Biology subjects

Peng, W.

Publications and source records attributed to Peng, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Site- and Structure-Specific Characterization of Glycoproteins of H11: Potent Vaccine Candidates against Parasitic Worm Haemonchus

Parasitic worms (helminths) infections pose significant threats to global health and livestock economies. While mass spectrometry (MS)-based glycomics have revealed that helminths express complex, immunomodulatory N-glycans, site- and structure-specific characterization of intact glycopeptides remain challenging. Here we employed advanced MS-based intact glycoproteomics to explore the N-glycosylation profile of H11 antigen - an important vaccine antigen from pathogenic parasite Haemonchus contortus. We successfully identified seven glycosylated aminopeptidases carrying 19 N-glycosylation sites with 31 distinct N-glycan structures. Notably, 13 N-glycopeptides were significantly enriched by H11-induced protective IgG antibodies. Our findings revealed a high degree of structural heterogeneity and abundant core fucosylation among the identified N-glycopeptides. Additionally, molecular docking studies demonstrated those IgG-recognized N-glycopeptides are situated on the protein surface or adjacent to the substrate-access channels, strongly indicating their potential as antigenic epitopes. Overall, our work represents the first comprehensive glycoproteome of an economically important parasitic worm. These results hold important implications for the rational design of vaccines against H. contortus and other related metazoan parasites.

pathology↗

bioRxiv2025

Conformational flexibility of tubulin dimers regulates the transitions of microtubule dynamic instability

Microtubules are highly conserved polymers of {beta}-tubulin dimers that undergo dynamic instability. While dynamic instability is conserved across eukaryotes, many of its associated conformational changes, like lattice compaction and twist, are not. Tubulin dimers sample multiple conformations in solution and undergo conformational changes during polymerization; the rate and extent of these changes describes their "conformational flexibility." Here, we investigate the relationship between the conformational flexibility of tubulins and the dynamic phenotypes of the microtubules they produce with a comparative study of Drosophila melanogaster tubulin (Dm-Tb) and Bos taurus brain tubulin (Bt-Tb). While these tubulins share high sequence and structural similarity, their microtubules display divergent dynamic phenotypes in vitro, with altered transition frequencies between phases of growth and shrinkage. Dm-Tb microtubules showed drastically longer lifetimes, lower barriers to nucleation, and a high rescue frequency, while maintaining a similar growth rate to Bt-Tb microtubules. 3D reconstruction of mature Dm-Tb microtubules showed high structural conservation with mammalian microtubules. However, when we performed molecular dynamics simulations of free tubulin dimers, we found Dm-Tb to be more rigid and adopt fewer conformational states than Bt-Tb. Biochemical characterizations experimentally confirmed this finding, leading us to hypothesize that differences in the conformational flexibility of tubulins may tune the frequency of transitions between the dynamic phases of microtubules, thereby altering their stability and overall dynamic phenotypes.

biophysics↗

bioRxiv2025

PCAGP, a parallel convolutional attention network-based method for crop genomic prediction

Genomic selection (GS) has emerged as a transformative breeding paradigm, leveraging genome-wide marker data to predict phenotypic outcomes and accelerate crop improvement cycles. Traditional statistical models face fundamental limitations in modeling the higher-order, non-linear genotype-phenotype relationships inherent in complex agronomic traits. Deep learning architectures have recently shown remarkable predictive performance in GS applications. Current deep learning approaches in GS predominantly employ a serial structure convolution kernel, this may lead to gradient vanishing and computational efficiency challenges. In this study, we propose a method based on a parallel convolutional attention network for crop genomic prediction (PCAGP), a novel deep learning framework for crop genomic prediction. The architecture uses a convolution kernel to transmit information through a parallel structure, combined with a coordinate attention mechanism that effectively integrates inter-channel relationships and spatial genomic information. This approach significantly improves the accuracy of phenotypic prediction. We compared PCAGP with six widely used GS methods on four benchmark datasets, including statistical method (GBLUP), machine learning approaches (SVR, RF), and deep learning models (DeepGS, DNNGP, and SoyDNGP). The experimental results demonstrate that PCAGP outperforms all baseline methods, and the average prediction accuracy is improved (0.4%-53.1%).

bioinformatics↗

bioRxiv2025

A Reductive Uric Acid Degradation Pathway in Anaerobic Bacteria

Uric acid is a key intermediate in purine degradation across diverse organisms, while its accumulation in humans leads to inflammation and gout disease. Aerobic organisms degrade uric acid via a well-known "oxidative pathway" involving dearomatization of the purine core catalyzed by uric acid oxidases or dehydrogenases. The ability to degrade uric acid is also widespread in anaerobic bacteria, including gut bacteria, although the mechanisms are incompletely understood. Here, we report the biochemical characterization of a recently identified uric acid degradation gene cluster from Escherichia coli, and show that it encodes a "reductive pathway" for uric acid degradation. In this pathway, uric acid is first reduced to isoxanthine (2,8-dioxopurine) by a xanthine dehydrogenase homolog (XdhD), followed by dearomatization of the purine core catalyzed by a flavin-dependent reductase (YgfK). Stepwise cleavage of the pyrimidine and imidazole rings forms 2,3-diureidopropionate, and stepwise cleavage of the 2- and 3-ureido groups then forms 2,3-diaminopropionate, which is cleaved by a pyridoxal 5-phosphate-dependent lyase (YgeX) to pyruvate and ammonia. Detection of isoxanthine in clinical serum samples suggests it is a physiologically relevant circulating metabolite. A probiotic E coli Nissle strain was engineered for constitutive overexpression of the gene cluster, and oral administration in a uricase-knockout hyperuricemic mouse model significantly reduced the serum uric acid level and alleviated associated kidney injury, suggesting a potential route towards uricolytic probiotics.

biochemistry↗

bioRxiv2025

Soluble Immune Factor Profiles in Blood and CSF Associated with LRRK2 Mutations and Parkinson's Disease

Background and ObjectivesMutations in the Leucine-rich repeat kinase 2 (LRRK2) gene are one of the most common genetic causes of Parkinsons disease (PD) and are linked to immune dysregulation in both the central nervous system and periphery. However, peripheral and central profiles of soluble immune factors associated with LRRK2 mutations and PD have not been comprehensively characterized. Using serum and CSF samples from the LRRK2 Cohort Consortium (LCC), this study aimed to probe a broad range of soluble immune biomarkers associated with LRRK2 mutations and PD. MethodsWe investigated the levels of soluble immune regulators in the serum (n=651) and cerebrospinal fluid (CSF, n=129) of LRRK2 mutation carriers and non-carriers, both with and without PD. A total of 65 cytokines, chemokines, growth factors, and soluble receptors were assessed by Luminex immunoassay. A multivariable robust linear model was used to determine levels associated with LRRK2 mutations and PD status, adjusting for age, sex, and sample cohort. Correlations were assessed using the Spearman correlation coefficient. LRRK2 G2019S knock-in mice were used to validate the associations identified in the LCC. ResultsIn this extensive discovery cohort, we identified several elevated serum immune regulatory factors associated with LRRK2 mutations. In particular, serum stromal cell-derived factor-1 alpha (SDF-1 alpha) levels, as supported by findings in LRRK2 G2019S knock-in mice, and tumor necrosis factor receptor II (TNF-RII) were significantly increased after multiple comparison adjustment. In contrast, LRRK2 mutations were associated with reduced soluble immune markers, including BAFF, CD40-Ligand, I-TAC, MIP-3 alpha, NGF beta, and IL-27 in CSF. Those with clinically diagnosed PD, with or without LRRK2 mutations, did not show strong signals in serum but reduced inflammatory analytes in CSF, including MIF, MMP-1, CD30, Tweak, and SDF-1 alpha. In addition, we found that the serum levels of these soluble immune factors display varied correlations with their corresponding CSF levels. DiscussionThis study highlights distinct immune profiles associated with LRRK2 mutations and PD in the periphery and CNS. Serum levels of SDF-1alpha and TNF-RII were elevated in LRRK2 mutation carriers, while CSF immune markers were reduced. In PD, irrespective of LRRK2 status, reduced CSF inflammatory analytes and weak serum signals were observed. These results provide insight into immune dysregulation linked to LRRK2 mutations. If replicable in independent datasets, they offer potential avenues for biomarker and therapeutic exploration.

neuroscience↗

bioRxiv2025

NitrOFF: An engineered fluorescent biosensor to illuminate nitrate transport in living cells

The duality of nitrate is nowhere best exemplified than in human physiology - a detrimental pollutant but also a protective nutrient and signaling ion - particularly as connected to reactive nitrogen oxides. Aside from limited insights into nitrate uptake and storage, foundational nitrate biology has lagged. Genetically encoded fluorescent biosensors can address this gap with real-time imaging. However, imaging technologies for mammalian cell applications remain rare. Here, we set out to design and engineer a two-domain chimera fusing the split green fluorescent protein EGFP and the nitrate recognition domain NreA from Staphylococcus carnosus. Over 7 rounds of directed evolution, 15 mutations were accumulated resulting in the functional biosensor NitrOFF. NitrOFF has a high degree of allosteric communication between the domains reflected in a turn-off intensiometric response (Kd {approx} 9 {micro}M). This was further reinforced by X-ray crystal structures of apo and nitrate bound NitrOFF, which revealed that the two domains undergo a large-scale conformational rearrangement that changes the relative positioning of the EGFP and NreA domains by 68.4{degrees}. Such a dramatic difference was triggered by the formation of a long helix at the engineered linker connecting the two domains, peeling the {beta}7 strand off the EGFP and thus extinguishing the fluorescence upon nitrate binding. Finally, as a proof-of-concept, we highlighted the utility of this first-generation biosensor to monitor exogenous nitrate uptake and modulation in a human embryonic kidney (HEK) 293 cell line. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/644677v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@1ba853eorg.highwire.dtl.DTLVardef@81bed9org.highwire.dtl.DTLVardef@18a313org.highwire.dtl.DTLVardef@17a5e80_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Literature-scaled immunological gene set annotation using AI-powered immune cell knowledge graph (ICKG)

Large scale application of single-cell and spatial omics in models and patient samples has led to the discovery of many novel gene sets, particularly those from an immunotherapeutic context. However, the biological meaning of those gene sets has been interpreted anecdotally through over-representation analysis against canonical annotation databases of limited complexity, granularity, and accuracy. Rich functional descriptions of individual genes in an immunological context exist in the literature but are not semantically summarized to perform gene set analysis. To overcome this limitation, we constructed immune cell knowledge graphs (ICKGs) by integrating over 24,000 published abstracts from recent literature using large language models (LLMs). ICKGs effectively integrate knowledge across individual, peer-reviewed studies, enabling accurate, verifiable graph-based reasoning. We validated the quality of ICKGs using functional omics data obtained independently from cytokine stimulation, CRISPR gene knock-out, and protein-protein interaction experiments. Using ICKGs, we achieved rich, holistic, and accurate annotation of immunological gene sets, including those that were unannotated by existing approaches and those that are in use for clinical applications. We created an interactive website (https://kchen-lab.github.io/immune-knowledgegraph.github.io/) to perform ICKG-based gene set annotations and visualize the supporting rationale.

bioinformatics↗

bioRxiv2025

Structural basis for postfusion-specific binding to Respiratory Syncytial Virus F protein by the canonical antigenic site I antibody 131-2a

The Respiratory Syncytial Virus (RSV) Fusion (F) protein is a major target of antiviral antibodies following natural infection or vaccination and responsible for mediating fusion between the viral envelope and the host membrane. The fusion process is driven by a large-scale conformational change in F, switching irreversibly from the metastable prefusion state to the stable postfusion conformation. Previous research has identified six distinct antigenic sites in RSV-F, termed sites O, I, II, III, IV, and V. Of these, only antigenic site I is fully specific to the postfusion conformation of F. A monoclonal antibody 131-2a that specifically targets postfusion F has been widely used as a research tool to probe for postfusion F and to define antigenic site I in serological studies, yet its sequence and precise epitope have remained unknown. Here we use mass spectrometry-based de novo sequencing of 131-2a to reverse engineer a recombinant product and study the epitope to define antigenic site I with molecular detail, revealing the structural basis for the antibodys specificity towards postfusion RSV-F.

immunology↗

bioRxiv2024

Unexpected Activities of CYP152 Peroxygenases towards Non-carboxylic Substrates Reveal Novel Substrate Recognition Mechanism and Catalytic Versatility

Exploring and exploiting the catalytic promiscuity of enzymes is a central topic and captivating challenge in enzymology. CYP152 peroxygenases are attractive biocatalysts for diverse reactions under mild conditions using H2O2 as cofactor. However, their substrate scope is limited by a carboxyl group required for acid-base catalysis, following the well-accepted principle that heme-dependent H2O2-utilizing enzymes employ a carboxyl group within their active sites to facilitate H2O2 activation. Herein, we reveal for the first time that several CYP152 family members can directly degrade various aromatic pollutants without any carboxyl group, exhibiting novel aromatic hydroxylation and dehalogenation activities. Through crystal structure analysis, isotope tracing experiments, and QM/MM calculations, we elucidate that the phenolic hydroxyl group activated by electron-withdrawing substituent(s) functionally replaces the carboxyl group, forming hydrogen bonds with the conserved arginine leading to Compound I formation. The oxygen atom of the newly formed hydroxyl group originates from water, bypassing the conventional oxygen rebound step. These findings provide first insights into the mechanisms of P450 peroxygenases towards non-carboxylic substrates, expanding our knowledge of biological C-H activation and C-halogen bond cleavage beyond canonical P450 reactions. This discovery holds immense potential for harnessing these enzymes in innovative strategies for industrial biocatalysis and environmental remediation.

biochemistry↗

bioRxiv2024

Structure of the ciliary tip central pair reveals the unique role of the microtubule-seam binding protein SPEF1

Motile cilia are unique organelles with the ability to autonomously move. Force generated by beating cilia propels cells and moves fluids. The ciliary skeleton is made of peripheral doublet microtubules and a central pair (CP) with a distinct structure at the tip. In this study, we present a high-resolution structure of the CP in the ciliary tip of the ciliate Tetrahymena thermophila and identify several tip proteins that bind and form unique patterns on both microtubules of the tip CP. Two of those proteins that contain tubulin polymerization-promoting protein (TPPP)-like domains, TLP1 and TLP2, bind to high curvature regions of the microtubule. TLP2, which contains two TPPP-like domains, is an unusually long protein that wraps laterally around half a microtubule and forms the bridge between the two microtubules. Moreover, we found that the conserved protein SPEF1 binds to both microtubule seams. In vitro, human SPEF1 not only binds to the microtubule seam but also crosslinks two parallel microtubules. Single-molecule microtubule dynamics assays indicate that SPEF1 stabilizes microtubules in vitro. Together, these data show that the proteins in the tip CP maintain stable microtubule structure and probably play important roles in maintaining the integrity of the axoneme.

cell biology↗

bioRxiv2024

Directed Evolution of a Genetically Encoded Indicator for Chloride

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/624492v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@8a9309org.highwire.dtl.DTLVardef@1bb6770org.highwire.dtl.DTLVardef@840dd4org.highwire.dtl.DTLVardef@1a7e2cb_HPS_FORMAT_FIGEXP M_FIG C_FIG Inarguably, the green fluorescent protein (GFP) family is an exemplary model for protein engineering, accessing a range of unparalleled functions and utility in biology. The first variant to recognize and provide an optical output of chloride in living cells was serendipitously uncovered more than 25 years ago. Since then, researchers have actively expanded the potential of GFP indicators for chloride through site-directed and combinatorial site-saturation mutagenesis, along with chimeragenesis. However, to date, the power of directed evolution has yet to be unleashed. As a proof-of-concept, here, we use random mutagenesis paired with anion walking to engineer a chloride-insensitive fluorescent protein named OFPxm into a functional indicator named ChlorOFF. The sampled mutational landscape unveils an evolutionary convergent solution at one position in the anion binding pocket and nine other mutations across eight positions, of which only one has been previously linked to chloride sensing potential in the GFP family.

biochemistry↗

bioRxiv2024

Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism

Human stem cell-derived {beta} (SC-{beta}) cells still exhibit limited glucose response required for insulin secretion due to glycolytic bottlenecks, yet how these metabolic abnormalities impact glucose response and functional maturation of SC-{beta} cells remains unclear. In this study, we identified a metabolic checkpoint located at PEP accumulation that impeded the functional maturation, which was rescued by restoration of pyruvate kinase 1 (PKM1). Glucose-tracing metabolomics in human stem cell-derived islets revealed abnormal glycolytic PEP accumulation at resting condition, resulting in impaired calcium response and insulin secretion upon high glucose or glycolytic metabolite stimulation. Mechanistically, elevated PEP significantly raised intracellular basal calcium levels, leading to downregulated expression of genes involved in TCA cycle elucidated by single cell transcriptomics. Furthermore, the activity of pyruvate kinase, which metabolizes PEP, was notably reduced due to low PKM1 expression. By overexpressing PKM1, the impairment of TCA-related genes caused by PEP accumulation was reversed via modulating PEP metabolism, resulting in enhanced calcium responses and insulin secretion upon high glucose stimulation. Together, we discovered a novel role of PKM1-regulated PEP metabolism in mediating the functional maturation of human SC-{beta} cells. This study highlights the importance of metabolic reprogramming in human SC-{beta} cell maturation, advancing cell therapy approaches for diabetes treatment.

cell biology↗

bioRxiv2024

The dynamics of wild Vitis species in response to climate change facilitate the breeding of grapevine and its rootstocks with climate resilience

Climate change poses significant challenges to agricultural suitability and food security due to the limited adaptability of domesticated crops, however, our understanding of their climate adaptability is still limited. In this study, we compare the potential distributional dynamics in response to future climate change between grapevine and its wild relatives (Vitis L.) based on ecological niche models (ENMs). We reveal that the annual mean temperature is the primary factor influencing the potential distribution of cultivated grapes (V. vinifera L.). By 2080, under RCP 8.5, suitable areas for wine and table grapes from V. vinifera are predicted to reduced by 15.04x105 km{superscript 2} and 13.26x105 km{superscript 2}, respectively. The results suggest that grape cultivation, particularly for table grapes, will face serious threats from future climate change. In contrast, seventy percent of wild grapes are well able to withstand future climate conditions. For example, under RCP 8.5, North American wild grapes like V. rotundifolia and V. labrusca, as well as East Asian wild grapes such as V. heyneana and V. davidii, are projected to demonstrate significant adaptability. These wild grapes have the potential to provide rootstocks that could enhance the adaptability of cultivated grapes and serve as invaluable resources for breeding programs aimed at developing new cultivars better suited to withstand the environmental pressures of climate change. Our results not only predict potential suitable distribution areas of wild grapes in the future, but also emphasize the essential impact of these wild genetic resources on grape breeding for promoting adaptation to future climate change.

plant biology↗

bioRxiv2024

Structural and immunological characterization of the H3 influenza hemagglutinin during antigenic drift

The quest for a universal influenza vaccine holds great promise for mitigating the global burden of influenza-related morbidity and mortality. However, challenges persist in identifying conserved epitopes capable of inducing protection. In this study, we explore the influence of glycan evolution on H3 hemagglutinin from 1968 to present day and its impacts on antigenicity and immunogenicity. We observe that the appearance of potential N-linked glycosylation sites in Sing/16 hemagglutinin head domain reduces the binding of broadly neutralizing antibodies and shifts the polyclonal immune response upon vaccination to target the stem. Furthermore, structural characterization of HK/68 and Sing/16 by cryo-electron microscopy shows that while HK/68 is resistant to enzymatic deglycosylation, removal of glycans destabilizes the hyperglycosylated head and membrane-proximal region in Sing/16. These insights expand our understanding of glycans beyond their role in protein folding and highlight the interplay among glycan integration and immune recognition to design a universal influenza vaccine.

immunology↗

bioRxiv2024

Identification and Validation of Mitophagy-Related Genes in Diabetic Retinopathy

BackgroundDiabetic retinopathy is one of the common chronic complications of diabetes, characterized by retinal microvascular and neurodegenerative impairment, and it is the primary cause of vision impairment and blindness in adults. Many studies have demonstrated that mitophagy plays a significant role in the pathological mechanism of DR. however, its mechanism is not yet fully clear and requires further research. MethodsWe obtained relevant datasets of diabetic retinopathy from the GEO database and used R language to screen for differentially expressed genes. We intersected these genes with mitophagy-related genes and identified differentially expressed mitophagy-related genes. We performed GO and KEGG analysis on the differentially expressed mitophagy-related genes, followed by PPI network analysis. Using Cytoscape software, we selected mitophagy hub genes. Finally, we further validated the expression of the mitophagy hub genes in an in vitro cell culture high-glucose model using quantitative real-time polymerase chain reaction (qRT-PCR). ResultsWe identified 27 differentially expressed genes related to mitophagy by using R language, with 10 genes upregulated and 17 genes down regulated. We performed GO and KEGG enrichment analysis using R software to further study the potential biological functions of differentially expressed genes. Through PPI network analysis and Cytoscape software, we selected 10 hub genes associated with mitophagy. Finally, through qRT-PCR validation of these 10 hub genes, we found that the mRNA expression differences of MFN1, BNIP3L, GABARAPL1, and PINK1 genes were consistent with our bioinformatics analysis results. ConclusionWe consider that MFN1, BNIP3L, GABARAPL1, and PINK1 may serve as potential biomarkers for diabetic retinopathy. The upregulation and downregulation of these genes provide new insights for further exploration of the role of mitophagy in the pathological mechanism of diabetic retinopathy. These genes can serve as new potential therapeutic targets for the treatment of diabetic retinopathy.

bioinformatics↗

bioRxiv2024

DMT1 knockout abolishes ferroptosis induced mitochondrial dysfunction in C. elegans amyloid beta proteotoxicity

Iron is critical for neuronal activity and metabolism, and iron dysregulation alters these functions in age-related neurodegenerative disorders, such as Alzheimers disease (AD). AD is a chronic neurodegenerative disease characterized by progressive neuronal dysfunction, memory loss and decreased cognitive function. AD patients exhibit elevated iron levels in the brain compared to age-matched non-AD individuals. However, the degree to which iron overload contributes to AD pathogenesis is unclear. Here, we evaluated the involvement of ferroptosis, an iron-dependent cell death process, in mediating AD-like pathologies in C. elegans. Results showed that iron accumulation occurred prior to the loss of neuronal function as worms age. In addition, energetic imbalance was an early event in iron-induced loss of neuronal function. Furthermore, the loss of neuronal function was, in part, due to increased mitochondrial reactive oxygen species mediated oxidative damage, ultimately resulting in ferroptotic cell death. The mitochondrial redox environment and ferroptosis were modulated by pharmacologic processes that exacerbate or abolish iron accumulation both in wild-type worms and worms with increased levels of neuronal amyloid beta (A{beta}). However, neuronal A{beta} worms were more sensitive to ferroptosis-mediated neuronal loss, and this increased toxicity was ameliorated by limiting the uptake of ferrous iron through knockout of divalent metal transporter 1 (DMT1). In addition, DMT1 knockout completely suppressed phenotypic measures of A{beta} toxicity with age. Overall, our findings suggest that iron-induced ferroptosis alters the mitochondrial redox environment to drive oxidative damage when neuronal A{beta} is overexpressed. DMT1 knockout abolishes neuronal A{beta}-associated pathologies by reducing neuronal iron uptake. HighlightsO_LIEnergetic imbalance is an early event in iron-induced loss of neuronal function C_LIO_LINeuronal A{beta} increases susceptibility to ferroptosis mediated oxidative damage C_LIO_LIDivalent metal transporter 1 knockout protects against iron-induced oxidative damage and ferroptosis C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=196 HEIGHT=200 SRC="FIGDIR/small/607074v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@927aaorg.highwire.dtl.DTLVardef@10b121forg.highwire.dtl.DTLVardef@1d2d6aforg.highwire.dtl.DTLVardef@10cb797_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Characterization of bronchiolitis and vaccine-induced enhanced respiratory disease in Syrian hamsters caused by respiratory syncytial virus infection

Respiratory syncytial virus (RSV) presents a significant health risk to pediatric and old populations. The quest for developing effective RSV vaccines and immunoprophylactic measures remains highly active, while the catastrophic enhanced respiratory disease (ERD) reaction triggered by RSV vaccines poses lingering concerns. Meanwhile, as the basis of vaccine research, the development of animal models of RSV infection has shown less substantial progress, with considerable disparities in immunological and pathological responses compared to humans. The Syrian hamster, which is reported to be susceptible to RSV infection, seems promising, but the lack of in-depth studies has hampered its application. Consequently, we have refined the RSV-infected hamster model by establishing infection models at different ages, reanalyzing virological and pathological data, and applying vaccination with heat-inactivated RSV virus for ERD reaction. In general, neonatal hamsters exhibited the highest level of viral amplification, while old hamsters displayed the most severe pathological manifestations, with adult hamsters in between. Although Syrian hamsters were moderately susceptible to RSV infection, they showed typical pathological changes of bronchitis in all age groups, with adult and old animals even showing clinical signs of coughing. In addition, hamsters demonstrated the typical ERD response to heat-inactivated virus, characterized by the exacerbation of lung injury with extensive neutrophil and eosinophil infiltration, as well as TH2 polarization. Collectively, these characteristics suggest that the Syrian hamster model has significant potential for investigating the pathogenesis of RSV infection, elucidating the mechanism of ERD, and evaluating vaccine efficacy and safety. ImportanceThe Syrian hamster has been shown in our study to be a potential model for respiratory syncytial virus (RSV) infection, according to the following characteristics: Hamsters of three different age groups all developed typical pulmonary bronchiolitis following RSV infection, whereas adult and old hamsters showed typical cough symptoms, comparable to those observed in clinical patients. Hamsters of different ages showed considerable variability. Neonatal hamsters tolerated more viral replication, while old hamsters suffered the most severe pulmonary pathology. Hamsters exhibited typical ERD responses after inoculation with heat-inactivated RSV virus, including enhanced lung pathology, pulmonary eosinophilic and neutrophil infiltration, and Th2 polarization, which was remarkable and more similar to the typical characteristics of the ERD response in humans.

microbiology↗

bioRxiv2024

PRMT1-SFPQ regulates intron retention to control matrix gene expression during craniofacial development

Spliceosomopathies, which are a group of disorders caused by defects in the splicing machinery, frequently affect the craniofacial skeleton and limb, but the molecular mechanism underlying this tissue-specific sensitivity remains unclear. Splicing factors and small nuclear ribonucleoproteins (snRNPs) are core components of splicing machinery, and splicing factors are further controlled by post-translational modifications, among which arginine methylation is one of the most prevalent. We determined the splicing mechanisms in the cranial neural crest cells (CNCCs), a multipotent developmental population that gives rise to the majority of the craniofacial skeleton, and focused on an upstream regulator of splicing proteins, protein arginine methyltransferase 1 (PRMT1). PRMT1 is the highest expressing arginine methyltransferase in CNCCs and its role in craniofacial development is evident from our earlier investigation, where CNCC-specific Prmt1 deletion caused cleft palate and mandibular hypoplasia. PRMT1 catalyzes arginine methylation of splicing factors to modify protein localization, expression and activity. In the present study, we uncover roles of PRMT1 in the regulation of intron retention, a type of alternative splicing where introns are retained in the mature mRNA. CNCCs from mandibular primordium of Prmt1-deficient embryos demonstrated an increase in the percentage of intron-retaining mRNA of matrix genes, which triggered NMD, causing a reduction in matrix mRNA abundance. We further identified SFPQ as a substrate of PRMT1 that depends on PRMT1 for arginine methylation and protein expression in the developing craniofacial structures. Depletion of SFPQ in CNCCs phenocopied PRMT1 deletion whereby matrix, Wnt signaling components and neuronal gene transcripts contained higher IR and exhibited lower expression. We further recognized gene length as a common feature among SFPQ-regulated genes in CNCCs. Altogether, these findings demonstrate that the PRMT1-SFPQ pathway modulates matrix gene expression via IR-triggered NMD in CNCCs during craniofacial development.

developmental biology↗