Biology subjects

Pu, J.

Publications and source records attributed to Pu, J..

At least 19 recordsLinked to original sources

bioRxiv2026

A pretrained unified model enables cellular functional profile prediction and multi-objective virtual drug screening

Cells are characterized by molecular states, coordinated molecular interactions, regulatory programs, and responses to perturbations. Systematic mapping of these cellular functional profiles across biological contexts remains experimentally costly and fragmented. Here we present InsilicoCell, a pretrained multi-modal, multi-task model that unifies prediction of cellular functional profiles spanning molecular states, molecular interactions, and perturbation-induced responses. Built on a supervised transformer architecture and pretrained on more than 88 million measurements across seven tasks, including drug sensitivity, drug-induced gene expression, and drug-protein binding, InsilicoCell learns a shared representation that links molecular profiles to cellular phenotypes, improves performance over task-specific models, and generalizes to unseen entities, contexts, and conditions. InsilicoCell extends beyond cell line systems to patient, spatial and single-cell settings, and enables multi-objective virtual drug screening. It identifies novel candidate compounds with experimental validation, including c-Myc activity inhibitors, antifibrotic agents and stemness-inducing compounds. Together, InsilicoCell provides a scalable framework for predictive cellular biology and therapeutic discovery.

bioinformatics↗

bioRxiv2026

Automating scientific annotations for open transcriptomic profiles via multi-stage agents

Public transcriptomic repositories contain millions of samples, yet their large-scale reuse is hindered by heterogeneous and inconsistently reported metadata. In the Gene Expression Omnibus (GEO), key biological information is often distributed across study- and sample-level records, requiring context-dependent interpretation. Here we present GEOMeta, a large language model (LLM)-based multi-stage workflow with task-specialized agents for automated GEO metadata curation. The pipeline separates metadata retrieval, task-specific information extraction, field standardization, ontology mapping and quality control. Using GEOMeta, we generated standardized annotations for approximately 600,000 human bulk RNA-seq samples. To demonstrate its utility, we benchmarked transcriptome representation models for predicting sex, age, tissue and disease from transcriptome embeddings. We further prospectively annotated newly submitted GEO studies and evaluated 22 frontier LLMs. Recent open-source Flash models achieved annotation quality comparable to leading reasoning models while reducing costs by an order of magnitude. GEOMeta provides a scalable resource and reproducible framework for metadata curation.

bioinformatics↗

bioRxiv2026

HSD17B11 maintains FSP1 localization on lipid droplets to support ferroptosis defense

Ferroptosis is a regulated form of cell death driven by iron-dependent lipid peroxidation, and lipid droplets (LDs) are increasingly recognized as important regulators of this process. Consistent with this role, the anti-ferroptotic factor ferroptosis suppressor protein 1 (FSP1) is known localizing on LDs through N-myristoylation-dependent membrane targeting, where it protects LD lipids from peroxidation. Here, we identify the LD protein HSD17B11 as an additional factor required for maintaining both FSP1 localization on LDs and cellular FSP1 abundance. Silver staining followed by mass spectrometry analysis of purified LD proteins identified reduced LD-associated FSP1 in HSD17B11-deficient cells, which was further validated by immunoblotting and imaging analyses. Mechanistically, HSD17B11 physically interacted with FSP1 and was required to preserve FSP1 association with LDs. Mutational analyses further demonstrated that both FSP1 N-myristoylation and an intact HSD17B11 interaction interface are necessary for LD targeting. Correspondingly, HSD17B11 deficiency reduced LD-associated and total cellular FSP1 levels and increased cellular sensitivity to lipid oxidative stress. Together, our findings identify HSD17B11 as a previously unrecognized regulator of LD-associated FSP1 and reveal an additional mechanism controlling compartmentalized ferroptosis defense.

cell biology↗

bioRxiv2026

Hex-MASP for Mapping the Whole-tissue Spatial Proteome and the Intra-brain Distribution of Monoclonal Antibodies

Whole-tissue spatial proteomics level provides critical insights into region-specific biological regulations but remains challenging. Previously, we introduced the Micro-scaffold Assisted Spatial Proteomics (MASP) concept for whole-tissue mapping. However, this prototype required substantial development in spatial resolution, practicality, and throughput for practical application. Here we present a next-generation MASP technique (hex-MASP) featuring i) a new design of hexagonal-micro-wells fabricated with optimized Projection Micro-Stereolithography (P{micro}SL) 3D-printing, achieving high spatial resolution, sampling robustness and mechanical strength for reproducibly compartmentalizing even tough tissues; ii) enhanced throughput/effectiveness in sample preparation and LC-MS analysis with high quantitative quality. Applied to mouse brain, hex-MASP for the first time achieved in-depth, whole-tissue mapping for >6,000 proteins in mouse brains, with high spatial accuracy and excellent data quality. The substantially improved resolution revealed critical regional details across the entire brain, that were not previously captured, enabling precise depiction of protein distribution heterogeneity. This technique enabled the discovery of many unreported regionally-enriched proteins across brain structures. We further applied hex-MASP to investigate the intra-brain distribution of intracerebroventricularly-dosed antibody therapeutics and related proteins, which to our knowledge, enabled whole tissue mapping of protein drugs for the first time and revealed novel mechanistic insights into antibody distribution and localized treatment effects. Hex-MASP represent a robust, scalable platform for whole-tissue spatial proteomics.

pharmacology and toxicology↗

bioRxiv2026

Integrative Multi-Omics Analysis Identifies a Functional Enhancer Driving Tumorigenesis in Head and Neck Squamous Cell Carcinoma

Enhancer is a critical epigenetic feature in head and neck squamous cell carcinoma (HNSCC), yet the functional roles of individual enhancers remain poorly understood. Here, we conducted an integrative multi-omics analysis based on publicly available ATAC-seq, H3K27ac ChIP-seq, transcriptomic profiling, and genetic association datasets to systematically map HNSCC-associated enhancers and their target genes. Integrating ATAC-seq and H3K27ac ChIP-seq, we identified 20,362 enhancers and 18,040 enhancer-associated genes, highlighting widespread regulatory complexity. Functional characterization of the TERT-associated enhancer GH05J001312 (GRCh38/hg38: chr5:1312099-1317743) revealed strong transcriptional activity in HNSCC. CRISPR-mediated deletion of a core sequence significantly reduced TERT expression, impaired cellular proliferation in vitro, and suppressed tumor growth in vivo, confirming its role as a key cis-regulatory element. RNA-seq analysis of enhancer-edited cells uncovered 742 differentially expressed genes enriched in cancer-related pathways, including MAPK and IL-17 signaling, indicating a broad transcriptional impact. Collectively, our findings establish GH05J001312 as a functional enhancer driving oncogenic programs in HNSCC and suggest enhancer-targeted strategies as a potential therapeutic avenue.

cancer biology↗

bioRxiv2025

Metabolomic, Lipidomic, and Enterohormone Changes in the Progression from MASLD to MASH

Background & AimsMetabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) and Metabolic Dysfunction-Associated Steatohepatitis (MASH) represent progressive stages of liver disease, with distinct metabolic and cellular alterations. This study investigates the progression from MASLD to MASH through metabolomics, lipidomics, and assessment of hormones. MethodsMale C57BL/6NTac mice were fed a high-fat diet for 16 weeks to induce MASLD and for 29 weeks to develop MASH. Aged-matched controls on a normal diet were used for comparison. Histology confirmed the progression of MASLD to MASH. We performed metabolomic and lipidomic profiling of liver, colon, and stool samples to identify metabolic and lipid alterations. Plasma enteroendocrine hormones and cytokines were quantified. Immunofluorescence was performed to assess enteroendocrine cells changes in the colon and the association of serotonin (5-HT) with fibronectin in the liver. ResultsMetabolomic and lipidomic analysis revealed significant alterations at different stages of the disease. Specifically, cholic acid was increased across the liver, colon, and stool in both MASLD and MASH mice compared to controls. Compared to the control group, MASLD mice exhibited an increase in enteroendocrine hormones, GLP-1, GIP, and PYY, whereas no changes were observed in MASH mice. Comparing MASLD to MASH livers, we found hepatic 5-HT levels were increased in MASH mice compared to MASLD mice. The MASH liver also exhibited a colocalization between fibronectin and 5-HT, suggesting a potential role of 5-HT in liver fibrosis. ConclusionsOur study provides novel insights into the progressive metabolic and hormonal changes from MASLD to MASH. The increase in cholic acid and differential enteroendocrine hormone responses highlight the complex interactions between the gut and liver in metabolic liver diseases. These findings suggest that enteroendocrine hormones may play a role in the progression of MASLD to MASH as well as liver fibrosis, offering potential therapeutic avenues for targeting the gut-liver axis in metabolic liver diseases.

cell biology↗

bioRxiv2025

Processing bodies promote lysosomal quality control and cell survival during recovery from lysosomal damage

Lysosomes are essential for cell survival but are highly susceptible to diverse physical and pathological stressors. Thus, the ability to initiate an acute damage response and promote recovery after stressor resolution is critical for maintaining cellular homeostasis and viability. Although recent studies have advanced our understanding of acute responses to lysosomal injury, the molecular mechanisms governing the recovery stage and distinguishing it from the acute phase remain poorly defined. Here, we delineate a key difference between these two stages in translational regulation and uncover lysosomal recovery from acute damage as a novel trigger for processing body (PB) formation. PBs are membraneless biomolecular condensates involved in RNA metabolism and translational reprogramming. We provide the first evidence that PBs are critical for lysosomal quality control and cell survival during recovery. Mechanistically, PBs are induced selectively during the recovery phase, but not during the acute damage response, through interactions with stress granules (SGs), distinct membraneless biomolecular condensates formed upon acute injury to stabilize damaged lysosomal membranes for repair. Functional analyses reveal that PBs promote lysosomal quality control by collaborating with SG-mediated membrane stabilization, while independently recruiting released cathepsins, thereby collectively supporting cell survival. Together, these findings establish PBs as central effectors of the lysosomal recovery program and underscore the broader relevance of biomolecular condensates in cellular responses to lysosomal damage and related disease processes.

cell biology↗

bioRxiv2025

Using Artificial Intelligence to Assess Cross-Species Transmission Potential of Influenza A Virus

Influenza A viruses (IAVs) pose pandemic threats through cross-species transmission, yet predicting their adaptive evolution remains challenging. We introduced Influenza A virus Adaptability to host X (FluAdaX), a deep learning framework that integrates a moving average-equipped gated attention mechanism using full-genome sequences. FluAdaX demonstrated robust host classification performance across endemic IAV strains, and outperformed traditional models in detecting avian-to-human transmission. Spillover score and adaptability score were introduced to evaluate host shift risk, which prioritized variants with elevated human adaptation potential, such as H7N9, H9N2 avian IAVs, and H1N1 swine IAVs. Besides HA and NA genes, PB2 and NS genes were found critical for zoonosis. Potential molecular markers associated with avian/human tropism were identified across PB2 and NS genes using XGBoost. FluAdaX provided a dynamic framework to decode IAV host adaptation, enabling real-time risk assessment of cross-species transmission of emerging IAV variants.

bioinformatics↗

bioRxiv2024

CEACAM1 Targets ABCA1 to Mediate Atrial Fibrillation via Lipophagy-Dependent Ferroptosis

Atrial fibrillation (AF) is one of the most common arrhythmias, imposing a significant burden on individuals due to its association with cerebrovascular events. The mechanisms underlying AF involve cardiac structural remodeling, electrical remodeling, and metabolic remodeling, with oxidative stress playing a crucial role. Our previous studies demonstrated that upregulation of CEACAM1 can increase oxidative stress, inhibit cell proliferation, and potentially contribute to cellular damage, while ferroptosis is closely associated with AF. In this study, we observed a significant increase in CEACAM1 expression in an AF model. Knocking out CEACAM1 revealed changes in mitochondrial membrane potential, reactive oxygen species (ROS) levels, intracellular Ca2+ concentration, channel proteins, and glycolipid metabolic enzymes. This knockout reversed electrical, structural, and metabolic remodeling in AF. Further investigation showed that CEACAM1 knockout inhibited ferroptosis, as evidenced by ferroptosis-related indicators. Using colocalization analyses of lipid droplets, lysosomes, and autophagosomes, we discovered that CEACAM1 knockout suppressed autophagy and lipophagy during AF. Supplementation with free fatty acids (FFAs) in the AF model post-CEACAM1 knockout suggested that the inhibition of ferroptosis was linked to a reduction in FFAs. Transcriptomic and non-targeted metabolomic analyses, along with ABCA1 interference studies, indicated that CEACAM1 knockout mitigates AF by promoting ABCA1 expression. In summary, CEACAM1 targets ABCA1 to alleviate AF through the regulation of lipophagy-dependent ferroptosis, as demonstrated in both cellular and animal models. BackgroundFerroptosis is a regulated form of cell death, but its connection with atrial fibrillation(AF) remains unclear. Since CEACAM1 knockout reduces oxidative stress and protects cells, we investigated the relationship among CEACAM1, ferroptosis, and AF to uncover the regulatory mechanisms of ferroptosis in AF. MethodsWe established AF models using HL-1 cells, human pluripotent stem cells, and rats. CEACAM1 expression levels were assessed in these models, along with changes in mitochondrial membrane potential, ROS levels, intracellular Ca2+ concentration, channel proteins, glycolipid metabolic enzymes, and ferroptosis-related indicators following CEACAM1 knockout. Through transcriptomics, non-target metabolomics, and immunoprecipitation screening, we identified ABCA1 as a downstream gene of CEACAM1 involved in protecting against AF. Subsequently, ABCA1 interference experiments were conducted, and colocalization analyses of lipid droplets, lysosomes, and autophagosomes were performed after the application of ferroptosis activators, lipophagy inhibitors, and lipophagy activators. FFAs were added to the AF model to evaluate changes in lipophagy and ferroptosis following CEACAM1 knockout. ResultsIn the AF model using HL-1 myocytes, CEACAM1 knockout reverse electrical, structural, and metabolic remodeling while inhibiting ferroptosis, with ABCA1 as a downstream gene. In the AF model derived from pluripotent stem cells differentiated into atrial myocytes, CEACAM1 knockout suppressed autophagy and lipophagy during AF, thereby inhibiting ferroptosis, which correlated with reduced FFA release. This process was regulated by ABCA1. In the rat AF model, ABCA1, identified as a downstream gene of CEACAM1, was further confirmed to inhibit ferroptosis by regulating FFA levels. ConclusionThis study reveals that CEACAM1 knockout inhibits ferroptosis in AF models by upregulating ABCA1 and reducing FFA levels, providing a novel regulatory mechanism for ferroptosis in AF. O_FIG O_LINKSMALLFIG WIDTH=172 HEIGHT=200 SRC="FIGDIR/small/625561v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@809c82org.highwire.dtl.DTLVardef@1a339d6org.highwire.dtl.DTLVardef@12a20d4org.highwire.dtl.DTLVardef@d14927_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Manipulation of Host Cholesterol by SARS-CoV-2

Cholesterol homeostasis relies on lysosomes, which release free cholesterol from degraded lipids. We show that SARS-CoV-2 blocks lysosomal cholesterol export through its protein ORF3a. ORF3a binds the HOPS subunit VPS39, and disrupting this interaction restores cholesterol trafficking. Two mechanisms underlie this defect. First, ORF3a-VPS39 interaction traps the sorting receptor CI-MPR and the retrieval complex retromer in endosomes/lysosomes, impairing trafficking of the cholesterol transporter NPC2. Retromer deletion reproduced these defects. Second, ORF3a reduces bis(monoacylglycerol)phosphates (BMPs), lysosomal lipids required for cholesterol export. Lipidomics and proteomics revealed altered metabolism of BMP precursors, mitochondrial phosphatidylglycerols (PGs), and reduced mitochondrial proteins at lysosomes. ORF3a-VPS39 interaction decreased lysosome-mitochondrion membrane contact sites (MCS), excluding autophagy or mitochondrion-derived vesicles as routes for PG transfer. VPS39 deletion decreased the MCS and BMPs. These findings identify VPS39 as a regulator of NPC2 trafficking and BMP biosynthesis and reveal that ORF3a disrupts both pathways to block cholesterol egress.

cell biology↗

bioRxiv2024

Synergistic Role of Amino Acids in Enhancing mTOR Activation Through Lysosome Positioning

Lysosome positioning, or lysosome cellular distribution, is critical for lysosomal functions in response to both extracellular and intracellular cues. Amino acids, as essential nutrients, have been shown to promote lysosome movement toward the cell periphery. Peripheral lysosomes are involved in processes such as lysosomal exocytosis, cell migration, and metabolic signaling--functions that are particularly important for cancer cell motility and growth. However, the specific types of amino acids that regulate lysosome positioning, their underlying mechanisms, and their connection to amino acid-regulated metabolic signaling remain poorly understood. In this study, we developed a high-content imaging system for unbiased, quantitative analysis of lysosome positioning. We examined the 15 amino acids present in cell culture media and found that 10 promoted lysosome redistribution toward the cell periphery to varying extents, with aromatic amino acids showing the strongest effect. This redistribution was mediated by promoting outward transport through SLC38A9-BORC-kinesin 1/3 axis and simultaneously reducing inward transport via inhibiting the recruitment of Rab7 and JIP4 onto lysosomes. When examining the effects of amino acids on mTOR activation--a central regulator of cell metabolism--we found that the amino acids most strongly promoting lysosome dispersal, such as phenylalanine, did not activate mTOR on their own. However, combining phenylalanine with arginine, which activates mTOR without affecting lysosome positioning, synergistically enhanced mTOR activity. This synergy was lost when lysosomes failed to localize to the cell periphery, as observed in kinesin 1/3 knockout (KO) cells. Furthermore, breast cancer cells exhibited heightened sensitivity to phenylalanine-induced lysosome dispersal compared to noncancerous breast cells. Inhibition of LAT1, the amino acid transporter responsible for phenylalanine uptake, reduced peripheral lysosomes and impaired cancer cell migration and proliferation, highlighting the importance of lysosome positioning in these coordinated cellular activities. In summary, amino acid-regulated lysosome positioning and mTOR signaling depend on distinct sets of amino acids. Combining lysosome-dispersing amino acids with mTOR-activating amino acids synergistically enhances mTOR activation, which may be particularly relevant in cancer cells.

cell biology↗

bioRxiv2024

An emerging PB2-627 polymorphism increases the pandemic potential of avian influenza virus by breaking through ANP32 host restriction in mammalian and avian hosts

Alterations in the PB2-627 domain could substantially increase the risk of an avian influenza virus (AIV) pandemic. So far, a well-known mammalian mutation PB2-E627K has not been maintained in AIV in poultry, which limits the spread of AIVs from avian to humans. Here, we discovered a variant, PB2-627V, which combines the properties of avian-like PB2-627E and human-like PB2-627K, overcoming host restrictions and posing a risk for human pandemics. Specifically, by screening the global PB2 sequences, we discovered a new independent cluster with PB2-627V emerged in the 2010s, which is prevalent in various avian, mammalian, and human isolates of AIVs, including H9N2, H7N9, H3N8, 2.3.4.4b H5N1, and other subtypes. And, the increasing prevalence of PB2-627V in poultry is accompanied by a rise in human infection cases with this variant. Then we systematically assessed its host adaptation, fitness, and transmissibility across three subtypes of AIVs (H9N2, H7N9, and H3N8) in different host models, including avian and human cells, chickens, mice, and ferrets where infections naturally occur. We found that PB2-627V facilitates AIVs to efficiently infect and replicate in chickens and mice by utilizing both avian- and human-origin ANP32A proteins. Importantly, and like PB2-627K, PB2-627V promotes efficient transmission between ferrets through respiratory droplets. Deep sequencing in passaged chicken samples and transmitted ferret samples indicates that PB2-627V remains stable across the two distinct hosts and has a high potential for long-term prevalence in avian species. Therefore, the mutation has the ability to continue spreading among poultry and can also overcome the barrier between birds and humans, greatly enhancing the likelihood of AIVs infecting humans. Given the escalating global spread of AIVs, it is crucial to closely monitor influenza viruses carrying PB2-627V to prevent a pandemic.

microbiology↗

bioRxiv2023

Tropism of AAV.CPP.16 in the respiratory tract and its application for a CRISPR-based gene therapy against SARS-CoV-2

Efficient gene delivery vectors are essential for developing gene therapies for respiratory diseases. Here, we report that AAV.CPP.16, a novel AAV9-derived adeno-associated virus vector, can efficiently transduce airway epithelium systems and lung parenchyma cells in both mice and non-human primates after intranasal administration. AAV.CPP.16 outperforms AAV6 and AAV9, two wild-type AAVs with demonstrated tropism to respiratory tract tissues, and can target major cell types in the respiratory tract and the lung. We also report an "all-in-one", CRISPR-Cas13d-based AAV gene therapy vector that targets the highly conserved RNA-dependent RNA polymerase (Rdrp) gene in SARS-CoV-2, and show the potential of such gene therapy against a broad range of circulating and emergent SARS-CoV-2 variants. Thus, AAV.CPP.16 could be a useful gene delivery vector for treating genetic respiratory diseases and airborne infections including for developing a potential prophilaxis to SARS-CoV-2.

bioengineering↗

bioRxiv2023

Quantitative Learning of Cellular Features From Single-cell Transcriptomics Data Facilitates Effective Drug Repurposing

In this study, we have devised a computational framework SuperFeat that allows for the training of a machine learning model and evaluate the canonical cellular states/features in pathological tissues that underlie the progression of disease. This framework also enables the identification of potential drugs that target the presumed detrimental cellular features. This framework was constructed on the basis of an artificial neural network with the gene expression profiles serving as input nodes. The training data comprised single-cell RNA-seq datasets that encompassed the specific cell lineage during the developmental progression of cell features. A few models of the canonical cancer-involved cellular states/features were tested by such framework. Finally, we have illustrated the drug repurposing pipeline, utilizing the training parameters derived from the adverse cellular states/features, which has yielded successful validation results both in vitro and in vivo. SuperFeat is accessible at https://github.com/weilin-genomics/rSuperFeat.

cell biology↗

bioRxiv2023

Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila

To survive in extreme environments such as hot-arid deserts, desert-dwelling species have evolved physiological traits to withstand the high temperatures and low aridity beyond the physiologically tolerable ranges of most species. Such traits which include reducing water loss have independently evolved in multiple taxa. However, the genetic and evolutionary mechanisms underlying these traits have thus far not been elucidated. Here we show that Drosophila mojavensis, a fruitfly species endemic to the Sonoran and Mojave deserts, had evolved extremely high desiccation resistance, by producing very long chained methylbranched cuticular hydrocarbons (mbCHCs) that contributes to a cuticular waterproofing lipid layer reducing water loss. We show that the ability to synthesize these longer mbCHCs is due to evolutionary changes in a fatty acyl-CoA elongase (mElo). CRISPR/Cas9 knockout of mElo in D. mojavensis led to loss of longer mbCHC production and significant reduction of desiccation resistance at high temperatures but did not affect mortality at high temperatures or desiccating conditions individually, indicating that this gene is crucial for desert adaptation. Phylogenetic analysis showed that mElo is a Drosophila specific gene with no clear ortholog outside Diptera. This suggests that while the physiological mechanisms underlying desert adaptation are general, the genetic mechanisms may be lineage-specific.

evolutionary biology↗

bioRxiv2023

Integrated Bioinformatics Analysis Reveals APEX1 as a Potential Biomarker for Septic Cardiomyopathy

BackgroundA severe threat to human health is septic cardiomyopathy (SCM), a condition with high morbidity and fatality rates throughout the world. However, effective treatment targets are still lacking. Therefore, it is necessary and urgent to find new therapeutic targets of SCM. MethodsWe obtained gene chip datasets GSE79962, GSE53007 and GSE13205 from the GEO database. After data normalization, GSE79962 was used as the training set and screened for differentially expressed genes (DEGs). Then, the module genes most related to SCM were identified via weighted gene co-expression network analysis (WGCNA). The potential target genes of SCM were obtained by intersection of DEGs and WGCNA module genes. We further performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function and pathway enrichment analyses on these genes. In addition, potential biomarkers were screened using machine learning algorithms and receiver operating characteristic (ROC) curve analysis. Gene Set Enrichment Analysis (GSEA) was then used to explore the mechanisms underlying the involvement of potential biomarkers. Finally, we validated the obtained potential biomarkers in test sets (GSE53007 and GSE13205). ResultsA total of 879 DEGs were obtained by differential expression analysis. WGCNA generated 2939 module genes significantly associated with SCM. The intersection of the two results produced 479 potential target genes. Enrichment analysis showed that these genes were involved in the positive regulation of protein kinase A signaling, histone deacetylase activity and T cell receptor signaling pathway, etc. Then, the results of machine learning algorithm and ROC analysis revealed that NEIL3, APEX1, KCNJ14 and TKTL1 had good diagnostic efficacy. GSEA results showed that these genes involved in signaling pathways mainly enriched in base excision repair and glycosaminoglycan biosynthesis pathways, etc. Notably, APEX1 was significantly up-regulated in the SCM groups of the two test sets and the AUC (area under curve) > 0.85. ConclusionsOur study identified NEIL3, APEX1, KCNJ14 and TKTL1 may play important roles in the pathogenesis of SCM through integrated bioinformatics analysis, and APEX1 may be a novel biomarker with great potential in the clinical diagnosis and treatment of SCM in the future.

bioinformatics↗

bioRxiv2022

Increased public health threat of avian-origin H3N2 influenza virus during evolution in dogs

Influenza A viruses in animal reservoirs repeatedly cross species barrier to infect humans. Once an animal-borne virus with novel antigenicity acquired the efficient human to human transmissibility, it will become epidemic in the population. Dogs are the closest animal companions to humans and canine respiratory tract expresses both SA2,3-(avian type) and 2,6-Gal (human type) receptors. However, the role of dogs in the ecology of influenza viruses is unclear. H3N2 avian influenza viruses transmitted to dogs around 2006 and have formed stable lineages. The long-term epidemic of avian-origin H3N2 virus in canine offers the best models to investigate the effect of dogs on the evolution of influenza viruses. Here, we carried out a systematic and comparative identification of the biological characteristics of H3N2 canine influenza viruses (CIVs) isolated in the worldwide over 10 years. We found that during the adaptation of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like SA2,6-Gal receptor, gradually increased HA acid stability and replication ability in human airway epithelial cells, and acquired a 100% transmission rate via respiratory droplet in ferret model, which were essential hallmarks of being adapted to humans. We also identified that the frequency of substitutions related to human adaptation has gradually increased in H3N2 CIVs, and determined four cumulative molecular changes responsible for the increased airborne transmission ability in ferrets. Our results suggested that canine may serve as an intermediate for the adaptation of avian influenza virus to human. Continuous surveillance coordinated with risk assessment for CIVs is necessary.

microbiology↗

bioRxiv2022

Integrated single-cell sequencing analysis reveals peripheral immune landscape across the human lifespan

Systematic understanding of immune dynamics across the entire human lifespan at single-cell resolution is currently lacking. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor (TCR)/B cell receptor (BCR) sequencing (scTCR/BCR-seq) on over 380,000 peripheral blood mononuclear cells collected from 45 healthy participants aged 0 to over 90 years. We revealed that the functions of T cell subsets were most susceptible to senescence among all PBMCs, featured by increased NF-{kappa}B signaling and IFN-{gamma} responses pathways, while reduced telomere maintenance and energy metabolism. We subsequently explored the rewiring of cell-cell interactions among different immune cells across the lifespan and revealed the major alteration of immune checkpoints in T cells within the cellular interaction networks. By combined analysis of scRNA-seq and scTCR-seq, we revealed that 1) GNLY+ CD8 Effector T cells exhibited a high clonal expansion with distinct functional signatures in children and the elderly; 2) Naive CD4+ T and naive CD8+ T cells displayed different aging patterns in both transcriptomes and immune repertoires; and 3) CD8+ MAIT cells showed a higher cell abundance and clonal diversity in adolescents. Furthermore, we identified a unique cytotoxic B cell subset enriched in children by scRNA-seq and scBCR-seq analysis and experimental validations. In summary, our work provided valuable insights and rich resources for understanding the development and aging of the human immune system across the lifespan.

immunology↗