Biology subjects

Guo, W.

Publications and source records attributed to Guo, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

CART-GPT: A T Cell-Informed AI Linguistic Framework for Interpreting Neurotoxicity and Therapeutic Outcomes in CAR-T Therapy

Chimeric antigen receptor (CAR) T cell therapy holds transformative potential for hematologic malignancies, yet predicting patient-specific treatment efficacy and neurotoxicity remains a major clinical challenge due to the complex and heterogeneous nature of the infused CAR-T cell populations. Here, we introduce CART-GPT, a transformer-based model fine-tuned on a curated atlas of 1.12 million CAR-T single-cell RNA-seq profiles annotated with clinical outcomes. CART-GPT is the first AI model developed for CAR-T therapy that predicts both treatment response and the risk of immune effector cell-associated neurotoxicity syndrome (ICANS), achieving state-of-the-art performance (AUC ~0.8) and marking a significant advance in the field. The model provides interpretable insights, revealing that neither therapeutic efficacy nor neurotoxicity is driven by individual cell types alone, but by the combined influence of discrete, distinct subsets across diverse T cell states and transcriptional programs. A novel cell aggregation strategy links single-cell predictions to patient-level metrics, enhancing both accuracy and biological relevance. As a contribution to this ever-evolving field, we also release a comprehensive, annotated single-cell CAR-T atlas as a community resource to facilitate future research in immunotherapy. These advances demonstrate the potential of foundation models in single-cell biology to inform precision CAR-T treatment planning and facilitate the rational design of next-generation cell therapies.

bioinformatics↗

bioRxiv2025

Novel combination of irreversible electroporation and allogenic chimeric antigen receptor (CAR) T-cell therapy synergizes therapeutic outcomes in a preclinical human pancreatic cancer mouse model

Irreversible electroporation (IRE) is a non-thermal ablation modality used clinically for treating unresectable tumors while preserving vital structures through controlled application of pulsed electric fields. Previous data suggest that patient outcomes are enhanced with the induction of an anti-tumor immune response, but current research focuses on using immune checkpoint inhibitors, which function through conventional immune pathways that may be downregulated by cancer or dysregulated by chemo-induced lymphodepletion. Chimeric Antigen Receptor (CAR) T-cells overcome this limitation, as they are engineered with synthetic receptors that redirect lymphocytes to recognize and target cells expressing tumor-specific structures. CARs are engineered to have an increased binding affinity compared to in-situ T-cell binding, amplify internal stimulation cascades, and release pro-inflammatory cytokines that can modulate the endogenous immune system. However, there are still major limitations for adoptive cell therapies in solid tumors, including life-threatening on-target off-tumor cytotoxicity, antigen escape, and failure to infiltrate and persist in solid tumors. Given the substantial evidence that IRE overcomes many of the challenges associated with immune infiltration and persistence in solid tumors, there is a strong premise for using targeted cell therapies following IRE, which would then target residual cancer that could repopulate the lesion. Here, we present the first proof-of-concept combination of IRE with an adoptive cell therapy. We validated that the cell membrane CAR target is not affected in electroporated cells that survive IRE, allowing for subsequent binding and elimination of residual tumor. The research demonstrates the feasibility and synergy of a novel combination of two clinically used techniques.

cancer biology↗

bioRxiv2025

Far-Red Light in Early Growth Stages Boosts Lettuce Biomass and Preserves Anthocyanins

Background and AimsLight plays a dual role in plants, serving as both an energy source and a regulator of development from seedling to senescence. Recently, far-red (FR) radiation has gained attention in the controlled environment agriculture (CEA) science and grower community for its potential to enhance yield through canopy expansion and improved light capture, contributing positively to photosynthesis. This study explores how supplemental FR light promotes lettuce growth and morphology across weekly intervals as well as analyzing photosynthetic parameters, pigment accumulation, and anthocyanin gene expression. MethodsRed leaf lettuce (Lactuca sativa Red Fire) was grown in a commercial plant factory with artificial light for six weeks. 5000K white (W) light was maintained at 300 mol m-2 s-1, and FR, when supplemented, was added at 100 mol m-2 s-1 in addition to the 300 mol m-2 s-1 of W light. Four lighting treatments were tested under a 16 h photoperiod: (1) W for all 6 weeks ("W"), (2) 4 weeks of W followed by 2 weeks of supplemental FR ("W to W+FR"), (3) 4 weeks of FR supplementation followed by 2 weeks of only W ("W+FR to W"), and (4) W+FR for all 6 weeks ("W+FR"). Key ResultsThe shoot dry weight after 6 weeks in "W+FR", "W+FR to W" and "W to W+FR" was greater than "W". Both "W+FR" and "W+FR to W" showed a tendency for greater canopy expansion compared to "W" as well as "W to W+FR". There were no significant differences in stomatal conductance among the treatments. On the other hand, in both "W" and "W+FR to W" plants, CO2 assimilation rates were enhanced when FR light was supplemented during measurement, compared to when FR was not provided. Anthocyanin accumulation was greater in both "W" and "W+FR to W", consistent with the expression of key genes involved in the anthocyanin biosynthesis pathway, including anthocyanin synthase (ANS), flavanone 3-hydroxylase (F3H) and dihydroflavonol 4-reductase (DFR). ConclusionsThis study demonstrates that FR supplementation during the early growth stages of lettuce promotes biomass accumulation by enhancing both canopy expansion and photosynthetic activity, while maintaining high levels of functional compounds such as anthocyanins.

physiology↗

bioRxiv2025

Potent Efficacy of Computer-Aided Designed Peptide Degrader Drug on PCSK9-Mediated Hypercholesterolemia

Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key regulator of low-density lipoprotein receptor (LDLR) degradation, which leads to increased levels of low-density lipoprotein cholesterol (LDL-C) and a heightened risk of hypercholesterolemia. Existing therapeutic strategies--such as monoclonal antibodies and gene-editing approaches--are limited by high production costs, potential safety concerns, and limited effectiveness in targeting intracellular PCSK9. Targeted protein degradation (TPD) represents a promising alternative capable of overcoming these limitations. In this study, we utilized computer-aided drug design (CADD) to develop a peptide-based degrader, Cadd4, aimed at selectively reducing PCSK9 levels. Through molecular docking and structural refinement, a peptide sequence with strong binding affinity to PCSK9 was identified. Functional evaluation was conducted both in vitro using human LX-2 cells and in vivo in high-fat diet (HFD)-induced hypercholesterolemic mouse models. Cellular uptake, PCSK9 degradation, and LDLR restoration were assessed via confocal microscopy, western blotting, and biochemical analysis. Safety was evaluated by monitoring liver enzyme levels and general physiological parameters. Cadd4 exhibited efficient intracellular delivery and selective PCSK9 degradation in LX-2 cell. In HFD-fed mice, hepatic PCSK9 expression was reduced by 38%, accompanied by a marked increase in LDLR levels. These changes translated into a 25% reduction in total plasma cholesterol and a 29% decrease in LDL-C concentrations. Biodistribution studies indicated liver-specific accumulation of Cadd4, consistent with its intended site of action. Experiments using human liver tissue further confirmed its ability to decrease PCSK9 and enhance LDLR levels. No signs of liver toxicity or adverse systemic effects were observed throughout the study. This work introduces Cadd4 as a CADD-designed peptide-based degrader capable of lowering plasma cholesterol by promoting LDLR recovery via PCSK9 degradation. Its intracellular mechanism of action addresses key gaps in current PCSK9-targeted therapies and supports the broader utility of TPD platforms in managing hypercholesterolemia. These findings offer a foundation for developing cost-effective, scalable therapies within the context of precision cardiovascular medicine.

pharmacology and toxicology↗

bioRxiv2025

Pentose Sugars Encode Sequence-Dependent DNA-RNA Segregation for Biomimetic Multiphase Condensates

The nucleus segregates DNA and RNA with high precision to safeguard genome stability and gene regulation despite their homologous structures, yet the underlying molecular principles have long evaded both understanding and synthetic translation. Here we show that a single atomic difference between the pentose sugars, a 2-OH in RNA versus a 2-H in DNA, suffices to drive their phase segregation with cationic peptides. This subtle chemical distinction makes RNA bind peptides more strongly than sequence-identical DNA, generating an asymmetry that, when modulated by sequence-encoded homotypic interactions, drives the formation of core-shell multiphase condensates. Using a supervised machine-learning approach, we distill these molecular principles into a predictive design rule and harness it to program a library of oligonucleotide pairs, termed SEGREGamers, that self-assemble into droplets with coexisting DNA- and RNA-rich domains. These synthetic condensates recapitulate nuclear compartment functions, including selective molecular partitioning and enhanced RNA catalysis. Our results establish a chemically encoded platform for engineering synthetic nuclear mimics and programmable biomolecular condensates, and suggest that sugar identity may have served as an ancient physical mechanism for organizing nucleic acids.

biophysics↗

bioRxiv2025

In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation

The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope into host cells. At least 27 Dot and Icm proteins are required for assembly and function of the system, yet the architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy cryo-electron microscopy to reveal in-situ structures of the Dot/Icm machine at near-atomic resolution. Importantly, two proteins essential for effector translocation, DotA and IcmX, form a pentameric protochannel at an inactive state. Upon activation, the DotA-IcmX protochannel undergoes extensive rearrangements to form an extended transenvelope passage capable of transporting effector proteins from the bacterial cytoplasm into host cells as revealed by cryo-electron tomography. Collectively, our findings suggest that the DotA-IcmX complex functions as the gatekeeper for effector translocation of the Dot/Icm T4SS.

molecular biology↗

bioRxiv2025

DR5 CAR-T cells target solid tumors and suppress MDSCs with minimal toxicity

Chimeric antigen receptor (CAR) T cell therapies have poor efficacy in solid tumors due to limited target specificity and an immunosuppressive tumor microenvironment. We investigated death receptor 5 (DR5) as a CAR target based on its high expression in both solid tumors and myeloid- derived suppressor cells (MDSCs). We engineered agonistic DR5-specific CAR constructs and evaluated their activity in multiple models, demonstrating DR5-expression-dependent tumor killing, confirmed by knockout and overexpression experiments. DR5-targeting single-chain variable fragments retained their pro-apoptotic activity when expressed on non-effector cells or extracellular vesicles. Among multiple CAR designs, we identified a construct with optimized binding affinity that maintained T cell viability while preserving strong tumor and MDSC-killing potency. To assess safety and efficacy in an immunocompetent setting, we also developed a murine DR5-targeted CAR. In multiple xenograft and syngeneic mouse models, DR5 CAR-T cells reduced tumor growth, prolonged survival, and did not cause detectable toxicity. In patient- derived organoids and tissue slices, DR5 CAR-T cells infiltrated tumor tissues, reduced MDSCs, boosted CD8+ T cell activity, and inhibited tumor growth. These findings support DR5-targeted CAR-T therapy as a promising strategy for treating solid tumors, which combines direct tumor cytotoxicity with immune activation and minimizes off-target effects. TeaserDR5 CAR-T cells eliminate tumor cells and MDSCs and activate tumor-resident CD8+ T cells within the TME.

cancer biology↗

bioRxiv2025

Senescent mast cells contribute to the progression of benign prostatic hyperplasia via SCF/c-KIT mediated endothelial-mesenchymal transition

Benign prostatic hyperplasia (BPH) is a common age-associated urological condition characterized by stromal expansion, but its cellular origins and regulatory mechanisms remain unclear. In this study, we identified endothelial-to-mesenchymal transition (EndMT) as a contributor to stromal cell accumulation in BPH. Using single-cell transcriptomic analysis, endothelial lineage tracing in mice, and validation in human samples, we showed that senescence-associated mast cells increased the expression of vascular endothelial growth factor A (VEGFA) and transforming growth factor-beta 1 (TGF-{beta}1) through the stem cell factor (SCF)/c-KIT-MAPK-JUND signaling pathway, thereby inducing EndMT in endothelial progenitor cells. Stromal fibroblasts express SCF, promoting mast cell activation and establishing a feedback loop that supports continued stromal proliferation. Intriguingly, inhibition of mast cell activation reduces EndMT and attenuates prostate enlargement in vivo. Thus, these findings revealed a senescence-linked immune-stromal interaction in the aging prostate and identify potential targets for therapeutic intervention in BPH.

cell biology↗

bioRxiv2025

Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms

BackgroundRespiratory syncytial virus (RSV) poses a significant public health threat, particularly to children and the elderly. Two protein-based vaccines and one mRNA vaccine have been approved, all targeting the prefusion conformation of the fusion (F) glycoprotein. However, it has been reported that the F protein transitions to the post-fusion state during storage, resulting in a reduction of the vaccines immunogenicity. MethodsIn this study, we engineered novel pre-F-based antigens to preserve pre-F-specific immunodominant epitopes while eliminating sub-potent ones. Based on this, we constructed a series of single-chain dimers and selected the one with the highest expression yield and melting temperature (Tm). Next, we created a heterodimer, scDimer AB. Structural and protein characterization analyses were conducted to verify our design. All monomeric and scDimer antigens were used to immunize rodent models. Additionally, we prepared the antigens in mRNA form and immunized BALB/c mice. Finally, we combined both antigen forms, administering intramuscular mRNA priming followed by intranasal protein delivery in mice. In all immunization strategies, viral challenges were performed in animals to evaluate the immunologic protective effects. FindingsThrough rational design, we developed a monomeric and two single-chain dimeric (scDimer) proteins with the expected characteristics, including complete II, V, and O epitopes and a partial III epitope. The scDimers elicited stronger binding and neutralizing antibody responses in rodent models compared to the monomer, and they also boosted T cell responses when combined with appropriate adjuvants. After three doses of scDimer immunization, live RSV was barely detectable in the tissues of infected animals. The copies of RNA encoding N-gene were significantly reduced in the immunized groups compared to the PBS-injected control groups. We also engineered mRNA versions of the antigens and verified their protective efficacy in mice. Notably, there were no significant differences between intranasal boost and intramuscular two doses after RSV challenged, suggesting that intranasal boost provided equivalent protection to intramuscular vaccination and could reduce the risk of vaccine-enhanced disease (VED) potentially. InterpretationThe scDimer-based RSV vaccines effectively protected rodents from RSV infections, highlighting their clinical potential. Our antigen design removed certain suboptimal epitope regions, enhancing the efficiency of antigen presentation and increasing the proportion of the most potent pre-F-specific neutralizing antibodies. This approach provides a novel perspective for future vaccine design. FundingNational Key R&D Program of China, National Science Foundation of China, Young Scientists in Basic Research, Chinese Academy of Sciences, and Special Program of China National Tobacco Corporation. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe licensed respiratory syncytial virus (RSV) vaccines were based on RSV pre-F structure. We conducted a PubMed search for articles published in English from databases inception to March 31, 2025, using the search terms "RSV" (interchanged with "respiratory syncytial virus"), "pre-F" (interchanged with "prefusion F") and "vaccine". Our search revealed that most of the articles focus on combining pre-F with RSV G protein or other proteins to form viral-like particles (VLPs) or nanoparticles. The second-largest category of articles examined the antibodies level elicited by the pre-F antigens in animal model or some special cohorts. Other studies addressed topics such as optimization of injection dosage and immunization strategies, methodologies for detecting pre-F-specific antibodies, and the development of mRNA-LNP vaccines. Notably, only 4 articles described novel designs of RSV pre-F antigens, all of which were trimeric and based exclusively on the RSV A subtype F protein sequence. Added value of this studyTo our knowledge, our design is the first single-chain dimer version of RSV pre-F antigen. The engineered antigens demonstrated high yield, thermostability, and immunogenicity comparable to that of DS-Cav1. Additionally, we developed the first chimeric RSV-antigen covering both subtype A and B, thereby broadening the potential protective spectrum. We further validated the immunogenicity of our designs in mRNA form and as a protein-mRNA combination. This research emphasizes the potential of constructing and combining minimized, stable antigen modules, offering a novel approach for future vaccine development. Implications of all the available evidenceIn this study, we present a novel approach for constructing and combining minimized, stable antigen modules for future vaccine design. The strong immunogenicity of our antigens underscores their potential for clinical application. Furthermore, given the structural similarities between the RSV antigen and those of other Pneumoviruses, such as human metapneumovirus (hMPV), our design strategy could be extended to the development of multivalent vaccines.

immunology↗

bioRxiv2025

Loss of tumor suppressor p53 upregulates stem cell factor SOX9 via Notch signaling

Basal-like breast cancer (BLBC) consists of the majority of triple-negative breast cancer subtype that has a higher degree of cellular plasticity owing to a greater number of stem-like cancer cells compared to other subtypes 1. BLBCs are thought to originate from the luminal progenitor cells despite their prominent basal-cell features. SOX9 is a key transcription factor which is expressed selectively in estrogen receptor-negative luminal progenitors in postnatal mammary glands. During BLBC progression, SOX9 upregulation is required for the de-differentiation of luminal cells to multipotent fetal mammary stem cell-like states, which are crucial for the malignant progression of BLBC. However, the mechanism driving SOX9 upregulation in BLBC remains unclear. Since p53 is mutated in nearly 90% of the BLBC and is considered as an early event in the BLBC transformation, we hypothesized that p53 loss could contribute to SOX9 upregulation during BLBC progression. Using primary mammary cell organoids, we showed that p53 loss not only induced the SOX9 expression but also stabilized the half-life of SOX9 protein. We further identified that p53 loss increased Psen2 expression to activate the Notch1 signaling, which induced SOX9 expression. Together, our work identified a molecular mechanism allowing loss of tumor suppressor p53 to coopt the cell fate determinant SOX9 to drive de-differentiation in BLBC.

cancer biology↗

bioRxiv2025

eSPred: Explainable scRNA-seq Prediction via Customized Foundation Models and Pathway-Aware Fine-tuning

Single-cell RNA sequencing (scRNA-seq) has been widely used for studying cellular heterogeneity, but its use for subject-level prediction and clinical applications is still limited. We introduce eSPred, a customized foundation model designed for predictive analysis of scRNA-seq. It integrates cell-type information through a grouping strategy during pre-training and leverages pathway information to guide network flow during fine-tuning. Across multiple datasets, eSPred improves prediction accuracy and highlights pathways linked to disease mechanisms. These results suggest that eSPred can help bridge the gap between single-cell data and subject-level clinical insights, supporting more precise diagnosis and better-informed treatment decisions.

bioinformatics↗

bioRxiv2025

cytoGPNet: Enhancing Clinical Outcome Prediction Accuracy Using Longitudinal Cytometry Data in Small Cohort Studies

Cytometry data, including flow cytometry and mass cytometry, are now standard in numerous immunological studies, such as cancer immunotherapy and vaccine trials. These data enable the monitoring of an individuals peripheral immune status over time, providing detailed insights into immune cells and their role in clinical outcomes. However, traditional analyses relying on summary statistics, such as cell subset proportions and mean fluorescence intensity, may overlook critical single-cell information. To address this limitation, we introduce cytoGPNet, a novel approach that harnesses extensive cytometry data to predict individual-level outcomes. cytoGPNet is designed to address four key challenges: (1) accommodating varying numbers of cells per sample; (2) analyzing the longitudinal cytometry data to understand temporal relationships; (3) maintaining robustness under the constraints of limited individual samples in immunological studies; and (4) ensuring interpretability to facilitate biomarker identification. We apply cytoGPNet to data from multiple diverse studies, each with unique characteristics. Despite these differences, cytoGPNet consistently outperforms other popular methods in terms of prediction accuracy. Moreover, cytoGPNet provides interpretable results at multiple levels, offering valuable insights. Our findings underscore the effectiveness and versatility of cytoGPNet in enhancing the analysis of cytometry data and its potential to advance immunological research.

bioinformatics↗

bioRxiv2025

Microengineered transplantation of human solid tumors for in vitro studies of CAR T immunotherapy

Treatment of solid malignancies using chimeric antigen receptor (CAR) T cells remains a significant challenge, but current efforts to advance this therapy are challenged by our limited capacity to probe and understand cancer-immune interactions in human solid tumors. Here, we present a microengineered platform for in vitro modeling of malignant solid tumors during CAR T therapy. This system makes it possible to vascularize human tumor explants and perfuse them with blood-borne immune cells in a controlled manner. We first present a microphysiological model of human lung adenocarcinomas infused with CAR-T cells and show how this system can be used to simulate, visualize, and interrogate tumor-directed trafficking and effector function of CAR T cells. We then demonstrate the proof-of-principle of testing a chemokine-directed CAR T cell engineering strategy in a model of malignant pleural mesothelioma and validating our in vitro assessment using a matching in vivo mouse model. Finally, we describe a potential therapeutic target discovered by single-cell RNA sequencing that can be pharmacologically modulated to increase the efficacy of CAR T cells for lung adenocarcinoma, for which we also present specific biomarkers identified by global metabolomics analysis. We believe that the bioengineering principle demonstrated here will make important contributions to developing new capabilities for preclinical studies of adoptive cell therapies for cancer and other complex diseases.

bioengineering↗

bioRxiv2025

Tumor-Initiating Cells Fine-tune the Plasticity of Neutrophils to Sculpt a Protective Niche

The abundant accumulation of neutrophils in various solid cancers has been well recognized, but the functions of tumor-associated neutrophils (TANs) remain controversial. TANs have long been believed to be immune suppressive and have thus been referred to as "myeloid-derived suppressor cells". However, effective tumor control induced by immunotherapy was recently found to be associated with strong neutrophil signatures. These seemingly contradictory findings highlight the unexpected degree of plasticity and heterogeneity unique to TANs. How the cellular plasticity and functional heterogeneity of TANs are regulated remains unknown. Here, we show that, while anti-PDL1/CD40 agonist immunotherapy can induce interferon responses to reprogram many TANs, allowing them to become plastic and regain anti-tumor activities in squamous cell carcinomas, a subset of TANs residing at the tumor-stroma interface can preserve their immune suppressive state. Importantly, by designing a reverse genetic screening, we identified a group of Sox2Hi tumor-initiating cells (TICs) at the tumor-stroma interface that could upregulate Fatty Acid Desaturase 1 (Fads1) to produce arachidonic acid. This TIC-specific pathway can disrupt the interferon responsive potentials of TANs, preventing the interferon-mediated reprogramming. Thus, by fine-tuning the plasticity of neutrophils, TICs shape neutrophil heterogeneity and sculpt a protective micro-niche to survive from immunotherapy and drive cancer relapse.

cancer biology↗

bioRxiv2025

An unrecognized and crucial role of chloroplast division in leaf variegation in Arabidopsis thaliana

Leaf variegation provides a valuable model for elucidating the molecular mechanisms that underlie chloroplast biogenesis, including both chloroplast development and division. While there has been notable advancement in comprehending the role of the Arabidopsis Yellow Variegated2 (VAR2), which encodes the AtFtsH2 subunit of the thylakoid FtsH metalloprotease complex, the exact mechanism governing leaf variegation formation remains elusive. In this study, time-course microscopy analyses of chloroplast number per cell from the first leaf pair revealed that most var2 cells lack chloroplasts. Interestingly, chloroplast biogenesis in the green sector of var2 leaves is significantly delayed but prolonged compared to the wild type (WT), leading to increased heterogeneity in chloroplast number and size among cells. These results suggest that chloroplast biogenesis in the green sector can partially compensate for the defect in the white sector. Additionally, approximately 15% of cells in var2 white sectors are devoid of plastids, and chloroplast number in guard cells is significantly lower in var2 than in WT, indicating that VAR2 mutations impair chloroplast division. Consistently, the var2 phenotype is exacerbated by knocking out key plastid division genes, including Paralog of Accumulation and Replication of Chloroplasts6 (PARC6) and Plastid Division1 (PDV1), but is fully rescued by overexpressing PDV1 or PDV2. Furthermore, VAR2 mutations inhibit etioplast development, while accelerating chloroplast biogenesis by knocking out Constitutively Photomorphogenic1 (COP1) rescues the var2 phenotype. Together, our findings reveal a novel role for VAR2 in plastid division and its essential function in chloroplast biogenesis, providing new insights into the mechanism underlying variegated leaf formation.

plant biology↗

bioRxiv2025

Modeling Masticatory Myalgia to Headache-like Referred Pain Triggers Local Gene Plasticity at Referred Pain Sites

Patients with myofascial pain in the head and neck area report widespread and referred pain, including headache. Existing preclinical models fail to replicate this clinical phenotype; therefore, we aimed to develop animal models mimicking referred pain phenomenon and investigate whether referred pain leads to gene plasticity at the referred sites. We modeled masticatory myalgia by stimulation of either the masseter (MM) or temporal muscle (TM) in mice. MM and TM were stimulated with a single high-dose injection of Collagenase-type II (Col), repetitive low-dose Col injections, repetitive gentle MM stimulation, or single or repetitive forceful mouth opening. Referred pain was assessed by measuring mechanical hypersensitivity in the periorbital area (representing headache-like behavior) and another masticatory muscle. Stimulation of the MM, whether through single or repetitive Col injections or mouth opening, produced inconsistent, short-lasting (1-2 days) headache-like behavior in both males and females. In contrast, stimulation of the TM, using different paradigms, triggered mechanical hypersensitivity in both the MM and the periorbital area. Referred headache-like behavior lasted longer in females compared to males, while referred myalgia in the MM was pronouncer in males. The referred pain in the MM and periorbital areas triggered by TM stimulation was associated with significant gene plasticity in the MM and dura mater. Transcriptional changes in the MM following Col injection into the TM resembled those observed after direct MM injections. Presented data imply that referred pain modeled by TM stimulation could be accounted by nociceptive signaling from multiple local sites involved in this referred pain network.

neuroscience↗

bioRxiv2025

Human giant GTPase GVIN1 forms an antimicrobial coatomer around the intracellular bacterial pathogen Burkholderia thailandensis

Several human pathogens exploit the kinetic forces generated by polymerizing actin to power their intracellular motility. Human cell-autonomous immune responses activated by the cytokine interferon-gamma (IFNg) interfere with such microbial actin-based motility, yet the underlying molecular mechanisms are poorly defined. Here, we identify the IFNg-inducible human giant GTPases GVIN1 as a novel host defense protein that blocks the bacterial pathogen Burkholderia thailandensis from high-jacking the hosts actin polymerization machinery. We found that GVIN1 proteins form a coatomer around cytosolic bacteria and prevent Burkholderia from establishing force-generating actin comet tails. Coatomers formed by a second IFNg-inducible GTPase, human guanylate binding protein 1 (GBP1), constitute a GVIN1-independent but mechanistically related anti-motility pathway. We show that coating with either GVIN1 or GBP1 displaces the Burkholderia outer membrane protein BimA, an actin nucleator that is essential for actin tail formation. Both GVIN1 and GBP1 coatomers require additional IFNg-inducible co-factors to disrupt the membrane localization of BimA, demonstrating the existence of two parallel-acting IFNg-inducible defense modules that evolved to target a virulence trait critical for the pathogenesis of numerous bacterial infectious agents.

immunology↗

bioRxiv2025

The Global Wheat Full Semantic Organ Segmentation (GWFSS) dataset

Computer vision is increasingly used in farmers fields and agricultural experiments to quantify important traits. Imaging setups with a sub-millimetre ground sampling distance enable the detection and tracking of plant features, including size, shape, and colour. Although todays AI-driven foundation models segment almost any object in an image, they still fail for complex plant canopies. To improve model performance, the global wheat dataset consortium assembled a diverse set of images from experiments around the globe. After the head detection dataset (GWHD), the new dataset targets a full semantic segmentation (GWFSS) of wheat organs (leaves, stems and spikes) covering all developmental stages. Images were collected by 11 institutions using a wide range of imaging setups. Two datasets are provided: i) a set of 1096 diverse images in which all organs were labelled at the pixel level, and (ii) a dataset of 52,078 images without annotations available for additional training. The labelled set was used to train segmentation models based on DeepLabV3Plus and Segformer. Our Segformer model performed slightly better than DeepLabV3Plus with a mIOU for leaves and spikes of ca. 90%. However, the precision for stems with 54% was rather lower. The major advantages over published models are: i) the exclusion of weeds from the wheat canopy, ii) the detection of all wheat features including necrotic and senescent tissues and its separation from crop residues. This facilitates further development in classifying healthy vs. unhealthy tissue to address the increasing need for accurate quantification of senescence and diseases in wheat canopies.

plant biology↗