Biology subjects

Kim, C.

Publications and source records attributed to Kim, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Behavioral Markers of Essential Tremor Correlate with Distributed Alteration of Brain Functional Connectivity

Essential Tremor (ET) is a common motor disorder characterized by involuntary oscillations of the upper limbs during voluntary movement. Although increasing evidence implicates dysfunction of the cerebello-thalamo-cortical pathway, ET remains a diagnosis of exclusion, as no definitive biological marker currently exists. To better characterize ET, we recently hypothesized that impaired compensation of sensorimotor delays within the long-latency feedback pathways may generate the tremor-like oscillations observed in ET. This theory suggests that the mean spectral amplitude (MSA), derived from limb kinematics, may serve as a potential marker of ET. Here we investigated the relationship between MSA, standard clinical assessment (Fahn Tolosa Marin Tremor Rating Scale; FTM-TRS), and brain connectivity derived from resting state functional magnetic resonance imaging (rs-fMRI). Using seed-based analyses, we replicated previous findings of reduced functional connectivity between the dentate nucleus and components of the cerebello-thalamo-cortical pathway in ET patients compared with neurologically intact (NI) age-matched participants. Graph-theoretical analyses of whole-brain functional networks revealed distributed alterations in network topology across motor-related cortical and subcortical regions. Several graph metrics correlated with FTM-TRS scores and/or MSA, particularly within motor-related cortical and subcortical circuits, including the thalamus, basal ganglia, and cerebellum in ET. These findings indicate that ET is characterized by distributed alterations in functional brain networks beyond reduced connectivity of dentate nucleus and highlights MSA as a candidate quantitative marker linking altered brain connectivity to sensorimotor delay-driven tremor oscillations.

neuroscience↗

bioRxiv2026

Single-cell profiling of physically interacting immune cells using image-guided sorting

Single-cell transcriptomics of cell-cell complexes offers key insights into in vivo immune interactions, yet distinguishing true physical contacts from artifacts remains challenging. Here, we integrated spectral imaging cell sorting with physical cell deconvolution to separate circulating T cell-monocyte doublets from tuberculosis patients into physically interacting (in-contact) and non-interacting (coincidental) populations. Single-cell sequencing of individual cell partners revealed that physical contact is associated with robust signatures distinct from singlets, including unidirectional monocyte-to-T cell RNA transfer, heightened metabolic activity and T cell cytotoxicity, and a trend toward antigen-specific enrichment. These signatures spanned all T cell and monocyte subpopulations, reflecting a global program of T cell-monocyte engagement. Coincidental doublets displayed intermediate transcriptional profiles between singlet and in-contact states, suggesting the presence of recently disrupted or forming physical pairs. This framework provides high-fidelity deconvolution of cellular interactions, uncovering signatures governing T cell-monocyte communication in human disease.

immunology↗

bioRxiv2026

Computational design of a versatile, zero-radius proximity labeling enzyme

The ability to map protein interactomes and organelle proteomes is foundational for achieving a molecular understanding of living cells. Proximity labeling (PL) provides a powerful strategy for this, but existing enzymes and photocatalysts are limited by their spatial resolution, reliance on biotin, and/or in vivo compatibility. Here we report FlexID, an engineered promiscuous ligase that catalyzes the rapid attachment of diverse small-molecule probes to proximal endogenous proteins. Critically, FlexID operates through a zero-radius, direct-contact mechanism, offering superior spatial precision compared to existing PL tools. We engineered FlexID by combining the strengths of sequence- and structure-trained computational models to enhance its catalytic activity and structural stability. Biophysical analysis revealed that specific conformational changes in FlexID improve its ability to recognize diverse target proteins while simultaneously preventing the premature release of the reactive intermediate. We demonstrate FlexID's versatility through in vivo proximity labeling, comprehensive organelle proteome mapping, and a high-throughput, fluorescence-based screen for molecular glues. Our work shows that computational methods can be harnessed to create mechanistically distinct PL enzymes and establishes FlexID as a flexible, high-resolution tool for mapping protein interactions and proteomes in living cells.

bioengineering↗

bioRxiv2026

Single-Cell and Spatial Analysis Reveals Retention of FCRL4⁺ Memory B Cells in Pediatric Tonsillar Hypertrophy

Pediatric tonsillar hypertrophy is a leading cause of sleep disordered breathing in children, yet the immune mechanisms sustaining tonsillar enlargement remain unclear. Using integrated single cell and spatial profiling of pediatric tonsils in a discovery cohort (n = 45) and independent validation cohort (n = 32), we identify a selective expansion and follicular retention of FCRL4+ memory B cells within the mantle zone of hypertrophic tonsils. These cells exhibit a quiescent, tissue-adapted phenotype characterized by NFATC1 repression and reciprocal RUNX1/RUNX2 regulation. Their accumulation is orchestrated by follicular type 1 regulatory T (Tr1) cells, which engage CTLA-4/CD86 checkpoint interactions to suppress plasma cell differentiation and reinforce a local immune tolerance program. Together, these interactions establish a persistent follicular niche enriched in regulatory FCRL4+ memory B cells. Our findings delineate a mechanistic Tr1/FCRL4+ B cell axis underlying follicular hypertrophy and highlight potential immunomodulatory targets for nonsurgical management of pediatric sleep-disordered breathing.

immunology↗

bioRxiv2026

Predator type shapes call-type composition and post-threat vocal dynamics in Japanese quail (Coturnix japonica): a pilot case-series

Japanese quail (Coturnix japonica) rely on an extensive vocal repertoire to coordinate social behaviour and respond to predation risk, yet how individual call types are modulated by predator identity remains poorly characterized. In this pilot case-series, two sexually mature Japanese quail (each contributing more than 2,000 classified vocalizations across repeated predator-exposure trials) were exposed to simulated aerial (hawk) and terrestrial (cat) predator stimuli across four social contexts, before, during, and after stimulus presentation. Vocalizations were classified, via blind dual-observer review, into 18 spectrographically distinct call types (an exploratory repertoire estimate, not independently statistically validated), of which 10 were acoustically characterized. Chi-square analyses of the full call-type composition revealed highly significant differences between hawk and cat exposure in both individuals (both p < 0.0001); call types 5 and 10 were significantly cat-biased and call type 2 was significantly hawk-biased in both individuals. An exploratory correlation suggested that call types with a higher maximum frequency tended to be relatively hawk-biased (Spearman rho = -0.67, p = 0.033, uncorrected for multiple comparisons). Independently, call-type composition shifted significantly between the pre- and post-exposure phases in all four individual-by-predator combinations (all p < 0.0001), driven substantially by a consistent post-exposure increase in call type 9 across both individuals and both predator classes. Additional exploratory analyses of social-context (mirror and concealed-conspecific) effects on call-type composition are presented in the supporting information. Given the small sample size (n = 2), these findings are presented as case-based, hypothesis-generating observations intended to justify and inform a fully powered follow-up study, rather than as population-level conclusions.

animal behavior and cognition↗

bioRxiv2026

A high-resolution blood immune cell doublet atlas via imaging spectral cytometry

Circulating cell-cell complexes (doublets) provide critical insights into in vivo immune interactions. Here, we leverage high-dimensional imaging spectral cytometry to systematically map the landscape of immune doublets in human peripheral blood. By integrating morphometric imaging features with a 22-color spectral panel, we established a gating workflow that cleanly segregates genuine, physically interacting complexes from coincidental transits and platelet contaminants, and resolved 12 highly pure homotypic and heterotypic immune doublet configurations in peripheral blood mononuclear cells (PBMC). At steady state, each doublet population displayed unique abundance, affinity and surface phenotypic profiles relative to circulating singlets. Principal component analysis (PCA) of quantitative imaging features further revealed lineage-specific topologies distinguishing singlet cells, homotypic doublets, and heterotypic pairs. Finally, comparative cohort analysis demonstrated that while doublet frequencies, affinities and surface phenotypes remain comparable between healthy donors and patients with tuberculosis (TB) disease, imaging-derived features uncovered disease-specific alterations in doublets morphology. Specifically, high-dimensional clustering using imaging parameters showed that TB disease significantly enriches for a tightly synapsed T cell-monocyte cluster characterized by high CD3-CD14 pixel correlation. Collectively, this study establishes a robust framework for mapping circulating cell-cell networks and demonstrates the superior sensitivity of imaging features over conventional fluorescence for capturing functional immune interactions in health and disease.

immunology↗

bioRxiv2026

Single-cell foundation models benefit from cross-modal training: adding proteomics data beats parameter scaling

Leading cellular foundation models have been trained on hundreds of millions of single-cell transcriptomes, with progress increasingly driven by larger datasets and model scaling. Here, we asked whether adding a proteomics modality can improve gene-level and cell-level representations beyond scaling RNA-only models. We introduce cross-modal continued pretraining, fine-tuning a published single-cell model (Tahoe-x1) on a large corpus of proteomic profiles. Training a 70M-parameter Tahoe-x1 model for a single epoch on 48843 proteomic samples from 440 diverse mass-spectrometry studies matched or exceeded 1B- and 3B-parameter RNA-only models across most of the original Tahoe-x1 evaluation benchmarks. This shows that with the right training recipe, heterogeneous proteomics data can improve the learned representations of single-cell RNAseq samples, demonstrating strong out-of-distribution generalization. Cross-modal pretraining also improves transfer to a held-out protein perturbation benchmark, where scaling the RNA-only model does not provide comparable benefits. These results demonstrate that careful targeted curation of proteomics data can provide larger benefits than increasing the model size alone and suggest that multimodal pretraining is a promising path toward more informative biological foundation models.

bioinformatics↗

bioRxiv2026

Exposure Duration Shapes the Hepatic Response to GenX: Divergent Acute and Chronic Transcriptomic Profiles Reveal Non-Monotonic Dose Effects and Increased Sensitivity in Human Liver Spheroids

Hexafluoropropylene oxide dimer acid (GenX), a replacement for legacy per- and polyfluoroalkyl substances (PFAS), is increasingly detected in the environment, yet its chronic toxicity remains poorly characterized. Current safety assessments rely largely on short-term, high-dose studies that may not capture the biological consequences of long-term, low-dose exposure. To address this gap, we employed 3D human liver (HepG2/C3A) spheroids cultured in a continuously rotating bioreactor system (ClinoStar) to systematically evaluate dose- and time-dependent mRNA changes in response to GenX under environmentally relevant conditions. Spheroids were exposed to GenX (0.08-50 M, spanning environmentally relevant to mechanistically informative concentrations) for acute (4 days) and chronic (4 weeks) durations, followed by genome-wide TempO-Seq transcriptomic profiling and benchmark dose (BMD) modeling. GenX elicited pronounced non-monotonic mRNA changes in acute exposure conditions, with the greatest number of differentially expressed genes (DEGs) observed at an intermediate concentration (0.4 M). In contrast, chronic exposure exhibited a generally concentration-dependent increase in DEGs, except for the 10 M condition, indicating a more consistent dose-response relationship than acute exposure. Notably, acute and chronic exposures elicited qualitatively distinct mRNA changes with low concordance across matched concentrations, demonstrating that exposure duration was a major determinant of mRNA changes. Acute low-dose GenX exposure preferentially modulated mRNA encoding components of cell cycle-related pathways, whereas acute higher dose exposures suppress mRNA levels of the constituents of lipid metabolic pathways and increase expression of mRNA encoding proteins involved in stress- and toxicity-associated signaling. Chronic exposure revealed a different pattern of changes in mRNA expression not observed under acute exposure conditions, including suppression of cellular components involved in lipid-related pathways at the lowest concentration tested. At higher concentrations, mRNA levels of components of multiple metabolic pathways were altered. Benchmark dose modeling identified a significantly lower transcriptomic point of departure (tPOD) for chronic exposure as compared to acute exposure, suggesting increased cellular sensitivity to prolonged GenX exposure and supporting the relevance of chronic models for human exposure assessment. Collectively, these findings demonstrate that GenX elicits time-dependent and non-monotonic changes in mRNA levels of human liver (HepG2/C3A) spheroids, with distinct responses depending on the exposure duration and dose. This study, therefore, highlights the importance of incorporating chronic, human-relevant in vitro models and transcriptomic endpoints into PFAS risk assessment and suggests that conventional short-term assays may underestimate the biological impact of sustained low-dose exposure. Key message (Impact of the study)This study provides systematic comparisons of short term (4 day) versus longer term (4 weeks), environmentally relevant GenX exposure in human liver spheroids, revealing non-monotonic, time-dependent changes in mRNA levels encoding cellular components of lipid metabolism-related pathways with potential implications for appropriate dose and time exposure parameters for use in New Approach Methods to be applied in risk assessment.

pharmacology and toxicology↗

bioRxiv2026

Sex Differences in Motor Unit Properties and Force Steadiness: Insights from Strength-Matched Elbow Flexion

Sex-related differences in force steadiness are often attributed to maximal strength and motor unit (MU) properties, but their independent contributions remain unclear. This study strength-matched females and males to remove the influence of maximal strength and determine whether MU properties are associated with sex-related differences in force steadiness. Twelve young adults (6 females) were matched for elbow flexion strength (females, 188.6{+/-}15.6 N; males, 199.7{+/-}24.8 N, p=0.4). Both groups performed submaximal isometric elbow flexion contractions at 2.5%, 5%, 10%, 15%, and 25% MVC. The MU recruitment thresholds (RT), discharge rates (MUDR), and coefficient of variation of interspike intervals (CVISI) were measured from intramuscular fine wire electromyography (EMG) electrodes. Force steadiness was quantified as the standard deviation (SD) and coefficient of variation (CV) of force. Across forces, SD and CV of force did not differ between females and males (p>0.05). Females had a higher recruitment threshold than males (p<0.05). Females had higher MUDR at 15% and 25% MVC (p<0.02), while males were higher at 5% MVC (p=0.02). The CVISI was greater in females (p<0.001) and positively correlated with SD of force (r=0.2) and negatively with CV of force (r=-0.2) in females and males. When strength was matched, sex-related differences in force steadiness were not evident. However, females exhibited higher MU recruitment thresholds, MUDR and CVISI. Despite greater CVISI in females, these differences did not translate into greater force fluctuations, suggesting that individual MU discharge variability is not a primary predictor of force steadiness when maximal strength is controlled. NEW & NOTEWORTHYO_LIStrength matching eliminated sex-related differences in elbow flexor force steadiness. C_LIO_LIFemales achieved similar force steadiness using higher MU recruitment thresholds and discharge rates, particularly in the short head of the biceps brachii. C_LIO_LIIn females, the greater variability in motor unit discharge was not associated with reduced force steadiness. C_LI

physiology↗

bioRxiv2026

The roles and synthesis of inorganic polyphosphate in Bacillus cereus

Inorganic polyphosphate (polyP) is a universally conserved biopolymer central to bacterial stress survival, yet understanding of its roles derives almost entirely from Gram-negative models in which polyP accumulates intracellularly following nutrient downshift. We examined polyP metabolism in the Gram-positive spore-forming bacterium Bacillus cereus using deletions of the polyP kinases PPK1 and PPK2 and the exopolyphosphatase PPX. Intracellular polyP synthesis required PPK1 and was opposed by PPX and PPK2: ppx mutants accumulated polyP in sporulation medium by 24 hours, ppx ppk2 double mutants accumulated more, and no ppk1 mutant accumulated any. A ppk1 ppx double mutant could not be generated, suggesting that unopposed PPK2 activity is lethal. Unlike Escherichia coli and Pseudomonas aeruginosa, B. cereus did not accumulate polyP after shift to minimal medium, increasing only modestly in stationary phase. Fluorescence and transmission electron microscopy localized intracellular polyP to electron-dense granules within ribosome-depleted cytoplasm. Cells bearing these granules remained membrane-intact yet failed to resume growth over 8 hours in rich medium, leading us to propose that polyP drives ribosome sequestration into condensates and a hibernation-like state. Unexpectedly, B. cereus also released close to 100{micro}M polyP extracellularly during late stationary phase, even in a ppk1 ppk2 mutant lacking both known synthetases. Extracellular polyP resisted hydrolysis by purified PPX even after deproteinization, indicating an atypical structure. Bacillus thuringiensis and Bacillus anthracis released similar amounts of extracellular polyP. Together these results identify two distinct polyP pools in the B. cereus group: a PPK1-dependent intracellular pool and an extracellular pool made by an uncharacterized pathway. ImportanceBacillus cereus is a spore-forming bacterium that causes foodborne illness and persists in soil and food-processing environments, where survival depends on managing phosphate and energy reserves during starvation. Inorganic polyphosphate (polyP), an ancient polymer used by nearly all cells to withstand stress, has been studied almost entirely as a molecule stored inside bacteria. We show that Bacillus cereus maintains two separate polyP pools. The internal pool is made by a known enzyme (PPK1) and is associated with dormant cells whose protein-making machinery appears to be packed away. The external pool is made without any known polyP-synthesizing enzyme, pointing to a novel polyP synthesis pathway that is shared with the close relatives Bacillus thuringiensis and Bacillus anthracis.

microbiology↗

bioRxiv2026

Covalent bond formation caught in a LOV photoreceptor

Light-oxygen-voltage (LOV) domains are blue-light photoreceptors of plants, algae and fungi, and among the most widely used tools in optogenetics. They switch on by forming a covalent thioether bond between a conserved cysteine and their flavin chromophore, in a reaction that needs a proton to cross from the cysteine to the flavin through a pocket containing essentially no water. Its mechanism has been debated for two decades1, and because the chemistry is over within a microsecond its elementary steps have stayed hidden. Here we combine 10 time-resolved serial femtosecond crystallography snapshots and infrared spectroscopy with QM/MM calculations to resolve the entire sequence of events at 1.4 [A] resolution: from excited-state distortion of the flavin ring (10-100 ps), through hydration of a surface channel (10 ns) and a single ordered water reaching the active site as the reactive cysteine shifts between its conformations (100-500 ns), to the thioether bond itself, caught half-formed at 1 {micro}s (half the molecules reacted, half still poised) and complete at 10-100 {micro}s. That water bridges the cysteine and the flavin and shuttles the proton, lowering the barrier from [~]35 to [~]15 kcal/mol and accelerating the reaction by roughly fourteen orders of magnitude (without it, the half-life would be [~]237,000 years), then departs before the bond forms. Proteins can therefore hydrate a dehydrated active site transiently and on demand to overcome otherwise prohibitive reaction barriers, a catalytic strategy that reaches well beyond photoreceptors.

biophysics↗

bioRxiv2026

Differential Regulation of Branched-Chain Amino Acids During Early Germination of Mungbean (Vigna radiata L.)

Branched-chain amino acids (BCAAs) are essential amino acids involved in protein synthesis and energy metabolism. Because animals cannot synthesize BCAA de novo, plant-derived BCAAs are important to human nutrition. Although mungbean sprouts are widely consumed as functional plant-based food materials, changes in individual BCAA accumulation and their transcriptional regulation during mungbean germination remain poorly understood. In this study, amino acid contents and transcriptomic profiles were analyzed at three germination stages, 8H, 24H, and 72H. Total BCAA content increased during germination, whereas individual BCAAs exhibited distinct temporal accumulation patterns. Isoleucine and valine increased until 72H, while leucine increased during early germination and decreased after 24H. Transcriptome analysis revealed time-dependent expression changes in BCAA biosynthesis and degradation genes associated with the leucine decrease after 24H. These findings suggest that 24H represents an important transition point for BCAA accumulation and compositional change during mungbean germination. This study provides molecular evidence for the regulation of BCAA metabolism during mungbean germination and supports the potential use of germinated mungbean as a plant-based amino acid resource.

plant biology↗

bioRxiv2026

Predicting Macroscopic Axon Topology from Microscopic Kinematics: An Interactive Tracking and Random Walk Pipeline for Substrate-Dependent Cortical Neurospheres

The cortical neuron is a fundamental building block of the mammalian brain, and the morphology of its axonal projections is central to how functional circuits assemble. The trajectory along which an axon grows is a key determinant of connectivity, yet the kinematics of cortical axon outgrowth remain poorly quantified. Characterizing these dynamics is most tractable in vitro, where axonal growth can be measured directly and under controlled, reproducible conditions. Even in culture, however, this remains challenging because cortical neurons require dense plating for viability, and their soma is motile, so growth behavior is highly sensitive to local density and population context, complicating reproducible measurement of intrinsic dynamics. To overcome these limitations, we used size-controlled cortical neurospheres, which provide a fixed spatial origin and a reproducible environment, together with a custom semi-automated tracking pipeline to quantify single-axon kinematics across two functionalized substrates and two developmental phases. This approach revealed a substrate-dependent divergence in outgrowth: during the later developmental phase, axons on poly-D-lysine with laminin (PDL-LA) substrate grew faster than those on PDL, with a mean step size of 0.436 versus 0.339 {micro}m /min. Decomposing trajectories into Katz dynamic states, we built a generative biased random walk model that reproduces axonal behavior at both microscopic (single-axon) and macroscopic (network topology) scales. This open, reproducible framework links single-axon kinematics to network architecture, enabling the structural connectivity of neurospherebased circuits in vitro to be predicted from measurable growth dynamics, a necessary foundation for future studies linking circuit structure to emergent function.

bioengineering↗

bioRxiv2026

Integrative multi-omic analysis identifies tumor-intrinsic p38 as a driver of immune exclusion in human epithelial cancers

Patients with tumors not responding to immune-checkpoint inhibition (ICI) often harbor a non-T cell-inflamed tumor microenvironment, characterized by the absence of IFN-{gamma}-associated CD8+ T cells and dendritic cell activation. While the role of p38 mitogen-activated protein kinases (MAPKs) in regulating dendritic and myeloid cells is established, the tumor-intrinsic immunomodulatory function of p38 remains underexplored. Here, we identify tumor cell-intrinsic p38 signaling as a target candidate associated with immune exclusion and reduced immunotherapy response. In human papillomavirus-negative head and neck squamous carcinoma (HNSCC), molecular analysis of 395 tumor tissues revealed a p38-centered network enriched in non-T cell-inflamed tumors. Multi-cancer single-cell RNA sequencing analysis of over 200,000 cells further identifies p38 activation as a potential immune-exclusion program across multiple epithelial tumor types, including HNSCC and lung squamous cell carcinoma (LUSC), supported by tissue validation in [~]250 human biospecimens using multispectral imaging and digital spatial profiling. Functional studies demonstrate that p38 knockdown or pharmacologic inhibition in HNSCC and LUSC cell lines increases T cell migration, with CXCL16 identified as a chemokine mediator in vitro; neutralization of CXCL16 attenuated this effect. Together, these findings identify tumor-intrinsic p38 activation as a driver of immune exclusion in epithelial cancers and support its potential as a therapeutic target to overcome immunotherapy resistance.

Cancer Biology↗

bioRxiv2026

Dissecting and directing pathology foundation models

Foundation models (FMs) are central to digital pathology, encoding histology images into dense embeddings for facilitating diagnostic classification, molecular alteration prediction, and clinical outcome modeling. However, the opacity of these embeddings renders FM-based systems "black boxes," limiting their trustworthiness for clinical translation and utility for scientific discovery. Here, we introduce PICASSO (Pathology Image Concept Atlas built via SparSe dictiOnary learning), a framework that makes pathology FMs interpretable and controllable. PICASSO decomposes FM embeddings into human-interpretable visual concepts using a sparse autoencoder. It is trained on more than 120 million tissue patches across 32 cancer types, producing the first pan-cancer atlas of histomorphological concepts. We demonstrate that PICASSO enables diverse downstream applications of FM embeddings by exposing interpretable structure within learned representations and supporting concept-level intervention. It enables auditing of clinical model behavior by revealing the morphological features driving predictions. Beyond transparency and validation, PICASSO enables the discovery of new biological insights; for example, it identified hobnailing epithelial morphology as a previously unrecognized biomarker of EGFR mutations in lung adenocarcinoma. By linking PICASSO-derived concepts with spatial transcriptomics, we uncover associations between morphological patterns and gene expression programs. Furthermore, PICASSO allows suppression of concepts associated with technical artifacts, thereby reducing model reliance on spurious signals. Finally, PICASSO enables controlled manipulation of learned concepts to generate counterfactual embeddings for exploratory therapeutic analysis, such as modulating tumour-infiltrating lymphocyte density to assess impacts on predict survival outcomes. Together, PICASSO provides a principled framework for transforming pathology FMs into platforms for mechanistic insight and discovery.

pathology↗

bioRxiv2026

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

Single cell transcriptomics has transformed our knowledge of reproductive tissues, yet studies remain largely organ-specific and temporally limited, leaving an incomplete picture of how cell types are distributed across the reproductive system over a lifetime. Gynaecological conditions affect more than one in four females and frequently span multiple organs and life stages. To advance our understanding and treatment of these conditions, an integrated cellular reference is essential. Here we present the Human Female Reproductive System Cell Atlas v1: a single-cell transcriptomic resource integrating more than 2M cells across the ovary, fallopian tube, uterus, cervix and vagina over the lifespan and menstrual cycle, further integrated with spatial transcriptomics and chromatin accessibility profiling to define 210 cell types through community-based annotation. Cross-organ integration resolves shared and organ-specific cellular states, identifying uterine-specific perivascular populations lining uterine spiral arteries, hypoxia-sensing type 3 innate lymphoid cells (ILC3s) enriched in the uterus, and lipid-associated macrophages with distinct subsets in each reproductive organ, including a previously undescribed population shared between the uterus and fallopian tube. Cross-organ integration enables detection of ectopic epithelial populations in otherwise healthy donors, including endometrial-like cells within a paediatric ovary consistent with early endometriosis. Integration with genome-wide association studies (GWAS) reveals that risk variants for major gynecological conditions act in mesenchymal cell states defined by specific transcriptional programmes and spatial or temporal context - for instance, heavy menstrual bleeding risk is enriched in basal fibroblasts (SFRP5) of the regenerative endometrial compartment. An integrated chromatin accessibility atlas provides peak-to-gene maps across reproductive cell types, enabling nomination of disease effector genes and providing the first regulatory evidence linking a Polyendocrine Metabolic Ovarian Syndrome (PMOS) risk locus to INHBB in granulosa cells. Together, this resource establishes a cellular and molecular framework for reproductive biology and the pathogenesis of neglected gynaecological conditions.

Cell Biology↗

bioRxiv2026

Tumor extracellular vesicle RNA profiling predicts treatment response in pediatric diffuse midline glioma

Detection of reliable markers of therapy response and drug resistance remains a major unmet need in brain cancer, as serial tumor biopsy is often not feasible. This challenge is particularly acute in diffuse midline glioma (DMG), a fatal pediatric brain tumor for which new targeted therapies are entering clinical use, yet tools for real-time molecular analysis of tumor evolution during therapy remain lacking. Here, we demonstrate that plasma tumor-derived extracellular vesicle (EV) profiling provides a minimally invasive and complementary approach for diagnosis and longitudinal molecular monitoring in H3K27M-mutant DMG. Across patient-derived tumor models and clinical plasma samples, EV mRNA levels correlated strongly with parental tumor transcriptomes. EV H3K27M mRNA enabled discrimination of DMG from non-DMG controls, and exploratory EV response-associated mRNAs were linked to radiographic response and progression-free survival in patients receiving ONC201. To enable tumor-selective EV enrichment and multiplexed molecular profiling within a clinically practical workflow, we developed a new integrated platform supporting same-day EV analysis from small plasma volumes. This work represents the first proof-of-concept demonstration of the diagnostic and treatment response relevance of tumor-derived EV RNA in pediatric DMG and establishes a generalizable framework for minimally invasive longitudinal molecular monitoring in diseases where tissue access is inherently limited.

cancer biology↗

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗