, including perversions and entanglements, and shows how these may be partially resolved through condensin activity and topoisomerase action. This framework bridges coarse-grained energy landscape models of chromosome dynamics and non-equilibrium molecular dynamics, advancing the understanding of chromosome organization during cell division and beyond.
    DOI:  https://doi.org/10.1038/s41467-025-66025-y
  32. Nature. 2025 Dec 10.
      All genomes have mobile genetic segments called transposable elements (TEs)1. Here we describe a system, which we term SOS splicing, that protects Caenorhabditis elegans and human genes against DNA-transposon-mediated disruption by excising these TEs from host mRNAs. SOS splicing, which seems to operate independently of the spliceosome, is a pattern-recognition system triggered by the base-pairing of inverted terminal repeat elements, which are a defining feature of DNA transposons. We identify three factors required for SOS splicing in both C. elegans and human cells: AKAP17A, which binds TE-containing mRNAs; the RNA ligase RTCB; and CAAP1, which bridges RTCB and AKAP17A to allow RTCB to ligate mRNA fragments generated by TE excision. We propose that SOS splicing is a previously undescribed conserved and RNA-structure-directed mode of mRNA splicing, and that an identified function of SOS splicing is to genetically buffer animals from the deleterious effects of DNA-transposon-mediated gene perturbation.
    DOI:  https://doi.org/10.1038/s41586-025-09853-8
  33. Nat Commun. 2025 Dec 06. 16(1): 10950
      Integrin-mediated cell adhesion and mechanotransduction are considered key innovations in animal evolution. Here, we show that these processes represent a specialization of an evolutionarily conserved force coupling mechanism that originated in unicellular organisms and is mediated by the actin-binding protein talin. In contrast to heterodimeric integrin receptors, talin is widely distributed in unicellular organisms, including amoebae. By comparing the molecular mechanics of talin-A from amoeboid cells with that of mammalian talin-1, we uncover a conserved role for talin in transmitting pN-scale forces, even in unicellular organisms lacking canonical integrin receptors but expressing the functional homologue SibA. Our data indicate that the critical evolutionary steps towards integrin-mediated cell adhesion in metazoan organisms were the specialization of talin as an adaptor protein allowing the activation of integrin receptors, the regulation of biochemical signaling by paxillin, FAK and YAP, and the control of cell adhesion turnover by KANK recruitment. Collectively, these experiments suggest a central but thus far underappreciated role for talin in the evolution of eukaryotic cell-substrate adhesion and force transmission.
    DOI:  https://doi.org/10.1038/s41467-025-67354-8
  34. Nature. 2025 Dec 10.
      Adipose tissue maintains energy homeostasis by storing lipids during nutrient surplus and releasing them through lipolysis in times of energy demand1,2. While lipolysis is essential for short-term metabolic adaptation, prolonged metabolic stress requires adaptive changes that preserve energy reserves2,3. Here we report that β3-adrenergic activation of adipocytes induces a transient and depot-specific infiltration of neutrophils into white adipose tissue (WAT), particularly in lipid-rich visceral WAT. Neutrophil recruitment requires the stimulation of both lipolysis and p38 MAPK in adipocytes, and is mediated by the secretion of leukotriene B4. Recruited neutrophils undergo activation in situ, and locally secrete IL-1β, which suppresses lipolysis and limits excessive energy loss. Neutrophil depletion or blockade of IL-1β production increases lipolysis, leading to reduced WAT mass after repeated β3-adrenergic stimulation. Together, these findings reveal a role of neutrophil-derived IL-1β in preserving lipid stores during metabolic stress, highlighting a physiological function of innate immune cells in limiting lipid loss and maintaining energy homeostasis.
    DOI:  https://doi.org/10.1038/s41586-025-09839-6