bims-ginsta Biomed News
on Genome instability
Issue of 2026–07–19
24 papers selected by
Jinrong Hu, National University of Singapore



  1. Cell Stem Cell. 2026 Jul 16. pii: S1934-5909(26)00233-X. [Epub ahead of print]
      Bone marrow aging compromises hematopoiesis and immunity, yet whether these processes are modifiable in primates remains unexplored. Here, we map the single-cell transcriptomic landscape of primate bone marrow aging and demonstrate that long-term oral vitamin C (VC) supplementation attenuates selected molecular and progenitor-level decline. Aging drives severe common lymphoid progenitor (CLP) depletion, myeloid-biased hematopoietic stem and progenitor cell (HSPC) output, and anatomical site-specific molecular adaptations. VC administration partially offsets these phenotypes, expanding the CLP pool and rebalancing lineage commitment trajectories. This aligns with a ∼4-year reduction in transcriptomic age estimates, cross-validated by an epigenetic clock. Cell-cell communication analyses revealed that VC remodels intercellular signaling, nominating a VC-responsive, progranulin (GRN)-linked candidate pathway. In parallel, human in vitro assays demonstrate that recombinant progranulin mirrors selected VC-associated molecular actions. Collectively, these findings delineate the molecular architecture of primate bone marrow aging and nominate modifiable pathways for further investigation.
    DOI:  https://doi.org/10.1016/j.stem.2026.06.006
  2. Dev Cell. 2026 Jul 17. pii: S1534-5807(26)00239-X. [Epub ahead of print]
      Fertilization involves dynamic sperm-egg interactions, yet has been primarily studied in static samples. Here, we use high-resolution live imaging to capture fertilization from the moment of sperm binding in zona-intact mouse oocytes. We identify two phases of sperm remodeling: a static phase, during which sperm remain beneath the oocyte cortex as DNA decondensation and histone loading occur, and a mobile phase characterized by stereotyped sperm movement. Initial displacement away from the spindle is driven by cytoplasmic streaming, with manipulations in mouse indicating that sperm movement requires chromatin decondensation and oocyte polarization. Subsequently, polar body cytokinesis generates convergent cortical flows that draw sperm toward the emerging female pronucleus. Finally, we capture sperm-egg fusion in human oocytes and characterize post-fusion events including meiotic resumption and sperm movement, offering a live-imaging description of human fertilization dynamics. Together, these findings provide a continuous spatiotemporal framework for mammalian fertilization, extended by initial observations in human oocytes.
    Keywords:  ICSI; IVF; chromatin remodeling; cortical flow; cytoplasmic streaming; fertilization; live imaging; oocyte; sperm; zygote
    DOI:  https://doi.org/10.1016/j.devcel.2026.06.015
  3. Mol Cell. 2026 Jul 16. pii: S1097-2765(26)00423-5. [Epub ahead of print]
      Nuclear stress bodies (nSBs) are stress-inducible membraneless organelles formed on HSATIII long noncoding RNAs (lncRNAs) that regulate pre-mRNA splicing during thermal stress recovery. During stress, dephosphorylated serine/arginine-rich splicing factors (SRSFs) accumulate in nSBs, whereas upon stress removal, their kinase CLK1 is recruited to rephosphorylate SRSFs, thereby promoting target intron detention. However, the mechanism underlying CLK1 localization to nSBs has remained unclear. Using HeLa cells and cell-free reconstitution, we identify CLK1 Ser341 phosphorylation as a critical determinant of its nSB localization and define its regulatory mechanism. Ser341 is phosphorylated under normal conditions, dephosphorylated by protein phosphatase 1(PP1) during stress, and rephosphorylated by RIOK2 during recovery, thus enabling CLK1 localization to nSBs specifically during recovery. We further identify PPP1R2, an entirely intrinsically disordered PP1 inhibitory subunit, as a reversible thermosensor that dissociates under stress to activate PP1. Together, our findings reveal multilayered thermosensing mechanisms that coordinate the staged localization of SRSFs and CLK1 to nSBs, thereby regulating temperature-dependent pre-mRNA splicing.
    Keywords:  intrinsically disordered protein; nuclear stress body; protein kinase; protein localization; protein phosphatase; splicing regulation; thermosensor
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.034
  4. Dev Cell. 2026 Jul 13. pii: S1534-5807(26)00238-8. [Epub ahead of print]
      The role of morphogenetic forces in cell fate specification is an area of intense interest. Using an ectopically expressed nonphosphorylatable mutant of β-catenin (Y654F) in human embryonic stem cell colonies, we provide evidence that impeding tension-dependent Src-mediated β-catenin phosphorylation compromises BMP4-driven Brachyury (T) expression. This impediment also disrupts the epithelial-to-mesenchymal transition essential for mesoderm specification. Mechanistically, the Y654F mutation prevents the translocation of the junctional and cytoskeletal pool of β-catenin to the nucleus. However, saturation of Wnt signaling with exogenous Wnt3a or the inhibition of GSK3β rescues mesoderm expression. These findings suggest that BMP4 initiates a force-dependent junctional β-catenin translocation upstream of both Wnt secretion and cytosolic Wnt/β-catenin stabilization to drive mesoderm specification. Ultimately, our work highlights the importance of force-dependent Wnt/β-catenin signaling in the self-organization of tissues during developmental processes, such as gastrulation, and emphasizes a role for fine-tuned molecular regulation of the Wnt signaling pathway.
    Keywords:  Wnt; cytoskeletal tension; gastrulation; gastruloids; human embryonic stem cells; mechanical forces; mechanotransduction; mesoderm; traction force microscopy; β-catenin
    DOI:  https://doi.org/10.1016/j.devcel.2026.06.014
  5. Science. 2026 Jul 16. eaeb0822
      Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostability. To combine these strengths, we used de novo protein design to generate small, nanomolar-affinity, high-selectivity binders (NovoTags) for three cell-permeable dyes spanning the visible spectrum. We show that the NovoTag fluorescent lifetimes can be tuned and demonstrate their application in lifetime and wavelength-based multiplexed fluorescence imaging. We further design a two-chain NovoTag that functions as a chemically induced dimerization system with fluorescent readout in living cells, or as a minimally perturbing proximity probe in fixed cells. Our approach combines the advantages of fluorescent proteins and small-molecule dyes, expanding the toolkit for cellular imaging.
    DOI:  https://doi.org/10.1126/science.aeb0822
  6. Science. 2026 Jul 16. 393(6808): eaea3075
      Aging disrupts tissue homeostasis across organ systems. Here, we identify tissue-resident macrophages (TRMs) as central coordinators of age-related organ decline through impaired clearance of senescent neutrophils, a process regulated by the immunomodulatory prostaglandin E2 (PGE2) receptor EP2. Reducing TRM EP2 signaling in aged mice preserved youthful mitochondrial fitness and prevented cognitive decline, frailty, sarcopenia, adiposity, cardiac impairment, and systemic inflammation. Plasma proteomics implicated the liver as a major source of age-associated immune change, in which reduced TRM EP2 signaling rescued neutrophil efferocytosis and prevented paracrine stress in neighboring cells. Elevated TRM EP2 expression and senescent neutrophils were also observed in aged and diseased human tissues. Pharmacologic EP2 inhibition restored youthful neutrophil clearance, establishing impaired TRM efferocytosis as a reversible driver of organ decline in aging.
    DOI:  https://doi.org/10.1126/science.aea3075
  7. Cell. 2026 Jul 16. pii: S0092-8674(26)00747-6. [Epub ahead of print]
      Cell and tissue functions arise from complex interactions among numerous genes, and a systematic understanding of these functions requires isoform-resolved transcriptomic analysis of single cells with high spatial resolution. Here, we introduce an in situ RNA amplification method and its integration with multiplexed error-robust fluorescence in situ hybridization (MERFISH) to detect short RNA sequences and enable whole-transcriptome-scale, isoform-resolved spatial transcriptomics of individual cells in intact tissues. Using this approach, we imaged ∼33,000 distinct RNAs-including ∼23,000 genes and ∼10,000 isoforms-in the mouse brain. Our data enabled systematic analyses of region- and cell-type-specific gene programs and ligand-receptor-based cell-cell communications. These data further revealed rich spatial diversity and cell-type specificity in isoform usage across numerous genes, as well as brain structures particularly rich in isoform specificity. We anticipate broad application of this method for characterizing the molecular and cellular basis of tissue functions, unlocking previously inaccessible discoveries in cell and organismal biology.
    Keywords:  MERFISH; RT&T-AMP; alternative splicing; brain; isoform; isoform-resolved spatial transcriptomics; single-cell transcriptomics; spatial genomics; spatial transcriptomics; whole-transcriptome imaging
    DOI:  https://doi.org/10.1016/j.cell.2026.06.027
  8. J Cell Biol. 2026 Sep 07. pii: e202605090. [Epub ahead of print]225(9):
      Fatty acids (FAs) are transported from lipid droplets (LDs) to mitochondria for β-oxidation during cell starvation. Starvation also triggers engulfment of LDs by autophagosomes and their subsequent degradation by lysosomes (lipophagy). The mechanisms coordinating these pathways remain unclear. Here, we demonstrate that PISD-LD, an LD-localized isoform of phosphatidylserine decarboxylase, facilitates FA transfer while inhibiting lipophagy. PISD-LD mediates LD-mitochondrion (LD-mito) contacts via interaction with mitochondrial PISD. In PISD-LD KD cells, LDs are larger, and FA trafficking and mitochondrial FA β-oxidation are suppressed. The lipid transfer proteins ATG2A/B are recruited by PISDs to mediate FA transfer from LDs to mitochondria. Disruption of PISD-LD-mediated LD-mito contacts activates lipophagy, aiding LD degradation. PISD-LD binds the lipophagy receptor Spartin and inhibits lipophagy by impeding Spartin-LC3 interaction. PISD-LD also regulates LD-mito contacts and lipid metabolism in mouse liver. Thus, PISD-LD serves as a switch between LD-to-mitochondrion FA transfer and lipophagy, ensuring efficient energy production.
    DOI:  https://doi.org/10.1083/jcb.202605090
  9. Nat Commun. 2026 Jul 17.
      Differentiated cells maintain their identity through active mechanisms that suppress alternative cell fates, but disrupting these barriers can enhance direct reprogramming for organ repair. Among the regulators of cell fate stability, glycosylation-associated genes have emerged as barriers to cardiac reprogramming. Here we show that carbohydrate sulfotransferases are central fate-stabilizing regulators, with CHST7 acting through CD44 to control nuclear JUNB levels, chromatin binding, and downstream transcriptional activity. Integrated RNA-seq and ATAC-seq analyses reveal that CHST7 maintains open chromatin at JUNB- and CTCF-enriched loci while restricting accessibility at MEF2C-enriched regions, collectively reinforcing fibroblast identity and suppressing cardiac fate acquisition. We further identify PIP4K2C as a downstream effector whose inhibition enhances cardiac reprogramming efficiency and improves myocardial repair in vivo. These findings define a sulfotransferase-dependent barrier to cell fate conversion with therapeutic implications for heart regeneration.
    DOI:  https://doi.org/10.1038/s41467-026-75583-8
  10. Nature. 2026 Jul 15.
      Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the effect of human genetic variation on disease1-6. Here we create and evaluate a resource of more than 92 million enhancer-gene regulatory interactions across 1,458 biosamples covering 369 cell types and tissues, by integrating predictive models, chromatin states, three-dimensional contacts and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,356 element-gene pairs measured in CRISPR perturbation experiments, more than 30,000 fine-mapped expression quantitative trait loci and 569 fine-mapped genome-wide association study (GWAS) variants linked to a probable causal gene. Using this framework, we develop ENCODE-rE2G, a predictive model achieving state-of-the-art performance across several prediction tasks, demonstrating that iterative perturbations and supervised machine learning can build increasingly accurate predictive models of enhancer regulation. Using ENCODE-rE2G, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes and improving analyses linking noncoding variants to target genes and cell types for common complex diseases. By interpreting the model, we find that beyond enhancer activity and three-dimensional enhancer-promoter contacts, additional features that guide enhancer-promoter communication include promoter class and enhancer-enhancer synergy. These genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.
    DOI:  https://doi.org/10.1038/s41586-026-10781-4
  11. Cell Rep. 2026 Jul 14. pii: S2211-1247(26)00761-8. [Epub ahead of print]45(7): 117683
      The branched structure of the vertebrate lung provides a high surface area-to-volume ratio that enhances diffusion-driven gas exchange. Generating this structure requires that epithelial branches avoid contacting one another during development, but the underlying mechanisms remain elusive. Using the embryonic chicken lung as a model system, we found that branch spacing is regulated primarily by signaling to the mesenchyme through transforming growth factor β (TGFβ). Although proliferation decreases in epithelial cells that are located in close proximity to an adjacent branch, these patterns emerge after regular branch spacing has been established. Instead, we find that TGFβ promotes the directed migration of mesenchymal cells, which form a condensation that physically displaces the adjacent epithelium and tunes branch spacing. Continuous disruption of TGFβ signaling prevents mesenchymal condensation and eventually results in contact between adjacent branches. These data suggest that the spacing between epithelial branches results from mesenchymal cell dynamics rather than from epithelial-intrinsic self-avoidance.
    Keywords:  CP: developmental biology; CP: molecular biology; mechanical stress; morphogen; tissue morphodynamics
    DOI:  https://doi.org/10.1016/j.celrep.2026.117683
  12. bioRxiv. 2026 Jul 07. pii: 2026.07.07.736946. [Epub ahead of print]
      Polyploid cells, which contain more than two copies of the genome, are widely present across plants and animals, where they are often found in tissues with high biosynthetic and metabolic demands, such as the mammalian liver and placenta. While somatic polyploidy is frequently associated with increased cell growth and biosynthetic capacity, unscheduled polyploidization in cell types that are not normally programmed to become polyploid is often linked to reduced cellular fitness and genome instability. To understand whether these divergent outcomes stem from distinct immediate cellular responses to increased ploidy, we systematically compared the early consequences of polyploidization across naturally occurring and experimentally induced systems. Specifically, we examined physiological polyploid cells in the Caenorhabditis elegans intestine and human hepatocyte organoids, alongside unscheduled polyploid human retinal pigment epithelial (RPE1) cells generated through cytokinesis failure. Using quantitative imaging, flow cytometry, and FUCCI-based cell-cycle reporters we measured cell size and protein translation dynamics during G1 in diploid and polyploid cells. Across all systems, we observed a strikingly conserved relationship between ploidy, cell size, and biosynthetic capacity: both cell size and protein translation showed similar scaling patterns after polyploidization, regardless of whether polyploidization occurred as part of normal development or by inducing cytokinesis failure. These findings indicate that the immediate cellular response to increased ploidy is broadly similar across contexts. However, in contrast to unscheduled polyploid RPE1 cells, polyploid human hepatocytes extend their G1 phase, leading to a higher accumulation of proteins before cell-cycle progression. Together, our findings suggest that polyploidization elicits similar growth responses across contexts, and that cell-type specific cell-cycle adaptations may determine whether polyploidy becomes advantageous or deleterious.
    DOI:  https://doi.org/10.64898/2026.07.07.736946
  13. Proc Natl Acad Sci U S A. 2026 Jul 21. 123(29): e2523230123
      The Hippo pathway governs cell growth, proliferation, and differentiation and is frequently deregulated in cancer. Yes-associated protein (YAP) is the central transcriptional coactivator of the Hippo pathway and interacts with β-catenin to coordinate YAP-Wnt signaling crosstalk. Both pathways are modulated by diverse upstream signals including mechanical cues, cell density, and cell polarity, yet how such signals are integrated remains poorly understood. Here, we demonstrate that Homer scaffolding proteins coordinate YAP and Wnt signaling downstream of the Crumbs polarity complex. Homers interact directly via their EVH1 domains with the Crumbs component PATJ and the NDR kinase scaffold Furry-like (FRYL). Homers antagonize FRYL to promote YAP activation while cooperating with FRYL to enhance Wnt/β-catenin signaling, revealing pathway-selective regulation. PATJ, in contrast, recruits Homers to the cortex and restrains YAP activity. We further show that Homers form biomolecular condensates in nonpolarized epithelial and colorectal cancer cells, whose assembly and signaling properties are differentially modulated by PATJ and FRYL. Whereas FRYL promotes the formation of cytoplasmic droplets, PATJ drives the assembly of phase-separated compartments at or near the plasma membrane. Collectively, our findings establish Homer-driven phase separation as a tunable signaling mechanism to translate polarity cues into transcriptional output.
    Keywords:  YAP; crumbs complex; homer; phase separation; wnt signaling
    DOI:  https://doi.org/10.1073/pnas.2523230123
  14. Nature. 2026 Jul 15.
      Diet composition shapes tissue function and disease risk by modulating nutrient availability, metabolic state and cellular dynamics1. In the gastrointestinal tract, obesogenic high-fat diets enhance small-intestinal stem cell activity and tumorigenesis2. However, the impact of ketogenic diets (KDs), which contain even higher lipid content but reduce circulating insulin and induce ketogenesis, remains poorly understood3. This is particularly relevant for patients with familial adenomatous polyposis who face a high risk of small-intestinal tumours4. Here we combine dietary, genetic and metabolic manipulations in mouse models of spontaneous intestinal adenoma formation to dissect the role of systemic and epithelial ketogenesis in intestinal cancer. We show that KD accelerates tumour burden and shortens survival, independent of ketone metabolites. Through genetic manipulation of the ketogenic pathway, we modulate the production of local and systemic ketone metabolites; however, neither inhibition nor augmentation of the ketogenic enzyme 3-hydroxy-3-methylglutaryl-coenzyme A synthase 2 nor disruption of ketolysis altered tumorigenesis. Combined intestinal loss of PPARα/δ/γ attenuates KD-driven intestinal stem cell expansion, proliferation and clonogenicity, whereas inhibition of downstream fatty acid oxidation through CPT1A loss limits adenoma formation specifically under KD, linking tumour initiation to fatty acid oxidation of dietary lipids rather than lipid accumulation. These findings reveal that dietary lipid content, through fatty acid oxidation rather than ketone metabolism, influences intestinal tumorigenesis and highlight the need for nuanced consideration of dietary strategies for cancer prevention in genetically susceptible populations.
    DOI:  https://doi.org/10.1038/s41586-026-10779-y
  15. Cell Rep. 2026 Jul 14. pii: S2211-1247(26)00747-3. [Epub ahead of print]45(7): 117669
      While mammalian limb regeneration is limited to the distal fingertips, axolotls can regenerate entire limbs, providing a model system to uncover conserved patterning mechanisms. Although anterior-posterior (A/P) signaling is required for limb regeneration, how A/P patterning is coordinated across limb segments remains unclear. Using spatial transcriptomics and our SpatialFlux analysis pipeline, we found that A/P genes are asymmetrically distributed along the proximal-distal (Pr/Di) axis of both uninjured and regenerating axolotl limbs. This asymmetric boundary coincides with distally enriched AP-1 and ERK signaling, with ERK inhibition disrupting both posterior and distal patterning programs, linking A/P organization to Pr/Di positional identity. Remarkably, a similar asymmetric boundary is present in fetal human limbs, revealing an evolutionarily conserved patterning paradigm. These findings challenge the long-standing model of a symmetrical A/P limb midline boundary and support a revised model, in which shifting A/P ratios regulate Pr/Di patterning.
    Keywords:  CP: Developmental biology; ERK signaling; axolotl; limb amputation; limb patterning; regeneration; spatial transcriptomics
    DOI:  https://doi.org/10.1016/j.celrep.2026.117669
  16. Nat Struct Mol Biol. 2026 Jul 15.
      Chromosome mis-segregation events that remain unresolved during cytokinesis threaten genome stability. Persistent ultrafine DNA bridges engage the Aurora B-dependent abscission checkpoint (termed NoCut), which delays abscission by phosphorylating components of the ESCRT complex. Here we show that NoCut surveillance repurposes human ESCRT-III, the membrane-remodeling complex that seals the reforming nuclear envelope in anaphase. In response to persistent ultrafine DNA bridges, ESCRT-III transfers from the reforming nuclear envelope to the mis-segregated DNA bridge and ESCRT-III complexes protect the DNA from damage, as evidenced by increased DNA damage upon CHMP1B depletion. Complementary in vitro assembly reactions show that the human ESCRT-III proteins CHMP1B and IST1 can copolymerize into double-stranded filaments that encase double-stranded DNA and nucleosomes and prevent nuclease digestion and cGAS recognition, demonstrating that ESCRT-III complexes can directly bind and protect DNA. Lastly, cells expressing a DNA-binding mutant of CHMP1B exhibit cytokinesis failure and binucleation when ultrafine DNA bridges persist, revealing a mechanism of safeguarding genome stability.
    DOI:  https://doi.org/10.1038/s41594-026-01841-4
  17. Mol Cell. 2026 Jul 15. pii: S1097-2765(26)00422-3. [Epub ahead of print]
      Pseudouridines (ψ) in mRNA are linked to alternative splicing, but their regulatory mechanisms remain unclear due to the lack of known reader proteins. Here, we identify SMD2, a core spliceosomal component, as a direct ψ reader. Through in vitro and ex vivo assays, we show that SMD2 preferentially binds to ψ-modified RNA over unmodified uridines in human cells. Specifically, SMD2 collaborates with ψ synthase (PUS) family enzymes to regulate alternative splicing by recognizing ψ residues near exon-intron junctions. Notably, SNRPD2, the gene encoding SMD2, is overexpressed in multiple cancers and is essential for tumor cell proliferation through modulating mRNA maturation. These findings establish a direct mechanistic link between ψ and spliceosomal function, which positions SMD2 as a key regulator of ψ-mediated splicing and a promising therapeutic target in cancer.
    Keywords:  RNA modification; SMD2; SNRPD2; cancer; mRNA; pseudouridine; spliceosome; splicing; tumorigenesis
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.033
  18. Sci Adv. 2026 Jul 17. 12(29): eady2267
      Pericentromeres are heterochromatic regions adjacent to centromeres that ensure accurate chromosome segregation. Despite their conserved function, they are composed of rapidly evolving A/T-rich satellite DNA. To test the functional consequences of this rapid sequence evolution, we establish hybrid mouse embryos as a model system to compare divergent satellite arrays from distinct species in a common cytoplasm. We show that variation in satellite sequence impacts heterochromatin formation, recruitment of the Chromosome Passenger Complex (CPC), and interactions with the mitotic spindle. Differences in satellite DNA sequence alter pericentromere packaging by Polycomb Repressive Complex 1 (PRC1), as satellite arrays that recruit PRC1 are enriched for specific A/T sequences that the PRC1 AT-hook preferentially binds. Furthermore, PRC1 heterochromatin modifies pericentromere function by inhibiting recruitment of the CPC, increasing microtubule forces on kinetochores during mitosis. Our results provide a direct link between satellite DNA composition and mitotic chromosome behavior and highlight early embryogenesis as a critical point in development that is sensitive to satellite DNA evolution.
    DOI:  https://doi.org/10.1126/sciadv.ady2267
  19. Cell Rep. 2026 Jul 16. pii: S2211-1247(26)00765-5. [Epub ahead of print]45(7): 117687
      Cortical layer 1 plays an essential role in neural networks, integrating many streams of information and undergoing plasticity during learning. Yet, we know little about the underlying molecular processes and whether layer-specific adaptations exist. Here, we show that layer 1 and its synapses actively synthesize proteins. Using laser capture RNA-sequencing and fluorescence in situ hybridization, we report an abundance of localized synaptic transcripts. We purify layer 1 excitatory and inhibitory mouse synapses and characterize their enriched transcriptomes, identifying proteins that can be locally synthesized and finding significant differences with deeper layer transcriptomes. Finally, we discover a strong similarity between cortical layer 1 and hippocampal stratum lacunosum moleculare, which suggests a conserved molecular architecture of these distal layers. Together, our results establish local protein synthesis as an important feature of cortical layer 1, and we provide the first comprehensive description of the transcriptomes of layer 1 and its synapses, which we make available online.
    Keywords:  CP: neuroscience; cortical layer 1; fluorescence-activated synaptosome sorting; laser capture transcriptomics; local translation; mRNA localization; metabolic labeling; molecular layer; neocortex; synapse diversity; synaptic transcriptomics
    DOI:  https://doi.org/10.1016/j.celrep.2026.117687
  20. Nat Cell Biol. 2026 Jul 15.
      Lysosomes are essential regulators of cellular homeostasis. Emerging evidence positions lysosomes as both vulnerable targets and active drivers of ageing biology. During ageing, lysosomes exhibit impaired biogenesis, defective acidification, reduced hydrolytic activity and compromised membrane integrity. These defects impair the clearance of damaged organelles and macromolecules and promote cellular stress responses, inflammageing and senescence, causing age-dependent functional decline across tissues. Lysosomal dysfunction has been increasingly linked to age-related diseases, including neurodegeneration, cardiometabolic disorders and increased susceptibility to infection, among others. Thus, lysosomal dysfunction is a hallmark of ageing that drives age-related pathology. Here we review recent progress in lysosomal biogenesis and quality control, discuss how lysosomes intersect with fundamental ageing mechanisms and evaluate emerging therapeutic strategies that target lysosomes to promote healthy ageing and potentially ameliorate age-associated pathologies.
    DOI:  https://doi.org/10.1038/s41556-026-02007-6
  21. EMBO Rep. 2026 Jul 15.
      Chemical reprogramming holds transformative potential for regenerative medicine. However, the regulatory mechanisms governing cell fate transitions are not well understood. Here, we identify Interleukin-1 Receptor-Associated Kinase 4 (IRAK4) as a barrier to multi-lineage reprogramming. Pharmacological inhibition of IRAK4 enhances the reprogramming of mouse embryonic fibroblasts (MEFs) through a chemically activated multi-lineage priming (CaMP) state and extraembryonic endoderm (XEN)-like intermediates, increasing colony formation, and the expression of core XEN regulators (Sox17, Gata4, Sall4, and Foxa2). Genetic knockdown of Irak4 similarly accelerates reprogramming, whereas its overexpression blocks cell fate transitions. IRAK4 inhibition enhances chromatin accessibility and reshapes cell cycle dynamics, characterized by G0/G1 shortening and G2/M lengthening, potentially contributing to multi-lineage state establishment. Furthermore, IRAK4 suppression enhances the direct conversion of MEFs to neuron-like and hepatocyte-like cells, which exhibit enhanced functional maturity, including increased glycogen storage and improved detoxification capacity. Our findings establish IRAK4 as a regulator that constrains cellular plasticity potentially by coordinating chromatin accessibility and cell cycle dynamics.
    DOI:  https://doi.org/10.1038/s44319-026-00855-9
  22. Nature. 2026 Jul 15.
      Molecular glues stabilize weak interactions to impart new functionalities to complexes1-3. Although molecular glues have been described in plant signalling and as human therapeutics4,5, it is unclear whether this modality provides endogenous regulation in human cells. Here we show that purine nucleotides are molecular glues that tether the rate-limiting enzyme in purine biosynthesis-phosphoribosyl pyrophosphate amidotransferase (PPAT)-to its inhibitor NUDT5. This mechanism allows cells to sense the levels of purines and to establish essential feedback control of their synthesis. We refer to such molecules as metabolite glues. Thiopurine chemotherapeutics6, which have been in clinical use since the 1950s, glue the same complex but adopt distinct orientations for enhanced function. Unlike most known glues, the PPAT-NUDT5 metabolite-glue pocket can adjust its conformation to notable compound alterations, enabling increased glue potency and improved on-target activity. We therefore identify endogenous metabolite glues as a mode of nutrient sensing that can be exploited for therapeutic benefit.
    DOI:  https://doi.org/10.1038/s41586-026-10790-3
  23. Nat Genet. 2026 Jul 14.
      Gene expression in mammalian cells is controlled by enhancers that are often dispersed across large cis-regulatory landscapes around a promoter. How enhancers determine transcription of their target genes and how this depends on their relative position within a cis-regulatory landscape remain unclear. Here we use live-cell imaging to track the activity of a promoter under the control of the same enhancer, but inserted at different positions across a simplified regulatory landscape with minimal complexity. Combined with mathematical modeling, this reveals that RNA production from the promoter occurs in clusters of transcriptional bursts, with enhancer position controlling the frequency at which clusters appear. This results in bursts being more frequent and occurring more uniformly across cells when the enhancer is genomically close to the promoter than when it is located at a large genomic distance. Mathematical modeling further indicates that the enhancer modulates the promoter's ability to transition from its basal transcriptional state to a regime in which clusters of bursts become more frequent. Our results reveal unexplored modes of mammalian promoter operation and show that enhancer position within a cis-regulatory landscape critically controls the timing and variability of transcriptional output in single cells.
    DOI:  https://doi.org/10.1038/s41588-026-02676-x
  24. J Cell Biol. 2026 Aug 03. pii: e202507107. [Epub ahead of print]225(8):
      Fam20C, the first protein kinase identified in the secretory pathway, governs the majority phosphorylation of the secretome. Although Fam20C has a high propensity for secretion, its kinase activity occurs intracellularly. How Fam20C clients are phosphorylated inside cells remains elusive. Here, we demonstrate that the pseudokinase Fam20A forms a heterocomplex with Fam20C on the Golgi membrane, anchoring the cleaved, mature form of Fam20C within the Golgi. Their Golgi localization is promoted by a set of cargo receptors ERGIC2 and ERGIC3, which drive the ER-to-Golgi transport of Fam20A-Fam20C. Importantly, both ERGIC2 and ERGIC3 are upregulated in the mammary gland during lactation, and Ergic2 or Ergic3 knockout mice display global changes in secretome phosphorylation, less phosphorylated β-casein in milk, and deficiency in offspring growth. Our findings uncover a previously unrecognized mechanism for the spatiotemporal regulation of Fam20 kinases, crucial for efficient phosphorylation of secretory proteins during lactation.
    DOI:  https://doi.org/10.1083/jcb.202507107