Nature Cell Biology

Liver injury induces rapid transcriptional responses in hepatocytes, yet the chromatin features that distinguish injured hepatocytes from healthy hepatocytes remain poorly understood. Using an integrated functional genomics approach combining bulk RNA-seq, ATAC-seq, and CUT&Tag profiling of H3K27ac and H3K27me3, we define the transcriptional and chromatin landscape of Sox9-expressing hepatocytes, which exhibit gene expression consistent with both hepatocyte and biliary identity. Under homeostatic conditions, Sox9+ hybrid hepatocytes (HybHeps) are rare and confined to the periportal space, while chronic injury induces an expansion of Sox9+ metaplastic hepatocytes (MetHeps). We identify three classes of differentially expressed genes associated with injury-responsive, state-associated, or shared regulatory programs and demonstrate that these classes are governed by distinct chromatin mechanisms. Injury-responsive transcription is driven primarily by dynamic chromatin accessibility remodeling at NF-{kappa}B- and AP-1-enriched regulatory elements, while state-associated and shared programs are reinforced through selective H3K27ac and H3K27me3 modification with comparatively stable accessibility. Relative to conventional hepatocytes, HybHeps encode a permissive chromatin landscape at injury-responsive loci under homeostatic conditions, consistent with epigenetic priming that facilitates rapid inflammatory activation. Projection of mouse-derived gene programs onto a human liver single-cell atlas encompassing both healthy and diseased hepatocytes confirms that SOX9-expressing hepatocytes preferentially engage injury-associated inflammatory modules while attenuating hepatocyte metabolic identity programs. Together, these findings define a chromatin-based regulatory dichotomy between inflammatory responsiveness and hybrid hepatocyte cell state stability, providing mechanistic insight into how differentiated epithelial cells integrate inflammatory signals while preserving cell state.

Differentiation of epidermal keratinocytes is accompanied by profound reorganization of intracellular architecture, but how organelle remodeling interfaces with cell fate control is not well understood. Here, we generate a compartment-resolved proteomic map of keratinocyte differentiation and identify extensive remodeling of lysosomes, mitochondria, autophagic vesicles, plasma membrane, and nucleus. Differentiating keratinocytes display coordinated enrichment of lysosomal degradative machinery, vesicular trafficking factors, and mitochondrial metabolic proteins, revealing organelle remodeling as a prominent feature of epidermal differentiation. From the lysosomal proteome, we identify Sorting Nexin 3 (SNX3) as a critical regulator of epidermal homeostasis. SNX3 increasingly localizes to LAMP1-positive vesicles during differentiation, and its loss impairs epidermal differentiation, suppresses Notch signaling, and promotes proliferative gene expression. In vivo, SNX3-deficient skin grafts fail to maintain normal epidermal architecture and instead develop into squamous cell carcinoma. Mechanistically, SNX3 mediates efficient Notch receptor activation, as SNX3 loss reduces nuclear Notch1 and NICD production, whereas NICD re-expression can rescue the differentiation defect. Our study defines a proteomic framework for organelle remodeling during epidermal differentiation and identifies lysosome-associated SNX3 as a key link between endolysosomal trafficking, Notch signaling, and epidermal tissue homeostasis.

At birth, the intestine must rapidly adapt to enable nutritional function and immune microbial tolerance. Here, integrating single-cell multi-omics and spatial transcriptomics we define the circuits underpinning this process. We identify asynchronous developmental trajectories with postnatal epithelial reprogramming characterised by coordinated changes in metabolism, junctional structure and innate defence. At birth epithelial stem cells demonstrate dynamic enhancer remodelling, with accessibility often preceding transcription. Fetal stemness elements remain accessible despite reduced transcription across epithelial lineages, retaining plasticity potential. Post-natal epithelia experience sequential homing of myeloid cells followed by innate T cells with peri-epithelial B cells localising later in infancy. Using developmentally staged organoids, we show that epithelial responses to inflammatory stimuli are age-dependent and constrained in early life. We identify BHLHE40 as an early-life regulator that attenuates the impact of interferon- and NF-{kappa}B-driven signalling. Altogether we define the events driving epithelial licensing and barrier adaptation at birth and through infancy.

Neural stem cells (NSCs) sustain lifelong neurogenesis through the tight regulation of quiescence, self-renewal and differentiation. Quiescent NSCs (qNSCs) exist in distinct substates, ranging from deep to shallow quiescence, yet the mechanisms governing these transitions remain unclear. In long-term self-renewing NSCs of the adult zebrafish pallium, we show that mTORC1 activity is specifically enriched during a prolonged quiescence phase in which NSCs acquire activation competence. Functional perturbations, analyzed in situ and using single-cell RNA sequencing, reveal that mTORC1 regulates cell progression during this phase, concomitantly ensuring the correct tempo for NSC transition towards activation and the preservation of stemness. These findings challenge the classical view of mTORC1 as a simple regulator of proliferation and identify it as a key regulator of NSC quiescence heterogeneity and dynamics under physiological conditions. By coordinating stemness maintenance with activation competence, mTORC1 emerges as a central player balancing long-term NSC preservation with neurogenic output in the adult brain.

How endothelial cell-cell junctions integrate cytoskeletal, adhesive, and local signaling networks to maintain vascular barrier integrity remains incompletely defined. Here, we identify junctional cadherin 5-associated protein (JCAD) as a modular scaffold that organizes endothelial tight junction architecture by coupling junctional condensates to actin and RhoA signaling. Genetic deletion of Jcad in mice does not affect baseline vascular permeability but causes inflammation-dependent barrier hyperpermeability. JCAD depletion in primary human endothelial cells disrupts tight junction continuity and increases paracellular permeability. Mechanistically, JCAD localizes to ZO-1-positive tight junctions independently of VE-cadherin, directly binds filamentous actin, and forms dynamic actin-associated condensates at cell-cell contacts. Structure-function analysis reveals separable domains mediating tight junction targeting and actin binding, establishing a bipartite architecture that distinctly coordinates junctional signaling and cytoskeletal coupling. Together, these findings identify JCAD as a cell-cell adhesion scaffold that integrates the phase-separated tight junction plaque with actin and RhoA-dependent mechanics, enabling endothelial barrier adaptation to inflammatory stress.

Chronic fibrotic disorders like idiopathic pulmonary fibrosis (IPF) are characterized by aberrant alveolar regeneration and severely limited treatment options. Identification of the mechanisms driving aberrant epithelial repair can lead to new viable therapeutic targets. Using integrated single nucleus ATAC- and RNA-sequencing on human lungs and an in vitro model of dysplastic repair, we identify two distinct regenerative trajectories for alveolar type 2 (AT2) cells: a resolvable euplastic repair trajectory and a persistent, non-resolving dysplastic repair trajectory. The latter is governed by a spatially restricted ITGB6/TGF{beta}1/SMAD3 signaling axis in fibrotic regions of IPF lungs and in murine lungs characterized by chronic epithelial remodeling. Mechanistically, SMAD3 directly regulates dysplastic transitional cell (DTC) markers, including KRT17 and Stratifin. We show that TGF{beta}1 signaling promotes a physical interaction between KRT17 and Stratifin at the leading edge of migrating DTCs in vitro and in vivo, which is essential for their migratory capacity. These findings collectively define the molecular regulation of AT2-driven dysplastic regeneration and identify TGF{beta}1-induced KRT17-Stratifin axis as a central driver of pathological epithelial remodeling in chronic fibrosis, which can be targeted therapeutically to tilt the balance in favor of euplastic regeneration.

Intercellular organelle exchange is increasingly recognized as a feature of the tumor microenvironment, but whether tumor-derived mitochondria functionally shape anti-tumor T cell immunity remains unclear. Here we show that tumor-infiltrating CD8+ T cells acquire functional mitochondria from tumor cells through a contact-dependent, TCR-independent mechanism requiring the mitochondrial trafficking machinery Trak1-Miro1. Transferred tumor mitochondria enhanced CD8+ T cell effector activity, increasing cytotoxic molecule expression and tumor-cell killing. Mechanistically, tumor-derived mitochondria carried sphingosine-1-phosphate (S1P), which engaged S1PR1 signaling in recipient T cells. Tumor-specific deletion of Sphk2 diminished mitochondrial transfer-associated T cell activation, impaired CD8+ T cell effector function, and accelerated tumor progression in vivo. These findings reveal tumor-to-T cell mitochondrial transfer as an unexpected immunostimulatory circuit in the TME and identify mitochondrial SPHK2-S1P signaling as a regulator of CD8+ T cell anti-tumor function.

AbstractsMembraneless organelles (MLOs) often exhibit internal architecture, yet whether the local transcriptome differentially partitions across MLO subdomains remains largely uncharacterized. Here we combine super-resolution imaging with in situ reverse transcription-based sequencing to profile transcriptomes within MLO subdomains. Using the human tripartite nucleolus as a model system, we identify distinct RNA populations in the fibrillar center (FC), dense fibrillar component (DFC), and granular component (GC). Pre-rRNA processing intermediates demonstrate a layered progression across nucleolar subdomains, reflecting the temporal order of the processing steps. Processing steps involved in large-small subunit separation show increased retention in the DFC in highly differentiated cells. Mature small nucleolar RNAs (snoRNAs) are preferentially enriched in the DFC and spatially segregated from their precursor transcripts. Many non-snoRNA-related transcripts, often derived from nucleolus-proximal genes, show modest enrichment in the GC. These results illustrate functional RNA organization across nucleolar subdomains and provide a framework for nanoscale transcriptome mapping of biomolecular condensates.

How developmental progenitors navigate divergent trajectories to either establish adult stem cell pools or undergo terminal differentiation remains a fundamental gap in stem cell biology. Here, we identify the well conserved Tet protein as an essential transcriptional regulator of intestinal stem cell (ISC) establishment. Developmental Tet depletion causes region-specific ISC loss and compromises adult lifespan, while adult-specific loss drives progressive stem cell exhaustion. Overexpression of Tet leads to ISC expansion in both developing and adult guts. Utilizing a comprehensive single-nucleus transcriptomic atlas spanning gut development, we demonstrate that Tet stabilizes progenitor identity by maintaining epithelial integrity, niche signaling, and fate maintenance. By defining this developmental trajectory, we reveal Tet as a critical factor that drives proper ISC maturation and maintains long-term adult epithelial homeostasis.

Embryonic pausing, including forms of diapause, enables development to be reversibly suspended during adverse conditions, but how paused embryos preserve cell fate patterning remains unclear. Using zebrafish, we show that developmental pausing results in the temporary collapse of Wnt, BMP, FGF, and Nodal signaling gradients, despite broad preservation of cell identity at the transcriptional level. In parallel, pausing induces a dormancy-enriched gene expression program (DEEP), which includes the non-canonical poly(A) polymerase tent5ba. Tent5ba promotes survival through pausing, sustains DEEP expression, and is required for robust reestablishment of axial patterning upon developmental re-entry. Poly(A)-tail and transcriptional profiling further link tent5ba to the stabilization of mRNA targets associated with robust developmental outcomes, supporting a model in which transcript polyadenylation safeguards patterning fidelity through suspended embryogenesis.

Lysosomes exhibit spatial heterogeneity, but establishing causal relationships remains challenging with existing relocalization strategies. We present a modular toolkit that rapidly repositions lysosomes on demand by recruiting inducible motors. This decouples the location of organelles from systemic stress. We demonstrate that peripheral lysosomes adapt quickly by exhibiting luminal alkalinization and reduced proteolytic capacity. Furthermore, peripheral sequestration impairs autophagic flux by creating a spatial "trafficking bottleneck". We use this system to provide an unbiased proteomic characterization of spatially distinct lysosomal populations using mass spectrometry. Our findings reveal a distinct set of proteins and complexes that are spatially partitioned between perinuclear and peripheral lysosomes. Perinuclear lysosomes are configured for metabolic recycling. They have a high density of V1 V-ATPase subunits and contain the nucleoside transporter SLC29A3. Conversely, peripheral lysosomes serve as secretory outposts that are enriched in cathepsin Z and the SPG11/SPG15/AP5 complex. These validated cell lines and extensive datasets provide a flexible framework for investigating the functional specialization of different lysosome populations.

Understanding how chromatin state contributes to developmental trajectories remains central to deciphering cell specification and differentiation. Using dual-modality nano-CUT&Tag, we profiled two antagonistic histone modifications--active H3K27ac and repressive H3K27me3--in thousands of single cells from Drosophila embryos across early lineage diversification and terminal differentiation. Joint embedding of both marks enabled robust cell-type classification and revealed increasing epigenetic specificity over developmental time. We ordered cells by developmental age and epigenomic similarity, and defined an epigenetic potential metric that visualizes repressive chromatin barriers as landscapes that predict transcriptional activity. While many genes conform to a classical model in which expression resides in low-potential epigenetic valleys, a substantial subset shows co-occurrence of H3K27ac, H3K27me3, and transcription within the same cell lineage. This indicates that Polycomb-mediated H3K27me3 repression frequently acts within, rather than solely between, lineages. Consistently, tissue-specific E(z) knockdown demonstrates that partial loss of H3K27me3 predominantly de-represses lineage-matched genes rather than inducing fate conversion. Systematic analysis showed that H3K27me3 occurs in multiple distributional modes, ranging from ubiquitous to highly cell-type-specific deposition, co-occuring with accessible but silent gene promoters. These findings demonstrate that cell-type-specific deployment of H3K27ac and H3K27me3 sculpts epigenetic potential landscapes that shape developmental gene expression patterns.

Transposable elements (TEs) pose a major threat to genome integrity in the germline, where the piRNA pathway ensures heritable TEs silencing. How the chromatin environment that enables piRNA biogenesis is first established during oogenesis remains unclear. Here, we identify the histone variant His2Av, the single H2A variant in Drosophila combining H2A.Z (transcriptional) and H2A.X (DNA repair) features, as a critical regulator of the earliest steps of piRNA pathway activation. Germline-specific depletion of His2Av disrupts transcription of piRNA pathway genes, abolishes dual-strand piRNA cluster transcription, and triggers strong TEs derepression. These defects are associated with loss of Rhino recruitment despite intact H3K9me3, suggesting that His2Av contributes to the establishment of a specialized heterochromatin permissive for noncanonical piRNA cluster transcription. His2Av depletion also causes DNA damage, replication stress, and activation of Chk2- and Claspin-dependent checkpoints, leading to oogenesis arrest. Remarkably, overexpression of RNase H, but not a catalytic-dead variant, robustly rescues oocyte development, suggesting that replication stress is a major source of DNA damage in His2Av mutants. Finally, using a separation-of-function approach with a C-terminal truncation inhibiting H2A.X-like activity, we show that the essential germline role of His2Av is transcriptional (H2A.Z-like). Together, our findings reveal that His2Av primes germline chromatin for piRNA pathway initiation while limiting transcription-replication conflicts during early oogenesis.

The final limb structure reflects coordinated deployment of molecular programs, defined not only by which genes are expressed but when they are activated and silenced across time. Existing omics analyses obscure the temporal unfolding of these programs and conflate program identity with deployment timing by assuming temporal equivalence between conditions. We developed WATER (Weighted Windowed Assignment of Temporal Expression of RNA), a framework that reconstructs temporal gene expression trajectories independently within each condition, enabling direct comparison of temporal program architecture between wild-type and perturbed systems. Applying WATER to U11-null mouse forelimb development revealed that minor spliceosome inhibition redistributes genes across inappropriate temporal trajectories. Minor spliceosome inhibition causes splicing defects in minor intron-containing genes such as the PRC2 component Eed, leading to reduced H3K27me3 deposition and chromatin-transcription divergence. Single-cell RNA sequencing revealed persistence of progenitor states, impaired chondrogenic progression, and p53-dependent apoptotic checkpoint activation. Orthogonal WATER analysis of Eed-knockout stem cells recapitulated key features of chromatin gating failure, including temporal redistribution of skeletal development programs and progenitor state persistence, confirming that Eed loss alone is sufficient to produce temporal program redistribution independently of other splicing defects. Trp53 ablation in U11-null limbs partially rescued distal limb structures without correcting the underlying splicing defects, establishing that checkpoint activation amplifies rather than initiates the timing disruption. The limb retains much of its molecular toolkit but executes it in the wrong order, demonstrating that developmental failure arises from mistimed deployment of intact molecular programs. Thus, temporal program architecture is a fundamental organizing principle of morphogenesis.

Clear cell renal cell carcinoma (ccRCC) is initiated by biallelic loss of the tumor suppressor VHL followed by additional genomic alterations, including loss of tumor suppressors PBRM1, BAP1 or SETD2. Although ccRCC is known to be intrinsically sensitive to ferroptosis, the contribution of PBRM1 to this vulnerability, and how it interfaces with VHL loss, has remained unexplored. Using isogenic ccRCC and non-transformed cell models, we show that re-expression of PBRM1 and/or VHL attenuates GPX4-inhibitor-induced ferroptosis, and that the two tumor suppressors act cooperatively: dual reconstitution confers the greatest protection, suppresses lipid peroxidation, and preserves redox homeostasis. Time-resolved RNA-seq reveals that PBRM1 and VHL establish additive, largely non-overlapping "ground-state" transcriptional programs. Integrated pharmacogenomic, CRISPR dependency, and lipidomic analyses converge on two protective axes: restricted labile iron and MUFA-biased membrane remodeling. These findings identify PBRM1 as a previously unrecognized modulator of ferroptosis and define a cooperative chromatin-metabolic axis that buffers ferroptotic cell death in ccRCC.

Cells dynamically regulate the size of their apical domain during epithelial morphogenesis. Multiciliated cells (MCCs) represent an extreme case, undergoing massive apical expansion to accommodate hundreds of basal bodies that generate an array of motile cilia. While actin-generated forces drive this expansion, the molecular mechanisms that govern actin assembly and organization remain poorly understood. We show that in Xenopus, depletion of Septin9 results in failure of filamentous actin assembly, apical domain expansion, and ciliogenesis. Notably, human Septin9 (SEPT9) localizes to cortical microtubules rather than actin filaments. Live-cell imaging and pharmacological studies reveal that SEPT9 and microtubules form a mutually stabilizing scaffold that directs actin assembly. Using isoform-specific depletion and rescue experiments that genetically separate the microtubule from its actin-bound functions of SEPT9, we demonstrate that SEPT9 association with microtubules is required for actin assembly. These results provide the first in vivo demonstration that microtubule-templated actin assembly via Septin9 drives apical surface expansion during epithelial morphogenesis.

Biogenesis of subcellular structures like centrioles is viewed as a physical transformation wherein elementary constituents form order without preexisting templates. Centrioles grow with precision from a composite scaffold known as the cartwheel, which is thought to self-assemble without templates and disassemble following centriole growth; however, the mechanism governing cartwheel assembly-disassembly dynamics remains obscure. Here, we identify ALMS1, a disease-linked, intrinsically disordered protein (IDP), as an external mediator of cartwheel dynamics that causes a seed for cartwheel--and thus centriole--formation without itself incorporating into the seed structure. The cartwheel seed (CS), characterized as a dense composite of CEP152/CEP63 protein complexes, forms in interphase and adopts a nanoscale, concentric ring from which the cartwheel grows. Upon mitotic entry, CSs recruit ALMS1 while disassembling into constituents associating with ALMS1 in proximity, correlating with cartwheel assembly-disassembly cycles. Hypomorph, disease-linked ALMS1 mutations trigger cartwheel expansion and shedding by its own grown procentriole, in turn forming ectopic centrioles, leading to perpetual reciprocal amplification. Without ALMS1, CS formation fails, negating centriole biogenesis, whereas reintroducing ALMS1 initializes biogenesis anew, creating diverse yet heritable architectures that evolve through selection, instead of generating a single canonical form. These results suggest that centriole biogenesis is grounded on adaptable transformation cues extrinsic to its constituents, propagating via IDP-mediated CS assembly-disassembly cycles, a process we conjecture involves memory.

Retromer drives endosomal cargo retrieval in combination with sorting nexin (SNX) adaptors, but how adaptor-cargo combinations specify coat architecture remains unclear. We identify sorting nexin 12 (SNX12) as the retromer adaptor required for human papillomavirus 16 (HPV16) infection and show that the viral L2 capsid protein tail directly engages SNX12-retromer complexes to trigger membrane tubulation. The crystal structure reveals a conserved cargo-recognition mode, whereas cryo-electron tomography of reconstituted assemblies shows retromer arches organized into two lattice configurations stabilized by membrane-proximal interfaces. These lattices assemble as multi-start helices and accommodate curvature through hinge-like motions between arches. These findings establish cargo and adaptor identity as co-determinants of retromer coat architecture, revealing retromer as a programmable system capable of generating route-specific transport carriers.

Acquired resistance to endocrine therapy remains a primary obstacle in the clinical management of estrogen receptor-positive (ER+) breast cancer. While resistance is frequently accompanied by transcriptional rewiring and lineage plasticity, how specific pharmacological modalities dictate divergent resistance trajectories remains poorly understood. Here, we integrate multi-omic profiling, spanning bulk and single-cell transcriptome, chromatin architecture (Hi-C), and the cistrome, to systematically compare the mechanisms involved in adaptive resistance to selective estrogen receptor modulators (SERMs, e.g., tamoxifen) and degraders (SERDs, e.g., fulvestrant), and the mechanism driven by constitutive ESR1 mutation, to characterize how mode of ER perturbation influences lineage identity and epithelial-mesenchymal state. We found that tamoxifen resistant (TamR) cells occupy a distinct transcriptional state characterized by coordinated luminal erosion, partial basal lineage activation, and stabilization of a partial epithelial-mesenchymal (pEMT) program. In contrast, fulvestrant resistant (FulR) cells primarily suppress ER signaling without extensive lineage reprogramming. Finally, ESR1 mutant cells recapitulate ligand-driven ER hyperactivation with limited engagement of mesenchymal and basal gene expression programs. Chromatin profiling further revealed that SERM resistance is accompanied by higher-order genome reorganization, including A-to-B compartment switching at luminal regulators such as GATA3 and ESR1, redistribution of ER and FOXA1 binding, and consequent activation of a pEMT program. Furthermore, we show that SERM-induced reprogramming is accompanied by a distinct mode of immune evasion where the reprogrammed cells do not engage classical T-cell exhaustion programs but instead exhibit coordinated loss of major histocompatibility complex (MHC) class I antigen presentation and establishment of a pro-tumorigenic signaling that strongly predicts adverse survival outcomes in patient cohorts. Together, these findings indicate that endocrine resistance does not converge on a single molecular endpoint but instead reflects drug-specific adaptive states defined by ER signaling context, lineage identity, and chromatin architecture. Our study establishes the basal-pEMT axis as a coordinated, epigenetically encoded module of SERM-induced plasticity and reframes endocrine resistance as a multidimensional evolutionary process shaped by therapeutic mechanisms of action.

Inference of cancer cell states is essential for understanding oncogenic mechanisms and predicting clinical outcomes, yet current reliance on transcriptomic profiling limits scalability and real-time monitoring. Here, we show that cell morphology provides a low-dimensional, observable representation of cellular identity and its dynamics. Using neuroblastoma (NB) as a model system, we establish a machine learning- morphology profiling framework that infers adrenergic (ADRN) and mesenchymal (MES) cell states directly from high-dimensional morphological fingerprints without reliance on transcriptomic measurements. By benchmarking against single-cell RNA sequencing (scRNA-seq), we demonstrate that morphology-defined states closely align with transcriptomic profiles at single-cell resolution. We further show that cell state transitions are represented as continuous trajectories within a morphology-defined state space. Perturbations targeting distinct regulatory layers, including ROCK signaling and epigenetic regulation via EZH2, drive convergent trajectories along a shared phenotypic axis. Together, these results establish cell morphology as a scalable and non-destructive readout of cell state with machine learning providing a unified framework for high-throughput phenotyping and real-time tracking of cancer cell state plasticity.