N Nature Cell Biology · Dec 03, 2025 A human epiblast model reveals dynamic TGFβ-mediated control of epithelial identity during mammalian epiblast development Pluripotency, the ability to generate all body cell types, emerges in a disorganized embryonic cell mass. After implantation, these cells form a columnar epithelium and initiate lumenogenesis. During gastrulation, some undergo epithelial-to-mesenchymal transition to form the primitive streak (PS). The signals controlling these events in humans are largely unknown. Here, to study them, we developed a chemically defined 3D model where conventional pluripotent stem cells self-organize into a columnar epithelium with a lumen, from which PS-like cells emerge. We show that early TGFβ family inhibition prevents epithelial identity, also in murine 3D embryo models and in embryos. ZNF398 acts downstream of TGFβ1, activating the epithelial master regulator ESRP1 while repressing mesenchymal factors CDH2 and ZEB2. After epithelium formation, TGFβ1 stimulation is dispensable for its maintenance. However, treatment via ACTIVIN—a distinct TGFβ family ligand—induces PS efficiently. Thus, signalling of the TGFβ family dynamically governs pluripotent epiblast epithelial identity. Embryonic stem cells Epithelial–mesenchymal transition Growth factor signalling biology
N Nature Cell Biology · Dec 02, 2025 Lineage-determining transcription factors constrain cohesin to drive multi-enhancer oncogene regulation Multiple enhancers, often separated by vast genomic distances, regulate key genes. However, how the folding of individual chromatin fibres enables cell-type-restricted multi-enhancer regulation remains unclear. Here, using acute protein degradation and time-resolved chromatin conformation capture in mantle cell lymphoma, we found that the B cell-lineage-determining factor EBF1 organizes multiple enhancers around sparsely distributed genes essential for B cell identity and oncogenesis. Time-resolved sub-diffraction optical tracing of more than 100,000 chromatin fibres further revealed diverse topological conformations that facilitate multi-enhancer interactions. Mechanistically, we discovered that enhancer positioning at local topological centres is required for promoter engagement, with EBF1 acting as a permeable barrier to loop-extruding cohesin at enhancers. Extending these findings to T cell leukaemia, we show that lineage-determining transcription factors such as EBF1 and TCF1 radially position enhancers within gene loci to enable multi-enhancer regulation of key oncogenes at the single-allele level. Epigenetics Oncogenes biology
N Nature Cell Biology · Dec 02, 2025 Karyopherins remodel the dynamic organization of the nuclear pore complex transport barrier Nuclear pore complexes (NPCs) mediate selective exchange of macromolecules between the nucleus and cytoplasm, but the organization of their transport barrier has been a matter of debate. Here we used high-speed atomic force microscopy, complemented with orthogonal in vitro and in vivo approaches, to probe the dynamic behaviour of the NPC central channel at millisecond resolution. We found that nuclear transport factors dynamically remodel intrinsically disordered phenylalanine-glycine (FG) domains tethered within the NPC channel, partitioning the barrier into two zones: a rapidly fluctuating annular region and a highly mobile central plug. Increased FG-repeat density in mutant NPCs dampened barrier dynamics and impaired transport. Notably, NPC-like behaviour was recapitulated in DNA origami nanopores bearing transport factors and correctly tethered FG domains but not in in vitro FG hydrogels. Thus, the rotationally symmetric architecture of NPCs supports a nanoscopic barrier organization that contrasts with many of the bulk properties of in vitro FG-domain assemblies. Atomic force microscopy Molecular biophysics Nuclear pore complex biology
N Nature Cell Biology · Dec 01, 2025 RASH3D19 mediates RAS activation through a positive feedback loop in KRAS-mutant cancer Therapeutic targeting of mutant KRAS pathways driving cancers is being actively investigated to identify feedback mechanisms responsible for the development of adaptive resistance to mutant KRAS inhibitors undergoing clinical trials. Here we report RASH3D19 as a mediator of RAS pathway activation through a positive feedback loop involving the KRAS–microRNA signalling axis. KRAS-induced miR-222 represses ETS1 expression and downstream transactivation of miR-301a leading to elevation of its target RASH3D19. RASH3D19 facilitates activation of RAS pathways by promoting dimerization and interaction of EGFR with the SOS2, GRB2, SHP2 and GAB1 complex. Genetic deletion of RASH3D19 in mutant KRAS-expressing cancer cells exhibits growth retardation in vitro, in vivo and sensitized pancreatic ductal adenocarcinoma and colorectal cancer cells, organoids and xenografts to mutant KRAS inhibitors, suppressing feedback reactivation of RAS pathways. Therapeutic targeting of RASH3D19 is expected to lead to tumour debulking and alleviating resistance to KRAS inhibitors in mutant KRAS-expressing cancers. Cancer therapeutic resistance Oncogenes Targeted therapies biology
N Nature Cell Biology · Nov 28, 2025 Proximal proteomics reveals a landscape of human nuclear condensates Nuclear condensates (NCs) are membraneless organelles that enable spatial and functional compartmentalization in the nucleus. Yet, the components and functional co-organization of NCs have been poorly studied. Here, we used PhastID to explore the proximal interactome of 18 NCs in HeLa cells. Our data revealed the organizational flow of gene control among these NCs. Crucially, we developed an algorithm to dissect the intricate internal relations of NCs. This algorithm led to key discoveries: the identification of an uncharacterized BUD13 condensate, and the recognition of specific co-organizations between nuclear gems and Cajal bodies for telomerase maturation, and between nuclear gems and histone locus bodies for histone gene pre-mRNA processing. We also created a global reference map to understand NC dynamics under stresses and how disease-related mutations differentially affect NC interactomes. Overall, our work provides a proximal proteome-based atlas for human NCs, substantially advancing our spatiotemporal understanding of nuclear biological events. Nuclear organization Protein–protein interaction networks biology
N Nature Cell Biology · Nov 28, 2025 WDR4 drives tumour-associated macrophage reprogramming and tumour progression via selective translation and membrane cholesterol efflux Tumour-associated macrophages (TAMs) play a pivotal role in shaping the immune microenvironment of hepatocellular carcinoma (HCC), influencing tumour progression and immunotherapy response. WDR4, a tRNA-binding cofactor of theN7-methylguanosine (m7G) methyltransferase complex, remains poorly understood in its independent functions. Here we show that WDR4 is significantly upregulated in HCC-associated TAMs and correlates with poor prognosis. Loss of WDR4 in monocyte-derived macrophages, but not in resident Kupffer cells, reprogrammes TAMs towards an antitumoral phenotype and suppresses HCC progression. Mechanistically, cytoplasmic WDR4 acts independently of m7G modification by directly interacting with eIF4E2 to enhance eIF4E-mediated selective translation of ABCA1, thereby promoting membrane cholesterol efflux and maintaining pro-tumoral polarization. Targeted silencing of WDR4 in TAMs using a CpG-small interfering RNA delivery system enhances antitumour immunity, inhibits tumour progression and improves the efficacy of anti-PD-1 therapy. Our findings identify WDR4 as a key regulator of TAM polarization and a promising therapeutic target to enhance immunotherapeutic outcomes. Cancer metabolism Hepatocellular carcinoma Tumour immunology biology mouse experiments
N Nature Cell Biology · Nov 28, 2025 Multi-omics identify hallmark protein and lipid features of small extracellular vesicles circulating in human plasma Extracellular vesicles (EVs) are an essential signalling entity in human plasma implicated in health and disease. Still, their core protein and lipid componentry, which lie at the centre of EV form and function, remain poorly defined. Here we performed high-resolution density gradient fractionation of over 140 human plasma samples to isolate circulating EVs, and systematically constructed their quantitative proteome (4,500 proteins) and lipidome (829 lipids) landscapes using mass spectrometry. We identified a highly conserved panel of 182 proteins (including ADAM10, STEAP23 and STX7) and 52 lipids (including PS, PIPs, Hex2Cer and PAs), providing a deep survey of hallmark molecular features and biological pathways characteristic to circulating EVs. We also mapped the surfaceome diversity, identifying 151 proteins on the EV surface. We further established a set of 42 proteins and 114 lipids features that served as hallmark features of non-EV particles in plasma. We submit ADAM10 and PS(36:1) as conserved EV biological markers that precisely differentiate between EV and non-EV particles. Our findings, which can be explored via an open-source Shiny web tool (evmap.shinyapps.io/evmap/), will serve as a valuable repository to the research community for a clearer understanding of circulating EV biology. Extracellular signalling molecules Membrane trafficking Organelles Systems analysis biology
N Nature Cell Biology · Nov 26, 2025 Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues Spatial omics technologies have transformed biomedical research by enabling high-resolution molecular profiling while preserving the native tissue architecture. These advances provide unprecedented insights into tissue structure and function. However, the high cost and time-intensive nature of spatial omics experiments necessitate careful experimental design, particularly in selecting regions of interest (ROIs) from large tissue sections. Currently, ROI selection is performed manually, which introduces subjectivity, inconsistency and a lack of reproducibility. Previous studies have shown strong correlations between spatial molecular patterns and histological features, suggesting that readily available and cost-effective histology images can be leveraged to guide spatial omics experiments. Here we present Smart Spatial omics (S2-omics), an end-to-end workflow that automatically selects ROIs from histology images with the goal of maximizing molecular information content in the ROIs. Through comprehensive evaluations across multiple spatial omics platforms and tissue types, we demonstrate that S2-omics enables systematic and reproducible ROI selection and enhances the robustness and impact of downstream biological discovery. Biotechnology Computational biology and bioinformatics Transcriptomics biology
N Nature Cell Biology · Nov 24, 2025 Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein Nucleoli are surrounded by pericentromeric heterochromatin (PCH), reflecting a conserved spatial association between the two largest biomolecular condensates in eukaryotic nuclei. Nucleoli are the sites of ribosome synthesis, whereas the repeat-rich PCH is essential for chromosome segregation, genome stability and transcriptional silencing, yet the mechanisms for their co-assembly are unclear. Here we use high-resolution live imaging duringDrosophilaembryogenesis and reveal that de novo establishment of PCH–nucleolar associations is highly dynamic, as PCH transitions from extending along the nuclear edge to surrounding the nucleolus. Elimination of the nucleolus by removing the ribosomal RNA genes disrupted this process causing increased PCH compaction, followed by its reorganization into a toroidal structure. Furthermore, in embryos lacking ribosomal RNA genes, nucleolar proteins were redistributed into new bodies or ‘neocondensates’, including enrichment in the PCH toroidal hole. Combining these in vivo observations with molecular dynamics simulations based on multiphase wetting theory revealed that nucleolar–PCH associations can be mediated by a hierarchy of interaction strengths between PCH, nucleoli and proteins with dual affinities for both compartments. We validate this model by identifying such a protein, a DEAD-box RNA helicase called Pitchoune, and show that modulation of its affinity for either nucleolar or PCH components alters nucleolar–PCH organization. Together, this study unveils a dynamic programme for establishing nucleolar–PCH associations during animal development and demonstrates how interaction hierarchies and dual-affinity molecular linkers co-organize compositionally distinct condensates. Chromatin Molecular biophysics Nucleolus biology
N Nature Cell Biology · Nov 24, 2025 Polyamines sustain epithelial regeneration in aged intestines by modulating protein homeostasis Ageing dampens the regenerative potential of intestinal epithelium across species including humans, yet the underlying causes remain elusive. Here we characterized the temporal dynamics of regeneration following injury induced by 5-fluorouracil, a commonly used chemotherapeutic agent, using proteomic and metabolomic profiling of intestinal tissues together with functional assays. The comparison of regeneration dynamics in mice of different ages revealed the emergence of proteostasis stress and increased levels of polyamines following injury exclusively in old epithelia. We show that delayed regeneration is an intrinsic feature of aged epithelial cells that display reduced protein synthesis and the accumulation of ubiquitylated proteins. The inhibition of the polyamine pathway in vivo further delays regeneration in old mice, whereas its activation by dietary intervention or supplementation of polyamines is sufficient to enhance the regenerative capacity of aged intestines. Our findings highlight the promising epithelial targets for interventions aimed at tackling the decline in tissue repair mechanisms associated with ageing. Proteomics Translation biology mouse experiments
N Nature Cell Biology · Nov 21, 2025 Transcription factors instruct DNA methylation patterns in plant reproductive tissues DNA methylation is maintained by forming self-reinforcing connections with other repressive chromatin modifications, resulting in stably silenced genes and transposons. However, these mechanisms fail to explain how new methylation patterns are generated. InArabidopsis, CLASSY3 targets the RNA-directed DNA methylation machinery to different loci in reproductive tissues, generating distinct epigenomes via unknown mechanism(s). Here we discovered that several different REPRODUCTIVE MERISTEM (REM) transcription factors are required for methylation at CLASSY3 targets specific to anther or ovule tissues. We designate these factors as REM INSTRUCTS METHYLATION (RIMs) and demonstrate that disruption of their DNA-binding domains, or the motifs they recognize, blocks RNA-directed DNA methylation. Furthermore, we demonstrate that mis-expression of RIM12 is sufficient to initiate siRNA production at ovule targets in anthers. These findings reveal a critical role for genetic information in targeting DNA methylation in reproductive tissues, expanding our understanding of how methylation is regulated to include inputs from both genetic and epigenetic information. DNA methylation Plant sciences biology
N Nature Cell Biology · Nov 18, 2025 Inhibiting ferroptosis enhances ex vivo expansion of human haematopoietic stem cells Improved ex vivo expansion of human haematopoietic stem cells (HSCs) would considerably advance transplantation and genome-engineered therapies, yet existing culture methods still allow substantial HSC loss. Here we show that this attrition is driven largely by ferroptosis, a metabolically regulated, iron-dependent cell-death pathway, and that it can be blocked to augment HSC expansion. Inhibiting ferroptosis with liproxstatin-1 or ferrostatin-1 markedly increases the expansion of cord blood and adult HSCs consistently across donors in both widely used serum-free cultures and recently reported chemically defined conditions. The expanded cells retain phenotypic and molecular stem cell identity and mediate improved durable, multilineage engraftment in xenotransplanted mice without genotoxicity or aberrant haematopoiesis. Mechanistically, ferroptosis blockade is accompanied by upregulated ribosome biogenesis and cholesterol synthesis, increasing levels of 7-dehydrocholesterol—a potent endogenous ferroptosis inhibitor that itself promotes HSC expansion. Crucially, this approach enhances yields of therapeutically genome-modified HSCs, paving a path for clinical applications. Bone marrow transplantation Cell death Haematopoiesis Haematopoietic stem cells biology mouse experiments
N Nature Cell Biology · Nov 17, 2025 DNA fragmentation factor B suppresses interferon to enable cancer persister cell regrowth Oncogene-targeted cancer therapies can provide deep responses but frequently suffer from acquired resistance. Therapeutic approaches to treat tumours that have acquired drug resistance are complicated by continual tumour evolution and multiple co-occurring resistance mechanisms. Rather than treating resistance after it emerges, it may be possible to prevent it by inhibiting the adaptive processes that initiate resistance, but these are poorly understood. Here we report that residual cancer persister cells that survive oncogene-targeted therapy are growth arrested by drug stress-induced intrinsic type I interferon signalling. To escape growth arrest, persister cells leverage apoptotic machinery to transcriptionally suppress interferon-stimulated genes (ISGs). Mechanistically, persister cells sublethally engage apoptotic caspases to activate DNA endonuclease DNA fragmentation factor B (also known as caspase-activated DNase), which induces DNA damage, mutagenesis and stress response factor activating transcription factor 3 (ATF3). ATF3 limits activator protein 1-mediated ISG expression sufficiently to allow persister cell regrowth. Persister cells deficient in DNA fragmentation factor B or ATF3 exhibit high ISG expression and are consequently unable to regrow. Therefore, sublethal apoptotic stress paradoxically promotes the regrowth of residual cancer cells that survive drug treatment. Apoptosis Cancer biology
N Nature Cell Biology · Nov 11, 2025 Reprogramming of H3K36me2 guides lineage-specific post-implantation de novo DNA methylation In mammals, DNA methylation is re-established after implantation following post-fertilization global erasure. Yet, the underlying mechanism remains elusive. Here we investigate H3K36me2 reprogramming in mouse early development and its role in post-implantation DNA methylation re-establishment. In oocytes, H3K36me2 accumulates in gene bodies upon transcription silencing and partially persists to the eight-cell stage. De novo H3K36me2 occurs at enhancers after zygotic genome activation, before spreading genome-wide after implantation, except on the inactive X chromosome. Mutation of the H3K36me2 methyltransferase NSD1 compromises global DNA methylation after implantation preferentially in extra-embryonic lineages and that at methylation-prone promoters, including those of germline-specific genes. However, DNA methylation establishment partially bypasses H3K36me2 through upregulated DNMT3B, a ‘leaky’ H3K36me2/3 reader. This contrasts with DNMT3A, which strictly requires H3K36me2/3 for DNA methylation through its PWWP domain. Finally, DNA methylation valleys escape de novo DNA methylation via PRC1/H2AK119ub1-mediated H3K36me2 exclusion. Thus, H3K36me2 reprogramming regulates lineage- and locus-specific post-implantation DNA methylation establishment. DNA methylation Embryogenesis Epigenomics biology mouse experiments
N Nature Cell Biology · Nov 11, 2025 Ca2+-driven PDIA6 biomolecular condensation ensures proinsulin folding The endoplasmic reticulum (ER) plays crucial roles in maintaining protein quality control and regulating dynamic Ca2+storage in eukaryotic cells. However, the proteostasis system involved in ER-mediated protein quality control has not been fully characterized. Here we show that Ca2+triggers the condensation of PDIA6, an ER-resident disulfide isomerase and molecular chaperone, into quality control granules. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the PDIA6 condensates recruit proinsulin, thereby accelerating the oxidative proinsulin folding and suppressing the proinsulin aggregation inside quality control granules, essential for secretion of insulin. Chaperones Endoplasmic reticulum biology
