Biology subjects

Xie, J.

Publications and source records attributed to Xie, J..

At least 19 recordsLinked to original sources

bioRxiv2026

Label-free volumetric dynamic atlas of fresh mouse organs using dynamic full-field optical coherence tomography

Dynamic full-field optical coherence tomography (D-FFOCT) enables label-free visualization of tissue microarchitecture and endogenous intracellular dynamics. Here, we establish a volumetric atlas of ten fresh mouse organs using a mobile D-FFOCT imaging platform. The system enables large-area imaging of approximately 1 cm2 within 15 min with 1,024 frames per field of view, achieving 0.75-{micro}m lateral resolution and imaging depths of up to 200 {micro}m. Large-area mosaics, three-dimensional reconstructions, and comparisons with conventional histology reveal diverse organ-specific tissue architectures. Beyond morphological characterization, quantitative analysis of dynamic intensity and mean fluctuation frequency across nine organs reveals distinct dynamic signatures and tissue heterogeneity. Longitudinal imaging of brain, liver, and intestinal tissues further demonstrates organ-dependent temporal changes in endogenous dynamics following excision. Finally, we publicly release raw D-FFOCT imaging datasets from all ten organs, providing an open resource for quantitative tissue characterization, algorithm development, and reproducible research. Together, this study provides a comprehensive, openly accessible optical atlas of fresh mouse organs, establishing a foundation for systematic tissue characterization and advancing the broader application of D-FFOCT in biomedical research.

biophysics↗

bioRxiv2026

Diacylglycerol Kinases Balance DAG Signaling to Control B Cell Maturation, Germinal Center Homeostasis, and Humoral Immunity

Diacylglycerol (DAG) is a critical second messenger downstream of the B-cell receptor (BCR), but how DAG signaling is regulated during B-cell development and humoral responses remains incompletely understood. Here, complementary gain- and loss-of-function approaches revealed stage-specific requirements for diacylglycerol kinase (DGK)-regulated signaling in B cells. Expression of the gain-of-function DGK{zeta} mutant DGK{zeta}{Delta}NLS had limited effects on early BM B-cell development but progressively impaired transitional and mature B-cell populations. DGK{zeta}{Delta}NLS attenuated BCR-induced ERK1/2 and mTOR signaling, activation, and proliferation and, when expressed in AID-expressing B cells, reduced GC B-cell survival and T-dependent IgG responses without detectably impairing GC B-cell proliferation in vivo. Conversely, combined DGK/{zeta} deficiency resulted in marked spontaneous GC B-cell expansion associated with enhanced ERK1/2, Akt, and S6 signaling and increased glucose uptake. Despite this steady-state GC expansion, DGK/{zeta}-deficient mice developed spontaneous autoreactivity and mounted impaired antigen-specific antibody responses. Thus, B-cell developmental stages exhibit differential sensitivity to altered DGK activity, and opposing perturbations of DGK-regulated signaling produce reciprocal effects on GC B-cell accumulation while both compromise productive humoral immunity. These findings identify DGKs as critical regulators that tune lipid signaling for B-cell maturation, GC homeostasis, and effective antibody responses.

immunology↗

bioRxiv2026

Direct visualization of lysosome-mediated intracellular transport and membrane anchoring of TNF-α in human T cells

Tumor necrosis factor-alpha (TNF-) represents a major pro-inflammatory cytokine associated with chronic inflammation. Enhanced understanding of intracellular trafficking of TNF- enables the identification of drug targets that modulate TNF- secretion at the cellular source. However, conventional cytokine assays provide only bulk measurements of secreted TNF- or static measurements in fixed cells and therefore cannot provide mechanistic information. Here, we report a fluorescence imaging platform to visualize and quantify intracellular TNF- trafficking in human T cells. Using a Jurkat T cell line stably expressing TNF- fused to mStayGold as a model system, we revealed through single-particle tracking (SPT) that T cell activation increased the motility of TNF- vesicles and that microtubule perturbation disrupted this increased motility. 3D structured illumination microscopy uncovered spatial associations between TNF- vesicles and lysosomes, and SPT further demonstrated their coordinated transport. Using total internal reflection fluorescence microscopy, we captured the sub-second splitting of single TNF- vesicles into multiple puncta that subsequently separated, suggesting delivery of TNF- from the vesicle to the plasma membrane. Confocal-based super-resolution microscopy further resolved TNF- vesicles fusing with the plasma membrane and transmembrane TNF-. Together, these imaging capabilities for tracking and super-resolving the intracellular transport and membrane delivery of TNF- in live T cells enable mechanistic studies of TNF- trafficking and release.

biophysics↗

bioRxiv2026

Circular Data Analysis for Spatial Omics

Many biological quantities in omics are inherently periodic or directional, including circadian phase, cell-cycle position, and cellular orientation. Treating such quantities as ordinary linear variables can introduce artificial discontinuities and obscure biological interpretation. Circular methods are well developed across directional statistics, bioinformatics, and spatial statistics, but practical guidance for omics applications remains limited. We present key considerations for circular data analysis in single-cell and spatial omics, including the provenance and observational unit of the circular quantity, the inferential or predictive objective, the distinction between tissue composition and residual spatial dependence, and the choice of appropriate models. We describe relevant approaches for circular representation, inference, clustering, regression, machine learning, and spatial analysis, together with representative R software. Their practical use is illustrated through spatial transcriptomic case studies of derived circadian peak phase in a mouse model of Alzheimer's disease and latent cell-cycle position in human ovarian cancer. These examples demonstrate how the definition of the angle, its observational unit, and tissue heterogeneity shape appropriate analysis and interpretation, including when spatial modeling is not warranted. We conclude with practical recommendations and directions for future methodological development.

bioinformatics↗

bioRxiv2026

Triazole Stress Induces Accelerated Degradation of Aspergillus fumigatus Hmg1

Triazole antifungals inhibit the lanosterol C14-demethylase Cyp51A/B and are the first-line treatment for invasive aspergillosis caused by Aspergillus fumigatus. We previously proposed that triazoles impose a secondary constraint on ergosterol biosynthesis through negative feedback regulation of HMG-CoA reductase (Hmg1) through its sterol sensing domain (SSD), and SSD mutations compromise this regulation to produce resistance. The molecular mechanism underpinning this feedback remained unknown. In this study, we show that voriconazole drives accelerated protein degradation of Hmg1 and that SSD mutation abolishes this regulated degradation. Triazole-induced Hmg1 degradation is proteasome-dependent and partially requires the ERAD E3 ubiquitin ligase, HrdA, and INSIG ortholog, InsA, both conserved regulators of HMG-CoA Reductase abundance. We provide genetic evidence that the initiating negative feedback signal is not triazole acting directly on Hmg1 but lanosterol accumulation resulting from Cyp51A/B inhibition. To test whether depleting Hmg1 protein could re-sensitize resistant strains, we utilized a GFP-targeted degradation system designed to target Hmg1 for degradation without engaging its SSD. Combining this system with voriconazole treatment reduced the MIC at least four-fold in both conidia and established hyphae in susceptible and resistant strains. Together, our findings support a model wherein triazole-induced lanosterol accumulation drives HrdA/InsA-dependent accelerated degradation of Hmg1 and establish that pharmacologically inducing this secondary mechanism can enhance triazole activity in both susceptible and resistant isolates.

microbiology↗

bioRxiv2026

Stressed alga-free coral cells can initiate coral bleaching

Coral bleaching is driving the rapid decline of coral reefs worldwide, yet a fundamental question remains unresolved: does the bleaching cascade begin in the coral host or in its intracellular algal symbionts, Symbiodiniaceae? Resolving where this process starts is critical for understanding how symbiosis collapses and where early intervention might be effective. Here we use transient stress to create a temporal window between the early cellular response and subsequent symbiosis breakdown. Across transient menthol and thermal stress in soft and stony corals, bleaching developed after the stress had ended. In Xenia sp., single-cell transcriptomics revealed a broad host response before detectable symbiont loss, including coordinated redox changes consistent with conditions favouring reactive oxygen species (ROS) accumulation. Cell-resolved imaging showed that alga-free coral cells were the first to become ROS-positive, whereas Symbiodiniaceae showed no detectable ROS signal. This early host response was transmissible. Conditioned medium from stressed cultures induced the emergence of ROS-positive host cells and subsequent symbiosis breakdown in unstressed recipients. Purified ROS-positive alga-free coral cells alone were sufficient to trigger symbiosis breakdown in recipient cultures without direct stress exposure. Suppressing the early emergence of ROS-positive coral cells markedly reduced later bleaching, whereas intervention after stress was substantially less effective. These findings identify a host-initiated, intercellularly propagating route to coral bleaching and reveal an early host response that can determine the subsequent fate of the symbiosis.

cell biology↗

bioRxiv2026

Cell-Lens: Advancing LLM Reasoning at Single-Cell Resolution

Recent work applies large language models (LLMs) to single-cell data, but the cell usually reaches the model as a short ranked list of genes. This list drops much of what defines a cell, so the model reasons from a partial view. Yet the information is not lost in the measurement, only in the text. Here, we introduce Cell-Lens, a training-free structured representation of the measured cell. It writes the cell as typed blocks, from paired measurements to marker-supported programs. On CellVerse, SOAR, CellPuzzles, and SC-Arena, across five model families, Cell-Lens improves performance by up to 27.1 points. It also narrows the model gap and reduces API-reported reasoning-token usage. The largest gains occur when a defining RNA marker falls out of the ranked list. In these cases, the paired protein data still capture the corresponding signal. Shuffling the added blocks removes the gain. The gain persists after selected label-associated proteins are removed. These controls link the improvement to cell-matched biological content. We also build and release CellSpectrum, a broader benchmark spanning eight sources and seven tasks with paired modalities. The gains hold there across tasks, tissues, and modalities. These results show that a better cell representation can improve single-cell reasoning without retraining the model. Code and CellSpectrum are publicly available at https://github.com/LiZaiyuan0619/Cell-Lens.

bioinformatics↗

bioRxiv2026

Spatiotemporal atlas resolves the mesenchymal-epithelial stem cell axis governing human hair follicle aging and pathology

How adult stem cell populations coordinate tissue regeneration across physiological and pathological states remains unclear. Hair follicles contain epithelial and mesenchymal stem cells that codetermine hair regeneration. Here, we integrate a multimodal spatiotemporal atlas with functional validation to define the mesenchymal-epithelial stem cell dynamics governing human hair follicle homeostasis, aging, and androgenetic alopecia. Aging is characterized by passive depletion of hDSC-derived regenerative cues, whereas AGA involves a shift of hDSC toward an inhibitory signaling hub that promotes HFSC dysfunction. We further pinpoint hDSC-secreted PTN as a key regenerative factor that promotes hair growth and counteracts androgen-induced growth suppression. This study provides a holistic framework of adult stem cell crosstalk across physiological and pathological states, offering a mechanistic roadmap to reinstate tissue regeneration.

cell biology↗

bioRxiv2026

Carcinogen-induced preinvasive human squamous lung cancer is characterised by a novel atypical basal cell state and presents opportunities for chemoprevention

There are no adequate carcinogen-induced models of the earliest stages of human squamous lung cancer (LUSC), limiting the development of effective chemoprevention strategies. We developed a novel human model of early LUSC by exposing differentiated primary human airway cells to a chemical carcinogen known to cause murine LUSC. Carcinogen exposure induced a phenotype recapitulating the earliest stages of human LUSC and associated with the emergence of a novel population of atypical basal cells (ABCs). ABCs express key cancer hallmark markers but without evidence of either common LUSC-associated mutations or an emergent major clonal/subclonal population. We established the clinical relevance of this model by demonstrating enrichment of the ABC expression profile in independent clinical precancer specimens. We then show that capivasertib, a clinically approved kinase inhibitor, prevented the emergence of the abnormal phenotype and the accumulation of cells with an active DNA damage response. Further, capivasertib reversed the established phenotype; and remained effective when nebulised in vitro, mimicking therapeutic inhalation. Together, these findings establish a tractable human model of carcinogen-induced early LUSC and provide a proof-of-principle for repurposing targeted therapies for the prevention of lung cancer.

cancer biology↗

bioRxiv2026

Biotinylation-dependent near-neighbor analysis for identification of septation regulators in Aspergillus fumigatus

Recent work has established septation as a critical process for virulence in A. fumigatus, as strains lacking septa are avirulent. While our work has focused on the well-studied Septation Initiation Network (SIN), understanding of septation machinery upstream and downstream of SIN remains limited in filamentous fungi. Proximity labeling techniques are powerful tools to study pathway interactions, especially those that are transient. Recent advances have seen TurboID used to study pathways and processes important for fungal pathogenesis. In this study, we adapt TurboID for use in Aspergillus fumigatus and use overlapping datasets of two SIN components, the terminal NDR kinase SidB and its binding partner MobA, to identify putative septation effectors. Many known septation effectors, including septins and cell wall synthesis proteins, were enriched in our datasets, validating the approach. Phenotypic characterization of hits identified by LC-MS/MS revealed several previously uncharacterized gene products involved in septum formation and cell wall stress tolerance. These included the PP2A regulatory subunit PabA and IQGAP SepG, which have been shown to regulate septation in Aspergillus nidulans. Thus, TurboID is a useful tool to study fungal signaling and physiology in A. fumigatus and may be used to improve understanding of pathogenic processes.

microbiology↗

bioRxiv2026

Integrating structural and biological evidence to rerank ESMFold2 protein-protein interactions

Large-scale protein structure prediction enables proteome-wide protein-protein interaction (PPI) screening, but distinguishing biologically meaningful interactions from spurious interfaces remains challenging. Here, we develop a scalable framework combining fast, MSA-free ESMFold2 prediction with PAE-guided domain parsing and evidence-based reranking. Three-recycle ESMFold2-Fast achieved 57% acceptable-or-better DockQ scores on FoldBench, comparable to AlphaFold2-Multimer while substantially reducing computation. PAE-guided parsing preserved 98.1% of XL-MS cross-links within parsed domain pairs. We then developed the Structure Prediction and Omics informed Classifier (SPOC)-ESMFold2, which integrates structural features with independent biological evidence to prioritize predicted interactions. SPOC-ESMFold2 achieved an AUROC of 0.93 and AUPR of 0.90, compared with 0.87 and 0.79 for a structural-only classifier. Under a 1:128 positive-to-negative ratio, SPOC-ESMFold2 achieved 17.2% recall at 5% false-discovery rate, substantially outperforming structural confidence metrics alone. This framework enables scalable PPI screening by integrating structural plausibility with orthogonal biological evidence to prioritize candidates for experimental investigation.

bioinformatics↗

bioRxiv2026

spaCraft: calibrated power analysis and sample-size planning for multi-sample spatial transcriptomics

Comparative spatial transcriptomics is now routine, yet the number of tissue sections per group is rarely determined by formal power analysis. Power depends jointly on between sample variation and domains recovered by clustering, a combination not represented by existing tools. We present spaCraft, which converts a replicated pilot into endpoint-specific per-group sample-size recommendations. It fits models of spatial expression, domain geometry and composition, then estimates power through a generate, recover, test loop that reestimates domains in every synthetic sample, allowing clustering uncertainty to enter the recommendation. Its differential-expression and composition endpoints are tested on recovered rather than assumed domains, yielding calibrated power rather than detection rates. We applied spaCraft to four cohorts spanning Visium, Stereo-seq, and Visium HD. In held-out validation, three-sample pilots predicted sample-size requirements in independent real samples, supporting the full chain from pilot fitting through domain recovery to endpoint testing. Sample size thereby becomes an explicit, reproducible property of the planned analysis rather than an informal guess.

bioinformatics↗

bioRxiv2026

Extracellular vesicles drive cross-genus mycovirus transmission and suppress two fungal diseases

Mycoviruses are typically transmitted vertically through fungal reproduction or horizontally via hyphal anastomosis, but identical viruses in phylogenetically divergent fungi hint at unknown inter-species transmission mechanisms. Here, we identify fungal extracellular vesicles (EVs) as mediators of cross-genus mycovirus transmission. Using the hypovirulent Botrytis cinerea strain IBc-374 (harboring 16 mycoviruses) as a donor, we show that up to 13 mycoviruses are horizontally transmitted to Sclerotinia sclerotiorum during dual culture or plant co-inoculation, even though these two fungi belong to different genera and are generally considered incapable of hyphal anastomosis. Electron microscopy reveals abundant vesicle structures in IBc-374 hyphae, and nanoparticle tracking analysis showed that the strain secretes >11-fold more EVs than a virus-free strain. RT-PCR detects genomic RNAs of 7 mycoviruses in purified EVs, and the full-length viral genome in EVs was further validated with BcHV5 as example by fluorescence in situ hybridization and RT-PCR. Incubation of protoplast-derived germlings of S. sclerotiorum or B. cinerea with IBc-374 EVs leads to infection by 4-6 donor mycoviruses, demonstrating EV-mediated cross-genus transmission. Injection of mycovirus-carrying EVs into tobacco leaves followed by fungal inoculation also transmits two hypoviruses to both species. Application of IBc-374 hyphal fragment suspension significantly reduces lesion sizes caused by both pathogens on plants, and rescued two pathogens carrying multiple mycoviruses exhibit hypovirulence and impaired growth. Our findings reveal EVs as a cell-free vector that bypasses vegetative incompatibility, providing a mechanistic basis for cross-species viral spread and opening avenues for EV-based virus cocktails to control multiple fungal diseases. IN BRIEFWu et al. discover that fungal extracellular vesicles (EVs) can package and transmit multiple mycoviruses across genera from Botrytis cinerea to Sclerotinia sclerotiorum. EV-mediated delivery overcomes vegetative incompatibility barriers and reduces disease caused by both fungal pathogens, offering a cell-free strategy for mycovirus-based biological control.

microbiology↗

bioRxiv2026

Temperature governs fitness effects of transgenes on plants non-monotonically: a global meta-analysis

The global expansion of genetically modified plants supports modern food and ecological security1, yet whether the fitness cost--widely assumed to limit their spread after escape--actually operates in the wild has remained unclear, with empirical evidence remaining mixed2-4. Here, a global meta-analysis of 518 experiments across 48 species reveals that this safety brake is real in the laboratory (fitness cost: [~]13%) but is largely attenuated in the worlds most intensively cultivated croplands. A phylogenetically robust, hump-shaped relationship between mean annual temperature and fitness effect is defined, with fitness benefits emerging specifically within 9.9-22.8{degrees}C. This buffer window overlaps the productive croplands5, where the high-risk proportion (HRP; the area-weighted posterior probability of non-negative fitness effect) consistently exceeds that in natural vegetation and expands with global warming (cropland: +18.4% versus natural vegetation: +8.3% under SSP5-8.5). Notably, constitutive expression or dual-resistance (resist to both abiotic and biotic stressors) transgene can effectively compress the HRP below 30%, providing a quantitative baseline for management. These findings establish a framework for climate-smart deployment that balances agricultural productivity with ecological safety.

ecology↗

bioRxiv2026

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

Understanding how cell types are organized across the central nervous system (CNS) is key to uncovering neural function. Here, we integrate single-nucleus Multiome (RNA+ATAC) sequencing, spatial transcriptomics, and computational analyses to map conserved cell type signatures in the adult mouse brainstem and spinal cord. We identify a shared core of neuronal and non-neuronal cell types, alongside region-specific specializations reflecting distinct functions. Spatial data reveal conserved cellular niches across the brainstem-spinal cord boundary, indicating a continuous organizational logic. Cross-region comparisons uncover recurrent gene expression modules and signaling programs that may support shared circuit features. Chromatin accessibility profiling highlights cell-type-specific regulatory programs and implicates Hox transcription factors in positional identity. Notably, cell-type and positional identities are largely orthogonal, with varying regional influence across neuronal classes: motor neurons show strong positional coupling, whereas glutamatergic and GABAergic interneurons show minimal entrainment. This work provides a reference for the shared molecular architecture of these CNS regions.

neuroscience↗

bioRxiv2026

Reachability-Preserving Minimum Edge Cut Problem and Applications in Biology

Biological pathway analysis often requires identifying interventions that block reachability to an undesirable state, such as a disease-associated module, toxic byproduct, or adverse phenotype, while preserving reachability among essential biological functions. Motivated by this setting, we study the Reachability Preserving Minimum Edge Cut (RPMEC) problem: given protected terminals s1 and s2 and a target terminal t, the goal is to remove a minimum-cost set of edges that separates s1 and s2 from t while keeping s1 and s2 connected. This formulation naturally models pathway-level intervention design, where one seeks to disrupt harmful signaling, metabolic, or interaction routes without breaking required functional connectivity. We revisit the three-terminal undirected edge-cut case and analyze a Dijkstra-style dynamic programming algorithm that is exact on planar graphs but fails on general graphs. We characterize the structural condition required for exactness, namely frontier-realizability of optimal source-side regions, and identify biological graph representations where this condition is likely to hold after appropriate preprocessing, including curated planar pathway maps, Reactome-style hierarchy trees, SCC-contracted feedback modules, metabolic building-block DAGs with dominator structure, and functional-module quotients of protein interaction networks. We further discuss directed variants, approximation strategies, and exact alternatives based on ASP, MILP, bounded-treewidth dynamic programming, and important separators. The results provide a graph-theoretic foundation for deciding when fast greedy computation is reliable for biological pathway intervention problems and when more expressive exact optimization methods are needed. Author SummaryMany real-world networks require interventions that separate harmful or undesirable states while preserving essential connectivity. This situation appears in biological pathway analysis, where one may want to block reachability to a disease-related module, toxic byproduct, or adverse phenotype without disrupting communication among essential genes, proteins, reactions, or metabolites. We study this problem through the Reachability Preserving Minimum Edge Cut formulation. Unlike ordinary minimum cut, the solution must satisfy both a separation requirement and a preservation requirement. We show why a natural Dijkstra-style algorithm works only under specific structural conditions, such as planar, laminar, or module-like pathway graphs, and why it may fail on general graphs. The results help identify when fast graph algorithms are reliable for biological intervention problems and when exact optimization tools such as Answer Set Programming or integer programming are more appropriate.

bioinformatics↗

bioRxiv2026

Co-delivered PD-L1 rescues the protective efficacy mediated by an AAV-expressed HIV-1 bNAb

Adeno-associated virus (AAV)-delivered anti-HIV-1 broadly neutralizing antibodies (bNAbs) could prevent and treat HIV-1 infection but are limited by host immune responses, specifically anti-drug antibodies (ADA). We tested whether PD-L1-mediated immune shielding could improve the consistency of AAV-delivered bNAb expression from muscle tissue in rhesus macaques. AAV9.PD-L1 co-delivery with AAV9.3BNC117 reduced the occurrence of ADA and T cell responses and improved the durability of 3BNC117 expression for one year post administration. Importantly, 5 of 6 macaques that received co-delivered AAV9.PD-L1 vectors were protected against ten repeated SHIVAD8-EO challenges. Histopathological and spatial transcriptomic profiling showed that AAV9.PD-L1 co-delivery prevented severe local inflammation, muscle injury, and tertiary lymphoid structure formation at the administration site. Thus, immune shielding could serve as a strategy to prolong transgene expression from muscle-directed AAV-delivered biologics.

immunology↗

bioRxiv2026

Overcoming host immune responses to an AAV-delivered HIV-1 bNAb in rhesus macaques mediated by co-delivery of PD-L1

Adeno-associated virus (AAV)-delivered anti-HIV-1 broadly neutralizing antibodies (bNAbs) have demonstrated promise for preventing and treating HIV-1 infection in preclinical models. However, host immune responses, specifically anti-drug antibodies (ADA), limit sustained bNAb expression. We have previously shown that PD-L1-mediated immune shielding improves the consistency of AAV-delivered bNAb 3BNC117 expression from muscle tissue in rhesus macaques. Here, we test the breadth of this approach with another bNAb, 10-1074. We show that AAV9.PD-L1 co-delivery with AAV9.10-1074 reduced the occurrence of ADA responses and improved the durability of bNAb expression for one year post administration. Notably 12 of 12 macaques that received AAV9.10-1074 vectors were protected against ten repeated SHIVAD8-EO challenges. Histopathological profiling showed that AAV9.PD-L1 co-delivery prevented severe local inflammation and tertiary lymphoid structure formation at the administration site. Thus, immune shielding could serve as a broad strategy to prolong transgene expression from muscle-directed AAV-delivered biologics.

immunology↗