Biology subjects

Guo, J.

Publications and source records attributed to Guo, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

RBM6-mediated alternative splicing facilitates the adaptation of Eurasian avian-like H1N1 swine influenza virus

The Eurasian avian{square}like (EA) H1N1 swine influenza virus (SIV), derived from avian influenza viruses (AIV), poses a serious threat to public health due to its capacity for cross{square}species transmission and pandemic emergence. The molecular determinants underlying its replication advantage over AIV remain poorly defined. Here, we identify RNA{square}binding motif protein 6 (RBM6) as a novel host factor that differentially regulates the replication of EA H1N1 SIV and AIV. Mechanistically, RBM6 binds to the critical M901 site of the viral M segment, thereby modulating RNA splicing. Substitution of M901C with M901T markedly reduced RBM6 binding, impaired M segment splicing, and attenuated viral replication both in vitro and in vivo. Conservation analysis revealed that M901T is common in avian strains, whereas M901C is predominantly maintained in swine strains, underscoring M901C as a determinant of swine adaptation. Complementation experiments further demonstrated that swine RBM6, but not avian RBM6, restored EA H1N1 SIV replication. Taken together, our findings uncover a previously unrecognized role of RBM6 in shaping influenza virus replication and highlight the RBM6-M901C axis may serve as potential targets for controlling influenza virus adaptation and interspecies transmission.

microbiology↗

bioRxiv2026

A Variant-Resistant Linear Epitope in the SARS-CoV-2 Nucleocapsid Protein for Antigen Detection

We previously generated a mouse monoclonal antibody, N179, against the SARS-CoV-2 nucleocapsid (N) protein and developed a colloidal gold-based immunochromatographic test strip. This assay achieved a detection limit of 2 ng/mL and displayed 98% concordance with RT-qPCR results. However, the precise epitope recognized by mAb N179 had not been defined. Using a panel of GST-fused N protein truncation fragments, we mapped the linear B-cell epitope recognized by mAb N179 to the flexible C-terminal tail of the N protein by Western blotting and ELISA. The minimal binding motif required for mAb N179 recognition was identified as 390QTVTLL395. Multiple sequence alignment of 11 representative SARS-CoV-2 lineages, including Alpha, Beta, Gamma, Delta, and Omicron subvariants BA.1, BA.2, and BA.3.2, revealed that this epitope was completely conserved across all variants analyzed. Stringent local pairwise alignment analysis using EMBOSS WATER further showed that the 390QTVTLL395 motif achieved a perfect 6/6 match exclusively in SARS-CoV-2; no identical sequence was detected in the seven common human coronaviruses, four influenza viruses, or five bat coronaviruses examined. Structural prediction analyses indicated that this region is surface-exposed and possesses a strong linear B-cell epitope propensity. Together, these findings identify 390QTVTLL395 as a specific molecular signature of SARS-CoV-2 among the viruses analyzed. Our results provide an epitope-level explanation for the sustained diagnostic reliability of the mAb N179-based assay against emerging variants, clarify the molecular basis for its lack of cross-reactivity, and may inform the rational design of SARS-CoV-2 diagnostics targeting conserved, mutation-resistant epitopes. ImportanceWe identified the exact nucleocapsid protein epitope recognized by monoclonal antibody N179, a diagnostic antibody used in a colloidal gold rapid assay. The identified 390QTVTLL395 motif at residues 390 to 395 was conserved among the SARS-CoV-2 variants analyzed and was not present as an identical continuous sequence in the related respiratory viruses examined. This work supports precise epitope mapping as a useful strategy for evaluating and revalidating diagnostic antibodies as respiratory viruses evolve.

microbiology↗

bioRxiv2026

A Cross-Species Systems Genetics Framework Identifies Causal Genes in Diabetic Nephropathy

Diabetic nephropathy (DN) is the leading cause of kidney failure in the developed world, but the genetic architecture of DN susceptibility is not well characterised. Here we apply a systems genetics approach in a mouse model of DN to discover novel QTLs for clinically relevant phenotypes including albuminuria, glomerulosclerosis, and macrophage infiltration. For context and prioritisation, we combined single-cell-transcriptomics-guided pQTL and eQTL mapping with cell-type-specific co-expression networks, identifying 192 candidate pGenes for albuminuria. While many were novel, 27% had prior genetic associations, and 40% were validated in a human diabetic cohort. Twelve genes belong to a podocyte network enriched for human GWAS signals. Among those, functional significance of the E3 ubiquitin ligases DCAF6 and ZNRF2 was confirmed by knockdown in Drosophila nephrocytes. Our systems genetics approach identified DN susceptibility genes previously validated in human GWAS while uncovering potential new genes and pathways that could be exploited for risk stratification and therapeutics development.

systems biology↗

bioRxiv2026

Cytokines driven by caspase-1 and RIPK3 are antagonistic

Pyroptosis, apoptosis, and necroptosis are thought to provide redundant protection against intracellular pathogens. We found that mice lacking inflammasomes, caspase-8, and MLKL were highly susceptible to infection by an environmental cytosol-invasive bacterium. Surprisingly, deletion of Ripk3 completely restored resistance despite the continued absence of all three cell death pathways. The infection outcome was determined instead by the production of antagonistic cytokines arising from these pathways. Deletion of Casp8 and Mlkl initiated an effector-triggered immunity-like response, in which RIPK3 induced type I interferons causing catastrophic susceptibility by impeding neutrophil responses. Opposing this, caspase-1-dependent IL-1{beta} production counteracted these type I interferons and restored resistance. Thus, susceptibility arose not from failure of regulated cell death, but from the activation of RIPK3-driven type I interferons unopposed by caspase-1-driven IL-1{beta}. Therefore, antagonistic cytokines embedded within cell death pathway signaling, distinct from cell death itself, can dictate the immune response to intracellular infection.

immunology↗

bioRxiv2026

Validation of MHPC512: A Publicly Available Special-Purpose Supercomputer for Molecular Dynamics Simulations of Biomolecular Systems

MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit fixed-point arithmetic to accelerate computation while controlling precision loss within an acceptable margin. The preprocessor is compatible with GROMACS and AMBER input formats and supports widely used biomolecular force fields (including CHARMM, AMBER, and OPLS/AA), the Neutral Territory method for short-range nonbonded interactions, the k-space Gaussian Split Ewald method for long-range electrostatics, and multiple thermostats, barostats, and integrators. We present a three-tier validation protocol--comparing static energy and virial components, examining ensemble distributions (NVE, NVT, NPT), and evaluating long-time statistical properties--demonstrating that MHPC512 reproduces results consistent with GROMACS and AmberTools. Application examples, including bulk water, dipeptide conformational sampling, folding of fast-folding peptides, membrane-protein systems, lipid self-assembly, and GPCR conformational transitions, further confirm its reliability. MHPC512 has been deployed at multiple supercomputing centers and is publicly accessible, representing a significant advance in high-throughput, large-scale biomolecular MD simulations.

Molecular Biology↗

bioRxiv2026

Small Molecule-Directed RNA Modification via Proximity-Driven Catalysis

Selective chemical modification of RNA is essential for RNA functionalization, probing RNA structure-function relationships and developing RNA-targeted therapeutics. Existing chemical strategies often rely on guanine accessibility or multiple helper DNA strands, restricting their generality and biological applicability. Inspired by DNA-guided DMAP catalysis and small-molecule binding-induced crosslinking, we report a small molecule-directed, DMAP-catalyzed, proximity-driven strategy for site-selective RNA functionalization. By appending a catalytic DMAP moiety to RNA-binding ligands, 2'-OH groups are selectively acylated in the presence of azide-bearing acyl donors, enabling subsequent installation of bioorthogonal handles. This approach was validated across diverse RNAs, including Pepper and Clivia RNA aptamers, G-quadruplex Broccoli RNA, and endogenous FMN riboswitch RNA. For a 400-nt Pepper-7SK fusion, selective modification of the Pepper motif was achieved with minimal perturbation to the nucleus localization function of 7SK RNA. Optimized PEG-pentafluorophenyl (PFP) acyl donors provided enhanced reactivity and low background. The method operates catalytically, decouples ligand recognition from the labeling moiety, and enables selective enrichment of target RNAs, offering a versatile platform for RNA functionalization, ligand profiling, and potentially live-cell applications.

biochemistry↗

bioRxiv2026

Intestinal Dysbiosis in Necrotic Enteritis: Dissecting the Roles of Eimeria and Clostridium perfringens

Necrotic enteritis (NE), caused by Clostridium perfringens, is a major enteric disease in poultry with substantial economic impact. NE is frequently triggered by co-infection with Eimeria spp., yet the relative contributions of Eimeria and C. perfringens to NE-induced dysbiosis and disease progression remain poorly defined. To address this, Cobb broiler chickens were challenged with Eimeria maxima, C. perfringens, or both, and ileal and cecal microbiota were analyzed using 16S rRNA gene sequencing and shotgun metagenomics. Temporal dynamics of intestinal microbiota shifts were further assessed at multiple time points post-infection. Our findings demonstrate that NE-associated dysbiosis is characterized by enrichment of pathobionts including C. perfringens, Escherichia, and Enterococcus cecorum, along with differential abundance of certain lactic acid-and short chain fatty acid-producing bacteria. Dysbiosis and disease progression were driven by synergistic interactions between E. maxima and C. perfringens, with E. maxima exerting a dominant influence. Notably, E. maxima alone promoted expansion of commensal C. perfringens or closely-related bacteria, even without prior exposure. Metagenomic analysis of the cecal microbiota further revealed a functional shift favoring utilization of host-derived glycans and simple carbohydrates over dietary fibers, in response to E. maxima and NE challenges. This transition coincided with E. maxima-induced epithelial damage, increased mucogenesis, and nutrient malabsorption. NE-associated dysbiosis emerged four days post-E. maxima infection and peaked 2-3 days following C. perfringens challenge. These findings suggest that Eimeria infection creates a permissive intestinal environment for C. perfringens colonization and proliferation, underscoring its pivotal role in NE pathogenesis. IMPORTANCENE is a major health and economic burden in poultry production, primarily driven by C. perfringens and potentiated by Eimeria infection. This study provides critical mechanistic insights into the distinct and synergistic roles of E. maxima and C. perfringens in NE disease progression. We show that Eimeria plays a dominant role in driving NE-associated dysbiosis and disease progression by inducing epithelial damage, inflammation, and nutrient malabsorption, which facilitate C. perfringens colonization, proliferation, and toxin production. Comprehensive characterizations of both structural and functional microbiome shifts revealed that NE-associated dysbiosis is marked by enrichment of facultative pathobionts that favors utilization of host-derived mucins and simple dietary carbohydrates, alongside depletion of strictly anaerobic, fiber-fermenting, SCFA-producing bacteria. These microbial shifts reflect disease progression and offer potential biomarkers for early diagnosis and therapeutic intervention. Our findings lay a foundation for microbiota-based diagnostics and interventions to mitigate NE and other enteric diseases.

systems biology↗

bioRxiv2026

Transient ATR inhibition following ionizing radiation enhances immune-mediated antitumor response and survival

BackgroundATR activation following DNA damage from cancer treatments such as radiation can mitigate anticancer efficacy, making ATR inhibitors (ATRi) an attractive therapeutic. In vivo and in vitro studies have shown enhanced tumor cell radiosensitivity with the ATRi ceralasertib, elimusertib, and berzosertib, however, the potentiating effect of ATRi on ionizing radiation (IR) through immune-based mechanisms has only been studied with ceralasertib. MethodsWe aimed to determine if antitumor immune responses observed with ceralasertib in combination with IR extend to the other ATRi class members in the preclinical CT26 mouse model. We also examined the relationship between exposure and immune stimulation, efficacy and survival outcomes of each ATRi when combined with IR. ResultsCeralasertib and elimusertib, not berzosertib, synergized with IR in a dose and schedule-dependent manner to modify tumor antigen-specific CD8+ T cell populations in the draining lymph node. Transient ATRi therapy, combined with IR, enhances antitumor efficacy, promoted tumor shrinkage, and increased survival. ATRi elicited differential inflammatory gene induction and dose-dependent unique cytotoxicity profiles in vitro. ConclusionThe immune mediated antitumor effect of ATRi combined with radiation is dose and schedule dependent, and while likely a class effect, may differ between ATRi compounds.

cancer biology↗

bioRxiv2026

Biosynthesis of bisbenzylisoquinoline alkaloids

Bisbenzylisoquinoline alkaloids (bisBIAs) are pharmacologically valuable plant metabolites with complex stereochemical architectures, yet the catalytic principles governing their assembly have remained largely unclear. Here, we elucidate the enzymatic pathway to cyclic bisBIAs and uncover a non-canonical redox-mediated mechanism for post-assembly stereochemical control. We identify cytochrome P450 enzymes that catalyze regioselective oxidative dimerization and macrocyclization of benzylisoquinoline monomers, establishing the macrocyclic scaffold. Subsequent stereochemical specification is achieved by a paired oxidase-reductase module that selectively epimerizes a single stereocenter through a transient imine formation, converting (R,S)-configured intermediates to (S,S)-products. Reconstitution of the pathway in yeast enabled production of both native bisBIAs and non-natural analogs, demonstrating pathway modularity and engineering potential. These results establish the biochemical principle underlying bisBIA biosynthesis and provide a framework for programmable biosynthesis of these complex natural products.

biochemistry↗

bioRxiv2026

TipQUANT: A robust algorithm for quantitative analysis of spatiotemporally dynamic activities in tip-growing cells

Cell polarity, essential for cell development and function, relies on dynamic subcellular distribution of structural and signaling molecules. Tip growth, an extreme form of polar growth, involves unidirectional expansion at the apical region of cells and requires precise spatiotemporal coordination to achieve periodic and directional growth. Understanding their spatiotemporal dynamics is critical for elucidating mechanisms and functions of cell polarity. However, manual quantification of such dynamics is extremely time-consuming, hindering advancements in the field. Current algorithms have limited power and flexibility in analyzing the distribution and dynamics of molecules and structures, particularly for tip-growing cells with oscillatory and dynamic behavior. To address this challenge, we present TipQuant, an automated analysis tool that robustly detects tips and analyzes spatiotemporal dynamics of fluorescently labeled molecules/structures on plasma membranes and in cytoplasm at apices of tip-growing cells, enabling quantitative understanding of signaling and structural components in these systems.

cell biology↗

bioRxiv2026

HESTIA: Scalable Multimodal Integration of Histology and High-Resolution Spatial Transcriptomics for Robust Spatial Domain Identification

Spatial omics has revolutionized molecular biology by providing invaluable insights into how native tissue microenvironments regulate cellular functions and disease mechanisms. Accurately capturing this structural complexity and decoding the underlying biological processes requires effectively integrating data from multiple modalities. However, transitioning to subcellular resolutions introduces massive data scales and severe transcriptomic sparsity, which challenge current analytical frameworks. To address this, we present HESTIA (Histology-Enhanced Scalable cross-Resolution inTegration for spatial trAnscriptomics), a highly efficient multimodal algorithm designed for identifying spatial domains in large-scale, high-resolution spatial omics data. By circumventing memory-intensive computations, HESTIA efficiently processes massive datasets on which existing algorithms fail due to memory constraints. HESTIA outperforms current multimodal methods in clustering accuracy and spatial continuity, accurately delineating fine structural boundaries. Furthermore, applying HESTIA to large-scale pathological samples successfully dissects clinically relevant intratumoral heterogeneity and maps distinct immune microenvironments in lung and colorectal cancers.

bioinformatics↗

bioRxiv2026

Reprogramming tumour-associated macrophages from immune suppressive to inflammatory state by Checkpoint kinase 1 inhibitor combination treatment

BackgroundTumour-associated macrophages (TAMs) play critical roles within the tumour microenvironment regulating immune evasion and therapeutic response. Previously, we have shown that the combination of Checkpoint kinase 1 inhibitor (CHK1i) with a subclinical dose of hydroxyurea (LDHU) reprograms the tumour immune microenvironment to a pro-inflammatory status. MethodsWe investigated a tumour-restricted Fcgr4 (Cd16.2) expressing macrophage population in multiple murine tumour models and the impact of CHK1i+LDHU on this population, using conventional and imaging flow cytometry as well as single-cell sequencing. ResultsTranscriptional profiling using CITE-seq and single-cell RNA sequencing reveals that Fcgr4 TAMs closely resemble Fcgr4- TAMs but display modest enrichment of interferon-associated and inflammatory gene programs, consistent with a functionally biased state rather than a distinct lineage. Importantly, we show that a highly tumour selective CHK1i+LDHU therapy shifts TAMs toward a more inflammatory phenotype while preserving dominant immunosuppressive features. Depletion of CSF1R macrophages enhanced CD8 T cell activation without influencing tumour growth but significantly augmented therapeutic efficacy of CHK1i+LDHU. ConclusionTogether, these findings define a novel TAM population and establish how targeted therapy reshapes, but does not fully overcome, TAM-mediated immune regulation.

cancer biology↗

bioRxiv2026

Histone modifications analysis reveals enhancers reprogramming during maternal-to-zygotic transition

Enhancers are important epigenetic regulatory components that coordinate spatiotemporal gene expression and play a crucial role in mammalian development, gene regulation, and illness. During early mammalian embryogenesis, histone modifications including H3K4me1, a canonical enhancer mark, and H3K27ac, which identifies active enhancers, are still poorly understood. This study profiles the genome-wide H3K4me1 and H3K27ac patterns in mouse oocytes and pre-implantation embryos using low-input CUT&RUN (cleavage under targets and release using nuclease) with input as low as 50 cells. Both markers are enriched in distal regions and exhibit distinct sequence preferences and reprogramming dynamics in pre-implantation embryos. H3K27ac, a mark of active enhancers, is reprogrammed at the 2-cell stage, whereas H3K4me1 is remodeled at the 4-cell stage and overlaps with H3K27ac, coinciding with accessible chromatin regions. Interestingly, H3K4me1 and H3K27ac are co-localized in promoter regions, where they are mutually exclusive to H3K4me3. Enhancers are dynamically remodeled during maternal-to-zygotic transition (MZT). there are three enhancer types: active enhancers (H3K4me1/H3K27ac), primed enhancers (H3K4me1), and poised enhancers (H3K4me1/H3K27me3). Active enhancers increase significantly after zygotic genome activation. Further, super-enhancers are present across the genome and are mainly enriched in promoters. The specific motifs enriched by super-enhancers may be associated with the variations of gene expressions at different stages.

developmental biology↗

bioRxiv2026

Do Larger Models Really Win in Drug Discovery?A Benchmark Assessment of Model Scaling in AI-Driven Molecular Property and Activity Prediction

The rapid growth of molecular foundation models and large language models (LLMs) has encouraged a scale centred view of AI in drug discovery, in which larger pretrained models are expected to supersede compact cheminformatics models based on classical machine learning (classical ML) and graph neural networks (GNNs) trained for individual tasks. We test this assumption across 26 endpoints grouped into ADME, toxicity and bioactivity classes, covering 165,541 endpoint level compound label records. The benchmark contains 78 endpoint and split entries, corresponding to 26 endpoints evaluated under three split protocols: random, Murcko scaffold and structure separated 5-fold cross validation (CV). Ordered from easiest to hardest, these splits approximate retrospective evaluation on a closed library, scaffold expansion in hit to lead, and library expansion on novel chemotypes. Each entry contributes two task and metric comparisons, giving 156 comparisons in total. Across these comparisons, classical ML provides the largest share of best performing entries (47.4%), followed by pretrained molecular sequence models (28.8%), GNNs (21.8%) and LLM based SAR baselines (1.9%). Classical ML dominates random split interpolation and remains the largest winner family overall. GNN and sequence models are competitive in selected harder split protocols under the primary optimal held-out readout, but their strict winner shares decrease under a fixed final-window readout, indicating that some of these gains depend on training settings and model selection. Paired bootstrap analyses indicate that small numerical differences between individual models should not be read as decisive victories. SAR knowledge from training folds improves many GPT5.5-SAR and Opus4.7-SAR metrics but does not make rule based reasoning a universal substitute for supervised predictors. Compact specialized models remain highly effective for molecular property and activity prediction. Larger models add value for SAR interpretation and reasoning in low data settings, but predictive performance depends on the fit among model, task and validation scenario, not on scale alone.

bioinformatics↗

bioRxiv2026

Survivin inhibition induces PD-L1 expression through cGAS stabilization and attenuates antitumor immunity

BackgroundSurvivin is a mitotic regulator frequently overexpressed in human cancers and an attractive therapeutic target. However, how Survivin inhibition influences tumor immune regulation remains incompletely understood. This study aimed to investigate whether Survivin inhibition modulates antitumor immunity and to elucidate the underlying mechanisms. MethodsProgrammed death-ligand 1 (PD-L1) expression was evaluated in multiple tumor cell lines following pharmacological or genetic inhibition of Survivin. Mechanistic studies included RNA sequencing, immunoblotting, flow cytometry, cGAS knockdown, and NF-{kappa}B inhibition. Immune profiling was performed using CD8 T-cell cytotoxicity assays, mass cytometry, flow cytometry, immunofluorescence and single-cell RNA sequencing. Clinical relevance was assessed using patient tumor specimens and public immunotherapy cohorts. ResultsSurvivin inhibition, either by YM155 treatment or genetic depletion, increased PD-L1 expression at both mRNA and protein levels in tumor cells. Mechanistically, Survivin inhibition stabilized cyclic GMP - AMP synthase (cGAS) by reducing its ubiquitination and activated NF-{kappa}B signaling, thereby promoting transcriptional upregulation of PD-L1. Functionally, the induced PD-L1 enhanced PD-1 engagement and suppressed CD8 T-cell cytotoxicity, promoting immune evasion. In immunocompetent ovarian cancer models, pharmacological inhibition of Survivin increased PD-L1 expression in tumor and immune compartments and attenuated cytotoxic immune activity. PD-L1 blockade restored antitumor immunity and significantly enhanced the therapeutic efficacy of Survivin inhibition. In addition, analyses of patient samples and public single-cell datasets revealed an inverse association between Survivin and PD-L1 expression, and high Survivin expression was associated with reduced benefit from PD-1/PD-L1 blockade. ConclusionsThese findings identify a Survivin-cGAS-PD-L1 axis linking mitotic stress to immune suppression and provide a mechanistic rationale for combining Survivin-targeted therapy with immune checkpoint blockade.

cancer biology↗

bioRxiv2026

NEURA: An agentic system for autonomous neuroimaging workflows

Neuroimaging research depends on heterogeneous software, multimodal data and multistage statistical workflows. Large language model (LLM)-based agents offer a route to automate these workflows, but their susceptibility to hallucination limits their credibility in scientific use. Here we introduce NEURA, a proof-carrying framework for hallucination-resistant neuroimaging automation. NEURA converts free-text research questions and neuroimaging datasets into executable analysis plans, validated outputs and structured reports. The system combines disease- and tool-aware planning with a deterministic verification layer inspired by formal proof: before any claim is retained for reporting, it must be checked against tool-derived evidence and domain axioms. On NeuroEval, an expert-curated benchmark of 110 neuroimaging tasks, NEURA achieved 89.5% planning accuracy, a 30.5% improvement over direct LLM queries. In a controlled hallucination-injection experiment, the verification layer detected all the injected error classes under the specified axiom bank and trust assumptions, with no false positives. In case studies of spinocerebellar ataxia type 3, NEURA reproduced cerebellar atrophy and abnormal diffusion patterns consistent with established pathology and independent expert analyses. Together, these findings show that coupling domain-grounded agency with proof-carrying verification can turn LLM-driven workflow automation from probabilistic self-checking into auditable scientific computation.

neuroscience↗

bioRxiv2026

Long-lived mammals contain more phosphorylation sites in the SIRT6 C-terminus that enhance PARP1 interaction and resistance to oxidative stress

Sirtuin 6 (SIRT6) is a protein deacetylase and ribosyltransferase that is a vital hub for maintaining epigenetic homeostasis, regulating the transcriptome, and repairing DNA double stranded breaks (DSBs). Comprehensive proteomic profiling of the SIRT6 post-translational landscape, however, remains elusive. The SIRT6 C-terminal domain contains multiple phosphorylation sites. We find that the presence and use of these sites is strongly correlated with maximum lifespan across mammals. Subsequent biochemical and in silico analyses revealed that SIRT6 hyperphosphorylation enhances its interaction with PARP1. Mutating the T294 phosphorylation site in human fibroblasts led to decreased survival after oxidative stress in the phospho-null T294A and improved oxidative stress resistance in the phospho-mimetic T294E. Together, these results suggest SIRT6 C-terminal phosphorylation increases stress resistance through interaction with PARP1, and that this effect has been enhanced by evolution in long-lived species.

molecular biology↗

bioRxiv2026

Longitudinal serum proteomics analyses reveal biomarkers for porcine influenza and coronavirus infections

Respiratory virus infections affect both humans and livestock, causing considerable mortality and morbidity. While respiratory pathogens such as swine influenza A virus (pH1N1) and porcine respiratory coronavirus (PRCV) often present with overlapping clinical symptoms, their pathological trajectories and outcomes differ. Given the propensity for pathogen spillover and the use of pigs as a physiologically relevant large-animal translational model, we aimed to characterise host serum protein signatures that detect and differentiate pH1N1 from PRCV, enabling improved disease monitoring and control. Using high-resolution mass spectrometry- based proteomics, we identified 162 serum proteins that were significantly dysregulated across 3 infection timepoints (1, 5, and 12 days post-infection (DPI)), with signatures correlating with viral shedding and lung pathology as early as 1 DPI. Notably, multiplexed targeted analysis of a subset of proteins in an independent cohort from a different breed and geographic location demonstrated detection, femtomole-level targeted quantitation, and validation of SRGN as a diagnostic marker for pH1N1 and PRCV (AUC=0.85). Further, SOD1 was validated as an early marker for PRCV, increasing as early as 1 DPI (AUC= 0.9). Finally, a multi-peptide signature composed of SRGN, SOD1, and RAN demonstrated reasonable predictive power for pH1N1 (AUC=0.75) and PRCV (AUC=0.65) at 1 DPI. Our data validate the proteomic screening, provide insights into the role of early protein markers in distinguishing respiratory viral infections, and pave the way for the development of point-of-care diagnostics and targeted prevention strategies, enhancing preparedness against emerging zoonotic threats.

biochemistry↗