bims-ginsta Biomed News
on Genome instability
Issue of 2026–05–10
33 papers selected by
Jinrong Hu, National University of Singapore



  1. EMBO J. 2026 May 02.
      Complex tissue architecture is achieved through multiple rounds of morphological transitions. Here, we analyzed cellular flows and tissue mechanics during avian skin development by employing chicken and transgenic quail skin explant models. We demonstrate how novel cellular flows initiate chemo-mechanical circuits that guide epithelial protrusion, folding, invagination, and spatial cell fate specification. During initial feather bud formation, stiff dermal condensates protrude vertically from the locally softened epithelial sheet. As the bud elongates, it stretches the epithelial cells at the base, thus mechanically activating YAP, which causes the epithelial sheet to fold downward and form a stiff cylindrical wall that invaginates into the skin. This stiff epithelial tongue is essential for the compaction and formation of the tightly packed dermal papillae. These topological transformational events are mechanically interconnected, and the completion of one circuit initiates the next. In contrast, during scale development, the rigid epithelial sheet restricts dermal cell flows, preventing further topological transformation. Based on these findings, we developed a topological transformation model describing how this process enabled the evolution of feather follicles from scales.
    DOI:  https://doi.org/10.1038/s44318-026-00771-7
  2. Nat Struct Mol Biol. 2026 May 07.
      The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not sufficiently understood. Here, we applied ribosome profiling to assess translation dynamics in combination with cryo-electron microscopy analysis of a COX1 ribosome-nascent chain complex to visualize cotranslational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation pausing events. Thus, our findings reveal a link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.
    DOI:  https://doi.org/10.1038/s41594-026-01803-w
  3. Sci Adv. 2026 May 08. 12(19): eaeb6691
      Nascent adhesions are early integrin-based assemblies that couple the extracellular matrix to the actin cytoskeleton and mature into focal adhesions. Many nascent-adhesion proteins interact through weak, multivalent contacts, suggesting that liquid-like organization may contribute to adhesion assembly. However, how phase separation shapes actin polymerization and organization remains unclear. Here, we compare two vasodilator-stimulated phosphoprotein (VASP)-recruiting adaptor proteins, zyxin and vinculin, to determine how adaptor identity tunes condensate properties and actin coupling. Both zyxin-VASP and vinculin-VASP assemblies drive integrin clustering and support actin filament growth. Notably, zyxin-VASP condensates remain fluid and redistribute along newly formed actin bundles, whereas vinculin-VASP condensates are more rigid and fail to spread along actin despite sustaining polymerization. These results suggest that differential VASP recruitment can modulate condensate properties and actin architecture, providing a potential mechanism for the maturation of nascent adhesions into focal adhesions.
    DOI:  https://doi.org/10.1126/sciadv.aeb6691
  4. EMBO J. 2026 May 05.
      p62/SQSTM1 self-assembles with polyubiquitin into liquid-like condensates ("p62 bodies") that function as stress-signaling hubs and selective autophagy cargo. We show that TBK1-dependent phosphorylation at Ser403 acts as a threshold-dependent modulator of a condensate's physical properties and promotes their rapid autophagic clearance. Phosphorylation within p62 bodies drives a transition from large, fluid droplets to compact, gel-like condensates that efficiently capture LC3-positive isolation membranes and accelerate the autophagic removal of ubiquitinated proteins. PP2A holoenzymes containing PPP2R5A/B/E, recruited via a KEAP1 bridge, counteract TBK1 by dephosphorylating Ser403. Homozygous p62S403E/S403E knock-in embryonic stem cells differentiate into post-mitotic neurons enriched in miniaturized, gel-like p62 bodies. Consistently, phosphorylation-mimetic knock-in mice show similar remodeling of p62 condensates in vivo, demonstrating that this phosphorylation-driven mechanism maintains proteostasis across scales. We propose that Ser403 phosphorylation functions as a molecular switch that couples the material state of p62 condensates to their stability and serves as a central control point for p62-mediated protein degradation.
    DOI:  https://doi.org/10.1038/s44318-026-00785-1
  5. Nat Cell Biol. 2026 May 07.
      The early organogenesis stage is a critical phase of embryogenesis that lays the foundation for organ development, and is characterized by dynamic and spatially organized transcriptional programs. However, limited spatial transcriptomic information has constrained our understanding of early primate organogenesis. Here we present a comprehensive three-dimensional (3D) spatial transcriptomic atlas of cynomolgus monkey embryos at Carnegie stages (CS) 9 and 10, capturing key morphogenetic events including cardiogenesis, gut tube regionalization, neurulation, axial mesendoderm patterning and early somitogenesis. Using high-resolution spatial transcriptomics and 3D reconstruction, we identify spatially defined lineage domains across germ layers and resolve regionally restricted gene expression, transcription factor activity, and signalling landscapes along major embryonic axes, exemplified by the emergence of dorsoventrally patterned spinal cord subpopulations during neurulation. Cross-species comparisons with human and mouse datasets reveal conserved and species-biased transcriptional programs. Together, this atlas provides a foundational reference for studying early primate development.
    DOI:  https://doi.org/10.1038/s41556-026-01956-2
  6. Nat Commun. 2026 May 05.
      Mitochondria are essential organelles whose functions depend on coordinated multiprotein complexes, yet their composition and organization remain incomplete. Here, we present a large-scale map of mitochondrial protein complexes by integrating affinity purification of 740 endogenously GFP-tagged mitochondrial proteins with biochemical co-fractionation of mitochondrial extracts from yeast (Saccharomyces cerevisiae) grown under respiratory conditions. Mass spectrometry identifies 13,716 high-confidence protein associations and defines 556 heteromeric complexes, many previously unknown. These assemblies reveal factors involved in coenzyme Q6 biosynthesis, membrane contact sites, phospholipid transport, and coordination with the MICOS complex during respiration. We further link 538 assemblies to 294 candidate human disease genes and construct a conservation map of 852,146 predicted mitochondrial interactions across 271 genomes, and validate key predictions in human cell lines and mouse brain tissue. Together, this work provides a comprehensive mitochondrial interactome, assigning functions to poorly characterized proteins, and offering insights into mitochondrial biology and disease-associated assemblies.
    DOI:  https://doi.org/10.1038/s41467-026-72525-2
  7. J Cell Biol. 2026 Jul 06. pii: e202306071. [Epub ahead of print]225(7):
      Actin networks undergo rearrangements that influence cell shape. Actin network organization is regulated by a host of actin-binding proteins. The Drosophila synaptotagmin-like protein, bitesize (Btsz), organizes actin at epithelial cell apical junctions in a manner that depends on its interaction with the actin-binding protein, moesin. Using RNAi, we showed that Btsz functions at earlier, syncytial stages of Drosophila embryo development. Btsz is required to stabilize pseudo-cleavage furrows, preventing metaphase spindle collisions and nuclear fallout prior to cellularization. While previous studies have focused on Btsz function through moesin, we find that phosphorylated moesin localized to the nuclear envelope and was not enriched at pseudo-cleavage furrows, suggesting a moesin-independent function for Btsz in syncytial embryos. Consistent with this, mutants that affected all moesin-binding domain isoforms did not recapitulate pan-isoform Btsz depletion and we find that the C-terminal half of Btsz cooperatively binds to and bundles F-actin. We propose that synaptotagmin-like proteins directly regulate actin organization during syncytial Drosophila development.
    DOI:  https://doi.org/10.1083/jcb.202306071
  8. bioRxiv. 2026 Apr 27. pii: 2026.04.26.720818. [Epub ahead of print]
      Sarcopenia, loss of muscle mass is a considerable health burden that demands immediate societal attention. Direct myogenic somatic cell reprogramming, a potential muscle regeneration method is constrained by an inability to control the signaling logic that governs cell fate. Here, we show that this barrier can be overcome using AI-designed receptor modulators. Screening de novo minibinders, we identify a synthetic protein cocktail, C6-DPC, that drives efficient human fibroblast-to-muscle transdifferentiation with robust structural and metabolic maturation. C6-DPC reprograms extracellular signaling by activating pro-myogenic FGFR1/2c pathways while suppressing anti-myogenic inputs through ALK1 and TGFBR2; targeted depletion of ALK1 is sufficient to lower the reprogramming barrier. Inflammatory signaling via gp130 emerges as a dominant checkpoint, and its inhibition further enhances conversion. Engineered tissues generate high twitch and tetanic forces in both wild-type and dystrophin-deficient human cells. These findings demonstrate that programmable synthetic ligands can rewrite receptor-level signaling to direct cell fate and enable functional tissue regeneration.
    DOI:  https://doi.org/10.64898/2026.04.26.720818
  9. Nature. 2026 May 06.
      A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states1-3, with major implications for biomedical science. However, a key gap in knowledge has been which ncORFs produce small microproteins or alternative protein molecules that contribute to the human proteome. Here we report the collaborative efforts of the TransCODE Consortium4 to produce a consensus landscape of protein-level evidence for ncORFs. We show that about 25% of a set of 7,264 ncORFs gives rise to detectable peptides in a large-scale analysis of 95,520 proteomics experiments. We develop an annotation framework for ncORF-encoded microproteins as human proteins and codify the new conceptual model of 'peptideins' as microproteins that have indeterminate potential as functional proteins. To probe the biological implications of peptideins, we create an evolutionary analysis approach, termed ORF relative branch length (ORBL), and determine that evolutionary constraint is common and associates with observation of ncORF-derived peptides. We then characterize a pan-essential cellular phenotype for one peptidein from the OLMALINC long non-coding RNA. Overall, we generate public research tools supported by GENCODE and PeptideAtlas and advance biomedical discovery for understudied components of the human proteome.
    DOI:  https://doi.org/10.1038/s41586-026-10459-x
  10. Res Sq. 2026 Apr 22. pii: rs.3.rs-9192680. [Epub ahead of print]
      MRE11 safeguards genome stability at stalled replication forks, where its activity must be tightly controlled to prevent nascent strand DNA degradation (NSD). However, the upstream signaling mechanisms that limit NSD remain poorly defined. Here, we identify Ser649 (S649) as a previously unrecognized phosphorylation site that limits MRE11 association with stalled forks. We show that S649 phosphorylation is robustly induced by replication stress or elevated cytosolic calcium levels, and is mediated by the calcium-responsive CaMKK2-AMPKα axis in concert with ATR, but independently of CHK1. Loss of S649 phosphorylation enhances MRE11 binding to DNA and increases its association with stalled forks, driving excessive NSD, elevated DNA damage, and increased sensitivity to PARP inhibition. We find that the ATM-mediated S676/S678 phosphorylation primes S649 phosphorylation, which in turn facilitates subsequent phosphorylation of SQ/TQ sites in MRE11. Moreover, we find that CaMKK2-AMPKα activation requires ATR but is independent of ATM. Collectively, our findings reveal a hierarchical signaling mechanism that couples calcium signaling with ATM/ATR pathways to prevent NSD at stalled forks and preserve genome integrity.
    DOI:  https://doi.org/10.21203/rs.3.rs-9192680/v1
  11. bioRxiv. 2026 May 01. pii: 2026.04.28.717272. [Epub ahead of print]
      Centromeres are essential regions of the genome that ensure chromosome segregation during mitosis. Yet, they are also hotspots for chromosome breaks and rearrangements in cancer. The mechanisms underlying this fragility is not fully elucidated. Here we show that oxidative DNA damage destabilizes centromeres and promotes chromosome instability. Using a chemoptogenetic system to generate singlet oxygen locally at centromeres, we uncouple centromeric oxidative damage from global oxidative stress. We find that oxidative base lesions activate base excision repair at centromeres but slow DNA synthesis, destabilize CENP-A chromatin, and are converted into DNA breaks that can persist into subsequent cell cycles. Single cell time lapse imaging reveals that the cellular fate of centromeric DNA damage depends on the cell cycle phase during which the oxidative lesions occur. Lesions induced before and during replication primarily induce cell cycle delays and often drive the cells into a state of quiescence, whereas lesions arising after replication allow mitotic progression but compromise the proliferative capacity of daughter cells. Finally, in pre-tumorigenic cells, centromeric oxidative lesions lead to mitotic defects, aneuploidy, and whole-arm chromosome translocations. Collectively, we identify centromeres as cell cycle-sensitive DNA damage sensors and oxidative stress as a direct driver of centromere fragility and chromosome instability.
    DOI:  https://doi.org/10.64898/2026.04.28.717272
  12. bioRxiv. 2026 Apr 21. pii: 2026.04.20.719509. [Epub ahead of print]
      Cell growth requires elevated protein synthesis, which depends on the production of ribosomes. Ribosome biogenesis is a complex, multi-step pathway in which newly transcribed precursor ribosomal RNA (rRNA) undergoes coordinated processing and assembly in the nucleolus to produce the small and large ribosomal subunits (SSU and LSU). 1-3 Oncogene activation stimulates rRNA transcription and processing, giving rise to enlarged nucleoli that produce thousands of ribosomes every minute. 4,5 However, efficient ribosome production requires tight coordination across numerous maturation steps, and it remains unclear if elevated rDNA transcription is proportionally converted into mature ribosomes, or whether imperfect coordination constrains the output yield. Here, we quantify pre-rRNA transcription (input) and compare it with newly-assembled cytoplasmic ribosomes (output), revealing that oncogene activation reduces the efficiency of ribosome production. Using a quantitative pulse-chase sequencing approach with mathematical modeling to resolve rRNA maturation kinetics, we found that oncogene activation creates late-stage processing bottlenecks, characterized by delayed precursor maturation and increased degradation. Perturbation of late-stage ribosome biogenesis factors preferentially impaired oncogene-driven cell growth, and limited tumor growth in mouse models, suggesting that these bottlenecks represent selective vulnerabilities in cancer, created by imbalanced biosynthetic flux. Together, these findings reveal that oncogene-driven ribosome production is imperfectly coordinated across maturation steps, and suggest that capacity limits in multi-step assembly pathways may be therapeutically exploitable in cancer and other diseases.
    DOI:  https://doi.org/10.64898/2026.04.20.719509
  13. Sci Immunol. 2026 May 08. 11(119): eadw5197
      Reactive oxygen species (ROS) produced by mononuclear phagocytes (MPs) are widely believed to drive tissue damage in multiple sclerosis (MS), yet the distinct roles of central nervous system (CNS)-resident versus CNS-invading MPs remain unclear. Here, we combined single-cell profiling and conditional gene targeting to map and modulate ROS production across CNS MPs in a preclinical mouse model of MS. We show that monocyte-derived macrophages (MdMs) exhibit a higher oxidative stress gene signature and produce more ROS than microglia (Mglia). Challenging previous assumptions, our findings reveal that phagocytic NADPH oxidase 2 is dispensable for neuroinflammation. In contrast, quenching mitochondrial ROS (mtROS) through mitochondria-targeted catalase (mCAT) expression in MdMs, but not in Mglia, ameliorated disease severity in acute neuroinflammation. Although core phagocyte functions were unaltered in mCAT-expressing MdMs, our results demonstrate a direct neurotoxic role of mtROS. In sum, we identify MdMs as the primary driver of ROS-mediated oxidative neurological tissue damage.
    DOI:  https://doi.org/10.1126/sciimmunol.adw5197
  14. Curr Top Dev Biol. 2026 ;pii: S0070-2153(26)00001-3. [Epub ahead of print]168 371-428
      Spermatogenesis is composed of three consecutive stages, mitosis, meiosis and spermiogenesis, during which spermatogenic cells undergo continuous molecular and cellular transformation. Regulation of gene expression has been underlying major molecular mechanisms that govern the progressive cell fate determination during spermatogenesis. Besides epigenetic and transcriptional controls, the un-coupled transcription and translation is a common phenomenon conserved across phyla during spermatogenesis. Translational regulation determines the dynamic proteomic landscapes in spermatogenic cells. Aberrant protein synthesis caused by mutations in RNA binding proteins (RBPs) and translation regulators often cast detrimental effects on spermatogenesis in a stage-specific manner, leading to male infertility. Regulation of gene expression at the post-transcriptional and translational levels bear advantages of fast and flexible responses to changing environment, coordination of cellular states including energy and nutrient availability, preservation of genomic fidelity and quantitative and qualitative control of proteins, the functional units of the cell. How cell type-specific translation is regulated during spermatogenesis is largely unclear. In this review, we will first introduce general features of protein synthesis and what have been revealed during mouse spermatogenesis when aberrant protein synthesis occurred. We will then analyze the differential signaling pathways and intracellular factors that cooperatively regulate proteomic landscapes in spermatogenic cells at various stages of spermatogenesis. Protein synthesis is a fundamental mechanism underlying cell fate determination. Taking advantage of current advancements in methodology, future research in this area will unveil the design principles that govern how cells program and maintain functional proteome during development and disease.
    Keywords:  AKT-mTORC1; Cell fate determination; Differentiation; Meiosis; Protein kinase A; Protein synthesis; Self-renewal; Spermatogenesis; Spermatogonial stem cells; Spermiogenesis
    DOI:  https://doi.org/10.1016/bs.ctdb.2026.01.001
  15. Proc Natl Acad Sci U S A. 2026 May 12. 123(19): e2522727123
      Cell behaviors in multicellular organisms are coordinated via both diffusible molecules and by signals based on direct cell-cell contacts. The mode of cell communication used influences the signaling range. In many developing epithelia, contact-based Notch-Delta lateral inhibition signaling is used to pattern cell fates. While previous work revealed that cells can use protrusions to extend the range of Notch-Delta signaling to alter these patterns, this is not a general feature of epithelia. In addition, it is not known how the complex three-dimensional (3D) shapes of epithelial cells influence cell communication. In exploring this question, we show that epithelial cells at the Drosophila wing margin, which lack basal protrusions, contact different neighbors at different heights along their apico-basal axis, effectively increasing the number of neighbors each cell touches. To quantitatively assess this behavior, we develop a mathematical modeling framework (Multilayer Signaling Model) to simulate Notch-Delta signaling over data-derived 3D cell topologies. The model predicts that lateral cell surface signaling is essential to tune the spacing between sensory organ precursors (SOPs). In agreement, we show that perturbing cortical stiffness and cell tortuosity in vivo modifies SOP spacing. These results emphasize the importance of 3D cell geometry and topology in fine-tuning signaling range.
    Keywords:  3D cell shapes; Notch signaling; development; mathematical modeling; patterning
    DOI:  https://doi.org/10.1073/pnas.2522727123
  16. Sci Adv. 2026 May 08. 12(19): eaed5283
      Accurate chromosome segregation requires dynamic kinetochore-microtubule attachments that, under the regulation of Aurora family kinases, biorient and align replicated chromosomes. In Caenorhabditis elegans, Aurora A acts with the TPX2-related activator TPXL-1 to regulate these attachments and control spindle length. We show that, in addition to prominent spindle pole localization, TPXL-1-AurA has a chromatin-associated pool positioned between the sister kinetochores. Structural modeling and biochemical analysis support TPXL-1 directly recognizing the nucleosome acidic patch via an arginine anchor. Disrupting this interaction selectively removed chromatin-bound TPXL-1-AurA and caused chromosome missegregation, whereas elevation of the chromatin pool disrupted chromosome alignment. These opposing perturbations inversely affected kinetochore recruitment of the microtubule-binding Ska complex. These results support spatially distinct TPXL-1-AurA populations acting sequentially, with the spindle pole pool controlling spindle length by switching kinetochores out of a depolymerization-coupled state, and the chromatin pool controlling attachment stabilization to ensure biorientation prior to anaphase.
    DOI:  https://doi.org/10.1126/sciadv.aed5283
  17. Cell. 2026 May 01. pii: S0092-8674(26)00439-3. [Epub ahead of print]
      The HOXA gene locus coordinates body patterning, hematopoiesis, and differentiation. While studying blood phenotype-associated variation within the HOXA locus, we identified a genetic variant, rs17437411, associated with globally reduced blood counts, protection from blood cancers, and variation in anthropometric phenotypes. We found that this variant disrupts the activity of a previously unstudied antisense long non-coding RNA (lncRNA) located between HOXA7 and HOXA9, which we named HOXA opposite-strand transcript, stem-cell regulator, antisense mid-cluster between loci (HOTSCRAMBL). The HOTSCRAMBL variant disrupts lncRNA function and reduces human hematopoietic stem cell (HSC) self-renewal. Mechanistically, HOTSCRAMBL enables appropriate expression and splicing of HOXA genes in HSCs, most notably HOXA9, in an SRSF2-dependent manner. Given the critical role of HOXA gene expression in some blood cancers, we also demonstrate that HOTSCRAMBL variation or deletion compromises HOXA-dependent acute myeloid leukemias. Collectively, we show how insights from human genetic variation can uncover critical regulatory processes required for effective developmental gene expression.
    Keywords:  HOXA9; SRSF2; clonal hematopoiesis; genetic variation; hematopoiesis; hematopoietic stem cell; leukemia; lncRNA; splicing
    DOI:  https://doi.org/10.1016/j.cell.2026.04.014
  18. Nat Cardiovasc Res. 2026 May 04.
      Although heart disease arises from different etiologies, treatment remains largely one-size-fits-all, leaving many patients without optimal benefit, which highlights the need for cause-directed therapies. Pathogenic variants in RBM20, a cardiac splicing factor, lead to an aggressive form of dilated cardiomyopathy with high risk of ventricular arrhythmias. We hypothesized that the splicing target calcium/calmodulin-dependent kinase II delta (CAMK2D) is disease causing in RBM20 cardiomyopathy. Here we show that Rbm20/Camk2d double knockout mice are protected from heart failure and sudden cardiac death. In Rbm20-deficient hearts, phosphorylation of CAMK2D targets was increased, indicating that RBM20 loss results not only in mis-splicing of Camk2d transcripts but also in functional activation of CAMK2D signaling. Reexpression of individual CAMK2D splice variants in Rbm20/Camk2d double knockout mice reintroduced cardiac dysfunction, demonstrating that overactivation, rather than mis-splicing, drives disease. Treatment of Rbm20-p.Arg636Gln knockin mice with the ATP-competitive CAMK2 inhibitor hesperadin improved cardiac function. These findings identify CAMK2D overactivation as a central mechanism in RBM20 cardiomyopathy and support CAMK2D inhibition as a promising cause-directed therapy.
    DOI:  https://doi.org/10.1038/s44161-026-00818-2
  19. Nat Commun. 2026 May 02.
      Cytoplasmic abundant heat-soluble (CAHS) proteins, a stress-responsive intrinsically disordered protein from tardigrades, have been discovered to form gel-like networks providing structural support during dehydration, thus enabling anhydrobiosis. However, the mechanism by which CAHS proteins protect the dehydrating cellular membrane remains enigmatic. Using giant unilamellar vesicles (GUVs) as a model membrane system, here we show that encapsulated CAHS12 undergoes a reversible structural transformation that reinforces membrane integrity and preserves encapsulated components, mimicking natural anhydrobiosis. CAHS12-containing GUVs demonstrated stability for weeks and mechanical robustness under dehydration, elevated temperature, and osmotic stresses. Molecular simulations suggest that CAHS12 forms a filamentous network within the vesicle lumen that mitigates membrane collapse and preserves compartmental architecture. Synthetic cells with cell-free transcription-translation capabilities withstand desiccation and recover biochemical activities, akin to the tun state of the tardigrade. This discovery opens up synthetic cell applications in bioengineering, cold-chain-independent biomanufacturing, and adaptive biointerfaces.
    DOI:  https://doi.org/10.1038/s41467-026-72328-5
  20. J Cell Biol. 2026 Jun 01. pii: e202411133. [Epub ahead of print]225(6):
      Macrophages coordinate inflammatory and immune responses to threats, yet how they interpret diverse danger signals to tailor inflammation remains unclear. Disturbances in extracellular and intracellular homeostasis alter cell volume, but the consequences for macrophage inflammatory responses are poorly understood. We demonstrate that macrophages use cell volume control as a danger-sensing mechanism to promote and augment inflammation. Using volume-regulated anion channel (VRAC)-deficient macrophages, which lack cell volume control under hypo-osmotic conditions, we show that cell volume disruptions drive transcriptomic reprogramming and induction of inflammation. Cell volume disruption induced type I interferon signaling through a DNA- and TBK1-dependent mechanism, but independent of cGAS and 2'3'-cGAMP transport. VRAC deficiency enhanced macrophage antiviral responses to influenza infection. Cell volume changes synergized with diverse pathogen-associated molecular pattern-mediated signaling to augment type I interferon responses and exacerbate the cytokine storm in mouse models of hyperinflammation. Our findings highlight cell volume as an important regulator in shaping inflammatory responses, expanding our understanding of how macrophages sense complex danger signals.
    DOI:  https://doi.org/10.1083/jcb.202411133
  21. EMBO J. 2026 May 02.
      Lysosomes and peroxisomes are essential for cellular homeostasis, yet how their activities are coordinated remains poorly understood. Here, we identify peroxisome-derived ether lipids as key regulators of lysosomal function. A genome-wide CRISPR/Cas9 screen in LYSET-deficient mucolipidosis V cells revealed that disruption of ether lipid synthesis genes or peroxins markedly reduces lysosome accumulation and restores degradative capacity. Genetic or pharmacological inhibition of ether lipid synthesis enhanced lysosomal exocytosis and promoted the clearance of undigested material independently of mannose-6-phosphate trafficking. Conversely, supplementation with the ether lipid precursor hexadecylglycerol increased lysosome abundance, while reducing their degradative capacity. These findings uncover a peroxisome-lysosome metabolic axis, in which ether lipids act as bidirectional regulators of lysosomal number and function independently of the lysosomal master regulator TFEB. Our findings reveal how peroxisome-localized lipid metabolism modulates lysosomal homeostasis, and suggest potential new strategies to combat lysosomal and peroxisomal disorders.
    DOI:  https://doi.org/10.1038/s44318-026-00791-3
  22. Cell Rep. 2026 May 04. pii: S2211-1247(26)00399-2. [Epub ahead of print]45(5): 117321
      Glucose serves not only as an energy source but also as a signaling molecule for organ growth. Intrauterine hyperglycemia elevates the risk of congenital heart defects independently of genetic factors, although its underlying mechanisms remain unclear. In this study, we investigated the impact of maternal hyperglycemia on cardiac development using a diabetic pregnancy mouse model and pluripotent stem cell-derived cardiomyocytes. Multi-modal analysis revealed that hyperglycemia disrupts mitochondrial structure and function in fetal hearts even before overt malformations appear, indicating that mitochondrial immaturity is an early signature of diabetic embryopathy. Metabolomic profiling revealed nucleotide imbalance and subsequent AMP-activated protein kinase (AMPK) suppression-contrasting with reports of increased AMPK activity observed in hyperglycemic neural tube defects. Notably, pharmacological activation of AMPK restored cardiomyocyte and mitochondrial function under high-glucose conditions in vitro. Our findings demonstrate that high glucose inhibits cardiomyocyte maturation through dysregulated nucleotide metabolism and AMPK suppression, advancing understanding of hyperglycemia-induced cardiac developmental defects.
    Keywords:  AMPK signaling; CP: metabolism; CP: molecular biology; cardiac maturation; cardiogenesis; diabetic embryopathy; hiPSC-derived cardiomyocytes; metabolism; mitochondrial dynamics; nucleotide metabolism
    DOI:  https://doi.org/10.1016/j.celrep.2026.117321
  23. Nat Methods. 2026 May 07.
      Metabolism unfolds within specific organelles in eukaryotic cells. Lysosomes are highly metabolically active organelles, and their metabolic states dynamically influence signal transduction, cellular homeostasis and organismal physiopathology. Despite the importance of lysosomal metabolism, a method for its in vivo measurement is currently lacking. Here we report a fluorescence-detected mid-infrared photothermal microscope (FILM) implemented with optical boxcar demodulation, artificial intelligence-assisted data denoising and spectral deconvolution, to map metabolic activity and composition of individual lysosomes in living cells and organisms. Using this method, we uncovered lipolysis and proteolysis heterogeneity across lysosomes within the same cell, as well as early-onset lysosomal dysfunction during organismal aging. In addition, we discovered organelle-level metabolic changes associated with diverse lysosomal storage diseases. This method holds the broad potential to profile metabolic fingerprints of individual organelles within their native context and quantitatively assess their dynamic changes under different physiological and pathological conditions, providing a high-resolution chemical cellular atlas.
    DOI:  https://doi.org/10.1038/s41592-026-03090-1
  24. bioRxiv. 2026 Apr 28. pii: 2026.04.27.721156. [Epub ahead of print]
      Actin-based membrane protrusions such as filopodia, microvilli, and stereocilia support a range of cell functions, from nutrient absorption to mechanosensation. In each case, membrane deformation is supported by a core bundle of actin filaments, organized in a unipolar 'barbed-end out' manner. Although their structures and proteomes are well characterized, mechanisms governing the growth and stability of these protrusions remain less clear. Factors that localize to the distal tips of these structures are of particular interest, as they are well positioned to control actin assembly at filament barbed ends. One such factor, EPS8, localizes to distal tip puncta in multiple protrusion types. While early biochemical studies suggested a role in filament capping, loss of EPS8 in multiple models shortened microvilli and stereocilia, suggesting roles in elongation. More recent studies in differentiating epithelial cells suggested that EPS8 promotes protrusion growth and stability. To clarify EPS8's function in the distal tip compartment, we leveraged acute loss-of-function experiments and titrated gain-of-function approaches in combination with live imaging. Acute sequestration of EPS8 led to rapid depletion of filopodia. Conversely, increasing cellular EPS8 levels elevated EPS8 per distal tip punctum, increased F-actin content within individual filopodia, reduced filopodia elongation rates, increased protrusion lifetimes, and protected filopodia against cytochalasin D-induced collapse. These findings suggest that EPS8 binds filament barbed ends as a 'leaky capper,' slowing monomer addition while stabilizing bundles and preventing collapse. These activities are likely critical for building and maintaining the large arrays of protrusions that are assembled by diverse epithelial cell types.
    DOI:  https://doi.org/10.64898/2026.04.27.721156
  25. Cell. 2026 May 07. pii: S0092-8674(26)00452-6. [Epub ahead of print]
      Small cell lung cancer (SCLC), a highly aggressive neuroendocrine malignancy, exhibits poor response to immunotherapy, and the underlying mechanisms remain unclear. Here, we identify a blood-brain barrier-like vascular gate (BVG) in SCLC, distinct from non-SCLC (NSCLC) and other cancers, composed of tightly connected endothelial cells, a thickened basement membrane, and dense pericyte coverage. Functionally, this blood-brain barrier-like vascular gate restricts immune cell infiltration, contributing to SCLC's immunotherapy resistance. Mechanistically, achaete-scute family basic-helix-loop-helix (bHLH) transcription factor 1 (ASCL1), the master transcription factor of SCLC, is essential for BVG formation by regulating insulin-like growth factor-binding protein 5 (IGFBP5), which activates the IGF1 signaling in endothelial cells. IGFBP5 knockout or treatment with the IGF1R inhibitor OSI-906 enhances CD8+ T cell infiltration and synergizes with anti-PD1 therapy. Furthermore, this ASCL1-IGFBP5-IGF1R axis and the BVG are conserved across multiple neuroendocrine cancers (NECs). Our findings reveal a previously unrecognized vascular gate in NECs and propose novel therapeutic strategies to enhance immunotherapy efficacy in these recalcitrant cancers.
    Keywords:  ASCL1-IGFBP5-IGF1R axis; OSI-906; SCLC; T cell infiltration; blood-brain barrier-like vascular gate; immunotherapy; neuroendocrine cancers
    DOI:  https://doi.org/10.1016/j.cell.2026.04.017
  26. bioRxiv. 2026 Apr 24. pii: 2026.04.22.720229. [Epub ahead of print]
      Accurate and timely repair of DNA double-strand breaks (DSBs) is essential for genome maintenance in all cells. Embryos are particularly vulnerable to DSBs. During zebrafish development, a single fertilized cell undergoes rapid divisions to form an embryo of 50,000 cells in the first 24 hours, subjecting its genome to intense replication stress and the inevitable formation of genomic DSBs. While we know that failure to repair these breaks can result in embryonic lethality, the kinetics, fidelity, and pathway choice of DSB repair during embryogenesis are not well understood. Here, we used light-activated CRISPR to generate targeted genomic DSBs across zebrafish embryo development. Importantly, DSB induction occurs within seconds after light stimulation, enabling precise measurements of repair kinetics within a single cell cycle. We found that DSBs were repaired within 15 minutes during the early, rapid-division stages. At later stages, the pace of DNA repair declines as the cell cycle slows. By leveraging mathematical modeling and mutants that disrupt DNA repair pathways, we uncovered a developmental transition from error-prone microhomology-mediated end joining to more faithful non-homologous end joining that correlates with the gradual shift in repair kinetics. To our knowledge, this is the first study to resolve DSB repair dynamics with high temporal resolution during embryo development. Our study establishes a framework for systematically interrogating the cellular responses to DNA damage in living model organisms.
    SIGNIFICANCE STATEMENT: This study reveals how developing embryos rapidly repair dangerous DNA breaks while balancing speed and accuracy. Using a light-activated CRISPR system, the authors precisely control when DNA damage occurs and measure repair in real time in living zebrafish embryos. They show that early embryos prioritize extremely fast but error-prone repair, then transition to slower, more accurate mechanisms as development progresses. This "fast-to-faithful" shift explains how embryos protect their genomes during rapid cell division. The work provides a new framework for studying DNA repair in vivo and has implications for understanding developmental disorders, genome editing outcomes, and how cells manage DNA damage under changing biological conditions.
    DOI:  https://doi.org/10.64898/2026.04.22.720229
  27. bioRxiv. 2026 Apr 28. pii: 2026.04.27.718938. [Epub ahead of print]
      Metabolic reprogramming is a hallmark of myocardial infarction (MI), in which cardiomyocytes shift from fatty acid oxidation to anaerobic glycolysis, leading to elevated lactate production and mitochondrial dysfunction. Lactylation, a recently described lysine post-translational modification, has emerged as a metabolic signaling mechanism; however, its role within mitochondria during MI remains poorly understood. Here, we define the mitochondrial lactylome following MI and examine how modulation of lactate transport influences mitochondrial metabolism and redox homeostasis. Using quantitative proteomics, we identify extensive remodeling of mitochondrial protein lactylation after MI, affecting enzymes involved in bioenergetics, redox regulation, and metabolic control. Pharmacological inhibition of monocarboxylate transporter-1 (MCT1) using AZD3965 further reshapes the mitochondrial lactylome, increasing lactylation of specific metabolic and redox-associated proteins without uniformly exacerbating mitochondrial dysfunction. Despite sustained impairment of global cardiac function, MCT1 inhibition attenuates post-MI fibrosis and inflammation and partially restores mitochondrial respiratory capacity. Consistent with in vivo findings, genetic or pharmacological inhibition of MCT1 in hypoxic cardiomyocytes-derived cells reduces mitochondrial reactive oxygen species, decreases inhibitory pyruvate dehydrogenase phosphorylation, and improves mitochondrial bioenergetics. Together, these findings reveal that mitochondrial lactylation is a context-dependent regulator of mitochondrial metabolism and redox balance following MI. Rather than acting solely as a pathological modification, lactylation integrates lactate availability with mitochondrial function to influence inflammatory and fibrotic remodeling, highlighting mitochondrial metabolic plasticity as a potential therapeutic target in ischemic heart disease.
    Highlights: Myocardial infarction (MI) increases mitochondrial protein lactylation, with 361 identified lactylated proteins.AZD3965-mediated MCT1 inhibition further elevates mitochondrial lactylation.Distinct alterations in mitochondrial proteins and pathways (TCA cycle, amino acid metabolism, gene expression) were observed.AZD3965 reduces cardiac fibrosis and inflammation and partly improves mitochondrial respiration post-MI, but cardiac function remains impaired.
    DOI:  https://doi.org/10.64898/2026.04.27.718938
  28. Nat Metab. 2026 May 08.
      Metformin is a versatile biguanide drug primarily prescribed for type II diabetes. Despite its extensive use, the mechanisms underlying its clinical effects, including attenuated postprandial glucose excursions and elevated intestinal glucose uptake, remain unclear. Here we map these and other effects of metformin to intestine-specific mitochondrial complex I inhibition. Using human metabolomic data and an orthogonal genetics approach in male mice, we demonstrate that metformin suppresses citrulline synthesis, a metabolite generated exclusively by small intestine mitochondria, and increases GDF15 by inhibiting the mitochondrial respiratory chain at complex I. This inhibition co-opts the intestines to function as a glucose sink, driving the uptake of excess glucose and its conversion to lactate and lactoyl-phenylalanine. We also find that glucose lowering by metformin is due to repeated bolus exposure rather than a cumulative chronic response. Notably, the efficacy of phenformin, another biguanide, and berberine, a structurally unrelated nutraceutical, similarly depends on intestine-specific mitochondrial complex I inhibition, underscoring a shared therapeutic mechanism.
    DOI:  https://doi.org/10.1038/s42255-026-01530-y
  29. Proc Natl Acad Sci U S A. 2026 May 12. 123(19): e2519341123
      During development, coordinated cell behaviors drive epithelial morphogenesis toward precise three-dimensional architectures essential for physiological function. How such coordination arises in epithelia composed of multiple cell types remains unclear. Here, we study development of the avian auditory epithelium comprising sensory hair cells (HCs) and nonsensory supporting cells (SCs). Initially, HCs and SCs are arranged into mosaics by Notch-Delta signaling. As development proceeds, HCs partially extrude from the epithelium, establish a tenfold gradient in apical surface area across the tissue, and rearrange with SCs to form near-hexagonal order. Using experiments combined with a three-dimensional vertex model, we show that increased contractility at apical junctions between SCs relative to HC-SC junctions drives spatial organization both within the epithelial plane and along the apical-basal axis. Consistent with experimental findings, our simulation shows systematic differences in HC apical area expansion generate opposing coordinated movements of HCs and SCs, establishing gradients in HC apical surface area and density while maintaining uniform hexagonal order. Together, these results demonstrate that spatial patterning of junctional contractility coordinates cell behavior across both the plane and depth of a mixed epithelium, producing quasi-stratified architecture and tissue-scale three-dimensional order.
    Keywords:  3D vertex model; basilar papilla; development
    DOI:  https://doi.org/10.1073/pnas.2519341123
  30. bioRxiv. 2026 Apr 21. pii: 2026.04.17.719304. [Epub ahead of print]
      Stratified epithelial tissues such as the skin epidermis maintain barrier integrity during development and homeostasis through the coordinated action of cell proliferation, differentiation, delamination, and tissue-scale mechanical forces. During development, the orientation of cell division within the basal layer plays a pivotal role in tissue stratification; however, the mechanical principles linking the orientation of the division plane to these processes across developmental stages remain poorly understood. Here, we expand a recently developed three-dimensional vertex model for stratified epithelia, composed of the basement membrane, basal, and suprabasal layers, to study the mechanical and structural impact of cell divisions with a wider range of orientations. The model integrates developmental stage via specific changes in heterotypic interfacial tensions (arising from actomyosin cortical contractility and adhesion molecules at the basal-suprabasal interface) and tissue stiffness that have been quantified previously in experiments. By systematically varying background mechanical parameters, we investigate how heterotypic tension, division orientation, and tissue fluidity collectively influence the outcome of cell division. Our goal is to uncover the strategies that the embryo may employ to generate stratified phenotypes at different developmental stages, recognizing that these strategies might evolve over time. Although our focus is on the embryonic developmental stages of the epidermis, this framework may also be extended to investigate transformed cells, such as in cancer, to explore how altered division orientation contributes to precancerous or transformed phenotypes.
    DOI:  https://doi.org/10.64898/2026.04.17.719304
  31. Proc Natl Acad Sci U S A. 2026 May 12. 123(19): e2523631123
      Protein kinases regulate almost every major signaling pathway. Visualizing spatiotemporal dynamics of kinase activity is thus essential to understand cell signaling. Here, we report a de novo-designed activity reporter of kinase, dubbed NOVARK, which contains a single polypeptide chain with multiple modular motifs that act as specific kinase substrates and reporters. NOVARK undergoes phosphorylation-induced higher-order assembly, which are detectable as ultrabright green fluorescent protein (GFP) droplets with a large dynamic range. We designed versions of NOVARK that rapidly and reversibly report intracellular activity of protein kinase A, C, and extracellular signal-regulated kinase (ERK) following stimulation/inhibition by upstream G protein-coupled receptor (GPCR) agonists. Our work provides a generalizable platform that enables the design of ultrabright biosensors for illuminating dynamic architecture of kinase signaling.
    Keywords:  de novo–designed activity reporter; kinase biosensor; live-cell imaging; protein design
    DOI:  https://doi.org/10.1073/pnas.2523631123
  32. Nat Chem Biol. 2026 May 05.
      Posttranslational modifications (PTMs) vastly expand the diversity of the human proteome, dynamically reshaping protein activity, interactions and localization in response to environmental, pharmacologic and disease-associated cues. However, their proteome-wide impact on small-molecule recognition-and, thus, druggability-remains largely unexplored. Here we present a chemical proteomic strategy to delineate how PTM states remodel protein ligandability in human cells. Using broad-spectrum photoaffinity probes, we identified more than 400 functionally diverse proteins whose ability to engage small molecules is impacted by phosphorylation or N-linked glycosylation status. Integrating binding site mapping with structural analyses reveals a diverse array of PTM-dependent pockets. Among these, we discovered that the phosphorylation status of common oncogenic KRAS mutants impacts the action of small molecules, including clinically approved inhibitors. These findings illuminate a previously underappreciated layer of proteome plasticity governed by PTMs and highlight opportunities to develop chemical probes that selectively target proteins in defined modification states.
    DOI:  https://doi.org/10.1038/s41589-026-02216-y
  33. Nat Commun. 2026 05 05. pii: 4073. [Epub ahead of print]17(1):
      The adult zebrafish heart can regenerate after injury, but the earliest gene expression changes that trigger this process remain poorly understood. Here we show that in vivo single-cell RNA metabolic labeling, which marks newly made RNA in individual cells, can capture rapid responses in the adult zebrafish heart after injury. Within the first 6 h, we detect activation of innate immune programs, including Toll-like receptor signaling, in a subset of macrophage-like immune cells. Analysis of a larger single-cell dataset indicates that neutrophils also contribute to this early response. Guided by these data, we show that macrophage-specific inhibition of the Toll-like receptor adaptor MyD88 reduces the pro-inflammatory macrophage response at the injury site and improves early hallmarks of regeneration. Our work establishes RNA metabolic labeling as a useful approach for measuring acute responses in vivo at single-cell resolution and identifies early immune-cell activation as a tunable component of heart regeneration.
    DOI:  https://doi.org/10.1038/s41467-026-72781-2