Biology subjects

Guo, W.

Publications and source records attributed to Guo, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Metastatic dissemination of breast cancer stem cells requires MenaINV for lung extravasation but not survival

Cancer stemness is a pivotal driver of tumor initiation, treatment resistance, and tumor cell survival. Cancer stem cells (CSCs), though constituting only a small fraction of primary tumor cells, are progressively enriched during metastatic progression: from circulating tumor cells traveling in the bloodstream, to disseminated tumor cells lodged in the lung vasculature, to extravasated tumor cells that have entered tissue parenchyma. However, whether CSCs have an intrinsic advantage for extravasation over cancer non-stem cells (CnSCs), or simply their increased representation in circulation renders them more likely to extravasate, remains unresolved. MenaINV, an invasive isoform of the actin regulatory protein Mena, promotes tumor cell transendothelial migration in primary and secondary sites, yet the direct mechanistic link between stemness and MenaINV in lung metastasis remains unresolved. Here, using a validated fluorescent stemness reporter (SORE6) to identify CSCs, we found that CSCs display elevated MenaINV expression relative to CnSCs. High-resolution intravital imaging showed that CSCs extravasate efficiently into lung parenchyma and survive at higher levels, robustly forming metastatic lesions, while CnSCs show limited extravasation, low survival, and poor colonization. Mechanistically, MenaINV disruption in CSCs specifically impaired extravasation without affecting survival, demonstrating that MenaINV is the key extravasation effector downstream of stemness, whereas stemness-associated factors independently confer survival advantages. Moreover, reintroduction of MenaINV in CnSCs restores their extravasation ability upon which extravasated CnSCs reactivate stem program and form metastases. Overall, we discovered a hierarchical framework where stemness regulates both survival and extravasation capacity, with MenaINV as the key CSC extravasation effector. Significance: This study reveals how breast cancer stem cells achieve metastatic dominance through separable pathways: MenaINV-dependent extravasation and MenaINV-independent survival, providing rationale for targeting stem program to improve patient outcome.

cancer biology↗

bioRxiv2026

Coacervate Droplets as a Liquefier for the Solid-to-Liquid Transition of RNA Aggregates

Biomolecular condensates are functionally gated by their material properties. While RNA is a primary structural scaffold, its sequence-specific interactions can aberrantly drive condensates into dysfunctional solid aggregates. Yet, actively reversing this solidification to restore function remains a fundamental challenge, impeding progress in synthetic biology and therapeutics interventions. Here, we establish that complex coacervates can be engineered as liquefiers to actively remodel solid RNA-peptide aggregates into functional liquid droplets. Integrating systematic experiments with all-atom simulations, we decode a multiscale mechanism: coacervate infiltration at the micrometer scale mediates molecular buffering at the nanometer scale, which fluidizes the crosslinked network to drive macroscopic liquefaction. This capability is governed by a design rule, where coacervates formed by small-molecular anions exhibit optimal efficacy. We deploy this principle to functionally rescue silenced RNA within a model of pathologically solidified ribonucleoprotein assemblies. Our work provides a general framework for the active, compositional control of biomolecular phase behavior, with direct implications for managing pathological aggregation and engineering functional condensates in synthetic and living systems.

biophysics↗

bioRxiv2025

Assembly and glycosylation of Helicobacter pylori sheathed flagella

The bacterial flagellum is a complex nanomachine essential for motility, colonization, and invasion in diverse species. Helicobacter pylori has evolved elaborate sheathed flagella that enable migration through the highly viscous gastric mucus layer to reach its colonization niche on the gastric epithelium, yet the molecular basis for these unique adaptations has remained elusive. Here, we use in-situ single particle cryo-electron microscopy to determine near-atomic structures of the flagellar filament within the membranous sheath of H. pylori. The major flagellin FlaA constitutes the bulk of the filament, whereas the minor flagellin FlaB contributes critically to the hook-proximal region. Both FlaA and FlaB form a conserved core surrounded by variable surface-exposed domains. Our structures further reveal that pseudaminic-acid glycans decorate these domains, where they mediate inter- and intra-subunit contacts that stabilize the filament and confer a negatively charged surface. Together, these findings support a model in which the filament rotates independently of the membranous sheath to drive H. pylori motility and provide a molecular framework for understanding how the sheathed flagellum enables colonization and persistence within the gastric niche. Significance StatementWe present the first in-situ near-atomic structure of the sheathed flagellar filament in Helicobacter pylori, revealing distinctive adaptations that underpin the pathogens unique motility and persistent infection. Our in-situ structures show that the two flagellins, FlaA and FlaB, assemble into an extended and exceptionally stable filament through an extensive hydrogen-bonding network. Pseudaminic acid glycans decorate the surface-exposed domains, where they stabilize inter-subunit packing and render the surface negatively charged and hydrophilic. These findings, which provide insight into the assembly of the flagellar filament and its relationship to the surrounding sheath, provide a structural framework for developing strategies to disrupt H. pylori motility and infection.

microbiology↗

bioRxiv2025

Transcriptome-wide mapping reveals an RNA-dependent mechanism of platinum cancer drugs.

Off-target interactions frequently compromise the clinical utility of anticancer agents by driving dose-limiting toxicity and therapeutic resistance. Although RNA has been predicted to be an off-target for numerous FDA-approved drugs, the extent and functional significance of RNA off-targeting among anticancer small molecules remain poorly understood. Using a systematic drug-binding screen, we identified cisplatin, a frontline chemotherapeutic that acts canonically through DNA adduct formation, as a prominent RNA binder. We employed cisplatin as a model compound to characterize the mechanistic basis and functional impact of RNA-small molecule off-targeting. To map transcriptome-wide cisplatin-RNA interactions, we developed PlatRNA-seq, a click-chemistry-enabled RNA-binding profiling platform. Genomic and functional analyses reveal that cisplatin preferentially accumulates at RNA G-quadruplex (rG4) structures near 5' transcript ends, inducing R-loop formation. Critically, we demonstrate that cisplatin cytotoxicity is partially mediated through RNA binding, revealing a noncanonical mechanism of action. Collectively, these findings illustrate the functional consequences of RNA-small-molecule off-targeting and provide a generalizable framework for investigating small-molecule-RNA interactions, opening new avenues for therapeutic innovation.

molecular biology↗

bioRxiv2025

Spatial Polarization-Induced Fluorescence Fluctuation Imaging (SPIFFI) Enables Single-shot Super-Resolution and Multidimensional Imaging

Fluorescence super-resolution microscopy has advanced optical imaging into the nanoscale regime, transforming biological and interdisciplinary research. However, conventional wide-field super-resolution techniques often compromise temporal resolution, thereby limiting the ability to capture rapid and transient biological events in living systems. Here, we introduce spatial polarization-induced fluorescence fluctuation imaging (SPIFFI), a multi-channel polarimetric method that enables single-shot super-resolution imaging and six-dimensional information extraction. By leveraging the inherently smaller point spread function (PSF) under polarized detection and capturing polarization-dependent spatial fluctuations across multiplexed channels, SPIFFI achieves instant resolution enhancement from a single exposure. This capability substantially enhances the feasibility of volumetric live-cell super-resolution imaging. Moreover, SPIFFI images can be seamlessly integrated with existing fluctuation-based methods for further post-processing and resolution improvement. We demonstrate the versatility of SPIFFI through experiments on both fixed and live cells, capturing rapid subcellular dynamics and enabling high-throughput, multidimensional imaging beyond the diffraction limit. SPIFFI thus offers a practical and robust platform for real-time super-resolution imaging in biological research.

biophysics↗

bioRxiv2025

Perturbational single-cell profiling of patient tumors defines lineage- and context-specific programs of innate immune resistance

AbstractDespite promise in preclinical models, most immuno-oncology drug candidates fail in clinical trials. These failures reflect limitations in our ability to directly model the response of human tumor and immune cells to immunotherapies. To address this gap and test the effect of innate immune agonists, we developed PERCEPT, an approach that uses ex vivo perturbational single-cell RNA sequencing to compare the response of immunomodulatory treatments with unstimulated controls directly in patient samples. Using PERCEPT, we tested cytokines and innate immune agonists in melanoma and Merkel cell carcinoma (MCC) and identified the dsRNA mimetic, RIG-I agonist, Stem Loop RNA (SLR) 14 as a powerful inducer of anti-viral states and enhancer of T cell activation. We compared transcriptional responder and non-responder patient samples and identified midkine (MDK), a multifunctional cytokine, as a potent repressor of IFN signaling in both tumor and immune cells. MDK expression dampened MHC-I presentation in human tumor cells and reduced activation of antigen-presenting cells, disrupting tumor immunity at multiple levels. In contrast to prior studies, we identified MDK as specifically enriched in neuroendocrine cancers such as MCC and small cell lung cancer compared with melanoma, suggesting the importance of lineage- and context-specific targeting. Our results demonstrate the utility of high-dimensional controlled perturbation of patient samples to identify mechanisms of innate immune response and resistance and demonstrate an actionable path towards clinical development of MDK-inhibiting therapies including FDA-approved ALK inhibitors in neuroendocrine cancers.

cancer biology↗

bioRxiv2025

Near-atomic in-situ architecture and membrane-coupled dynamics of the Vibrio cholerae sheathed flagellum

The sheathed flagellum of Vibrio cholerae is a self-assembling membranous organelle that must coordinate axial assembly, sheath biogenesis, and rapid motor rotation. Here, we determine in-situ near-atomic structures of the sheathed flagellar motor inside intact cells. The motor anchors to the outer membrane through lipidated HL-rings without forming a membrane pore, thereby allowing axial assembly to drive sheath formation. Conserved LP-rings act as slide-rotary bushings that permit high-speed rotation within a dynamic envelope yet can constrict to seal the pore upon stress-induced ejection. We further show that stator activation requires a specific PomB-MotX interaction rather than peptidoglycan engagement. Together, these findings reveal how the distinctive architecture and dynamics of the sheathed flagellum promote V. cholerae motility, environmental survival, and persistent colonization of the human gut.

microbiology↗

bioRxiv2025

Dynamics-enhanced Molecular Property Prediction Guided by Deep Learning

Molecular property prediction (MPP) is a key challenge in computational biology and drug discovery. Traditional approaches mostly rely on feature representations yielded from static structures of molecules, ignoring their dynamic nature. The scarcity of dynamics data in public databases and the complexity of learning such high-dimensional data made it more difficult for dynamics-involved studies. Accordingly, we built a series of dynamics datasets for MPP tasks by performing comprehensive molecular dynamics (MD) simulations on different molecules. In addition, we proposed a dynamically enhanced molecular representation (DEMR) method with multiple sampling strategies for the dynamics frames. Besides, two deep learning pipelines were employed for mapping DEMR to the molecular properties in various tasks. Our models achieved better performance in different MPP tasks, with a practical guidance in efficient frame selection. This study highlights the significance of integrating MD data into MPP tasks and opens new avenues for structure-based drug design. The generated MD datasets are publicly available in a Zenodo repository at https://doi.org/10.5281/zenodo.15788151.

bioinformatics↗

bioRxiv2025

QutRNA2: Robust tRNA modification discovery from Nanopore direct tRNA sequencing

Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequencing with Oxford Nanopore Technologies enables positional modification analysis but is challenged by tRNAs short length, redundancy, and dense modifications. We present QutRNA2, a scalable workflow featuring GPU-accelerated local alignment, statistical filtering, pairwise error profile comparison, and customizable visualization. Achieving up to 25-fold speed gains over CPU methods, QutRNA2 identifies enzyme-dependent modifications in nuclear- and mitochondrial-encoded tRNAs, demonstrated in human and mouse samples. This open-source solution provides a comprehensive, multiplexing-compatible framework for tRNA analysis, addressing a key gap in current tools.

bioinformatics↗

bioRxiv2025

Hippocampal transformations occur along dimensions of memory interference

The role of the hippocampus in resolving memory interference has been greatly elucidated by considering the relationship between the similarity of visual stimuli (input) and corresponding similarity of hippocampal activity patterns (output). However, these input-output functions can take surprisingly different forms. Here, we reconcile seemingly conflicting findings by considering the possibility that the hippocampus prioritizes different dimensions of visual similarity across different stages of learning. First, we generated a set of natural scene images from two visual categories and rigorously characterized visual similarity using a wide array of methods: neural networks, artificial intelligence models, and human perceptual and memory decisions. We then identified two orthogonal dimensions of visual similarity that each predicted memory interference, but that did so at distinct stages of learning. Using high-resolution fMRI, we then tested for dimension-specific input-output functions within the hippocampus. Within CA3 and dentate gyrus (CA3/DG), we show that dimensions of visual similarity were inverted (repulsion) at stages of learning when they contributed to memory interference. In contrast, CA3/DG preserved similarity when dimensions did not contribute to interference. These findings reveal that hippocampal representations of visually-similar stimuli are highly dynamic and critically depend on the dimensions of similarity that currently contribute to memory interference.

neuroscience↗

bioRxiv2025

Pharmacological Induction of Irreversible Senescence in Drug-Tolerant Persister Cells Prevents Tumor Relapse

Despite substantial advances in targeted therapies, most patients with advanced cancers ultimately relapse. This relapse is frequently seeded by drug-tolerant persister cells (DTPs), which persist as minimal residual disease (MRD) by adopting a reversible quiescent state and later reacquire proliferative capacity under ongoing treatment. To address this, we sought to convert quiescent DTPs into an irreversible, non-proliferative state by pharmacologically inducing senescence. Through large-scale chemical screening and combination optimization, we identified SAHA plus tilorone dihydrochloride (SIC) as a regimen that robustly induces senescence in melanoma DTPs and abolishes their proliferative potential in vitro. Mechanistically, SAHA relieves HDAC1-mediated repression of HMGA2, a key senescence driver, while tilorone synergistically inhibits autophagy to promote a fully senescent state. In a melanoma xenograft mouse model receiving MAPK-targeted therapy, SIC treatment significantly suppressed MRD progression. Importantly, SIC also induced robust senescence across diverse DTP models irrespective of tumor origin, mutational background, or prior treatment. Collectively, these findings provide proof-of-concept that converting DTPs from reversible quiescence to permanent senescence represents an effective strategy to prevent relapse under targeted therapy and position SIC as a broadly applicable pharmacological approach for durable control of residual disease in advanced cancers.

cancer biology↗

bioRxiv2025

Efineptakin alfa (NT-I7) improves overall survival and induces tertiary lymphoid structures in murine lung tumors

Tertiary lymphoid structures (TLSs) are emerging as good predictive biomarkers of response to cancer immunotherapy. However, therapeutic strategies to induce these structures are currently limited. We evaluated the therapeutic benefit of efineptakin alfa (NT-I7), a long-acting form of IL-7, and its ability to induce TLSs in a murine lung tumor model. NT-I7 improved overall survival in tumor-bearing mice. It also increased the abundance of T, B, dendritic cells, and stem-like CD8 T cells and promoted the formation of immune aggregates in the tumor microenvironment (TME). Stem-like CD8 T cells were preferentially located in the immune aggregates. Spatial transcriptomic analyses of the TME further demonstrated that the immune aggregates induced by NT-I7 included TLSs with enrichment of Cd274 (PD-L1) transcripts and genes involved in antigen processing and presentation. Upregulation of Cd274 in the TLSs may provide opportunities for synergy between NT-I7 and PD-1-targeted immunotherapy. STATEMENT OF SIGNIFICANCEThis study demonstrates the ability of efineptakin alfa (NT-I7) to potentially augment the clinical efficacy of cancer immunotherapy by inducing tertiary lymphoid structures in the tumor microenvironment.

immunology↗

bioRxiv2025

Dual-LLM Adversarial Framework for Information Extraction from Research Literature

Information Extraction (IE) is a fundamental task in Natural Language Processing (NLP) that aims to automatically identify relevant information from unstructured or semi-structured data. Information extraction from lengthy research literature, particularly in multi-omics studies, faces significant challenges due to their complex narratives and extensive context. To address this, we present a novel dual-LLM adversarial framework in which one large language model (LLM) performs the extraction and another provides iterative feedback to refine the results. This process systematically reduces errors, enhances consistency across heterogeneous data sources, and converges toward more accurate outputs. We evaluated our approach against manual and single-LLM extraction, using LLMs as evaluators. Experimental results show that our adversarial framework outperforms these baselines, highlighting its effectiveness for extracting structured information from lengthy scientific texts.

bioinformatics↗

bioRxiv2025

SpatialZoomer: multi-scale feature analysis of spatial transcriptomics

Single-cell resolution spatial transcriptomics (ST) provides a great opportunity to explore the complex cellular contents in different tissues. In this study, we introduce SpatialZoomer, a spectral graph-based method that applies a set of low-pass filters to efficiently extract spatial molecular features from ST data at multiple resolutions or scales, including the single cell scale, the niche scale with dozens of closely interacting cells, and the domain scale with spatially-organized cell contents. The corresponding "critical" scales can be automatically identified by partitioning a cross-scale similarity map. Results show that SpatialZoomer can identify disease-progression signals at specific scales in Alzheimers Disease, and spatial context dependent cell subtypes in tumor microenvironment. The extracted multi-scale features also uncovered spatially heterogeneous niches in cancer. SpatialZoomer also takes advantage of high computational efficiency and low hardware requirements.

bioinformatics↗

bioRxiv2025

Hypoxia/HIF Signaling Negatively Regulates Bone Marrow Adiposity after Radiation Exposure

Radiation therapy is an essential cancer treatment, yet collateral damage to normal tissues remains a major clinical challenge. In bone, radiation-induced toxicity is characterized by loss of hematopoietic function, reduced bone volume, and increased marrow adipose tissue (MAT). Importantly, cancer patients who undergo radiotherapy exhibit significantly higher fracture risk compared to those receiving similar treatments without radiation exposure, underscoring the clinical consequences of bone microenvironment (BME) injury. The BME is inherently hypoxic resulting in the activation of by hypoxia-inducible factor (HIF) signaling. Here, we demonstrate that radiation induces a rapid and persistent accumulation of MAT, with adipocytes localizing preferentially to hypoxic regions of the marrow. To investigate the role of hypoxia/HIF signaling in this process, we generated aP2Cre;Hif-1 fl/fl;Hif-2fl/fl conditional knockout mice. Surprisingly, these mice exhibited increased MAT expansion following radiation compared to controls, suggesting that HIF deletion in aP2-expressing cells exacerbates radiation-induced adipogenesis. Analysis aP2CreRosa26tdTomato/+ mice revealed that most aP2-expressing cells did not give rise to mature adipocytes, macrophages, or endothelial cells, pointing instead to an uncharacterized stromal population that influences MAT formation. In contrast, conditional ablation of HIF transcription factors in LepRCre-expressing skeletal stem cells, which contain a subpopulation of skeletal progenitors which directly contribute to marrow adipocytes, had no effect on radiation-induced MAT expansion. Collectively, these findings identify a previously unrecognized population of adipocyte-regulatory cells whose HIF-dependent activity constrains stress-induced marrow adiposity. This work provides new mechanistic insight into how radiation disrupts the marrow microenvironment and expands MAT, advancing our understanding of the cellular and molecular drivers of radiation-induced bone fragility. One Sentence SummaryLoss of HIF signaling in aP2Cre expressing cells enhances radiation induced marrow adiposity.

developmental biology↗

bioRxiv2025

Unveiling Eukaryotic Membrane Proteins in High Resolution Using Peptide Solubilization

Integral membrane proteins are vital for numerous biological functions and are typically studied using X-ray crystallography and cryo-electron microscopy (cryo-EM). However, these techniques require the extraction of target membrane proteins from their native membranes using detergents, which might disrupt the lipid environments and alter protein behavior. In this study, we present a novel method for solubilizing membrane proteins using a peptide, thereby eliminating the need for detergents throughout the procedure. We demonstrate that the 4F peptide effectively solubilizes a range of membrane proteins and complexes into peptidiscs, while preserving their functionality and structural integrity. Converting these peptidiscs into nanodiscs further enhances particle homogeneity and facilitates high-resolution structural determination of membrane proteins. Our findings highlight the potential of membrane-solubilizing peptides to advance membrane protein research. HighlightsO_LI4F peptide can effectively solubilize eukaryotic membrane proteins C_LIO_LI4F-peptidisc can be converted to MSP-wrapped nanodisc for high resolution cryo-EM studies C_LIO_LI4F solubilization can preserve endogenous ligands bound to the target membrane protein C_LI

biophysics↗

bioRxiv2025

Arabidopsis Group I Pumilio RNA-binding factors are vital for embryo development and balancing between growth and stress resistance

Pumilio (PUM) RNA binding proteins are crucial for regulating gene expression by binding to a conserved motif in the 3'-untranslated region (3'-UTR). Despite their importance, the role of PUM in plants is largely unexplored. Here, we investigated the functions of Arabidopsis group I PUMs (APUM1-APUM6), which are ubiquitously expressed and localized in the cytosol. While single apum mutants exhibit no visible phenotypes, CRISPR/Cas9-generated apum1 apum2 apum3 triple mutants (apum1/2/3) display reduced growth in both vegetative and reproductive organs, alongside hypersensitivity to various stresses. Remarkably, apum1/2/3/4 quadruple mutants are embryonically lethal, highlighting their essential role in embryo development. Transcriptomic profiling revealed that differentially expressed genes (DEGs) upregulated in apum1/2/3 are enriched in pathways related to photosynthesis, stress responses and anthocyanin biosynthesis, while downregulated DEGs are associated with biotic stress defense and hydrogen peroxide metabolism. This suggests that APUM1/2/3 act as molecular hubs balancing plant growth and stress adaptation. Biochemical assays showed that recombinant APUM homologous domains bind to the 5-UGUGUAUA-3 core motif in the 3-UTR of the transcription factor Production of Anthocyanin Pigment1 (PAP1), crucial for anthocyanin biosynthesis. Notably, single nucleotide substitutions, except for the third U, do not affect binding, while multiple mutations disrupt interaction. Consistently, apum1/2/3 mutants accumulate significantly more anthocyanin than wild-type plants. Furthermore, we predicted 7053 potential target genes for APUM1/2/3, with 1609 present among the upregulated DEGs in apum1/2/3. Taken together, our findings demonstrate that group I APUMs are vital posttranscriptional regulators, providing a new perspective on the trade-offs between growth and stress resilience in plants.

plant biology↗

bioRxiv2025

Texas 2-Step: A new Model for YcgR::c-di-GMP Action at the Flagellar Motor

YcgR is a c-di-GMP effector that inhibits chemotaxis and swimming speed in Escherichia coli and Salmonella. Genetic, biochemical, and structural studies suggest that YcgR interacts with both the bidirectional flagellar rotor and the stator to bias rotation toward counterclockwise (CCW) and reduce motor speed, but the underlying mechanism remains unresolved. Recent cryo-EM structures revealing conformational changes in the rotor-stator complex during directional switching suggested to us a mechanism by which YcgR acts. We call this the Texas 2-Step model, after the country dance in which partners move smoothly in a CCW arc with quick steps followed by slow ones. In this model, YcgR first binds a MotA subunit when the rotor adopts the CCW conformation, in which stators are largely displaced from the C-ring. In the next step, the rotating MotA pentamer delivers YcgR to the rotor protein FliG, thereby slowing motor speed. We provide evidence for the first step of this model, offering testable predictions for future work. ImportanceThe mechanism of YcgR action has been investigated by multiple laboratories using diverse approaches, yet no consensus has emerged. Some studies implicate the rotor, others the stator. A key complication is the involvement of four interacting proteins--MotA, FliG, FliM, and YcgR--with multiple contact sites in several of them. Recent rotor-stator cryo-EM structures revealing conformational changes during directional switching suggested a mechanism that we set out to test. Our experiments show that rotor conformation is crucial for YcgR function.

microbiology↗