Biology subjects

Xu, B.

Publications and source records attributed to Xu, B..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Chemokine-Dependent Natural Killer Cells Prevent Pulmonary Metastasis in a Newly Established Mouse Osteosarcoma Model

Rampant genomic instability of osteosarcoma (OS) and associated inter- and intratumoral heterogeneity convey a high risk of metastasis despite contemporary multimodal therapy. A mouse primary OS tumor model, originating from Myc-overexpressing Trp53-null mesenchymal progenitor cells, closely mimics cardinal genetic features and gene expression patterns of human OS samples. Subcutaneous injection of OS cells into immunocompromised NSG mice produced extensive metastases, whereas many fewer metastases occurred in T cell-deficient nude mice, suggesting a principal role for innate immunity in controlling OS dissemination. Depletion of natural killer (NK) cells in nude mice facilitated OS metastasis. OS cells released a suite of chemokines, with CCL2 the most prominent. A genome-wide CRISPR/Cas9 screen in OS cells identified 11 genes, including Ccl2, whose loss facilitated pulmonary metastasis in nude mice. Disruption of CCL2 in OS cells partially phenocopied the effects of antibody-dependent NK cell depletion, underscoring a plausible OS-NK signaling pathway that limits OS metastasis. SignificanceOsteosarcoma exhibits complex genomic instability and a propensity for pulmonary metastasis that limit chemotherapeutic response and patient survival. Despite the plethora of heterogeneous genetic alterations that connote poor prognosis, a novel preclinical in vivo model for studying metastasis highlights potentially targetable signaling between osteosarcoma cell-derived chemokines and pulmonary NK cells.

cancer biology↗

bioRxiv2026

Catalytic rewiring of RuvC-II catalytic site activates trans-cleavage in Fanzor2

Fanzors are eukaryotic RNA-guided endonucleases that mediate programmable cis-cleavage in eukaryotic cells, but their potential target-induced collateral (trans) cleavage activity remains largely unexplored. Here, we show that catalytic rewiring of the RuvC-II catalytic site activates robust trans-cleavage activity in Acanthamoeba polyphaga mimivirus Fanzor2 (ApmFz2). The representative variant ApmFz2-EP displayed DNA- and RNA-triggered trans-cleavage, attenuated cis-cleavage, minimal TAM dependence, and activation by as few as seven nucleotides of guide-target complementarity. Mechanistic analyses indicate that relieving steric constraints surrounding the conserved alternative glutamate within the RuvC-II activates trans-cleavage and reshapes target-recognition specificity. Coupling ApmFz2-EP with nucleic acid amplification enabled FINDER, a Fanzor-based diagnostic platform for sensitive pathogen detection and broad detection across genetically diverse target subtypes. In addition, the mismatch-sensitive ApmFz2-EA variant enabled specific single-nucleotide variant (SNV) genotyping. Together, this work expands the functional scope of Fanzors and identifies catalytic-center engineering as a strategy for developing compact, programmable nucleic acid diagnostics.

bioengineering↗

bioRxiv2026

Evaluation of analysis modes for RNA coexpression in single-cell and bulk tissue

Coexpression of transcripts presents the most common means of computational inference of transcription factor regulation, and is often combined with other data types to infer regulatory networks. With the growing popularity of single-cell approaches, there are questions about how best to extract coexpression information from the data. Recently we reported a simulation study that explored the differences among coexpression performed at different levels: across single cells (xCell, per cell type), across subjects from pseudobulked single-cell data (xSubject, per cell type), or across subjects using bulk tissue samples (xBulk). Here we test predictions made by those models using real data. We consider both preservation (consistency of coexpression findings across different levels of analysis of the same data) and replicability across independent studies, as well as biological interpretability. We find that preservation across levels is limited, indicating the choice of analysis level will affect outcomes. We show that xCell coexpression is more replicable across studies compared to xSubject. xBulk coexpression is dominated by patterns driven by variability in cellular composition and fails to capture much coexpression that is reliably detected at finer resolutions. While all modes of analysis exhibit some enrichment for known regulatory relationships, it was highest with the xCell mode. Finally, we present a case study of the effect of analysis modes on a schizophrenia-associated pattern, reinforcing the importance of analytic choices in the interpretation and replicability of coexpression analyses. Together with our modeling study, this work emphasizes the importance of understanding sources of expression covariation as they relate to the goals of the analysis, and recommend single-cell-based data with biological replicates should be the focus of attempts to infer dynamic regulatory interactions that are more likely to be replicable by others.

bioinformatics↗

bioRxiv2026

Persistent Post-Inflammatory Matrix Stiffening Defines a Premalignant Mechanical Niche in Ulcerative Colitis-Associated Neoplasia

Patients with long-standing ulcerative colitis (UC) remain at risk for colorectal neoplasia even after overt inflammatory activity improves, suggesting that repaired mucosa may retain residual tissue-level abnormalities. Whether extracellular matrix remodeling leaves a persistent mechanical cue that contributes to early neoplastic remodeling is unknown. Here we identify post-inflammatory matrix stiffening as a premalignant mechanical niche in UC-associated neoplasia. In human colonic biopsies, collagen remodeling and atomic-force-microscopy-based mucosal stiffness increased from non-UC controls to UC and UC-associated dysplasia. A stiffness-associated transcriptional program was also enriched in histologically non-dysplastic mucosa from patients with UC-associated neoplasia. In mouse models, colonic stiffness increased along the colitis-to-tumorigenesis axis and remained elevated during apparent recovery, when epithelial permeability, junctional protein loss, crypt proliferation and nuclear {beta}-catenin accumulation persisted despite reduced disease activity. Stiffness-controlled intestinal epithelial cultures showed that stiff substrates were sufficient to disrupt ZO-1 organization and enhance {beta}-catenin redistribution, particularly under TNF- stimulation. Pharmacological matrix normalization with {beta}-aminopropionitrile partially restored barrier organization and attenuated early epithelial remodeling in vivo. Single-cell profiling identified a stiffness-associated MMP7-positive/YAP-active epithelial state that was enriched in collagen-rich regions and reduced after matrix softening. Inhibition of YAP or MMP7 attenuated stiffness-associated junctional disruption and {beta}-catenin redistribution. These findings suggest that inflammatory recovery and mechanical recovery can be uncoupled, and that persistent mucosal stiffening provides a tissue-level mechanism by which chronically injured UC mucosa may remain biologically vulnerable to premalignant epithelial remodeling.

Cancer Biology↗

bioRxiv2026

Incorporation of single-neuron projectome-based connectivity motifs enhances the cortex-specific performance of artificial neural networks

The organizational principles of natural neural networks could inspire the new architecture design of artificial neural networks (ANNs). Analysis of single-neuron connectomes of mouse brains revealed distinct profiles of three-node connectivity motifs in various cortical areas and hippocampal formation. A connectome-informed neural network algorithm ("CINA") was developed to incorporate natural connectivity motifs into ANN algorithms represented by recurrent neural network (RNN) and transformer-based large language model (LLM). We found that incorporation of the average profile of cortical motifs improved the RNNs performance in noise-resistant categorization and motor learning benchmark tasks, as compared with RNNs with random connectivity. Notably, incorporating cortex-specific motifs further elevated the RNNs performance in tasks related to the cortical function, and this effect was enhanced by artificially increasing the bias in the motif profile. Similar experimental results were verified on an LLM using Motif-Transformer for natural language question answering and brain-signal decoding tasks. Graph-theoretic analyses showed that incorporating natural motifs drove the emergence of modular and small-world properties in ANNs. Together, we demonstrated not only connectome-inspired optimization of ANN architecture but also functional significance of specific motif profiles in various cortices.

neuroscience↗

bioRxiv2026

mRNA concentration-dependent translation enables rapid and sharp patterning in resource constraint Drosophila embryos

One of the fundamental challenges in protein expression during embryogenesis is the establishment of dynamic protein patterns under the resource constraint. This constraint is particularly stringent in enclosed Drosophila early embryogenesis, where protein synthesis relies exclusively on maternally supplied resources, yet its zygotic protein patterns still exhibit sharp boundaries and dynamic abundance changes for body plan development. Here, by integrating single-molecule imaging with mathematical modeling, we reveal that an mRNA concentration-dependent translation enables sharp and dynamics patterning even under resource constraint in embryos. Firstly, we reveal pronounced spatial heterogeneity in the fraction of hunchback (hb) mRNAs engaged in translation, challenging the conventional assumption of uniform translation rates. We further demonstrate that hb mRNA concentration is a dominant predictor of this heterogeneity, showing an increasing-saturation relationship between this translating fraction and mRNA abundance. This regulatory strategy enables combination of sharp Hb protein boundaries and close tracking of protein level to mRNA concentration decline under slow protein turnover rates, correlated to the resource efficiency in embryos. Together, our findings identify a translational control strategy that links molecular-scale regulation to embryonic pattern formation under resource constraints and highlight mRNA concentration-dependent translation as an effective way simultaneously enabling dynamic and economical spatial gene expression in biological systems.

biophysics↗

bioRxiv2026

S-nitrosylation of protein kinase A is required for its activation by GPCRs

Stimulation of many G protein-coupled receptors (GPCRs) increases cyclic adenosine monophosphate (cAMP) and nitric oxide (NO). While cAMP-dependent activation of protein kinase A (PKA) is a central regulatory mechanism, a parallel role for NO in GPCR transduction has not been established. Here we show that upon stimulation of multiple GPCRs in heart, brain, and fat, the regulatory subunits of PKA undergo enzymatic S-nitrosylation by SNO-CoA-assisted nitrosylase (SCAN). S-nitrosylation by SCAN is required for dissociation of PKA holoenzymes and activation of PKA. In transgenic and cardiovascular disease models, impaired adrenergic stimulation is identified with deficient S-nitrosylation of PKA, which can be rescued by the drug sodium nitroprusside. Our work suggests a new understanding of GPCR physiology with direct application to the clinical setting.

physiology↗

bioRxiv2026

Specification of bone marrow sinusoids requires TIE2-mediated positive feedback involving COUPTFII and VEGFR3

The bone marrow (BM) vascular network plays crucial roles in driving bone development and supporting hematopoiesis, yet the mechanisms governing its specialized architecture, particularly sinusoidal morphogenesis, remain inadequately characterized. We show in this study that TIE2 (Tek) was highly expressed by BM sinusoidal endothelial cells (SEC) and the endothelial Tek excision led to BM sinusoidal capillarization. Particularly, the BM sinusoids displayed thinner vessel diameter with the aberrant mural cell coverage in the Tek mutants. Mechanistically, TIE2 insufficiency led to a dramatic decrease of VEGFR3 in BM-SECs while its expression in hepatic sinusoids was not obviously altered. The RNA-seq analysis showed that GO terms enriched for the downregulated genes were related to the biological processes including sinusoidal development while pathways related to arterial ECs and angiogenesis were upregulated in the bone marrow of Tek mutants. The alteration of sinusoidal VEGFR3 expression occurred within 48 h after the induced endothelial deletion of Tek. Consistently, the defective BM sinusoidal formation was validated with the induced Tek deletion in VEGFR3+ SECs. The insufficiency of TIE2 ligand ANGPT1 also led to reduced sinusoidal VEGFR3, accompanied by similar BM sinusoidal defects. Furthermore, disruption of sinusoidal morphogenesis was observed in mutant mice with the endothelial excision of Nr2f2 (COUP-TFII), displaying a decreased expression of BM sinusoidal TIE2 and VEGFR3. These findings suggest that ANGPT1/TIE2 and COUP-TFII form a reciprocal regulatory loop to coordinate BM sinusoidal specification via regulating VEGFR3.

developmental biology↗

bioRxiv2026

Active repression of muscle fate preserves neural lineage identity during cerebellum development

Cell fate commitment is commonly thought to entail progressive restriction of developmental potential, enforced by passive, heterochromatin-based silencing of alternative lineage programs. Here we show that maintenance of neural identity during cerebellum development instead requires active repression of a starkly divergent fate by the TEAD-INSM1 transcriptional complex. Loss of TEAD1/2 or INSM1 activates the myogenic master regulator Myod1, resulting in neural cells acquiring transcriptional, structural, and metabolic features of skeletal muscle cells. Deletion of Myod1 fully suppresses neural-to-muscle conversion while partially rescuing neural developmental defects. Our results uncover a latent alternative lineage during neurodevelopment and a surprising role for sequence-specific transcription factors in enforcing lineage boundaries, including those previously thought essentially unbreachable, with implications for understanding aberrant differentiation in disease contexts and cell-type evolution.

developmental biology↗

bioRxiv2026

BRD4 recruitment desilences transcription without erasure or depletion of repressive chromatin

How genes are desilenced within mesoscale repressive chromatin is a crucial yet poorly understood phenomenon. Prevailing models posit that methylation of lysine-9 of histone H3 (H3K9me3) engages heterochromatin protein 1 (HP1) to drive chromatin compaction and transcriptional silencing. The erasure of this repressive mark and its replacement with acetyl/acyl groups recruits positive factors such as BRD4/BET to elicit gene transcription. We report that in Friedreichs ataxia, a synthetic gene regulator (SynGR1) drives transcription across repressive chromatin without removal or replacement of H3K9me3 or HP1. By selectively recruiting BRD4/BET into repressive GAA-repeats in frataxin (FXN), SynGR1 creates a paradoxical state where gene transcription and repressive chromatin co-exist. Contrary to convention, we find that BRD4 readily partitions into phase separated HP1 condensates in vitro and into HP1 puncta in patient-derived cells, thus presenting a mechanistic explanation for desilencing transcription without the dispersal of mesoscale repressive chromatin. Epigenetic drugs that gate sequential steps in transcription, synergistically stimulate FXN expression while concomitantly increasing, rather than eliminating, repressive H3K9me3 and HP1 levels. More broadly, this study highlights the dynamic nature of repressive chromatin and the context-dependence of epigenetic marks in regulating gene expression.

cell biology↗

bioRxiv2026

Dissecting heterogeneous brain development and aging using voxelwise normative models

Brain disorders are often characterized by biological heterogeneity that is poorly captured by group-average analyses. Normative modeling has emerged as a promising tool to parse out such heterogeneity, yet existing lifespan reference models rely on coarse parcellations, which may obscure individual variability. Using an aggregated reference sample (n=58,597 scans from n=51,107 participants), we provide openly available normative models of brain morphometry at the voxel level across the lifespan, and we illustrate their potential utility with two complementary applications. First, we investigated long-term brain development after preterm birth across two independent cohorts (n=284; n=304) and found individualized, replicable and persistent brain alterations. Second, we extracted high-resolution patient-level morphometric deviations in two samples with rare, genetic neurodegenerative disorders (spinocerebellar ataxia type 1 and 3; n=29, n=15), which showed marked heterogeneity. Together, our findings highlight that voxelwise normative modeling can detect clinically relevant, individualized deviations from a reference model with high spatial precision.

neuroscience↗

bioRxiv2026

Deep-Palm：an integrated deep learning framework for structure-aware prediction of protein S-Palmitoylation

Protein S-palmitoylation is a reversible lipid modification that regulates protein localization, trafficking, and signaling. Its dysregulation has been implicated in cancer and therapeutic resistance, making accurate site annotation important for understanding disease-related regulatory mechanisms. However, experimental identification of S-palmitoylation sites remains labor-intensive, highlighting the need for computational tools that can support large-scale candidate-site prioritization. S-palmitoylation-site recognition requires the integration of multiple levels of information surrounding candidate cysteine residues, including sequence context, local protein properties and structural features. Here, we present Deep-Palm, a deep learning framework that integrates four complementary branches: amino acid sequence, physicochemical properties, ESM embedding and spatial structure. On the testing set, Deep-Palm achieved an AUC of 0.950 and outperformed the compared predictors, including pCysMod, MusiteDeep and GPS-Palm. Deep-Palm also showed stable performance across diverse cysteine sequence contexts and Gene Ontology functional groups. Feature-level analyses revealed distinct spatial structural and protein property patterns between palmitoylated and non-palmitoylated peptide windows. Independent mass spectrometry datasets further demonstrated the ability of Deep-Palm to sensitively identify previously unannotated S-palmitoylation sites. Together, Deep-Palm provides an accurate and biologically informative framework for S-palmitoylation-site prediction, facilitating the discovery of novel candidate S-palmitoylation sites.

bioinformatics↗

bioRxiv2026

Application of large language models to the annotation of cell lines and mouse strains in genomics data

Accurate, consistent and comprehensive metadata are essential for the reuse of functional genomics data deposited in repositories such as the Gene Expression Omnibus (GEO), however, achieving this often requires careful manual curation that is time-consuming, costly and prone to errors. In this paper, we evaluate the performance of Large Language Models (LLMs), specifically OpenAIs GPT-4o, as an assistive tool for entity-to-ontology annotation of two commonly encountered descriptors in transcriptomic experiments - mouse strains and cell lines. Using over 9,000 manually curated experiments from the Gemma database and over 5,000 associated journal articles, we assess the models ability to identify relevant free-text entries and map them to appropriate ontology terms. Using zero-shot prompting and retrieval-augmented generation (RAG) to incorporate domain-specific ontology knowledge, GPT-4o correctly annotated 77% of mouse strain and 59% of cell line experiments, and uncovered manual curation errors in Gemma for over 200 experiments. GPT-4o substantially outperformed a regular expression-based string-matching method, which correctly annotated only 6% of mouse strain experiments due to low precision. Model errors often arose from typographical mistakes or inconsistent naming in the GEO record or publication, and resembled those made by human curators. Along with annotations, our approach requests that the model output supporting context and quotes from the sources. These were typically accurate and enabled rapid curator verification. These findings suggest that LLMs are not ready to fully replace manual curators, but can already effectively support them. A human-in-the-loop workflow, in which LLMs annotations are provided to human curators for validation, may improve the efficiency and quality of large-scale biomedical metadata curation.

bioinformatics↗

bioRxiv2026

Endocardial TIE1 synergizes with TIE2 to regulate the atrial internal muscular network assembly

Atrial cardiomyopathy is characterized by altered atrial structures, yet its underlying genetic basis remains inadequately explored. TIE1 mutations are reported in lymphedema patients, but whether they exhibit cardiac defects alongside lymphatic abnormalities remains unknown. Here, single-cell RNA sequencing showed high Tie1 and Tek expression in atrial endocardial cells. TIE1 deficiency severely disrupted atrial morphogenesis, with only minor ventricular defects. Bulk RNA-seq showed reduced transcripts for endothelial development and cardiac trabeculation in Tie1 mutants. Separate RNA-seq analysis of the atria and ventricles further confirmed these findings, revealing a more pronounced downregulation of trabecular genes, including Tek, in the atria upon Tie1 loss. Endothelial deletion of Tek impaired trabeculation, particularly in atria. Consistently, Tie1 loss combined with a single null Tek allele disrupted both atrial and ventricular trabeculation. Strikingly, atrial morphogenesis defects appeared within 48 hours of induced endothelial Tie1 loss coupled with Tek heterozygous deletion, implying a critical endocardial role in organizing the atrial muscular network. The synergy of TIE1 and TIE2 in remodeling atrial trabeculae was confirmed postnatally, whereas TIE1 insufficiency alone had no effect. Together, TIE1 is differentially required for atrial versus ventricular development, acting synergistically with TIE2 to regulate endocardial cell-coordinated assembly of atrial internal muscular network.

developmental biology↗

bioRxiv2026

A biofidelic Goat Model of Traumatic Optic Neuropathy with Optic Canal Fracture via Transnasal Endoscopy

Traumatic optic neuropathy (TON) is a major cause of irreversible vision loss following blunt cranial trauma, yet the absence of clinically relevant large animal models that faithfully recapitulate human TON has significantly impeded translational research. Current rodent models do not reproduce optic canal fracture, a key injury mechanism in many patients with TON. Here, we combined high-fidelity finite element analysis (FEA) with iterative engineering to establish a reproducible goat model of TON. We first built a high-resolution human-head finite element model to characterize force transmission to the optic nerve. Across clinically relevant periorbital impacts, stress preferentially concentrated in the intracanalicular segment, reaching a peak force density of approximately 500 N/m2 at 50.6 ms, about fivefold higher than in the intraorbital segment. Simulations further showed that direct optic canal impact reproduced comparable intracanalicular stress with a markedly lower input force: 195 N, compared with 3900 N for periorbital impact. Guided by these insights, we developed transnasal endoscopic impact systems capable of inducing optic canal fractures in goats. TON was confirmed within 24 hours by a characteristic relative afferent pupillary defect (RAPD), and at 1 month post-injury goats (n = 14) exhibited a 10%-20% reduction in ganglion cell complex (GCC) thickness and 40%-65% reductions in flash visual evoked potential (FVEP) and pattern electroretinogram (PERG) amplitude ratios (all P [≤] 0.001), with structural and functional preservation of the fellow eye. This study presents a robust, standardized, and clinically relevant large-animal platform for investigating TON pathophysiology.

neuroscience↗

bioRxiv2026

Pharmacological recruitment of a VTA glutamatergic arousal circuit by the natural product BN3 drives broad-spectrum emergence from general anesthesia

Pharmacological control of emergence from general anesthesia remains strikingly limited. Clinically available antagonists are largely drug-class specific, leaving recovery dependent on anesthetic clearance rather than to an actively programmable switch in brain state. Through phenotypic screening of a structurally diverse natural-product library, we identified BN3 (L-(-)-camphor) as a broad-spectrum emergence agent. BN3 robustly shortened recovery from propofol anesthesia across species--from mice and rats to rabbits, dogs, and rhesus monkeys--and remained effective after continuous infusion. In rodents, BN3 also accelerated emergence from mechanistically distinct anesthetics, including etomidate, remimazolam, sodium {gamma} - hydroxybutyrate, midazolam, ketamine, sodium pentobarbital, and isoflurane. EEG recordings revealed a rapid cortical shift from slow-wave dominance to a wake-like high-frequency spectrum. Mechanistically, BN3 preferentially recruited ventral tegmental area (VTA) glutamatergic neurons: chemogenetic silencing abolished the BN3-evoked EEG spectral shift and strongly attenuated behavioral acceleration of emergence, whereas optogenetic activation of these neurons was sufficient to promote recovery. BN3 increased glutamate release in the nucleus accumbens and medial prefrontal cortex, and projection-specific inhibition of VTA[->]NAc or VTA[->]mPFC outputs blunted BN3-induced emergence. These findings define a VTA-centered glutamatergic arousal circuit that can be pharmacologically recruited as a common gateway for anesthetic-independent emergence.

neuroscience↗

bioRxiv2026

Cell phenotypes in the biomedical literature: a systematic analysis and text mining corpus

The variety of cell phenotypes identified by single-cell technologies is rapidly expanding, yet this knowledge is dispersed across the scientific literature and incompletely represented in structured resources. We present the CellLink corpus, a manually annotated collection of over 22,000 mentions of human and mouse cell populations in recent journal articles, distinguishing specific cell phenotypes, heterogeneous cell populations, and vague cell populations, and linking to Cell Ontology (CL) terms as either exact or related matches, covering nearly half of the terms in the current CL. A systematic analysis reveals lineage-specific patterns in how authors utilize anatomical context, molecular signatures, functional roles, developmental stage, and other attributes in cell naming. We show that fine-tuning transformer-based models on CellLink yields strong performance for named entity recognition, while embedding-based approaches support zero-shot entity linking and distinguishing exact from related matches. We further demonstrate the utility of CellLink to expand and refine the chondrocyte branch of CL.

bioinformatics↗

bioRxiv2026

Nonanticoagulated Heparin Derivatives Mediate Goblet Cell Differentiation to Restore the Mucosal Barrier for Ulcerative Colitis Therapy

Epithelial mucus barrier dysfunction is a pathological hallmark of ulcerative colitis (UC), yet current clinical therapeutic strategies primarily suppress inflammation, lacking reliable approaches for restoration of the mucosal layer. Here, through a systematic screen of our established library of deanticoagulated heparins, we identified NALHP, a non-anticoagulant low-molecular-weight heparin derivative, and its representative fraction S6 as orally active epithelial repair-promoting glycans. NALHP/S6 restored crypt architecture, mucus production and epithelial barrier integrity in experimental colitis. In UC patient-derived colonic organoids, NALHP/S6 reduced aberrant stem/proliferative programs while promoting secretory, absorptive and junctional maturation. Single-cell transcriptomics and temporal validation identified a transient repair-secretory transitional state (RSTS) positioned between classical Wnt-associated stemness and mature barrier-forming epithelial states. Transcriptomic analysis revealed coordinated attenuation of Wnt and Notch signaling, whereas pharmacological reactivation of these pathways opposed NALHP/S6-induced epithelial state progression. These findings define mucosal repair as a regulated epithelial-state transition and identify NALHP/S6 as glycan-based modulators capable of restoring this progression in UC epithelium.

pathology↗