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Zheng, J.

Publications and source records attributed to Zheng, J..

At least 55 records · Page 3Linked to original sources
bioRxiv2025

SIMAIS: A swarm intelligence inspired biosensor for rapid protein detection

Swarm intelligence, the collective behaviour of animals such as birds, fish, and ants, arises from simple local interactions and enables survival, efficient foraging, and decision-making without central control. Inspired by this principle, we aimed to harness swarm intelligence for biosensing applications. Conventional assays often struggle with limited sensitivity, long processing times, and the need for specialised instruments, restricting their use in decentralised healthcare. Here we developed a swarm intelligence of microbead-inspired, artificial intelligence (AI)-assisted, and smartphone-based (SIMAIS) biosensing platform that can transform invisible molecular recognition into visible, macroscale patterns. Millions of antibody-coated magnetic microbeads (MBs) organise into magnetically induced structures upon binding protein biomarkers, with the resulting patterns correlating directly to biomarker concentration. Using interferon-gamma (IFN-{gamma}) as a model biomarker, we demonstrate that this approach delivers results within 10 minutes and achieves a tenfold increase in sensitivity compared to conventional lateral flow assays. Robust performance in human serum and urine confirms clinical applicability. By mimicking natural swarm behaviour, this platform introduces a new biosensing paradigm that bridges biology and engineering. Its versatility, speed, and ease of use highlight its potential for decentralised diagnostics, early disease detection, and broader applications in point-of-care healthcare.

biophysics↗
bioRxiv2025

Intrinsically Disordered Protein Coating for Oral Delivery of Peptide Drugs

AbstractAdvancing oral delivery of peptide therapeutics requires innovative materials that overcome gastrointestinal barriers. We introduce the first engineered synthetic intrinsically disordered protein (SynIDP) that self-assembles into an enteric coating, encapsulating peptide drugs to enhance gastric acid resistance and intestinal targeting. This SynIDP recapitulates the molecular design principles and phase transitions of native IDPs to exhibit temperature-controlled condensation and pH-controlled solidification--both transitions being reversible and precisely tuned to intestinal cues. Through detailed analysis of the kinetics of the liquid-to-solid phase transition, we achieve control over the nano-to-microscale morphology of the protein coating, optimizing drug encapsulation and protection. The coating protects peptide-based weight loss drugs for over 60 minutes in simulated gastric conditions, then dissolves to release the active compound. Oral delivery to obese mice results in more consistent weight loss compared to the unencapsulated drug. This modular protein-based coating is a promising platform technology for enhancing oral peptide drug delivery and improving patient compliance.

bioengineering↗
bioRxiv2025

Order-Selective Cells Tile Temporal Space and Predict Order Memory in Humans

Remembering the temporal order of events is critical for episodic memory, allowing us to link individual events into sequences. While the medial temporal lobe and prefrontal cortex are essential for this process, the underlying neural mechanisms remain poorly understood. Here we characterized the representation of order information at the level of single neurons and field potentials recorded from human neurosurgical patients watching naturalistic videos of everyday events and later recalling the order and content of the events depicted. We found order-selective cells (OSCs) in the human hippocampus, amygdala, and orbitofrontal cortex that responded selectively to specific event orders, independent of event content or absolute time. OSCs exhibited transient theta phase precession following their preferred order during both memory encoding and retrieval, the strength of which predicted participants order memory accuracy. During retrieval, OSC spike timing relative to theta varied with the relative position of their preferred event within the recalled event sequence, enabling selective retrieval of relevant events. These findings reveal a neural substrate for representing, encoding into and retrieving from memory absolute and relative ordinal relationships between discrete events. OSCs tile temporal space into discrete ordinal positions, thereby weaving episodic experiences into coherent temporal narratives.

neuroscience↗
bioRxiv2025

Decoding the Glycan Signature: Unraveling N-Glycosylation Alterations in Glycogen Storage Disease Ia and Ib

Glycogen storage disease (GSD) types Ia and Ib are rare inherited metabolic disorders caused by pathogenic variants in G6PC or SLC37A4, respectively. These defects disrupt glucose homeostasis and may affect protein glycosylation. We systematically profiled sera N-glycomes from retrospectively collected GSD Ia (n=17), GSD Ib (n=8), and control (n=21) samples. Derived traits analyses revealed distinct, subtype-specific, and shared glycomic alterations, including shifts from 2,3-to 2,6-sialylation in both subtypes. GSD Ia showed enhanced branching and reduced fucosylation, whereas GSD Ib displayed elevated fucosylation, bisection, and reduced branching. In GSD Ia patients with hepatocellular adenoma/carcinoma (HCA/HCC), further enrichment of oligomannosidic and 2,3-sialylation was observed. Several individual N-glycans showed strong discriminatory performance, supporting their potential as biomarkers for GSD I subtyping and HCA/HCC surveillance. This study provides the first comprehensive characterization of systemic N-glycans in GSD Ia and Ib, revealing glycomic remodeling as a potential biomarker of disease subtypes and tumor progression. Take-home message (synopsis) of the articleSerum/plasma N-glycomic profiling reveals distinct glycosylation signatures in GSD Ia and GSD Ib, including tumor-associated shifts in GSD Ia, highlighting novel biomarkers for disease subtyping and surveillance of hepatic complications.

biochemistry↗
bioRxiv2025

Cross-Species Insights from ART-D to Uncover Evolutionarily Conserved Oncogenic Mechanisms

Cancer arises from oncogenic clones, yet the dynamic mechanisms governing their stepwise evolution toward malignancy remain incompletely understood. Here, we establish the Atlas of Ras-driven Tumors in Drosophila (ART-D), a systematic, cross-species platform that dissects the molecular and phenotypic trajectories of tumorigenesis through ten genetically defined RasV12-driven models. By integrating longitudinal phenotypic profiling, we define three conserved stages of tumor development--initiation, promotion, and progression--distinguished by dynamic changes in tumor burden and tumor-induced cachexia. Transcriptomic dynamics reveal stage-specific signaling rewiring: early tumorigenesis is marked by co-activation of JAK/STAT, NF-{kappa}B/Toll, and MAPK pathways, whereas malignant progression is driven by Notch hyperactivation and Hippo pathway inactivation. Through integrative multi-omics and machine learning, we uncover an evolutionarily conserved pathogenic network involving coordinated JNK, NF-{kappa}B/Toll, Notch, and Hippo signaling that is functionally validated across species. ART-D provides a transformative resource that bridges Drosophila genetics and human cancer biology, offering a framework for decoding conserved oncogenic principles and enabling precision targeting of stage-specific vulnerabilities in RAS-driven cancers.

genetics↗
bioRxiv2025

Targeting the host factor HGS-viral membrane protein interaction in coronavirus infection

While current antivirals primarily target viral proteins, host-directed strategies remain underexplored. Here, we performed a genome-wide CRISPRi screening to identify the host protein, Hepatocyte Growth Factor-Regulated Tyrosine Kinase Substrate (HGS), as essential for the pan-coronaviruses infection both in vitro and in vivo. Mechanistically, HGS directly interacts with the viral membrane (M) protein, facilitating its trafficking to the ER-Golgi intermediate compartment (ERGIC) for virion assembly. Conversely, HGS deficiency caused M retention in the ER, blocking assembly. Leveraging this interaction, we designed M-derived peptides and screened over 5,000 FDA-approved drugs, identifying riboflavin tetrabutyrate (RTB). Both the peptides and RTB bind HGS and disrupt its interaction with the M protein, leading to M retention in the ER and subsequent blockade of virion assembly. These agents demonstrated broad anti-pan-coronavirus activity in vitro and in vivo. Collectively, our findings establish HGS as a druggable host target and identify RTB as a promising broad-spectrum antiviral candidate.

microbiology↗
bioRxiv2025

Targeting Endothelial PERK Accelerates Lymphoid Regeneration by Enhancing DLL4-NOTCH3 Signaling at the Pre-B Niche

Delayed immune recovery after hematopoietic stem cell (HSC) transplantation is associated with a poor clinical outcome, yet strategies to enhance lymphocyte regeneration are limited. We studied the role of unfolded protein response (ER stress) in hematopoietic regeneration within the bone marrow (BM) microenvironment. We revealed that PERK activation is a prominent feature of BM endothelium in leukemia patients and is a hallmark response in mouse BM following ionizing irradiation. Ablating endothelial Perk boosted Notch ligand DLL4 expression and promoted DLL4-dependent early HSC and B progenitor regeneration. Single-cell analysis shows that endothelial DLL4 activates NOTCH3 expressed by mesenchymal stroma cells, and that the PERK-DLL4 axis coordinates the regulation of lymphoid commitment and niche cytokine production. NOTCH3 is critical for the upregulation of IL7 following irradiation and for supporting the expansion of lymphoid progenitors in mesenchymal sphere cultures. These findings not only unveil a previously unrecognized ER stress-controlled vascular-stroma signaling mechanism in regenerative hematopoiesis but also highlight PERK blockade as a promising therapeutic strategy to improve immune recovery after myeloablative transplantation. SummaryZou et al unravel that the adaptive ER stress response in bone marrow blood vessels restricts the post-transplant regeneration of immune progenitor cells by attenuating the expression of Notch ligand DLL4. Targeting ER stress sensor PERK can accelerate immune recovery after transplantation by enhancing DLL4-NOTCH3 signaling and IL7 cytokine production.

cell biology↗
bioRxiv2025

Discovery of AVI-6451, a Potent and Selective Inhibitor of the SARS-CoV-2 ADP-Ribosylhydrolase Mac1 with Oral Efficacy in vivo

The COVID-19 pandemic made plain the need for effective antivirals acting on novel antiviral targets, among which viral macrodomains have attracted considerable attention. We recently described AVI-4206 (1), a potent and selective inhibitor of the SARS-CoV-2 ADP-ribosylhydrolase Mac1 based on a 9H-pyrimido[4,5-b]indole core, the first Mac1 inhibitor to demonstrate antiviral efficacy in mouse models of SARS-CoV-2 infection, but requiring IP administration and frequent dosing. Herein we describe an extensive, structurally enabled medicinal chemistry effort to identify orally bioavailable Mac1 inhibitors by addressing permeability and efflux liabilities of 1 and many of its analogs. Multiple strategies were pursued to overcome these issues, including replacing a urea function to reduce hydrogen bond donor count. While heterocyclic urea mimetics could deliver analogs like AVI-6318 (3) with potencies and ADME profiles similar to 1, abrogation of the P-gp liability was finally achieved with entirely non-polar substituents in place of urea. Thus, AVI-6451 (4) is a potent Mac1 inhibitor lead with low intrinsic clearance, high oral bioavailability, and antiviral efficacy with once-daily oral administration in a mouse model of SARS-CoV-2 infection.

pharmacology and toxicology↗
bioRxiv2025

Localization of Fascin to Dendritic Protrusions Regulates Postsynaptic Plasticity

The Fascin family of actin-bundling proteins is best known for organizing actin filaments (F-actin) into tightly packed bundles that drive dynamic membrane protrusions such as filopodia. In neurons, fascin has been thought to primarily function in axons, as previous studies reported its absence from dendritic filopodia and spines. Here, we demonstrate that fascin is both present and functionally important in dendritic compartments. Using optimized immunocytochemistry and CRISPR-based endogenous tagging of fascin1 in cultured hippocampal neurons, we show that fascin is concentrated in developing dendritic filopodia and enriched in mature dendritic spines. Super- resolution imaging further reveals that fascin is organized into discrete nanoscale foci within spine heads, but not the spine neck. Finally, we show that CRISPR-mediated knockout of fascin1 in mature hippocampal neurons impairs synaptic potentiation, without affecting baseline excitatory synaptic transmission. Together, our findings uncover a previously overlooked aspect of actin organization in dendritic spines and establish fascin as a critical regulator of postsynaptic plasticity. Summary StatementThe actin bundling protein fascin localizes to dendritic filopodia and spines, where it regulates activity-dependent synaptic plasticity.

neuroscience↗
bioRxiv2025

De Novo Design of Anti-Aging Peptides

Aging, a universal biological process in complex organisms, is increasingly recognized to be driven by progressive loss of epigenetic information, as proposed in the Information Theory of Aging (ITOA). However, research on anti-aging peptides remains scarce, with most existing efforts confined to derivatives of natural proteins, while systematic design attempts are virtually absent. This limitation not only restricts discovery within the evolutionary sequence space but also hampers the identification of candidates with novel mechanisms and improved efficacy. Here, we present ElixirSeeker2, the first computational framework for de novo design of anti-aging peptides. By integrating modeling of known anti-aging peptides, activity scoring from the IC50 database, and penalty constraints from toxic peptides, ElixirSeeker2 enables large-scale virtual screening and identification of novel peptide candidates. Several lead peptides demonstrated significant effects in delaying cellular senescence, restoring cellular functions in vitro and in enhancing locomotor activity of aged Caenorhabditis elegans. This study not only validates the feasibility of de novo design in anti-aging interventions but also establishes a strategy for the development of next-generation biologics.

bioinformatics↗
bioRxiv2025

Magnesium isoglycyrrhizinate alleviates alcohol-associated liver disease through targeting HSD11B1

While magnesium isoglycyrrhizinate (MgIG) is a clinically approved therapy for alcohol-associated liver disease (ALD), its precise molecular targets and mechanisms remain uncharacterized. This study aimed to define MgIGs hepatoprotective actions in chronic-binge ALD mouse models and ethanol/palmitic acid-exposed AML-12 hepatocytes. Through an integrated strategy encompassing RNA sequencing, molecular docking, and microscale thermophoresis, we discovered that MgIG directly binds to hydroxysteroid 11-beta dehydrogenase 1 (HSD11B1) at residue 187, a finding corroborated by molecular dynamics simulations. In vivo, MgIG markedly attenuated alcohol-induced liver injury, evidenced by ameliorated histological damage, reduced hepatic steatosis, and normalized liver-to-body weight ratios. In vitro, it effectively reduced lipid accumulation, inflammation, and apoptosis. Mechanistically, RNA sequencing identified isopentenyl diphosphate delta isomerase 1 (IDI1) as a key downstream effector. Hepatocyte-specific genetic manipulations confirmed that MgIG modulates the SREBP2-IDI1 axis, thereby suppressing lipogenesis, inflammatory responses, and apoptotic pathways. We reveal HSD11B1 as a novel direct molecular target of MgIG and elucidate its therapeutic mechanism through the HSD11B1-SREBP2-IDI1 signaling axis, which profoundly impacts ALD pathogenesis. These findings not only validate MgIGs clinical utility but also highlight a promising new therapeutic target for ALD.

pharmacology and toxicology↗
bioRxiv2025

Enterococcus faecalis delivers Obg GTPase via extracellular vesicles to instigate mTOR activity and promote HCC tumorigenesis

Hepatocellular carcinoma (HCC) is a malignant tumor that has been associated with dysbiosis of the gut microbiota. However, how the gut microbiota plays an oncogenic role in HCC remains largely unknown. Here, we show that Enterococcus faecalis (E. faecalis) is highly enriched in liver tumor tissues and is positively correlated with pathogenesis of HCC. E. faecalis promotes liver cancer cell proliferation, protein translation, cell migration and tumorigenesis. Mechanistically, we found that EF-derived extracellular vesicles (EF-EVs) deliver EF-Obg GTPase to activate host mTOR, thereby promoting liver cancer progression. Intriguingly, the EF-Obg protein exerts its influence on the mTOR pathway via a Ras-like G domain involved in GTP binding. EF-Obg exhibits a striking homology with the G1 site of the G domain of Rheb, a key positive regulator of mTOR. Obg gene is critical for E. faecalis to activate mTOR to promote hepatocarcinogenesis based on an engineered obg knockdown strain by CRISPR interference experiment. Clinically, abundant EF-Obg protein expression is correlated with enhanced activation of mTOR, leading to poor overall survival in HCC patients. Significantly, treatment of mTOR inhibitor Everolimus confers effectiveness in EF-colonized liver cancer orthotopic model, suggesting that Everolimus therapeutic approach can be effective for liver cancer patients with enriched E. faecalis. Taken together, we provide mechanistic and functional evidence to verify a direct causal relationship between tumor-resident E. faecalis enrichment and liver carcinogenesis, revealing that EF-Obg functions as a previously unidentified cross-kingdom activator of mTOR to promote liver tumorigenesis.

cell biology↗
bioRxiv2025

Binding Affinities of Disheveled PDZ Protein-Ligand Complexes

Wnt/{beta}-catenin signaling is critical for cell growth and development, with its hyperactive dysregulation implicated in the development of cancer. Current therapeutic research on inhibition of Wnt/{beta}-catenin signaling is impeded by the high cost of experimentally determining binding affinities. Consequently, interest has risen in screening potential inhibitors binding affinities with computational tools to reduce costs. Here, we test the validity of a computational molecular dynamics simulator, Binding Free Energy Estimator 2 (BFEE2), for determining peptide ligand affinity for Wnt/{beta}-catenin signaling. We focus on the Dishevelled (DVL) PDZ domain, a key mediator in WNT signaling through its ability to bind to various peptide ligands. We analyze the binding affinities of several DVL PDZ domain-peptide against previously established results to determine the validity of computational analysis. We conclude that computational molecular dynamics simulations were successful for peptide-ligand complexes.

bioinformatics↗
bioRxiv2025

Evolutionary patterns and repeated adaptive strategies of deep-sea anemones

Sea anemones occupy the full depth of the oceans, yet their evolutionary patterns and adaptive strategies to the enigmatic deep sea have remained contentious and poorly resolved. Here, we assemble genomes (n = 13) and transcriptomes for 15 species collected between 432 and 6,000 m and integrate them with all publicly available actiniarian data. Phylogenomic analyses reveal a mosaic topology among deep-sea and shallow-water clades. Using a novel framework that contrasts convergent gene-loss patterns, we show that a large number of light-associated gene families-- including the complete circadian toolkit--were independently deleted after lineages entered the aphotic realm, whereas comparable loss in shallow taxa is negligible, providing decisive support for a shallow-water origin followed by multiple descents. Intriguingly, some deep-sea lineages further streamline energy budgets by recurrent loss or pseudogenisation of key meiotic genes (e.g., Meiosin, Ythdc2, Spo11, Rad21, Mlh3), indicating a shift towards asexual reproduction. Despite this extensive genomic erosion, deep-sea anemones exhibit sophisticated molecular tuning: specific amino-acid substitutions enhance protein stability and activity under deep-sea conditions, while selective expansions of gene families related to neural excitability, membrane systems, etc., likely mitigate the suppressive environmental effects on vital physiological processes. Enzyme activity assays in the yeast system confirm that the deep-sea variants exhibit superior activity and enhanced growth at 4{degrees}C. These results define a "loss-optimization-innovation" triad that underlies bathymetric adaptations and may apply to other deep-sea fauna worldwide.

evolutionary biology↗
bioRxiv2025

N6-Methyladenine DNA modification regulates pathogen virulence in nematodes

Understanding the global regulatory mechanisms that control pathogen virulence gene expression is essential for elucidating the molecular basis of pathogenicity. N6-methyladenine (6mA) plays a crucial role in regulating gene expression in response to various environmental stresses; however, its role in pathogen virulence remains largely unexplored. Here, we report the widespread occurrence of 6mA across 17 nematode isolates and map its genomic landscape in six notorious agriculturally important pathogen root-knot nematodes (RKNs). We demonstrated that 6mA is characterized by a conserved GAG motif across nematodes, but exhibits species-specific distribution patterns and distinct effects on gene expression. In particular, its enrichment in transposable elements differs between polyploid and diploid nematodes, suggesting lineage-specific epigenetic regulation potentially associated with polyploidy. We further identified two functional 6mA demethylases, MiNMAD-1 and MiNMAD-2, and confirmed their catalytic activity and active sites. Host-induced gene silencing of minmad-1 significantly increased plant resistance to three polyploid RKN species. A detailed functional analysis revealed that minmad-1 knockdown disrupted virulence gene expression during the parasitic stage, thereby reducing nematode infectivity. Together, our findings suggest 6mA demethylase as a key epigenetic regulator of RKNs virulence, providing new insights into nematode biology and offering promising targets for the development of sustainable control strategies. Significance Statement6mA methyltransferase regulates the expression of virulence genes in certain pathogenic bacteria and plays a critical role in their infectivity. However, the regulation of virulence gene expression in eukaryotic pathogens, particularly plant pathogens, remains poorly understood. Most studies on pathogen virulence have focused on individual effectors, with little insight into global regulatory mechanisms. Here, we demonstrate that 6mA broadly shapes virulence gene expression patterns in polyploid RKNs. Moreover, transgenic tobacco, tomato, and rice plants expressing dsRNA against nematode demethylases showed significantly enhanced resistance to RKNs. These findings establish 6mA demethylase as a promising epigenetic target for controlling plant-parasitic nematodes.

molecular biology↗
bioRxiv2025

Geographical variation drives adaptive equilibrium of the P. falciparum sickle-associated mutations

The recent discovery of genetic mutations in Plasmodium falciparum--the most lethal malaria parasite--that enable it to overcome the protective effects of sickle cell trait, raises fundamental questions about the underlying biological and evolutionary interactions. Here we develop a geostatistical model to compare sickle haemoglobin genotype frequencies to the Plasmodium falciparum sickle-associated alleles across global populations, and find a robust association at multiple geographical scales, implying that sickle drives positive selection for these parasite mutations. A model of parasite evolution and an analysis of local haplotype patterns suggest that key features of these mutations - that they are polymorphic in all African populations and are mutually correlated despite lying in different genome regions - are caused by geographical variation in selection pressure, and that the alleles may have been maintained by balancing selection over timescales comparable to the age of the sickle mutation itself. The predicted impact of this host-parasite interaction on disease outcomes varies widely across populations, and functional data are needed to discover the biological mechanisms involved.

genetics↗
bioRxiv2025

SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis

With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core and 3 auxiliary classes based on object-oriented modeling. SEA CDM uses interoperable ontologies for data standardization and knowledge inference. Building on the SEA CDM, we developed the Ontology-based SEA Network (OSEAN) relational database and knowledge graph, along with a set of ETL (Extract, Transform, Load) and query tools, and further applied them to represent 1,278 immune studies with over two million samples from three resources: VIGET, ImmPort, and CELLxGENE. Using simple, robust queries and analyses, our research identified multiple scientific insights into sex-specific immune responses, such as neutrophil degranulation and TNF binding to physiological receptors, following live attenuated and trivalent inactivated influenza vaccination. The novel SEA CDM system lays a foundation for establishing an integrative biodata ecosystem across biological and biomedical domains.

bioinformatics↗