bims-ginsta Biomed News
on Genome instability
Issue of 2026–05–24
37 papers selected by
Jinrong Hu, National University of Singapore



  1. Cell. 2026 May 19. pii: S0092-8674(26)00508-8. [Epub ahead of print]
      The mammalian genome is safeguarded within the confines of the interphase nucleus. However, genomic instability can trigger the mislocalization of nuclear DNA to the cytoplasm within micronuclei or as fragmented chromosomes. Beyond activating cell-autonomous signaling programs, whether such cytoplasmic DNA can elicit non-cell-autonomous consequences to nearby cells remains unclear. Here, we show that cytoplasmic DNAs undergo intercellular transfer through contact-dependent, cytoskeleton-based nanotube structures connecting adjacent human cells. Diverse sources of genomic instability-including exposure to mitotic spindle poisons, ionizing radiation, and Cas9-induced chromosome breakage-promote nanotube-mediated DNA transfer in both cancerous and non-cancerous cells. Transferred DNA fragments are stably inherited as functional extrachromosomal genetic elements in the recipient host genome, thereby conferring heritable phenotypic traits to the recipient cell. Our findings uncover a horizontal gene transfer-like mechanism through which direct cell-cell contact can propagate genomic instability and reshape mammalian genomes.
    Keywords:  DNA damage; chromothripsis; cytoplasmic DNA; ecDNA; genomic instability; horizontal gene transfer; intercellular transfer; micronuclei; mitosis; tunneling nanotubes
    DOI:  https://doi.org/10.1016/j.cell.2026.04.041
  2. Dev Cell. 2026 May 21. pii: S1534-5807(26)00160-7. [Epub ahead of print]
      Embryo shape is determined by cell mechanics, intercellular interactions, and geometrical constraints. Models based on surface tensions at cell interfaces can predict 3D static cellular arrangements within aggregates. However, predicting the dynamics of such arrangements is challenging because temporal changes in tension are unknown. Here, we characterize the spatiotemporal changes in cellular tensions shaping early nematode embryos using atomic force microscopy (AFM), live microscopy, and tension inference. Using excoriated embryos, we validate a hybrid inference pipeline that temporally calibrates relative inferred tensions using cortical myosin enrichment and absolute tensions obtained by AFM. Applying this approach to embryos within their native shell provides a spatiotemporal map of absolute tensions. This reveals that ABa, ABp, and EMS compaction is driven by increased cell-medium tension, whereas P2's initial exclusion is due to high cell-cell contact tension. We further uncover a direct contribution of cadherins to cell-cell contact tension, comparable in magnitude to cadherins' indirect contribution via actomyosin regulation.
    Keywords:  C. elegans embryo; cadherin; foam simulation; myosin; surface tension; tension inference
    DOI:  https://doi.org/10.1016/j.devcel.2026.04.013
  3. Proc Natl Acad Sci U S A. 2026 May 26. 123(21): e2534871123
      Bleb-based cell migration involves rapid plasma membrane expansion driven by intracellular pressure. How the membrane reorganizes its curvature and protein composition during this process remains unclear. Here, we identify a distinct inward membrane structure, termed the sub-bleb invagination (SBI), that forms de novo at the bleb base during expansion. SBIs display strong positive curvature and transiently sequester curvature-preferring integral membrane proteins such as Caveolin-1 and Piezo1 without endocytosis. Live-cell imaging shows that these proteins transiently accumulate at the SBIs in concert with bleb growth, indicating that bleb expansion dynamically redistributes membrane curvature and protein localization. Overexpression of curvature-preferring proteins markedly inhibited bleb enlargement and induced the aberrant formation of SBI-like membrane invaginations, suggesting that their excessive accumulation limits the membrane from unfurling. Our findings reveal a curvature-based mechanism for membrane protein sorting during bleb expansion and highlight how the interplay between membrane curvature and integral membrane protein organization shapes PM dynamics.
    Keywords:  Caveolin-1; bleb; curvature-preferring proteins; membrane curvature; plasma membrane invagination
    DOI:  https://doi.org/10.1073/pnas.2534871123
  4. Nat Commun. 2026 May 21.
      Cell competition is a fundamental surveillance mechanism that preserves epithelial integrity by eliminating aberrant "loser" cells through interactions with surrounding "winner" cells. However, how winner cells sense and eliminate transformed neighbours remains poorly understood. Here, using a synNotch-based transcriptomic screen, we identify a mechanosensor-mechanotransducer axis linking the actin crosslinker filamin to the ETV4/5-PRKG2 pathway that mediates extrusion of oncogenically transformed cells through cell competition. Within an epithelial monolayer, transformed cells increase their volume, inducing membrane stretching. In adjacent normal cells, filamin senses the increased membrane tension and triggers activation of ETV4/5. Activated ETV4/5 then upregulate PRKG2, which promotes volume expansion of normal cells, consequently pushing back and driving the extrusion of transformed cells. These findings reveal that dynamic changes in cell volume can trigger mechanotransduction-driven cell competition, uncovering a fundamental pathway by which epithelial tissues maintain homoeostasis and defend against oncogenic transformation.
    DOI:  https://doi.org/10.1038/s41467-026-73504-3
  5. Dev Cell. 2026 May 18. pii: S1534-5807(26)00158-9. [Epub ahead of print]
      Stem cell proliferation drives tissue formation and homeostasis. Whether and how niche cell mechanics act in vivo to control this process remains unclear. Here, we identify a triad of cell adhesion molecules from the immunoglobulin superfamily, which physically link neural stem cells (NSCs) to their glial niche in Drosophila. Disrupting this connection increases actomyosin activation and tensile forces in the glial cells, reciprocally causing mechanical stress in NSCs. This promotes lamin accumulation, which causes nuclear deformation and acts as a protective response safeguarding NSC mitosis. However, this response is insufficient, and NSCs display abnormal spindle morphologies and impaired mitotic progression. Ultimately, the loss of NSC and niche mechanical interplay compromises NSC proliferative potential and genome integrity. This study uncovers a fundamental role for niche cell mechanics and members of the immunoglobulin superfamily, acting as mechanoregulators, in controlling stem cell proliferation.
    Keywords:  Drosophila melanogaster; actomyosin complex; immunoglobulin superfamily of cell adhesion molecules; lamin; mechanics; mitosis; neural stem cell; niche; nuclear mechanotransduction; spindle
    DOI:  https://doi.org/10.1016/j.devcel.2026.04.011
  6. Trends Cell Biol. 2026 May 18. pii: S0962-8924(26)00067-X. [Epub ahead of print]
      Cell competition is a highly conserved mechanism through which cells with lower fitness levels than surrounding cells are actively removed from tissues. Differences in fitness may result from intrinsic tissue heterogeneity or be caused by differentiation, infections, or mutations. The resulting competition dynamics act as a key regulator of various biological processes during development and homeostasis. The underlying mechanical factors often remain unclear. Here, we discuss the biophysical principles of cell competition and elimination via extrusion or delamination. Recent advances have uncovered how fitness is determined by cellular mechanical properties, which can regulate winning or losing, and how cells use forces to outcompete each other. Furthermore, forces can influence the fate and direction of eliminated loser cells, which govern functional tissue development and disease progression.
    Keywords:  cell competition; cell extrusion; epithelia; force transmission; tissue mechanics
    DOI:  https://doi.org/10.1016/j.tcb.2026.04.009
  7. Mol Cell. 2026 May 22. pii: S1097-2765(26)00271-6. [Epub ahead of print]
      Somatic stem cells are characterized by their low overall protein-synthesis rates, a feature implicated in driving their stemness. However, how aging reshapes the translational landscape of stem cells remains poorly understood. Here, we present an in vivo single-cell ribosome profiling strategy to monitor tissue-wide translational landscapes of the epidermis during aging. By implementing ribosomal elongation-inhibited cell isolation and switching to RNase I, we expand the applicability of single-cell ribosome profiling to in vivo systems and facilitate the evaluation of triplet periodicity, a hallmark of high-quality data. Leveraging this strategy, we document the in vivo translational landscapes of the major epidermal cell types, outline cell-type-specific translational efficiencies, and identify a pronounced translational reprogramming of AP-1 subunits specifically in aged epidermal stem cells. Our study illustrates the power of in vivo single-cell ribosome profiling to map cell-type-specific translational programs and offers a scalable strategy for tissue-wide interrogation of translational landscapes.
    Keywords:  AP-1; aging; epidermis; mRNA translation; ribosome profiling; single-cell biology; translational control
    DOI:  https://doi.org/10.1016/j.molcel.2026.04.017
  8. Nat Commun. 2026 May 21.
      Post-myocardial infarction remodeling is a major cause of heart failure, with contributions from multiple organs. Brown adipose tissue protects against cardiovascular disease, but the mediators of brown adipose tissue-heart crosstalk and their roles in cardiac remodeling remain elusive. Here, we show that mitochondria-derived vesicles from brown adipose tissue transfer to cardiac macrophages and attenuate pathological remodeling via anti-inflammatory effects. Vesicles containing mitochondrial membranes, rather than mitochondrial matrix, mobilize from brown adipose tissue to the heart in response to stress. VPS35 translocation to mitochondria drives protein packaging into mitochondria-derived vesicles for secretion through extracellular vesicle trafficking machinery. Becn1 deficiency impairs VPS35 translocation, alters mitochondria-derived vesicle cargo, and abolishes brown adipose tissue-mediated cardioprotection. Proteomics identifies mitochondrial respiratory chain complex V as a hallmark of protective mitochondria-derived vesicles. These vesicles enhance reparative cytokine production and oxidative phosphorylation rewiring in macrophages. Purified mitochondria-derived vesicles markedly improve remodeling in male mice. Our study uncovers an interorgan transfer of bioenergetic units that contributes to tissue repair.
    DOI:  https://doi.org/10.1038/s41467-026-73388-3
  9. bioRxiv. 2026 May 09. pii: 2026.05.07.722278. [Epub ahead of print]
      A comprehensive cell fate map of mammalian embryogenesis has remained out of reach due to the scale, cellular diversity, and non-deterministic nature of development in utero . Here, we use PEtracer to continuously install heritable genetic marks as cells divide, reconstructing lineage trees that resolve ∼75% of cell divisions across >1.5 million cells from 16 mouse embryos collected at half-day intervals from E7.5-E10.0. We pair these trees with deep transcriptional profiling to chart the landscape of cell fate decisions during gastrulation and early organogenesis. Using these data, we quantify cell fate biases, restriction timing, progenitor pool sizes, and lineage relationships across the embryo, revealing strikingly reproducible lineage architecture across replicate embryos despite the regulative flexibility of mammalian development. We further show how lineage, spatial position, and signaling jointly determine fate outcomes and timing, with their relative influence varying by tissue. This dataset provides a quantitative framework for understanding cell fate specification and a lineage-resolved reference for generating and contextualizing developmental hypotheses at organismal scale.
    DOI:  https://doi.org/10.64898/2026.05.07.722278
  10. Nat Commun. 2026 May 19.
      Accurate genome duplication requires tight-regulation of replication fork progression, and disruptions to this process are a major source of genomic instability, yet how fork dynamics are controlled during unperturbed S-phase remains unclear. We found replication forks elongate slowly in early S (ES) and faster in late S, independent of transcription or nucleotide availability. Elevated origin firing coupled with low TOP2A in ES generates torsional stress, causing replisome uncoupling, reduced fork speed, and basal ATR-CHK1 activation. Overexpression of TOP2A enhances fork speed and reduces replication stress in ES. Thus, TOP2A is a limiting replication factor during unperturbed ES, and basal ATR-CHK1 signaling is driven by transient replisome uncoupling. Also, TOP2A overexpression suppresses oncogene-driven replication stress. Given that TOP2A is frequently upregulated in cancers, it may function as a compensatory response to oncogene-induced replication stress. Together, these findings establish TOP2A as a central regulator of replication fork dynamics.
    DOI:  https://doi.org/10.1038/s41467-026-73330-7
  11. Nat Cell Biol. 2026 May 20.
      Trafficking of secretory proteins from the endoplasmic reticulum (ER) to the Golgi apparatus comprises the first, essential steps towards the appropriate localization of 30% of eukaryotic proteins. Coat protein complexes COPII and COPI are involved in the forward and retrograde transport of cargo and cargo receptors between the ER and the Golgi, respectively. Although COPII forms coated vesicles in vitro, the biogenesis, morphology and organization of transport carriers in mammalian cells is subject to debate. Here we use in situ cryo-electron tomography and super-resolution fluorescence microscopy to reveal the molecular architecture of ER exit sites in human cells that were not perturbed with drugs, temperature blocks or overexpression systems. We visualize ribosome-exclusion zones enriched with COPII- and COPI-coated vesicles and thus resolve the debate regarding the existence of COPII-coated vesicles. COPII vesicles derive from ER membranes, whereas COPI vesicles originate from vesicular-tubular clusters that constitute the ER-Golgi intermediate compartment (ERGIC). We quantify coated vesicle morphology and positioning with respect to other ER exit site components, providing a molecular description of the organization of the mammalian early secretory pathway.
    DOI:  https://doi.org/10.1038/s41556-026-01964-2
  12. Cell Genom. 2026 May 18. pii: S2666-979X(26)00115-1. [Epub ahead of print] 101253
      Mammalian genomes host a diverse array of RNAs, including protein-coding and noncoding transcripts. However, the functional roles of most long noncoding RNAs (lncRNAs) remain elusive. Using RNA-targeting CRISPR-Cas13 screens, we probed how the loss of ∼5,500 lncRNAs impacts cell fitness across five human cell lines and identified 788 lncRNAs with context-specific or broad essentiality. We confirm their essentiality through individual perturbations and find that the majority of essential lncRNAs operate independently of their nearest protein-coding genes. Using transcriptome profiling in single cells, we discover that loss of essential lncRNAs impairs cell cycle progression and drives apoptosis. Many essential lncRNAs demonstrate dynamic expression across tissues during development. Using ∼9,000 primary tumors, we pinpoint those lncRNAs whose expression in tumors correlates with survival, yielding new biomarkers and potential therapeutic targets. This transcriptome-wide survey of functional lncRNAs advances our understanding of noncoding transcripts and demonstrates the potential of transcriptome-scale noncoding screens with Cas13.
    Keywords:  CRISPR-Cas13; MALAT1; MIR17HG; Noncoding RNA; RNA targeting; essential genes; human development; lncRNA; transcriptome-scale; tumor biomarkers
    DOI:  https://doi.org/10.1016/j.xgen.2026.101253
  13. Nat Aging. 2026 May;6(5): 987-1006
      Aging impairs coordinated organelle dynamics essential for lipid metabolism, causing a decline in intracellular metabolic flexibility. However, the drivers of organelle collapse and their temporal order remain unclear. Here we identify peroxisomal function as a critical regulator of metabolic flexibility during youth and low-energy states. Using Caenorhabditis elegans, we show that fasting robustly induces peroxisomal function in youth, whereas this response is blunted during aging. Loss of peroxisomal import via PRX-5 declines over age, causing pathological lipid droplet expansion, dysfunctional mitochondrial bioenergetics and metabolic inflexibility. Although targeted PRX-5 degradation recapitulates metabolic aging, its overexpression preserves lipid dynamics and mitochondrial integrity. Notably, dietary restriction maintains peroxisomal pathways and organelle coordination into late life and peroxisomal function causally underpins dietary restriction-mediated longevity. Our findings highlight peroxisomes as central upstream regulators of a dynamic interorganelle cascade driving metabolic plasticity and highlight peroxisomal maintenance as a key determinant of metabolic flexibility during aging.
    DOI:  https://doi.org/10.1038/s43587-026-01122-1
  14. Nat Rev Mol Cell Biol. 2026 May 19.
      The nucleolus is the site of ribosomal RNA synthesis and ribosome biogenesis. Advances in high-resolution imaging and next-generation sequencing have unveiled unprecedented details of its intricate architecture and dynamic organization. In this Review, we focus on the dynamic organization of mammalian nucleoli, while drawing selective comparisons with other organisms to highlight conserved and divergent principles of nucleolar organization. We discuss recent progress in deciphering the multilayered compartments of nucleoli, the physical principles driving their organization and dynamics, and their functional interplay during stepwise ribosomal RNA processing, ribosome assembly and maintenance of compartment integrity. We also discuss how disruptions of nucleolar structure-function relationships can drive cellular stresses and diseases, offering new opportunities for therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41580-026-00975-z
  15. Nat Commun. 2026 May 16.
      For tissues to spread, they must deform while staying intact. How spreading tissues balance flexibility with integrity is not yet well understood. Here, we show that keratin intermediate filaments adapt tissue mechanical resilience to the stresses arising in epithelial tissues during spreading. By analyzing the expansion of the enveloping cell layer (EVL) over the yolk cell in zebrafish embryos in vivo, we find that keratin network maturation in EVL cells is promoted by stresses building up within the spreading tissue. Through genetic interference and tissue rheology experiments, complemented by a vertex model with mechanochemical feedback, we demonstrate that stress-induced keratin network maturation in the EVL increases tissue viscosity, to prevent tissue rupture. Further, keratins are required in the yolk cell for mechanosensitive actomyosin network contraction and flow, the forces pulling the EVL. These dual mechanosensitive functions of keratins enable a balance between pulling force production and EVL mechanical resilience, ensuring uniform and robust tissue spreading.
    DOI:  https://doi.org/10.1038/s41467-026-72366-z
  16. bioRxiv. 2026 May 09. pii: 2026.05.07.723638. [Epub ahead of print]
      The ATR-enforced S/G2 checkpoint activates during DNA replication to restrain CDK1-dependent phosphorylation of FOXM1 and subsequent transactivation of the G2/M gene network until the end of S phase. However, the extent to which this checkpoint ensures the completion of DNA replication and whether it safeguards genomic integrity has remained unknown. Here, we induce S/G2 checkpoint failure throughout S phase in non-malignant human epithelial cells using multiple ATR pathway inhibitors. Consequently, the mitotic kinase complex cyclin B1-CDK1 prematurely shuts-down the DNA replication program, preventing the completion of genome duplication. In turn, this leads to the retention of inactive replisomes on chromatin and unfired origins into the G2 phase, which induce subsequent accumulation of pan-nuclear ᵧH2AX and mitotic failure. Collectively, these findings indicate the S/G2 checkpoint ensures replication completion and genome stability.
    DOI:  https://doi.org/10.64898/2026.05.07.723638
  17. Nature. 2026 May 20.
      L-2-Hydroxyglutarate (L-2-HG) is a low-abundance metabolite in mammals because the mitochondrial enzyme L-2-HG dehydrogenase (L2HGDH) oxidizes L-2-HG to 2-oxoglutarate (2-OG) to prevent its accumulation1. In humans, a lack of L2HGDH activity leads to L-2-HG accumulation and causes L-2-hydroxyglutaric aciduria2. Thus, L-2-HG is often classified as a toxic metabolite2-5. However, whether L-2-HG has any physiological function is unclear. Here we investigate whether L-2-HG qualifies as a physiological signalling metabolite by testing three criteria: regulated levels, defined molecular targets and a measurable physiological function. We report that an increase in mitochondrial NADH/NAD+ ratio drives malate dehydrogenase 2 (MDH2) to reduce 2-OG into L-2-HG. Moreover, L2HGDH oxidizes L-2-HG back to 2-OG in the mitochondrial matrix without requiring a functional electron transport chain. Through proteome integral solubility alteration assays, we show that the KDM4 family of H3K9 demethylases are L-2-HG-responsive targets. L-2-HG represses the nascent transcription of specific genes in mouse embryonic stem cells and increases H3K9me3 (a repressive histone mark) at these loci. In vivo, early embryonic L2HGDH overexpression in mice systemically reduces L-2-HG levels, impairs postnatal growth, causes mortality and produces selective functional and histological renal vulnerabilities. In postnatal kidneys, this reduction in L-2-HG causes H3K9me3 loss at L1MdTf retrotransposons and their derepression, which coincides with the activation of the integrated stress response and inflammation pathways. Our findings establish mitochondrial L-2-HG as a physiological signalling metabolite and indicate that metabolites previously regarded as toxic may also have crucial physiological functions.
    DOI:  https://doi.org/10.1038/s41586-026-10564-x
  18. Cell. 2026 May 15. pii: S0092-8674(26)00471-X. [Epub ahead of print]
      Spermatogenesis features the seminiferous epithelial cycle, a periodic progression of germ-cell differentiation along the seminiferous tubules. Using seqFISH+ spatial transcriptomics, we profiled 2,653 genes in 867,062 mouse testis cells, revealing tubule-level transcriptional patterns that recapitulate the cycle and enable high-resolution temporal mapping of cells. Unlike other somatic cells, Sertoli cells exhibit a cyclic transcriptional profile synchronized with spermatogenesis. This cyclicity persists in germ-cell-depleted testes (busulfan and W/Wv), although with gene-specific dephasing and reduced amplitude, supporting an intrinsic Sertoli cyclic program. We identify retinoic acid (RA) as a permissive signal: germ-cell-depleted Sertoli cells cycle RA enzymes, while inhibiting RA synthesis via WIN 18,446 arrests them mid-cycle. Ligand-receptor analysis reveals bidirectional germ-Sertoli signaling. Notably, Wnt inhibition with LGK974 partially recapitulates germ-cell-depletion dephasing and amplitude changes. These findings support an integrative model where an intrinsic Sertoli program maintains baseline periodicity, while germ-cell signals refine the cycle to coordinate spermatogenesis.
    Keywords:  Sertoli cells; Wnt signaling; biological oscillator; blood-testis barrier; cell synchronization; cell-cell signaling; mouse testis; permissive signal; retinoic acid; seminiferous epithelial cycle; seqFISH+; spatial biology; spatial transcriptomics; spermatogenesis; temporal dynamics
    DOI:  https://doi.org/10.1016/j.cell.2026.04.036
  19. bioRxiv. 2026 May 05. pii: 2026.05.01.722310. [Epub ahead of print]
      The formation of functional corneal endothelial cells during development requires tight coordination between tissue-scale growth and cell-scale organization, yet how these processes are integrated in three dimensions remains poorly understood. Here, we combine high-resolution confocal imaging with quantitative analysis to reconstruct the morphogenesis of the chick corneal endothelium across embryonic development. Using a pipeline integrating 3D nuclear segmentation, Voronoi-based topological mapping, and spatial statistics, we link macroscopic globe expansion to single-cell geometry and lattice organization. We identify a multiphasic relationship between tissue growth and cell density, driven by temporal decoupling of organ expansion and proliferation. During early development, rapid globe expansion induces cellular stretching and spatial heterogeneity, followed by a phase of density accumulation and geometric refinement. Despite these dynamic conditions, the endothelial sheet maintains a robust monolayer architecture with minimal z-axis stratification. Quantitative topological analysis reveals that hexagonal packing is preserved from early stages and progressively refined through reduction of area variability and spatial clustering. Nearest-neighbor and Clark-Evans analyses demonstrate a transition from localized clustering to a more uniform spatial distribution, consistent with increasing packing regularity. Transient out-of-plane deviations coincide with key mechanical transitions, suggesting a role for 3D remodeling in accommodating mechanical stress. Concomitantly, junctional and cytoskeletal organization undergo progressive maturation. N-cadherin is established early at cell-cell interfaces, while Zonula Occludens-1 (ZO-1) transitions from diffuse localization to apically enriched tight junctions aligned with cortical actin. In parallel, microtubule organization becomes increasingly polarized to the apical domain, coinciding with the emergence of primary cilia. Together, these changes reflect coordinated establishment of epithelial polarity, barrier function, and mechanical stability. Overall, our study provides a multiscale, imaging-driven framework for understanding how epithelial tissues achieve and maintain geometric order under mechanical strain, establishing the corneal endothelium as an exemplar for linking developmental mechanics, 3D architecture, and epithelial topology.
    Summary Statement: Using 3D imaging and quantitative analysis, this work reveals how corneal endothelial cells stay organized and form a regular pattern during growth, despite ongoing changes in tissue size and shape.
    DOI:  https://doi.org/10.64898/2026.05.01.722310
  20. Nature. 2026 May 20.
      Quasisymmetric icosahedral viral capsids achieve larger sizes than possible with strictly symmetric icosahedra by tessellating pentagons and hexagons using a single subunit that adopts different conformations in symmetrically non-equivalent locations1,2. Recapitulating such quasisymmetric architectures through computational design is a considerable challenge in nanomaterials engineering. Here we introduce a computational design strategy based on geometric frustration to generate two-component, quasisymmetric protein cages with customizable properties. We designed complementary trimeric and dimeric protein components that co-assemble into positively curved local hexagonal assemblies. Hexagonal lattices cannot tile spherical surfaces; instead, the components form closed sphere-like cage assemblies through incorporation of curvature-inducing pentagonal defects, as evidenced by electron microscopy. By designing dimers that encode different local curvatures, we programmed cage dimensions ranging from 40 to over 200 nm in diameter and with molecular weights from 2 MDa to over 50 MDa, comparable with natural virus capsids. We further functionalized these large cages with additional protein domains to enable ribonucleoprotein cargo loading and cellular uptake. Fluorescently labelled cage assemblies expressed in mammalian cells function as rheological probes and cargo recruiters, enabling a systematic study of size-dependent cytoplasmic diffusion and protein localization. Thus, the quasi-symmetry that has long fascinated structural biologists can now be achieved by computational protein design, with immediate applications to biologics delivery and molecular cell biology.
    DOI:  https://doi.org/10.1038/s41586-026-10464-0
  21. Nat Commun. 2026 May 20.
      Eukaryotic cells license far more potential replication origins than they use, but how origin firing rate is tuned in S phase, especially under replication stress, remains unclear. Here, we identify a regulatory mechanism by which cyclin-dependent kinase (CDK) activity controls the abundance and chromatin recruitment of the origin firing factors TRESLIN and MTBP to promote dormant origin activation. Inhibition of WEE1 kinase during S phase increases CDK activity, which blocks the PCNA-CRL4CDT2-dependent degradation of TRESLIN and enhances its chromatin association along with MTBP. This increased loading is required for elevated helicase recruitment and DNA synthesis under CDK-hyperactive conditions. We define a sequence within TRESLIN required for its degradation and show that TRESLIN stabilization is necessary but not sufficient for CDK-driven origin firing. Replication stress regulates TRESLIN destruction in a dose- and time-dependent manner. Acute high-dose hydroxyurea suppresses CDK activity and reduces chromatin-bound TRESLIN, whereas prolonged low-dose hydroxyurea is accompanied by elevated CDK activity and increased chromatin loading of TRESLIN-MTBP and CDC45. Altogether, these findings uncover a control point in replication origin usage with implications for genome stability and therapeutic kinase inhibition.
    DOI:  https://doi.org/10.1038/s41467-026-73333-4
  22. J Cell Sci. 2026 May 15. pii: jcs264498. [Epub ahead of print]139(10):
      Polyploidy is a widespread phenomenon in development and evolution and is frequently associated with altered cellular physiology and developmental robustness. However, how genome doubling influences an embryonic robustness to environmental stress remains poorly understood. Here, we investigated developmental traits and osmotic responses in tetraploid Caenorhabditis elegans embryos. Tetraploid animals exhibited increased body and tissue sizes and produced larger embryos than diploids, accompanied by moderately delayed development and partial embryonic arrest. When exposed to a range of osmotic environments, both diploid and tetraploid embryos swelled or shrank in response to external osmolarity. Strikingly, tetraploid embryos at the early stage maintained normal cell division across a broader range of osmotic conditions than diploids. Quantitative analyses further revealed that tetraploid embryos exhibited reduced cytoplasmic mass density, primarily reflecting lower protein concentration, while lipid and RNA levels remain unaffected. These compositional differences likely buffer cellular size fluctuations and underlie the enhanced osmotic tolerance of tetraploid embryos. Together, our findings demonstrate that genome doubling reshapes embryonic cellular physiology in a non-proportional manner to ploidy, thereby enhancing robustness during early development.
    DOI:  https://doi.org/10.1242/jcs.264498
  23. Nucleic Acids Res. 2026 May 05. pii: gkag350. [Epub ahead of print]54(9):
      Ribosomal DNA (rDNA) arrays are among the most highly transcribed repetitive regions of the genome and therefore require specialized mechanisms to maintain their stability. The nucleolar DNA damage response (n-DDR) safeguards rDNA integrity and is coordinated by the repair scaffold TOPBP1 and the fibrillar center (FC) protein Treacle. Here, we show that Treacle promotes phase separation of TOPBP1 within the FC to establish a spatially confined signaling platform that amplifies nucleolar DDR signaling and coordinates rDNA repair pathway engagement. Using an inducible TOPBP1 oligomerization system together with physiological models of rDNA damage, we demonstrate that phosphorylation of Treacle by CK2 and ATR/ATM enables its interaction with TOPBP1 and nucleates TOPBP1 condensation in the nucleolus. Functionally, Treacle-dependent condensation promotes robust ATR/ATM activation, γH2AX signaling, and recruitment of DNA repair factors. Disruption of this process does not impair the initial removal of rDNA double-strand breaks but shifts repair toward rapid DNA-PK-dependent nonhomologous end joining while attenuating ATR/ATM signaling and reducing engagement of homologous recombination-associated pathways. Treacle-knockout cells exhibit accelerated early rDNA repair but incomplete damage resolution at later stages. Together, our findings identify Treacle-dependent TOPBP1 condensation as a nucleolar signaling platform that promotes accurate maintenance of highly repetitive rDNA arrays.
    DOI:  https://doi.org/10.1093/nar/gkag350
  24. Nat Aging. 2026 May 19.
      DNA methylation changes are reliable biomarkers of aging, but the driving mechanisms remain poorly understood. Here we present SCARLET (Stem Cells and Age-ReLated Epigenetic Trajectories), a parsimonious mathematical model that describes how methylation changes in blood arise and propagate through hematopoietic stem cell divisions. Using a large human cohort, we demonstrate that seemingly distinct age-related methylation patterns can be explained by a unifying mechanistic model. We show that SCARLET captures known drivers of epigenetic aging, with accelerated individuals showing reduced ratios of stem cell pool size to division rate (N/s). Applying SCARLET to methylation data from 11 mammalian species reveals that N/s scales with maximum lifespan, suggesting that evolutionary adjustments to stem cell dynamics, rather than epigenetic maintenance efficiency, drive the previously observed relationship between methylation rates and lifespan. Our findings provide a quantitative framework for understanding epigenetic aging and suggest that stem cell dynamics may be a key driver of aging across mammals.
    DOI:  https://doi.org/10.1038/s43587-026-01125-y
  25. Genome Biol. 2026 May 23.
      Resistance to cancer therapy is driven by both cell-intrinsic and microenvironmental factors. We use spatial transcriptomics and single-cell RNA sequencing to uncover distinct resistance programs in melanoma cells shaped by intrinsic cellular states and the tumor microenvironment. Consensus non-negative matrix factorization reveals shared intrinsic resistance programs across cell lines. In patient samples, these resistance programs coexist within individual tumors and associate with diverse immune signatures. Single-cell resolution spatial transcriptomics in xenograft models reveals both intrinsically determined and extrinsically influenced resistant fates. This work demonstrates that therapy-resistant fates coexist within distinct microenvironments and that tissue features influence which fate is adopted.
    DOI:  https://doi.org/10.1186/s13059-026-04112-z
  26. Sci Adv. 2026 May 22. 12(21): eaeh0301
      Amyloid precursor protein (APP) gives rise to amyloid-β, a pathological factor in Alzheimer's disease. However, the physiological role of APP and its homolog amyloid precursor-like protein 2 (APLP2), which are also widely expressed outside the nervous system, is largely unknown. Here, we show that endothelial APP and APLP2 are required for postischemia angiogenesis after myocardial infarction (MI). We found that hypoxia induced the endothelial expression of α-secretases, resulting in nonamyloidogenic processing of APP and APLP2 into the soluble forms APPsα and APLP2sα. Loss of endothelial APP and APLP2 led to decreased neovascularization as well as increased heart failure and mortality after MI, a phenotype that could be rescued by endothelial expression of APPsα. APPsα and APLP2sα exerted their proangiogenic effect by positive allosteric modulation of the endothelial receptor tyrosine kinase KIT, which promotes postischemia neovascularization. Our data identify a function of APP and APLP2 in endothelial cells, which is required for postischemia tissue repair, and suggest approaches to improve regeneration after MI and other ischemic diseases.
    DOI:  https://doi.org/10.1126/sciadv.aeh0301
  27. bioRxiv. 2026 May 08. pii: 2026.05.04.721738. [Epub ahead of print]
      Resilience to cardiac stress is essential for health, yet the relationship between cardiomyocyte (CM) stress response and local microenvironment remains unclear. Here, we combined MERFISH spatial transcriptome profiling with Cellouette , an improved cell segmentation method, to determine CM-microenvironment relationships in a mouse model of ventricular pressure overload. We report the shape, transcription profile, spatial organization, and physical connectivity for >400,000 cells across stressed and healthy tissues. Under stress, CMs adopted a spectrum of emergent transcriptional states, with advanced states marked by a metabolic and pro-fibrotic shift. To discover CM-environment relationships, we performed a network analysis of physical cell connectivity combined with cell-type-specific profiling. We found that pro-fibrotic CM progression was tightly linked to distinct local microenvironments, and CM metabolic shifts could be inferred from transcriptional patterns in neighboring non-CM cells, revealing microenvironmental imprints of disease. We thus provide a resource for understanding the heterogeneity of outcome during cardiac pressure overload.
    Highlights: Cellouette provides accurate segmentation for single-cell spatial transcriptomics in cardiac tissue.Pressure overload creates spatial gradients of cardiomyocyte pro-fibrotic states.Cardiomyocyte pro-fibrotic progression is linked to changes in local cell composition and gene expression.Transcriptional states of non-muscle cells predict metabolic state of adjacent cardiomyocytes.
    DOI:  https://doi.org/10.64898/2026.05.04.721738
  28. Proc Natl Acad Sci U S A. 2026 May 26. 123(21): e2528309123
      The uterine microenvironment is critical for establishing pregnancy and sustaining embryonic development. Embryo attachment induces profound endometrial transformation, including stromal differentiation and vascularization, termed decidualization. This process, conserved in humans and rodents, supports the embryo even before placentation. Poorly formed decidua leads to fetal growth restriction or placental defects, yet underlying mechanisms remain unclear. Here, we used single-cell RNA-seq of mouse and human endometria, including patient samples, to uncover key regulators. We identified that collagen-related extracellular matrix (ECM) remodeling depends on TAZ, a central effector of Hippo signaling, and is essential for decidual formation. ECM pathways were enriched in differentiating stromal cells alongside upregulation of TAZ and associated transcription factors. Conditional uterine knockout of TAZ (Wwtr1flox/floxPgrCre/+; Wwtr1-uKO) caused pregnancy failure in mice, marked by defective trophoblast invasion, early embryonic degradation, and severe subfertility. Spatial transcriptomic and histological analyses of TAZ-deficient endometria further revealed impaired decidualization, ECM remodeling, and vascularization. Thus, TAZ promotes temporal ECM remodeling at the feto-maternal interface, ensuring functional decidual zone formation and healthy pregnancy outcomes.
    Keywords:  embryo implantation; extracellular matrix; pregnancy; reproduction
    DOI:  https://doi.org/10.1073/pnas.2528309123
  29. EMBO J. 2026 May 20.
      Intestinal stem cells (ISCs) continuously renew the gut epithelium by producing specialised cell types, yet the mechanisms that couple ISC renewal with lineage commitment remain poorly characterised. Here, we identify a self-limiting transcriptional program, mediated by the zinc-finger transcription factor Chronophage (Cph), that promotes both ISC maintenance and differentiation into enteroendocrine (EE) cells in the Drosophila midgut. Cph expression is transiently induced by the proneural factor scute at the onset of ISC-to-EE specification. Genetic and single-cell transcriptomic approaches revealed that Cph is required to reprogramme ISCs and sustain normal lifespan. Cph binds to genes involved in proliferation and differentiation, and directly represses its own expression. This autoinhibitory feedback safeguards ISCs from accumulating autophagosomes and undergoing cell death, thus preserving ISC function. Our findings uncover a key regulatory mechanism that balances stem cell maintenance and differentiation, highlighting principles relevant to regenerating tissues.
    DOI:  https://doi.org/10.1038/s44318-026-00808-x
  30. Nat Struct Mol Biol. 2026 May 22.
      At the onset of reproduction, oviparous animals synthesize large amounts of yolk in somatic tissues to provide lipids and other nutrients to their progeny. However, whether the yolk transports other molecules, such as RNAs with gene-regulatory functions, remains largely unexplored. Here, we biochemically purified the yolk granules in the nematode Caenorhabditis elegans and show they contain microRNAs (miRNAs). We provide evidence that the yolk transports miRNAs from the intestine of the mother to the embryos by the lipoprotein yolk receptor RME-2. These yolk-enriched miRNAs inherited by the embryos regulate the transcriptomes of developing larvae. Moreover, environmental stresses and maternal age modulate the transfer of yolk-enriched miRNAs, contributing to stress-resilience benefits to progeny. This discovery establishes an alternative paradigm in intergenerational gene regulation, where the gut-germline axis orchestrates the transmission of environmental cues through yolk-enriched miRNAs. Our work, thus, reveals a mechanism underlying the soma-to-germline transfer of epigenetic information in animals.
    DOI:  https://doi.org/10.1038/s41594-026-01816-5
  31. Nat Commun. 2026 May 22.
      Inflammasomes are cytosolic multiprotein complexes facilitating the maturation and release of the inflammatory cytokines interleukin (IL)-1β and IL-18 and pyroptosis. ASC (apoptosis-associated-speck-like protein containing a CARD) is the central inflammasome adaptor. ASC polymerization is crucial for inflammasome assembly, and ASC particle release propagates inflammasome responses to bystander cells. However, control of inflammasome and ASC particle assembly to limit chronic inflammation and the emergence of autoinflammatory diseases is still incompletely understood. Here, we show that the E3 ubiquitin ligase TRIM (tripartite-motif-containing protein) 21, a common autoantigen in autoimmune diseases, is involved in inflammasome assembly. Specifically, TRIM21 binds to and ubiquitinates ASC to facilitate ASC/NLRP3 interactions, ASC polymerization and the release of ASC/TRIM21-containing particles during pyroptosis in human and mouse macrophages. Furthermore, we detect systemic ASC/TRIM21 particles and autoantibodies in human and mouse autoinflammatory disease. Thus, our findings highlight a previously unrecognized role of TRIM21 as an inflammasome component and driver of autoinflammation.
    DOI:  https://doi.org/10.1038/s41467-026-73350-3
  32. Nat Genet. 2026 May 18.
      Polycomb repressive complex 2 (PRC2)-mediated histone H3 K27 trimethylation (H3K27me3) recruits canonical PRC1 (cPRC1) to maintain heterochromatin. In early development, Polycomb-regulated genes can display long-range three-dimensional interactions, many of which resolve during lineage differentiation. Here we report that Polycomb-anchored looping is controlled by H3K27me3 spreading and regulates target gene silencing to influence cell fate specification. Using glioma-derived H3 Lys27-to-Met (H3K27M) mutations as tools to restrict H3K27me3 spreading, we show that H3K27me3 confinement concentrates the chromatin pool of cPRC1, resulting in heightened three-dimensional interactions that mirror the chromatin architecture of pluripotency. Conversely, H3K27me3 spread in pluripotent stem cells dilutes local cPRC1 chromatin concentration, weakening Polycomb loop contact frequencies. Disruption of cPRC1 binding or aggregation compromises stringent repression of Polycomb genes and induces differentiation and tumor regression of H3K27M-mutant glioma. These results identify the regulatory principles and disease implications of Polycomb looping and show that histone-modification-guided distribution of reader complexes is an important mechanism for nuclear compartment organization.
    DOI:  https://doi.org/10.1038/s41588-026-02586-y
  33. Proteomics. 2026 May 18. e70144
      Cardiac fibrosis is a hallmark of progressive cardiac remodeling and heart failure, characterized by excessive extracellular matrix (ECM) deposition and complex cellular interactions. While bulk proteomic studies have provided insights into global protein alterations associated with fibrosis, they inherently average signals across heterogeneous cardiac cell populations, limiting resolution of cell-type-specific protein regulation. In this study, we applied single-cell proteomics by mass spectrometry (SCoPE2) to generate a proteomic atlas of cardiac fibrosis in an isoproterenol-induced mouse model. Across 1,163 high-quality single cells (ISO: 581; Control: 582), we quantified 4,251 proteins and resolved five major cardiac cell populations, including cardiomyocytes, endothelial cells, fibroblasts, M2 macrophage-like cells, and smooth muscle cells. Single-cell analysis revealed extensive cell-type-specific and discordant protein regulation that was largely masked in bulk proteomic measurements. These fundings demonstrate the utility of single-cell proteomics for resolving cellular heterogeneity in fibrotic cardiac tissue and provide a resource for future integrative studies of cardiac remodeling.
    Keywords:  SCoPE2; bulk proteomics; cardiac fibrosis; cell‐type heterogeneity; discordant protein regulation; single‐cell proteomics
    DOI:  https://doi.org/10.1002/pmic.70144
  34. Nat Phys. 2026 ;22(5): 770-783
      The nuclear pore complex regulates nucleocytoplasmic transport. It was recently shown that the global mechanical stability of proteins regulates their nuclear import rate. On the basis of these findings, we hypothesize that the main principles governing protein translocation through narrow biological pores-in which locally unstructured and unfolded regions determine cargo orientation and translocation kinetics-can help rationalize protein trafficking across the nuclear pore complex. Inspired by single-molecule studies showing that proteins exhibit different mechanical stability when pulled from different termini, here we show that the rate of both nuclear import and export is enhanced when the translocating protein is threaded through the nuclear pore from the specific region exhibiting lower local nanomechanical stability and increased structural disorder. We demonstrate this for a range of model proteins with different folds and stabilities by combining single-molecule magnetic tweezers with single-cell optogenetic experiments, complemented by steered molecular dynamics simulations and biochemical binding assays. Our bioinformatics survey then shows that in human transcription factors, the termini containing the nuclear localization signal sequence exhibit a higher degree of structural disorder. We propose that protein orientation might offer an additional layer of structural and mechanical control of the kinetics of nuclear transport.
    Keywords:  Biological physics; Nanoscale biophysics
    DOI:  https://doi.org/10.1038/s41567-026-03242-2
  35. Nat Commun. 2026 May 20.
      Angiogenesis is essential for development and tissue repair after ischemia. Reactive oxygen species (ROS) act as signaling molecules that promote angiogenesis in endothelial cells (ECs) which mainly rely on aerobic glycolysis for energy production. However, how redox signaling couples to endothelial metabolism remains unclear. Here, we identify endothelial Drp1 as a redox sensor that links VEGF-induced H₂O₂ signaling to metabolic reprogramming and angiogenesis. Loss of Drp1 in ECs suppresses VEGF-driven angiogenic responses. Mechanistically, VEGF rapidly induces NOX4-dependent sulfenylation of Drp1 at Cys644, promoting disulfide bond with the metabolic kinase AMPK and subsequent oxidation of AMPK at Cys299/304 via mitochondrial fission-derived ROS. This pathway enhances endothelial glycolysis and angiogenesis. In vivo, mice with endothelial Drp1 deficiency or CRISPR-engineered redox-dead Drp1 (Cys to Ala) knock-in exhibit impaired retinal angiogenesis and post-ischemic neovascularization. Thus, endothelial Drp1 integrates mitochondrial redox signaling with glycolysis through cysteine oxidation-mediated Drp1-AMPK redox relay, thereby driving reparative neovascularization.
    DOI:  https://doi.org/10.1038/s41467-026-73128-7
  36. Cold Spring Harb Perspect Biol. 2026 May 18. pii: a041915. [Epub ahead of print]
      The Hippo signaling pathway, first identified in Drosophila, is a conserved regulator of organ size and tissue homeostasis that balances proliferation and apoptosis. In mammals, its core kinases mammalian Sterile 20-like kinases 1 and 2 (MST1/2) and large tumor suppressor kinases 1 and 2 (LATS1/2) restrict the transcriptional coactivators Yes-associated protein 1 (YAP) and transcriptional coactivator with PDZ-binding motif (TAZ), whose nuclear translocation drives cell proliferation and survival. In the intestine, YAP/TAZ activity is normally repressed to maintain homeostasis, but transient activation following injury promotes regeneration. Injury-induced YAP signaling triggers a regenerative transcriptional program marked by fetal gene re-expression and the emergence of Clusterin (Clu)-positive revival stem cells (revSCs), which restore leucine-rich repeat-containing G-protein-coupled receptor 5-positive (Lgr5+) intestinal stem cells and epithelial integrity. Cross talk between Hippo, Wingless-related integration site (WNT), transforming growth factor β (TGF-β), and p53 signaling orchestrates this dynamic repair process, with precise temporal control of YAP essential for successful regeneration. Dysregulation of these interactions contributes to colorectal cancer tumorigenesis, highlighting the Hippo pathway as a central hub linking intestinal homeostasis, regeneration, and cancer.
    DOI:  https://doi.org/10.1101/cshperspect.a041915
  37. Nat Metab. 2026 May 18.
      Loss of host-microbiota balance promotes gut inflammation, colitis and inflammatory bowel disease. Yet, whether host or microbial factors are the critical driver of the pathology remains unclear. Here, we investigate how cardiolipin maintains metabolic fitness of regulatory T (Treg) cells to preserve gut-immune homeostasis. We discover that deleting the cardiolipin-synthesizing enzyme protein tyrosine phosphatase mitochondrial 1 (PTPMT1) in T cells predisposes mice to colitis due to impaired Treg cell function in the absence of dysbiosis. Subsequent pathobiont infections accelerate the progression and severity of gut inflammation. Mechanistically, the absence of cardiolipin impairs Treg cell metabolic fitness and triggers a maladaptive integrated stress response, which can be reversed pharmacologically or genetically, restoring gut homeostasis and extending lifespan in PTPMT1 ΔT mice. Barth syndrome, a genetic disorder marked by severe cardiolipin deficiency, also exhibits gastrointestinal symptoms and inflammation associated with helper T cell imbalance and an active integrated stress response signature. Overall, these results suggest that a cardiolipin-mediated mitonuclear axis in T cells preserves gut-immune homeostasis and dictates outcome in pathobiont infections.
    DOI:  https://doi.org/10.1038/s42255-026-01533-9