Biology subjects

Huang, Z.

Publications and source records attributed to Huang, Z..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Hydrophobic interactions of FG-nucleoporins are required for dilating nuclear membrane pores into selective transport channels after mitosis

Nuclear envelope (NE) reformation after mitosis is essential for daughter cell viability and requires tightly coordinated nuclear pore complex (NPC) assembly and nuclear membrane reformation. To reveal how these processes are mechanistically linked, we combined acute molecule perturbations in live cells with correlative 3D electron tomography or MINFLUX super-resolution microscopy. We show that degrading Nup62 during mitosis arrests NPC assembly at an intermediate step with smaller membrane pores and removes the whole central transport channel. Molecular dynamics simulations predicted that 32 copies of the central channel subcomplex, recruited into the previously unoccupied pore center, can self-associate via hydrophobic interactions to occupy the volume required for full pore size and exert an outward pushing force; indeed, disrupting these interactions during NPC assembly blocked pore dilation. Later in mitotic exit, perturbed cells exhibited impaired nuclear import, smaller nuclei, and looser NE spacing. Acute inhibition of nuclear import recapitulated these NE defects without affecting NPC assembly. Together, our findings reveal a new, two-step molecular mechanism linking NPC assembly and NE reformation. First, hydrophobic FG-nucleoporins dilate the assembling nuclear pore to its full width by forming the central transport channel, which then allows nuclear import-driven nuclear expansion leading to tight, regular NE membrane spacing.

cell biology↗

bioRxiv2025

VAMP8 function reveals tight linkage between endocytic recycling and endocytosis

Clathrin-mediated endocytosis (CME) is a multistage process that involves the initiation and stabilization of clathrin-coated pits (CCPs) that invaginate and finally detach from the plasma membrane to form clathrin-coated vesicles (CCVs). Given that SNARE proteins are essential for downstream vesicle targeting and fusion events, their recruitment into nascent CCVs has been suggested to be a prerequisite for CME progression. However, which and how SNARE proteins regulate CME remains to be explored. Here, we showed that siRNA-mediated knockdown of the R-SNARE, VAMP8 impairs CCP initiation, stabilization and invagination and strongly inhibits CME. Mechanistically, recruitment of VAMP8 to CCVs is not required for CME. Instead, depletion of VAMP8 inhibits recycling of endocytic cargoes and as exemplified here by transferrin receptor, skews their trafficking toward lysosomal degradation. VAMP8 depletion therefore indirectly impairs CCV formation and inhibits CME by depleting endocytic cargo. Overall, our study provides new insights into the crosstalk between endocytosis and endocytic recycling of CME cargo and demonstrates the critical role for cargo recruitment in stabilizing nascent CCPs to regulate CME. Significance StatementWe demonstrate that VAMP8 depletion inhibits recycling of endocytic cargo and reroutes transferrin receptors toward lysosomal degradation, thereby impairing endocytic vesicle formation and inhibiting clathrin-mediated endocytosis. Thus, the work uncovers a critical link between endocytic recycling and endocytosis, highlighting the importance of recycling pathways in maintaining membrane dynamics. However, the recruitment of VAMP8 into nascent clathrin-coated pits by CALM is not required for CME. While SNARE recruitment is essential for formation of COPI and COPII vesicles, our findings suggest that this requirement is not generalizable to endocytic CCVs.

cell biology↗

bioRxiv2025

Microbubble Track-based Functional Ultrasound Localization Microscopy in Awake Mice

Functional neuroimaging with ultrafast ultrasound is an emerging neuroimaging tool for studying neural activities in the rodent brain. Existing methods, however, are challenged by the compromise between functional imaging sensitivity (i.e., sensitivity in detecting neural responses) and spatial resolution. For example, functional ultrasound (fUS) uses native red blood cells (RBCs) as imaging targets, which offers high functional imaging sensitivity but limited spatial resolution that is confined by the diffraction limit of ultrasound. On the other hand, functional ultrasound localization microscopy (fULM) employs intravenously injected microbubble (MB) as contrast agent to achieve super-resolved spatial resolution but at the cost of functional imaging sensitivity. This study aims to address this challenge by developing a novel, MB track-based hemodynamic activity estimation method to enhance the functional imaging sensitivity of fULM. Our approach involves conducting functional correlation analysis using the MB signals acquired from the entire MB movement track rather than individual MB centroid locations, which overcomes the signal sparsity issue in fULM. To further boost the functional sensitivity of fULM, we developed a novel approach based on indwelling jugular vein catheters to achieve fULM imaging in awake mice. The in vivo imaging results demonstrate that the proposed techniques successfully enhanced the functional imaging sensitivity of fULM without compromising its high spatial resolution. In the whisker stimulation experiments, the proposed technique enabled detection of significantly activated brain regions within fewer than five stimulation cycles (5 minutes of acquisition), reducing the required time by over 50% compared to conventional fULM.

bioengineering↗

bioRxiv2025

Pathology-Specific Modulation of Corticostriatal Circuitry by Chronic Alcohol Consumption in Alzheimers Disease Mouse Models

Chronic alcohol use is a major modifiable risk factor for Alzheimers disease (AD), yet the mechanisms by which it modulates AD pathophysiology remain unclear. Here, we examined circuit-level and pathological changes in two distinct AD mouse models, humanized A{beta} knock-in (hAPP-KI) (A{beta}-driven) and PS19 (tau-driven), subjected to a chronic intermittent alcohol exposure paradigm. In hAPP-KI mice, alcohol increased A{beta} accumulation and excitatory transmission in the medial prefrontal cortex (mPFC) while reducing corticostriatal transmission and striatal cholinergic output. These alterations were accompanied by enhanced recruitment of microglia around A{beta} plaques. In contrast, alcohol-exposed PS19 mice displayed elevated mPFC-to-dorsomedial striatum (DMS) glutamatergic transmission and increased tau phosphorylation without significant changes in microglial activation or local mPFC excitatory drive. In wild-type mice, microglial depletion enhanced glutamatergic transmission onto cortical neurons, suggesting a homeostatic role for microglia in maintaining excitatory balance. Together, these findings reveal pathology-specific effects of alcohol on circuit dysfunction and propose microglia as an important modulator of alcohol-induced synaptic remodeling in the early stage of AD. HighlightsO_LIChronic alcohol exposure modulates glutamatergic transmission and neuroimmune responses in pathology-specific manners across A{beta}- and tau-driven Alzheimers disease mouse models. C_LIO_LIIn hAPP-KI mice, alcohol increases mPFC excitatory input, A{beta} plaque burden, and microglial activation, while impairing corticostriatal transmission and striatal cholinergic signaling. C_LIO_LIIn PS19 mice, alcohol enhances mPFC-to-striatum excitatory transmission and tau phosphorylation without altering local microglial activation or mPFC excitability. C_LIO_LIMicroglial depletion in wild-type mice recapitulates alcohol-induced glutamatergic changes in hAPP-KI mice, revealing a homeostatic role for microglia in regulating cortical excitatory balance. C_LI

neuroscience↗

bioRxiv2025

SpatialFinder: A Human-in-the-Loop Vision-Language Framework for Prioritizing High-Value Regions in Spatial Transcriptomics

Sequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent routine H&E slides offers a practical alternative, but there is (i) no reliable way to identify the most informative areas from standard H&E images alone; and (ii) limited solutions for clinicians to prioritize the microenvironment of their own interests. Here we introduce SpatialFinder, a framework that combines a biomedical vision-language model (VLM) with a human-in-the-loop optimization pipeline to predict gene expression heterogeneity and rank high-value ROIs across routine H&E tissue slides. Evaluated across four Visium HD tissue types, SpatialFinder consistently outperforms baseline VLMs in selecting regions with high cellular diversity and tumor presence, achieving up to 89% correlation with ground truth rankings. These results demonstrate the potential of human-AI collaboration to make spatial transcriptomics more cost-effective and clinically actionable.

bioinformatics↗

bioRxiv2025

Cyclin-dependent kinase 9 inhibitors as oncogene signaling modulators in combination with targeted therapy for the treatment of colorectal cancer

BackgroundColorectal cancer (CRC) is the second deadliest cancer worldwide and new treatment options are urgently needed. Cyclin dependent kinase 9 (CDK9) promotes aberrant RNA transcription in cancer and is a promising target for cancer therapies. MethodsUsing CRC cell lines as well as newly established patient-derived organoid models of CRC, we studied the clinically promising CDK9 inhibitors (AZD4573, BAY1125152/VIP152/enitociclib, and NVP2) to determine their therapeutic potential. We investigated the efficacy and mechanisms of action through cell growth and cytotoxicity assays, RNAseq, immunoblotting, and IHC. ResultsWe found CDK9 inhibitors to be highly potent against CRC, through suppression of proliferation and induction of apoptosis. Our results demonstrated CDK9 inhibitors to be broadly active against a set of CRC models derived from a diverse patient population. Our mechanistic studies showed significant suppression of the Mitogen-active protein kinase (MAPK) signaling pathway due to CDK9 inhibitor treatment, suggesting that CDK9 inhibitor efficacy could be enhanced when combined with MAPK pathway inhibitors. As proof-of-concept, we found that CDK9 inhibitors and MEK inhibitors could be combined to synergistically suppress CRC growth and survival. ConclusionsCDK9 inhibitors show promising activity against patient-derived models of CRC. MAPK signaling is particularly suppressed by CDK9 inhibitors. Combining CDK9 inhibitors and targeted therapy against MAPK signaling pathway may be a viable strategy worthy of further investigation preclinically and clinically. State of translational relevanceNovel therapies for chemotherapy-refractory CRC remain urgently needed. Rapid validation of efficacy in appropriate translational models can provide the necessary rationale to test new therapies in clinical trials. Using newly established patient-derived organoids, we validate the preclinical efficacy of transcriptional CDK9 inhibitors against CRC. This is a therapeutic class that has been scarcely evaluated for efficacy against CRC. We found that CDK9 inhibitors potently inhibit patient-derived organoid models of CRC. Our mechanistic work also reveals that clinically achievable concentrations of CDK9 inhibitor treatment results in suppression of MAPK signaling. As proof-of-concept of the potential actionability of our findings, we demonstrate that CDK9 inhibitors can be combined with MEK inhibitors to synergistically suppress CRC growth. Our study provides new patient-derived CRC models as a resource available to others for therapeutic testing, as well as a roadmap for novel hypotheses about synergistic combination treatments using CDK9 inhibitors.

cancer biology↗

bioRxiv2025

Approaching an Error-Free Diploid Human Genome

Complete human genomes now resolve regions long inaccessible to genetic analysis, yet repetitive and structurally complex sequences remain prone to assembly errors because of limitations in current assembly algorithms. We introduce a support-based framework founded on the principle that each sequencing read provides independent evidence for the underlying genome sequence. Implemented through Sufficient Alignment Support (SAS), the framework identifies regions lacking concordant read support, localizes residual errors, and guides correction. Applying SAS to T2T-YAO, a haplotype-resolved Han Chinese genome, produced a support-validated assembly in which nearly all sequences outside unresolved rDNA arrays and long homopolymer tracts are supported by independent sequencing evidence. This work establishes a scalable framework for genome validation and provides a support-validated East Asian diploid reference for investigating human genomic diversity.

genomics↗

bioRxiv2025

DANCE 2.0: Transforming single-cell analysis from black box to transparent workflow

Preprocessing is a critical step in single-cell data analysis, yet current practices remain largely a black-box, trial-and-error process driven by user intuition, legacy defaults, and ad hoc heuristics. The optimal combination of steps such as normalization, gene selection, and dimensionality reduction varies across tasks, model architectures, and dataset characteristics, hindering reproducibility and method development. We present DANCE 2.0, an automated and interpretable preprocessing platform featuring two key modules: the Method-Aware Preprocessing (MAP) module, which discovers optimal pipelines for task-specific methods via hierarchical search, and the Dataset-Aware Preprocessing (DAP) module, which recommends pipelines for new datasets via similarity-based matching to a reference atlas. Together, MAP and DAP execute over 325,000 pipeline searches across six major tasks - clustering, cell type annotation, imputation, joint embedding, spatial domain identification, and cell type deconvolution - yielding robust and generalizable recommendations. MAP-recommended pipelines consistently outperform original method defaults, with substantial gains across all tasks. Beyond automation, DANCE 2.0 reveals interpretable preprocessing patterns across tasks, methods, and datasets, transforming preprocessing into a transparent, data-driven process. All resources are openly available at https://github.com/OmicsML/dance to support broad community adoption and future methodological advances.

bioinformatics↗

bioRxiv2025

Post-Domestication selection of MKK3 Shaped Seed Dormancy and End-Use Traits in Barley

Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crop plants (1). In cereals, shortening dormancy provides rapid and even post-harvest germination, but increases the risk of weather-induced pre-harvest sprouting (PHS) with harvest losses estimated at beyond 1 billion USD a year (2, 3, 4). Our understanding of how, why, when and where diversification of cereal dormancy arose is fragmentary. Here, we show in the founder cereal crop barley (Hordeum vulgare) that the Mitogen-Activated Protein Kinase (MAPK) pathway regulates dormancy primarily through a mosaic of locus haplotypes comprising copy-number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 (MKK3). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shape dormancy levels according to changing climatic pressures. Understanding the regulatory landscape of MKK3 provides a genetic framework to balance short grain dormancy and PHS-avoidance during a period of rapid climate change.

plant biology↗

bioRxiv2025

Genomic Surveillance Reveals Global Spread of Macrolide-Resistant Bordetella pertussis Linked to Vaccine Changes

The resurgence of whooping cough in regions utilizing acellular pertussis vaccines underscopes emerging public health challenges. Here, we characterized 178 Bordetella pertussis isolates collected from patients across all age groups in Shanghai (2018-2024) to assess genomic evolution and antibiotic susceptibility. Macrolide resistance to erythromycin, azithromycin, clarithromycin and clindamycin escalated from [≤]50% (pre-2020) to nearly 100% (post-2020), mechanistically linked to the 23S rRNA A2047G mutation. Genome-based analysis identified a genotype MT28-ptxP3-MRBP rapidlly dominated post-2020, exhibiting significantly higher prevalence in adults versus than age groups. Phylogenetic analysis of 178 Shanghai and 1596 global genomes revealed two major lineages corresponding to ptxP1 and ptxP3 alleles. MT28-ptxP3-MRBP cluster was identified in France, Japan and the United States in 2024, indicating potential cross-border dissemination. These findings advocate for intergrated surveillance spanning all ages and international borders to contain the global spread of macrolide-resistant Bordetella pertussis. HighlightsO_LIAfter 2020, MT28-ptxP3-MRBP lineage rapidly dominated, comprising 61.7% of isolates. C_LIO_LIMT28-ptxP3-MRBP exhibits a significant transmission advantage among older individuals. C_LIO_LIThe primary affected group shifted from [≤]36 months (pre-2020) to 37 months-18 years (post-2020). C_LIO_LIMacrolide resistance rose from [≤]50% pre-2020 to nearly 100% post-2020, with all resistant isolates carrying the A2047G mutation. C_LI

microbiology↗

bioRxiv2025

Thioredoxin-1 inhibits granulosa cell ferroptosis to rescue ovarian aging through mitophagy-dependent activation of BNIP3L

Ovarian aging is closely associated with a decline in fertility and an increase in reproductive dysfunction. Ovarian granulosa cells (GCs) support oocyte homeostasis and development, yet insight into GC dysfunction during aging is limited. Here, we show that aged GCs of humans and mice have indications of elevated ferroptosis, including increased ferroptosis-related metabolites, lipid peroxidation, and iron accumulation. The ferroptosis inhibitor Ferrostatin-1 reversed ovarian impairment and fertility of aged mice in vivo. We show that the age-related reduction in the expression of TXN (thioredoxin) leads to ferroptosis in human and mouse GCs by blocking BNIP3L-dependent mitophagy. Exogenous activation of TXN could promote mitophagy, thereby clearing excessive ROS and inhibiting ferroptosis. These results suggest that anti-ferroptosis-related treatments may assist in treating aging-related reproductive disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/664497v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1b97e8forg.highwire.dtl.DTLVardef@123f8d0org.highwire.dtl.DTLVardef@a44c61org.highwire.dtl.DTLVardef@92b32e_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsO_LIFerroptosis signatures are upregulated in aged GCs from human and mouse ovaries C_LIO_LITXN is deregulated in aged GCs, leading to mitochondrial and ROS metabolic dysfunction C_LIO_LITXN binds to DNA to regulate autophagy and mitophagy genes, including BNIP3L C_LIO_LIInhibition of ferroptosis can ameliorate GC dysfunction C_LI

cell biology↗

bioRxiv2025

f-BGM enables fungi-specific genome mining in high accuracy and interpretability

Emerging artificial intelligence (AI)-based genome mining methods have revolutionized the paradigm of bacterial secondary metabolite (SM) discovery. Fortunately, recent data accumulation of fungal biosynthetic gene clusters (BGC) fairly offers opportunities for systematic development and evaluation of fungi-specific pipelines. In this work, we proposed a deep learning framework termed as f-BGM specifically for fungal genome mining. By designing a novel self-attention-based architecture to augment inter-domain associations in local genomic contexts, f-BGM exhibits superior performance over existing AI-based methods in both in-distribution and out-of-distribution benchmark tests for BGC detection. Further analyses demonstrate that f-BGM is of decent interpretability on deciphering single-domain and -protein importance, as well as inter-domain partnership. By establishing additional binary classification models, f-BGM also achieves high-quality identification of core enzymes within given BGCs. Finally, case studies of f-BGM-driven genome mining in marine fungi uncovers biosynthetic potential underestimated by the rule-based method antiSMASH, as supported by experimental and computational validation.

bioinformatics↗

bioRxiv2025

The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS

G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1 in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1 that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1G93A mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.

neuroscience↗

bioRxiv2025

MetaNet: a scalable and integrated tool for reproducible omics network analysis

Network analysis is a powerful strategy for uncovering complex relationships in high-throughput omics datasets. However, current tools often lack scalability, flexibility, and native support for multi-omics integration, posing significant barriers for exploring complex biological networks. To address these limitations, we developed MetaNet, a high-performance R package designed to construct, visualize, and analyze biological networks from multi-omics datasets. MetaNet supports highly efficient correlation-based network construction, scalable to datasets with over 10,000 features, and includes extensive layout algorithms and visualization options compatible with both static and interactive platforms. It also provides a comprehensive suite of topological and stability metrics for in-depth network characterization. Benchmarking results show that MetaNet outperforms existing R packages by up to 100-fold in computation time and reduces memory usage by up to 50-fold. We demonstrate its utility through two case studies: (1) a longitudinal analysis of microbial co-occurrence networks showing the dynamics of the airborne microbiome, and (2) an integrative exposome-transcriptome network of more than 40,000 features, uncovering distinct regulatory impacts of biological and chemical exposures. MetaNet bridges the gap between network theory and omics application by offering a robust, reproducible, and biologically informed framework for large-scale, interpretable, and integrative network analyses across diverse omics platforms, advancing systems-level understanding in modern life sciences. MetaNet is available on the Comprehensive R Archive Network (https://cran.r-project.org/web/packages/MetaNet).

bioinformatics↗

bioRxiv2025

Intestinal Epithelial C/EBPβ Deficiency Impairs Colitis-Associated Tumorigenesis by Disrupting CXCL1 /CXCL2/CXCL5-CXCR2-Mediated Neutrophil Infiltration

Dysregulated transcription factors critically link chronic inflammation to oncogenesis in colitis-associated colorectal cancer (CAC), but their mechanistic roles remain incompletely understood. By integrating microarray and transcriptome sequencing data from ulcerative colitis (UC), colitis-associated cancer (CAC), and colorectal cancer (CRC) patients, we identify C/EBP{beta} as a key transcriptional regulator whose elevated expression inversely correlates with survival. In azoxymethane (AOM)/dextran sulfate sodium (DSS)-induced CAC models, intestinal epithelial C/EBP{beta} is upregulated during tumor progression, correlating with exacerbated tumor burden and neutrophil infiltration. Mice with intestinal epithelial-specific Cebpb deletion (Cebpb{Delta}IEC) show resistance to carcinogenesis, accompanied by reduced neutrophil infiltration and tumor growth. Mechanistically, C/EBP{beta} transcriptionally activates CXCR2 ligands (CXCL1, CXCL2, and CXCL5) to drive neutrophil recruitment. Pharmacological inhibition of CXCR2 phenocopies the anti-tumor effects of Cebpb{Delta}IEC deletion, further validating this axis as a therapeutic target. Correlation analysis in patient tissues confirms positive relationships between C/EBP{beta}, CXCR2 ligands, and neutrophil infiltration, suggesting that targeting the C/EBP{beta}-CXCL1/2/5-CXCR2 axis may offer a novel strategy for CAC treatment.

cancer biology↗

bioRxiv2025

Inactivating a β1 subunit of SnRK1 promotes broad-spectrum disease resistance in rice

Rice is a staple crop for over half of the worlds population, and its sustainable production is vital to ensure global food security. However, rice is highly susceptible to several devastating fungal diseases1, including blast disease caused by Magnaporthe oryzae, sheath blight by Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by Bipolaris oryzae, bakanae by Fusarium fujikuroi, and head blight by F. graminearum. The mechanisms underlying the susceptibility of rice to these fungal diseases remain unclear. Here, we report that the {beta} subunit of SnRK1, SnRK1{beta}1A, confers broad-spectrum susceptibility to these fungal diseases. Our findings reveal that diverse rice fungal pathogens have convergently evolved an effector, Gas2, which interacts with SnRK1{beta}1A to prevent its ubiquitination-mediated degradation and promotes its nuclear translocation. While SnRK1{beta}1A is expressed at low levels in healthy plants, its expression is markedly induced upon fungal infections, facilitating susceptibility by inhibiting SnRK11, the subunit of SnRK1, whose overexpression has been shown to enhance broad-spectrum resistance in rice2. Notably, rice lines with disrupted SnRK1{beta}1A are resistant to multiple fungal diseases without compromising growth and yield in the field. Together, this study demonstrates that broad-spectrum disease resistance in crops can be achieved by disrupting inducible susceptibility genes whose encoded proteins are targeted by effectors conserved in multiple pathogens.

plant biology↗

bioRxiv2025

A Novel 'Three-in-one' Mucosal Vaccine Elicits Broad Protection against Three Distinct Clusters of ACE2-using Sarbecoviruseses

With the persistent risk of coronavirus epidemics, the development of universal vaccines is urgently needed and challenging to achieve. In this study, we aimed to design a multivalent immunogen to provide broad protection against diverse ACE2-using sarbecoviruses, which pose a significant threat to global health. Our analysis revealed that the receptor-binding domains (RBDs) of ACE2-using sarbecoviruses segregate into three antigenically distinct clusters, including one cluster that encompasses viruses related to SARS-CoV-2. Based on these findings, we engineered a three-in-one immunogen, designated as 3Rs-NC, which incorporates representative RBDs from all three clusters. 3Rs-NC preserved the natural epitope configuration of each monomeric RBD component, and efficiently elicited high levels of neutralizing antibodies against representative viruses and closely related sarbecoviruses. When administered intranasally with flagellin-based mucosal adjuvant KFD, 3Rs-NC induced robust and durable RBD-specific serum IgG and mucosal IgA responses in mice. Furthermore, KFD-adjuvanted 3Rs-NC conferred sustained protection in both the upper and lower respiratory tracts against SARS-CoV-2 Omicron BA.1 and SARS-like coronavirus WIV1. Additionally, 3Rs-NC immunization protected mice from lethal challenge of SARS-like coronavirus rRsSHC014S, with more efficient protection observed in female mice than male mice. This needle-free three-in-one vaccine represents a promising candidate for a universal mucosal vaccine against ACE2-using sarbecoviruses and could serve as a foundational component of three-in-one vaccine series to form a comprehensive coronavirus vaccine package. HighlightO_LInovel three-in-one immunogen 3Rs-NC induced a high level of neutralizing antibodies against three distinct ACE2-using Sabecovirus clusters. C_LIO_LIadministration of 3Rs-NC plus KFD adjuvant (3Rs-NC+KFDi.n) generated potent and long-lasting RBD-specific serum IgG and mucosal IgA. C_LIO_LI3Rs-NC+KFDi.n provided long-term protection in both upper- and lower-respiratory tracts in mice. C_LIO_LI3Rs-NC+KFDi.n could serve as a foundational component for next-generation coronavirus vaccine strategies. C_LI

immunology↗

bioRxiv2025

Targeting HMGA1-driven leukemic transformation in myeloproliferative neoplasms with pacritinib

Progression of myeloproliferative neoplasms (MPNs) to secondary acute myeloid leukemia (sAML) is a lethal transition lacking reliable early biomarkers and effective therapies. Integrating multi-omics analyses, a cohort of 240 patient biopsies, and functional studies, we identify High Mobility Group A1 (HMGA1) as a critical driver and predictor of this transformation. HMGA1 expression, readily detectable by immunohistochemistry, progressively increases from chronic MPN phases to sAML, outperforming established markers (CD34/CD117) in predicting impending leukemic transformation (AUC = 0.96). Mechanistically, HMGA1 cooperates with JAK2V617F and TP53 mutations to promote leukemogenesis. Clinically, high HMGA1 levels correlate with resistance to first-generation JAK inhibitors and portend poor overall survival. Importantly, the next generation JAK2/FLT3 inhibitor pacritinib abrogates HMGA1-driven proliferation and significantly extends survival in preclinical models, offering an immediate therapeutic strategy for this high-risk population. Our findings establish HMGA1 as an actionable biomarker for risk stratification and early intervention, and a therapeutic target to overcome therapeutic resistance in MPN-sAML. HighlightsO_LIHMGA1 IHC staining serves as a readily implementable biomarker, outperforming existing marker for early prediction of MPN progression to sAML and identifying patients at high risk. C_LIO_LIElevated HMGA1 expression correlates with resistance to first-generation JAK inhibitors and predicts poor overall survival in MPN-sAML patients, highlighting a critical unmet therapeutic need. C_LIO_LIThe next-generation JAK2 inhibitor pacritinib effectively overcomes HMGA1-driven aggressive disease and therapy resistance, offering a rational, clinically available treatment strategy for HMGA1-high MPN-sAML. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/657170v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@18b835org.highwire.dtl.DTLVardef@e5b31dorg.highwire.dtl.DTLVardef@5245caorg.highwire.dtl.DTLVardef@163f5de_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗