Biology subjects

Peng, C.

Publications and source records attributed to Peng, C..

At least 55 records · Page 3Linked to original sources

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

Evaluation of Multiplexed Liquid Glycan Array (LiGA) for Serological Detection of Glycan-binding Antibodies

We test the performance of the multiplexed liquid glycan array (LiGA) technology in serological assays. Specifically, we use LiGA to detect ABO blood group antibodies in human serum. This LiGA, which we name ABO-LiGA, contains ABO blood group trisaccharide glycans with an ethylazido aglycone conjugated to groups of ten multi-barcoded M13 particles carrying dibenzocyclooctyne (DBCO) on p8 proteins. ELISA clonal binding assays to anti-A/B antibodies confirmed the functional performance of ABO-clones and aligned with next-generation sequencing (NGS) of the mixed clones. Multiple DNA-barcoded technical replicates in LiGA allow for quantification of reproducibility and robustness as determined by the Z-score using NGS. We then tested ABO-LiGA for specific detection of IgG and IgM anti-A and anti-B IgG and IgM antibodies in human serum samples. Comparison of antibody binding responses in sera from 31 healthy donors to ABO-LiGA with an ABO-Luminex-based method revealed consistent responses to LiGA-ABO but also minor deficiencies of ABO-LiGA such as low robustness of the current assay format and a limited ability to detect low intensity antibody responses. Some results point to undesired interactions of serum antibodies with small-footprint glycans conjugated to phage via the bulky DBCO moiety. This report illuminates the path for future development of LiGA-based serological assays and suggests the need to develop alternative methods for conjugating glycans to phage to avoid liabilities of the hydrophobic DBCO moiety.

biochemistry↗

bioRxiv2025

The intratumoral microbiome is negatively associated with malignancy in dermatofibrosarcoma protuberans

In recent years, growing evidence demonstrated the critical roles of intratumoral microbes in tumors. However, the characteristics of intratumoral microbiome in dermatofibrosarcoma protuberans (DFSP) and their associations with tumor malignancy remains unexplored. Here, 106 whole-genome sequencing (WGS) data of the paired biopsy and blood samples from 53 DFSP patients were utilized, in which we extracted high-quality non-human reads to assign microbial taxonomic annotation by Kraken2 and PlusPF database. Meanwhile, significantly elevated non-human reads, microbial abundance, and bacterial load were detected in tumor compared to blood samples. To minimize the impact of contaminants and noise, we conducted a series of filtering procedures and treated blood samples as negative controls. Notably, we found that over 98% of intratumor microbes belonged to bacteria, and that the dominant taxa and alpha-diversity of intratumoral bacteria all exhibited significantly negative correlations with Ki67 expression in tumors. Specifically, the 84 key intratumoral species were identified to be associated with the reduced tumor malignancy, as evidenced by the diminished Ki67 expression, decreased tumor volume, and fewer COL1A1-PDGFB fusion events. These findings highlighted the tumor-suppressive potential of intratumoral microbiome, thereby providing a novel insight into DFSP pathogenesis and clinical management. IMPORTANCETo our knowledge, this is the first study to explore the intratumoral microbiome in DFSP. Microbial DNA signatures could be detected by whole-genome sequencing (WGS) and enabled a comprehensive view of the microbial landscape, thus we analyzed 106 WGS data of the paired biopsy and blood samples from 53 DFSP patients. Our analysis revealed that the dominant taxa and alpha-diversity of intratumoral microbiome all showed significantly negative correlations with Ki67 expression of tumor samples. This study indicated the tumor-suppressive role of intratumoral microbiome in DFSP and highlighted the potential clinical significance in understanding DFSP pathogenesis and guiding therapeutic management strategies.

microbiology↗

bioRxiv2025

Differential Regulation of Hepatic Macrophage Fate by Chi3l1 in MASLD

Metabolic dysfunction-associated steatotic liver disease (MASLD) progression involves the replacement of protective embryo-derived Kupffer cells (KCs) by inflammatory monocyte-derived macrophages (MoMFs), yet the regulatory mechanisms remain unclear. Here, we identify chitinase 3-like 1 (Chi3l1/YKL-40) as a critical metabolic regulator of hepatic macrophage fate. We observed high expression of Chi3l1 in both KCs and MoMFs during MASLD development. Genetic deletion of Chi3l1 specifically in KCs significantly exacerbated MASLD severity and metabolic dysfunction, whereas MoMF-specific Chi3l1 deletion showed minimal metabolic effects. Mechanistic studies revealed that this cell type-specific regulation arises from differential metabolic requirements: KCs display elevated glucose metabolism compared to MoMFs. Chi3l1 directly interacts with glucose to inhibit its cellular uptake, thereby selectively protecting glucose-dependent KCs from metabolic stress-induced cell death while having negligible effects on less glucose-dependent MoMFs. These findings uncover a novel Chi3l1-mediated metabolic checkpoint that preferentially maintains KCs populations through glucose metabolism modulation, providing important new insights into the pathogenesis of MASLD and potential therapeutic strategies targeting macrophage-specific metabolic pathways.

molecular biology↗

bioRxiv2025

Dual function of DOT1L suppresses tumor intrinsic immunogenicity in hepatocellular carcinoma

Immune checkpoint inhibitor (ICB) therapy for many cancers remains limited in patients overall response rate. Discovery and development of more effective combinatorial approaches is urgent. Here, through CRISPR/Cas9 genetic screens, we identify DOT1L as a versatile epigenetic factor that functions to suppress tumor-intrinsic immunity through a dual mechanism. Depletion of DOT1L induces the expression of transposable elements and subsequent type I interferon (IFN) response, and meanwhile lowers ZEB1 levels to further unleash the expression of immune-related genes. In turn, we demonstrate that DOT1L loss or treatment with the clinical stage inhibitor EPZ-5676 sensitizes tumors to ICB with increased immune infiltration in mice. More importantly, EPZ-5676 treatment alone is sufficient to enhance antitumor immunity in humanized mice. TCGA data analysis reveals an inverse correlation between DOT1L expression and IFN signatures across multiple cancer types. These findings provide a rationale for targeting DOT1L to improve tumor immunogenicity and overcome immunotherapy resistance. One Sentence SummaryCRISPR genetic screens identified DOT1L as a potential suppressor of tumor intrinsic immunogenicity

cell biology↗

bioRxiv2025

Genome-wide analysis reveals the genetic basis of key agronomic traits and modern wheat breeding in Henan Province

Despite the continuous improvement of wheat cultivars in Henan Province, the largest Chinese wheat-producing area, there have been no reports of studies on their breeding advances in the past decades. This study aims to elucidate their genetic basis and breeding advances. A total of 351 landraces and 265 cultivars in Henan Province were employed in selective sweep studies and genome-wide association studies. All the wheat accessions were planted in five locations in Henan Province in 2016-2017, 2017-2018 and 2018-2019. Candidate genes were identified through differential expression, GO annotation, gene homology, and haplotype analyses. Breeding advances were summarized based on four breeding periods (1950s, 1960s-1970s, 1980s-1990s, and post-2000s) of all 265 cultivars. The results demonstrated that 263 known genes with selection signals were found to be associated with important traits. Around the detected quantitative trait loci, 51 genes had been previously reported, while 252 genes were identified as candidate genes. Of the 303 genes and loci identified, 80 genes and 50 loci contributed to the improvement of 12 traits like plant height, and 12 key candidate genes was verified by qRT-PCR, while superior haplotypes of 24 genes explained cultivar climate adaptation. The superior haplotypes of 164 genes are available for future breeding. Transmission of superior haplotypes in four varietal pedigrees revealed pyramiding of superior haplotypes in elite cultivars. The analysis of post-2000 cultivars suggests a broader range of germplasm resources should be considered in parental selection than only recent accessions. This study provides a genetic basis and guide for wheat improvement.

genetics↗

bioRxiv2025

The Pesticide Chlorpyrifos Increases the Risk of Parkinson's Disease

Background and PurposePesticides have been associated with an increased risk of Parkinsons disease (PD), but it is unclear which specific pesticides contribute to this association and whether it is causal. Since chlorpyrifos (CPF) exposure has been implicated as a risk factor for PD, we investigated its association to incident PD and if this association is biologically plausible using human, rodent, and zebrafish (ZF) studies. MethodsThe association of CPF with PD was assessed using the UCLA PEG study (829 PD and 824 control subjects), and proximity-based exposure estimates from living or working near agricultural CPF use. For the mammalian studies, 6 months old male C57BL/6 mice were divided into two groups, CPF and controls, for open field, rotarod, and wire hang behavioral testing. Mice were then exposed to CPF in an inhalation chamber (0.65-2.9 mg/m3/day) for 6 hrs./day 5 days/wk., whereas control mice were exposed to vehicle alone. Behavioral tests were performed before and 2.5 months after CPF exposure following a 3-day washout. Mice were then perfused for immunohistochemical analysis. For the mechanistic studies, ZF embryos were treated with CPF (250 nM) 24 hours post fertilization for 5-7 days. Behavioral testing was performed using the Viewpoint Imaging System. Neuronal loss and microglial activation were determined using immunohistochemistry. Neuronal autophagic flux was determined using autophagy modulators in GFP-LC3 transgenic ZF and Western blots. ResultsLong-term residential CPF exposure was linked to an increased risk of developing PD with an odds ratio of 2.68 (CI 1.58-4.55). Mice exposed to aerosolized CPF developed motor impairment and a significant loss of dopaminergic neurons in the substantia nigra and activation of microglia. TH positive neurons in the substantia nigra (SN) had significantly higher levels of phosphoserine 129 (pS129) -synuclein (-syn), a marker for pathological phosphorylated -syn, and ubiquitin. In contrast, neither pS129 -syn or ubiquitin accumulated in TH neurons in the VTA after CPF exposure. Consistent with the mice data, CPF exposure resulted in impairment of locomotor activity and selective loss of aminergic neurons in ZF. We also found an increase in neuronal apoptosis and microglial activation. Importantly, dopamine neuron loss was found to be at least partially dependent on {gamma}1-synuclein (closest functional homologue to human -syn) as neuronal loss did not occur in {gamma}1-synuclein knockout ZF. Using an in vivo ZF assay, we found impaired autophagic flux and an increase in lysosomal labelling within the zebrafish brain. CPF exposure also led to elevated {gamma}1-synuclein and p62 (autophagic cargo protein) levels consistent with impaired degradation. Furthermore, induction of autophagy was protective, supporting the hypothesis that impaired autophagic flux is at least partially responsible for neuron loss following CPF exposure. ConclusionsCPF exposure is associated with an increased risk of developing PD and this association is likely causal since PD-like pathology was recapitulated in animal models. Furthermore, impaired autophagic flux appears to underly this toxicity, a pathway implicated in the pathogenesis of PD.

neuroscience↗

bioRxiv2025

Distinguish risk genes functioning at presynaptic or postsynaptic regions and key connectomes associated with pathological α-synuclein spreading

Previous studies have suggested that pathological -synuclein (-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: (1) How many and which connections in the connectome are necessary for predicting the progression of pathological -Syn? (2) How to identify risk gene that affects pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, we addressed these key questions with novel mathematical models. Strikingly, the spreading of pathological -Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. We further explored the genes that are responsible for the selective vulnerability of different brain regions to transmission to distinguish the genes that play roles in presynaptic from those in postsynaptic regions. Those risk genes were significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses were then conducted to identify key drivers of genes responsible for selective vulnerability and overlapping with Parkinsons disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, our study has demonstrated for the first time that these are functionally distinct processes.

neuroscience↗

bioRxiv2025

ERGA-BGE genome of Androsace saussurei Dentant, Lavergne, F. C. Boucher & S. Ibanez, a recently described plant from the rooftops of Europe

The reference genome of Androsace saussurei (Ericales: Primulaceae: Primuloideae) provides a valuable resource for understanding the mechanisms of plant adaptations to the most extreme environments where flowering plants can thrive and the speciation mechanisms of plants dwelling on high alpine sky islands. The entirety of the genome sequence was assembled into 20 contiguous chromosomal pseudomolecules. This chromosome-level assembly encompasses 413 Mb, composed of 253 contigs and 101 scaffolds, with contig and scaffold N50 values of 4.95 Mb and 21.2 Mb, respectively.

genomics↗

bioRxiv2025

Investigation of All Disease-Relevant Lysine Acetylation Sites in α-Synuclein Enabled by Non-canonical Amino Acid Mutagenesis

Aggregates of -synuclein (S) are hallmarks of synucleinopathies, including Parkinsons Disease (PD) and Multiple System Atrophy (MSA). We have recently shown that S lysine acetylation in the soluble monomer pool varies between healthy controls, PD, and MSA patients. We used non-canonical amino acid (ncAA) mutagenesis to express and purify all 12 currently known disease-relevant variants of S and studied their binding to membranes as well as their aggregation propensities. We found that acetylation of lysine 12, 43, and 80 had particularly strong effects. To understand the implications for acetylation of monomeric S found in healthy cells, we performed NMR experiments to study protein conformation and fluorescence correlation spectroscopy experiments to quantify lipid binding. We also investigated the effects of acetylation at lysine 12, 43, and 80 on fibril seeding in neurons. Collectively, our biochemical and cell biological investigations indicated that acetylation of K80 could inhibit aggregation without conferring negative effects on monomer function in healthy cells. Therefore, we studied the structures of fibrils with K80 acetylation through cryo-electron microscopy to uncover the structural basis for these effects. Finally, we identified inhibition of HDAC8 as a way of potentially increasing acetylation at K80 and other inhibitory sites for therapeutic benefit.

biochemistry↗

bioRxiv2025

Atom-level Machine of Protein-glycan Interactions and Cross-chiral Recognition in Glycobiology

Cross-chiral recognition in glycobiology is the interactions between biologically conventional proteins and the enantiomers of biological glycans (e.g., L-proteins binding with L-hexoses) from organisms across all kingdoms of life. By symmetry, it also describes the interactions of chirally mirrored proteins with normal D-glycans. Knowledge of cross-chiral recognition is critical to understanding the potential interactions of existing life forms with artificial mirror-life forms, but currently known rules of protein-glycan interaction are insufficient. To build a methodology for learning such interactions, we used machine learned models that can predict binding strength between a set of proteins and glycans represented as graphs of atoms, rather than monosaccharides. Atomic q-gram and Morgan fingerprint (MF) based representation of glycans made it possible to train ML models that predict lectin binding properties of glycans, glycomimetic compounds, and enantiomers of all natural glycans. Critical to this training was merging disparate data--some with relative fluorescence units (RFU) from glycan microarrays and others with Kd values from ITC--using a universal "fraction bound" parameter f at a specific lectin concentration. A fully-connected neural network architecture, MCNet takes a MF and concentration (C) as inputs and returns f for 147 lectins. Performance of MCNet is comparable to the GlyNet models, and by proxy to other state-of-the art models that predict strength of protein-glycan interactions. MCNet effectively predicts binding of glycomimetic compounds to Galectins 1, 3, and 7. Breaking from a monosaccharide-based description makes it possible for MCNet to predict cross-chiral recognition. We employed a Liquid Glycan Array to validate some predictions, such as the lack of interactions of L-mannose with D-mannose binding lectins, purified ConA, and DC-SIGN displayed on cells, and weak binding of L-Man to galactose-binding lectins and L-Glc binding by canonical fucose binding lectins. MCNets atom-level input makes it possible to agglomerate protein-glycan data from diverse glycans across all kingdoms of life and non-glycan structures (e.g. glycomimetic compounds). The universal fraction bound parameter makes it possible to unify disparate quantitative observations (Kd/IC50, RFU, chromatographic retention times, etc.). We believe that such an approach will facilitate a merger of knowledge from diverse glycobiology datasets and predict protein interactions with uncommon/unnatural glycans not attainable from current ML models.

biochemistry↗

bioRxiv2024

Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all

Comprehensive metagenomic sequence classification of diverse environmental samples faces significant computing memory challenges due to exponentially expanding genome databases. Here, we present Kun-peng, featuring a unique ordered 4GB block database design for ultra-efficient resource management, faster processing, and higher accuracy. When benchmarked on mock communities (Amos HiLo, Mixed, and NIST) against Kraken2, Centrifuge, and Sylph. Kun-peng matched Sylph, achieving the highest precision and lowest false-positive rates while demonstrating superior time and memory efficiency among all tested tools. Furthermore, Kun-pengs efficient database architecture enables the practical utilization of large-scale reference databases that were previously computationally prohibitive. In comprehensive testing across 586 air, water, soil, and human metagenomic samples using an expansive pan-domain database (204,477 genomes, 4.3TB), Kun-peng classified 69.78-94.29% of reads, achieving 38-43% higher classification rates than Kraken2 with the standard database. Unexpectedly, Sylph failed to classify any reads in air samples and left > 99.85% of reads unclassified in water and soil samples. In terms of computational efficiency, Kun-peng processed each sample in 0.2[~]11.2 minutes using only 4.0[~]35.4GB peak memory. Remarkably, these processing times were comparable to Kraken2 using the standard database (81GB, 5% of the pan-domain database). Memory-wise, Kun-peng required only 35.4GB peak memory with the pan-domain database, representing a 473-fold reduction compared to Kraken2. When compared to Sylph, Kun-peng processes samples up to 46.3 times faster while using up to 20.6 times less memory. Overall, Kun-peng offers an ultra-memory-efficient, fast, and accurate solution for pan-domain metagenomic classifications.

bioinformatics↗

bioRxiv2024

A Wearable Spiral Ultrasound Patch for Focused Ultrasound Peripheral Neuromodulation of Diabetic Neuropathic Pain

Diabetic foot disease, a severe complication of diabetes, frequently results in diabetic neuropathic pain, which diminishes quality of life and increases the risk of amputation. Current treatment options are limited in their effectiveness and can present adverse effects. We have demonstrated a first-of-its-kind wearable spiral ultrasound patch for focused ultrasound peripheral neuromodulation to alleviate diabetic neuropathic pain. This innovative, stretchable ultrasound device reliably delivers focused ultrasound to peripheral nerves. The devices ultrasound elements are arranged in a phyllotaxis spiral pattern, enhancing transmitted acoustic focus performance and minimizing grating and side lobes. Using a diabetic foot rat model, we confirmed peripheral neuropathy through behavioral assessments of mechanical allodynia and heat hyperalgesia, which showed significant pain relief after two weeks of ultrasound treatment. Additionally, nerve conduction velocity improved. Biological safety tests indicated no adverse effects on nerve tissues or cells. Our approach offers a non-invasive solution for managing diabetic neuropathic pain and provides critical insights into its underlying mechanisms, paving the way for more effective therapies.

bioengineering↗

bioRxiv2024

Global Scientific Trends in Organoids from 2004 to 2023: A Data Bibliometric and Visualized Analysis

To conduct a bibliometric analysis of organoids to describe international research trends and visualize current research directions. This cross-sectional bibliometric analysis examined the development of organoid research from 2004 to 2023. The current study used VOS-viewer to assess and analyze 13,174 documents. Literature data were collected on a specific date (Feb 19, 2024) and downloaded in plain text from Web of Science Core Collection. In this paper, 13,174 organoid papers were retrieved from Web of Science Core Collection. There were only 114 organoid studies in 2004, and from 2015 onward, the number of annual publications on this topic began to proliferate, reaching 10,023 from 2019 to 2023, accounting for as much as 76.1% of the total number of published papers. The United States proudly leads the way in both the volume of articles published and the number of citations garnered, standing tall as the undisputed frontrunner. Among the illustrious institutions, Harvard University and the University of Washington are among the most prolific. Hans Clevers has worked with 121 prolific authors and has the most publications. With the use of organoids in cancer modeling, drug screening, and regenerative medicine, organoid technology has attracted much attention in medicine, and the significant increase in the number of published papers and citations signifies the expanding influence and global collaboration in the field of organoid research. This study contributes to our understanding of current trends and potential future advances in the field of organoid research by identifying five distinct clusters in the field.

cancer biology↗

bioRxiv2024

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-Treated Adult Zebrafish as a Model for Parkinsons Disease

Dopamine (DA) is a catecholamine neurotransmitter that works to regulate cognitive functions. Patients affected by Parkinsons Disease (PD) experience a loss of dopaminergic neurons and downregulated neural DA production. This leads to cognitive and physical decline that is the hallmark of PD for which no cure currently exists.. Danio rerio, or zebrafish, have become an increasingly popular disease model used in PD pharmaceutical development. This model still requires extensive development to better characterize which PD features are adequately represented. Furthermore, the great majority of PD zebrafish models have been performed in embryos, which may not be relevant towards age-related human PD. As an improvement, mature D. rerio were treated with neurotoxic prodrug 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) through intraperitoneal injection to induce parkinsonism. Behavioral analysis confirmed disparities in movement between saline-injected control and the MPTP-injected experimental group, with swim distance and speed significantly lowered seven days after MPTP injection. Simultaneously, cognitive decline was apparent in MPTP-injected zebrafish, demonstrated by decreased alternation in a y-maze. RT-qPCR confirmed trends consistent with downregulation in Parkinsonian genetic markers, specifically DA transporter (DAT), MAO-B, PINK1. In summary, mature zebrafish injected with MPTP present with similar movement and cognitive decline as compared to human disease. Despite its benefits, this model does not appear to recapitulate full pathophysiology of the disease with the full profile of expected gene downregulation. Because of this, it is important that researchers looking for pharmacological interventions for PD only use this zebrafish model when targeting the human-relevant PD symptoms and causes that are represented.

neuroscience↗

bioRxiv2024

Molecular Architecture of Monkeypox Mature Virus

Since the 2022 mpox outbreak, MPXV has caused [~]100,000 infected cases with [~]200 deaths across 117 countries. and was declared a public health emergency of international concern by the WHO. The causative pathogen, monkeypox virus (MPXV), is a zoonotic double-stranded DNA orthopoxvirus. To investigate the structures and replication mechanism of MPXV, the MPXV recombinant proteins and vaccinia virus (VACV) particles have been studied by cryo-EM, however, in situ structural insights into major structural proteins and assembly of the authentic MPXV particles are missing. In this work, we isolated two MPXV strains from the first imported mpox case and the first local mpox case in mainland China. From the two strains, we propagated and purified mature viruses, and applied cryo-electron tomography (cryo-ET) and sub-tomogram averaging (STA) to unveil the architecture of intact MPXV virus. Interestingly, we also discovered irregularly-shaped mature virions with distorted core walls. To our knowledge, these in situ structural insights in MPXV have not been reported before.

biophysics↗

bioRxiv2024

Molecular basis of Ad5-nCoV Vaccine-Induced Immunogenicity

In response to coronavirus disease 2019 (COVID-19), numerous vaccines have been developed to protect against SARS-CoV-2 infection. Ad5-nCoV (Convidecia) is a vaccine listed for emergency use by the WHO and has been administrated to millions of people globally. It comprises a series of human adenovirus 5 (Ad5) replication-incompetent vectored vaccines that transduce the spike protein (S) gene of various SARS-CoV-2 strains. Despite promising clinical data demonstrating its safety and effectiveness, the underlying molecular mechanism of its high immunogenicity and incidence of adverse reactions remains less understood. Here we combined cryo-ET, fluorescence microscopy and mass spectrometry to characterize the in situ structures, density and site-specific glycan compositions of the Ad5-nCoV_Wu and Ad5-nCoV_O vaccine-induced S antigens, which encode the unmodified SARS-CoV-2 Wuhan-Hu-1 S gene and optimized Omicron S gene, respectively. We found that the vaccine-induced S are structurally intact, antigenic and densely distributed on the cell membrane. Compared to Ad5-nCoV_Wu induced S, the Ad5-nCoV_O induced S demonstrate significantly better stability and is less likely to induce syncytia among inoculated cells. Our work demonstrated that Ad5-nCoV is a prominent platform for antigen induction and cryo-ET can be a useful technique for vaccine characterization and development.

biophysics↗

bioRxiv2024

Poxvirus A52 is a host range factor for modified vaccinia virus Ankara (MVA) and promotes viral replication by disturbing the formation of autolysosomes

Many members of the poxvirus family are important zoonotic pathogens that pose a significant threat to human and animal health worldwide. Autophagy is a multi-step degradation pathway within cells, and one of its primary biological functions includes the clearance of invading viruses. Nevertheless, the interplay between poxviruses and host cell autophagy has not been fully elucidated. Here, we demonstrate that vaccinia virus (VACV) and lumpy skin disease virus (LSDV) induce incomplete autophagy and inhibit the fusion of autophagosomes and lysosomes, while modified vaccinia virus Ankara (MVA), an attenuated strain of VACV unable to replicate in almost all human cells, does not. Additionally, we screened and identified the VACV protein A52 as a key factor that obstruct the formation of autolysosomes. Mechanistically, A52 interacts with SNAP29 and inhibits its interaction with STX17 and VAMP8, both of which are binding partners of SNAP29 and are essential for complete autophagy. Moreover, A52 promotes the proteasomal degradation of SNAP29, which facilitates viral replication. We further revealed that SNAP29 functions as a restriction factor for MVA, as the suppression of SNAP29 allowed the replication of MVA in human cells. In summary, our data present a molecular mechanism by which poxviruses manipulate the cellular autophagic machinery and provide additional explanation for the restriction of MVA in human cells.

microbiology↗