Biology subjects

Zhao, J.

Publications and source records attributed to Zhao, J..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

Accelerated genome shuffling associated with rapid evolution of sexual conflict in seed beetles

Structural variation (SV) has an extensive impact on the evolution of the genome. The diverse SV provide a material basis for genome evolution, which can affect gene expression, 3D genome structure, and even changes in complex chromosomal features through regional recombination, copy number variation, and chromosome rearrangement. Here, we assemble and compare the chromosome-level assemblies of three species (Acanthoscelides obtectus, Callosobruchus chinensis, and C. maculatus) in Bruchinae, a clade of Coleoptera that is often used as models to study sexual conflict, to investigate the influence of SV on the changes of various genomic characteristics during species evolution. Through comparative genomic analysis of Coleoptera species, we reveal extensive structural variants (SVs) within the Bruchinae family, which is linked to the ongoing activity of LINE transposons. We show that SV drive the rapid evolution of sex chromosomes and correlated with dynamic evolution of sex-biased gene expression in seed beetle species. Our analysis highlights the acquisition of novel genes on the Y chromosome through frequent gene translocations, gradually shaping them into genes exhibiting male-biased expression patterns. This underscores the Y chromosomes role in promoting sexual dimorphism evolution. Our findings reveal the significant contributions of SV to genome evolution, specifically through their influence on sex chromosome evolution and the evolutionary dynamics of sex-biased genes.

evolutionary biology↗

bioRxiv2025

The first chromosomal-level genome assembly of an allotetraploid oyster

Tetraploid oysters are used to cross with diploids to produce triploid oysters that have become an important part of the oyster aquaculture industry worldwide. Although most tetraploid oysters are artificially induced autotetraploids, allotetraploids can be produced between closely related species, providing new opportunities for polyploid breeding and studying genome interactions. Using PacBio sequencing, Illumina sequencing, and high-throughput chromosome conformation capture scaffolding, we assembled the first high-quality genome assembly of an artificially induced allotetraploid between the Pacific oyster Crassostrea gigas and Portuguese oyster Crassostrea angulata. The assembled genome is 1.23 Gb, with a contig N50 of 2.56 Mb and a scaffold N50 of 57.22 Mb, and anchored to 20 chromosomes. The assembly contains 58,330 protein-coding genes, 98.34% of which are functionally annotated. The heterozygosity and the ratio of repetitive sequences is 5.50% and 46.43%, respectively. This chromosomal-level genome assembly of an allotetraploid oyster provides a valuable genetic resource for studying genome biology of molluscs and for advanced breeding of polyploids that are critical for the oyster aquaculture industry.

genomics↗

bioRxiv2025

Optimizing Metagenome Analysis for Early Detection of Colorectal Cancer: Benchmarking Bioinformatics Approaches and Advancing Cross-Cohort Prediction

Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2,053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent dynamic patterns of microbial signatures are the fundamental for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability, advances the application of non-invasive approaches for the early screening and prevention of CRC.

bioinformatics↗

bioRxiv2025

Synergistic RAS-MAPK and AKT Activation in MYC-Driven Tumors via Adjacent PVT1 Rearrangements

MYC-driven (MYC+) cancers are aggressive and often fatal. MYC dysregulation is a key event in these cancers, but overexpression of MYC alone is not always enough to cause cancer. Plasmocytoma Variant Translocation 1 (PVT1), a long non-coding RNA (lncRNA) adjacent to MYC on chromosome 8 is a rearrangement hotspot in many MYC+ cancers. In addition to being co-amplified with MYC, the genomic rearrangement at PVT1 involves translocation, which has had obscure functional consequences. We report that translocation at the PVT1 locus cause asymmetric enrichment of 5-PVT1 and loss of 3-PVT1. Despite being classified as a non-coding RNA, the retained 5 region of PVT1 generates a circular RNA (CircPVT1) that codes for the novel peptide we call Firefox (FFX). FFX augments AKT signaling and synergistically activates MYC and mTORC1 in these cells. Further, the 3 end of PVT1, which is lost during the translocation, codes for a tumor-suppressing micropeptide we named as Honeybadger (HNB). We demonstrate that HNB interacts with KRAS and disrupts the activation of KRAS effectors. Loss of HNB leads to activation of RAS/MAPK signaling pathway, and enhances MYC stability by promoting phosphorylation of MYC at Ser62. These findings identify PVT1 as a critical node that synchronizes MYC, AKT, and RAS-MAPK activities in cancer. Our study thus identifies a key mechanism by which rearrangements at the PVT1 locus activate additional oncogenic pathways that synergize with MYC to exacerbate the aggressiveness of MYC+ cancers. This newfound understanding explains the poor prognosis associated with MYC+ cancers and offers potential therapeutic targets that could be leveraged in treatment strategies for these cancers.

cancer biology↗

bioRxiv2025

Structure-based analysis unveils co-origin of LPOR and nitrogenase-like proteins

Structures of nitrogenases, dark-operative protochlorophyllide oxidoreductases, and light-dependent protochlorophyllide oxidoreductases (LPOR) have been resolved. However, their evolutionary relatedness remains elusive. Here, we show, through structural alignment, that all subunits of nitrogenase-like proteins originated from a co-ancestral archaic one-subdomain precursor. LPOR evolved from the BchX/BchY subunits of nitrogenase-like chlorophyllide a oxidoreductase (COR), and the intermediary retinol dehydrogenase through possible genetic recombination. We thus establish previously unknown structural links among key enzymes involved in biological nitrogen-fixation (BNF) and photosynthesis, unraveling structure-guided functional evolution from a single-subunit iron protein to multi-subunit nitrogenase-like COR, and to the single-subunit LPOR for phototrophic metabolism via bacteriochlorophyll, retinal, and chlorophyll. This work also demonstrates structural similarities are imperative for inferring distant origins of functionally divergent proteins, particularly those lacking primary amino-acid sequence identity. Moreover, our findings coupled with AI may be exploited to design innovative light-driven CORs and/or light-utilizing nitrogenases with enhanced efficacy of photosynthesis and BNF. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/634645v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@9f9a2aorg.highwire.dtl.DTLVardef@4243ecorg.highwire.dtl.DTLVardef@796b4corg.highwire.dtl.DTLVardef@17373da_HPS_FORMAT_FIGEXP M_FIG C_FIG Video abstracthttps://www.youtube.com/watch?v=b0qBE1JMaH0 HighlightsO_LILPOR evolves from BchX and BchY subunits of the nitrogenase-like protein (NGLP) COR C_LIO_LIAll subunits of NGLPs can be traced back to the ancestral one-subdomain precursor C_LIO_LIRetinol dehydrogenase acts as a crucial intermediate in the COR to LPOR evolution C_LIO_LIStructure-based design of LUN is showcased to revolutionize protein engineering C_LI

evolutionary biology↗

bioRxiv2025

DNA G-quadruplex Profiling Reveals Functional and Mechanistic Role of G-quadruplexes in Skeletal Muscle Stem Cells

DNA G-quadruplexes (G4s) are non-canonical secondary structures formed in guanine-rich DNA sequences and play important roles in modulating biological processes through a variety of gene regulatory mechanisms. Emerging G4 profiling permits global mapping of endogenous G4 formation. Here in this study, we map the G4 landscapes in adult skeletal muscle stem cells (MuSCs) which are essential for injury induced muscle regeneration. Throughout the myogenic lineage progression of MuSCs from quiescent to activated and further differentiated cells, we uncover dynamic endogenous G4 formation with a pronounced G4 induction when MuSCs become activated and proliferating. We further demonstrate that the G4 induction promotes MuSC activation thus the regeneration process. Mechanistically, we found that promoter associated G4s regulate gene transcription through facilitating chromatin looping. Furthermore, we found that G4 sites are enriched for transcription factor (TF) binding events in activated MuSCs; MAX binds to G4 structures to synergistically facilitate chromatin looping and gene transcription thus promoting MuSC activation and regeneration. The above uncovered global regulatory functions/mechanisms are further dissected on the paradigm of Ccne1 promoter, demonstrating Ccne1 is a bona fide G4/MAX regulatory target in activated MuSCs. Altogether, our findings for the first time demonstrate the prevalent and dynamic formation of G4s in adult MuSCs and the mechanistic role of G4s in modulating gene expression and MuSC activation/proliferation.

molecular biology↗

bioRxiv2025

Variation analysis of fruit phenotypic traits of different provenances of ancient Cinnamomum camphora in Jiangxi Province of China

Exploring fruit phenotypic diversity of different provenances of ancient Cinnamomum camphora in Jiangxi Province of China, it will provide a theoretical basis for the collection, selection and improvement of germplasm resources. Taking the naturally distributed ancient Cinnamomum camphora in 45 counties of 11 cities in Jiangxi Province as the research object, nested ANOVA, Pearson correlation analysis, principal component analysis and other methods were used to statistically analyze 10 phenotypic traits such as fruit thousand-grain weight, fruit volume, fruit side diameter, fruit horizontal diameter, fruit vertical diameter, and peel thickness in different provenances. The resuit was as follows. (1) The fruit phenotypic traits of ancient Cinnamomum camphora in Jiangxi Province were rich in variation among and within provenances, and the variation among provenances was the main source of phenotypic variation. The mean value of phenotypic differentiation coefficient among provenances was 80.1%. The coefficients of variation of fruit phenotypic traits among different provenances was ranged from 2.64% to 25.45%, with the largest coefficient of variation for peel thickness. The mean value of coefficient of variation among provenances(9.65%) was larger than that within provenances(8.52%). (2) Significant or highly significant correlations were existed among the fruit phenotypic traits of ancient Cinnamomum camphora in Jiangxi Province. Fruit thousand-grain weight was significantly positively correlated with fruit volume, fruit side diameter, fruit horizontal diameter, fruit vertical diameter, peel thickness, fruit side diameter-fruit horizontal diameter ratio, fruit side diameter-fruit vertical diameter ratio, fruit horizontal diameter-fruit vertical diameter ratio (P<0.05), while fruit horizontal diameter and fruit vertical diameter were significantly negatively correlated with fruit thousand-grain weight to fruit volume ratio(P<0.05). (3) There was a significant correlation between fruit phenotypic traits of ancient Cinnamomum camphora and latitude, longitude and climate factors in Jiangxi Province. Among them, fruit thousand-grain weight and fruit volume were highly significant negatively correlated (P<0.01) with annual average sunshine duration and mean temperature in July, and highly significant positively correlated with mean temperature in January and mean altitude factor (P<0.01). (4) The cumulative variance contribution of the first three principal components in the principal component analysis reached 78.78%, and the fruit side diameter, fruit side diameter-fruit vertical diameter ratio, and fruit side diameter-fruit horizontal diameter ratio could comprehensively reflect the information and ranking of the 10 traits. (5) In the cluster analysis, it was divided into two groups A and B at the distance coefficient of 1.2, and further divided into different subgroups at the distance coefficient of 0.9. The fruit morphology indexes from subgroup B2 were bigger. In conclusion, fruit phenotypic traits of ancient Cinnamomum camphora in Jiangxi Province were rich in variation, and the variation of among provenances was more than within provenances. At the same time, there was a certain geographic variation pattern of the phenotypic traits of Cinnamomum camphora. The results would provide an important direction for the selection and breeding of excellent germplasm resources in Jiangxi Province, China.

plant biology↗

bioRxiv2025

Glycosylphosphatidylinositol biosynthesis restricts coronavirus infection via the regulation of LY6E

Coronaviruses, including SARS-CoV-2, rely on host factors for their replication and pathogenesis, while hosts deploy defense mechanisms to counteract viral infections. Although numerous host proviral factors have been identified, the landscape of host restriction factors and their underlying mechanisms remain less explored. Here, we conducted genome-wide CRISPR knockout screens using three distinct coronaviruses--SARS-CoV-2, HCoV-OC43 (a common cold human virus from the genus Betacoronavirus) and porcine epidemic diarrhea virus (Alphacoronavirus) to identify conserved host restriction factors. We identified glycosylphosphatidylinositol (GPI) biosynthesis as the pan-coronavirus host factor that restrict viral entry by disrupting spike protein-mediated membrane fusion at both endosomal and plasma membranes. GPI biosynthesis generates GPI moieties that covalently anchor proteins (GPI-anchored proteins [GPI-APs]) to the cell membrane, playing essential roles in various cellular processes. Through focused CRISPR knockout screens targeting 193 GPI-APs, we identified LY6E as the key downstream effector mediating the antiviral activity of the GPI biosynthesis pathway. These findings reveal a novel role for GPI biosynthesis as a conserved host defense mechanism against coronaviruses and highlight LY6E as a critical antiviral effector. This study provides new insights into virus-host interactions and the development of host-directed antiviral therapies.

microbiology↗

bioRxiv2025

Multi-Omics Analysis of Wound Microbiome and Staphylococcus aureus in Pressure Ulcer

This study employs a multi-omics approach to investigate the wound microbiome and Staphylococcus aureus in pressure ulcers. Metagenomic sequencing and associated technologies were utilized to examine bacterial populations, identify dominant species, and study biofilm formation in S. aureus through metabolomic and proteomic characteristics. The results revealed a significant reduction in microbial diversity in pressure ulcer samples compared to controls, with Staphylococcus, Corynebacterium, and Klebsiella being the most prevalent genera. Functional prediction analysis indicated differences in pathogenic invasiveness and biofilm formation factors among the groups. The presence of antimicrobial resistance genes was higher in the pressure ulcer group, particularly in Staphylococcus spp. strains. Whole-genome sequencing of 29 S. aureus isolates identified various clonal complexes and spa types, with the majority possessing genes conferring resistance to {beta}-lactam antimicrobials and virulence factors. Histopathological examination and fluorescent in situ hybridization confirmed the presence of S. aureus in biofilm structures. In vitro biofilm formation tests and metabolomic and proteomic analyses provided insights into the interactions between S. aureus strains and their biofilm formation, revealing enriched pathways related to metabolic processes and membrane composition. This research offers a scientific foundation for understanding the colonization patterns of S. aureus biofilms in pressure ulcer wounds.

microbiology↗

bioRxiv2025

Knockoff procedure improves causal gene identifications in conditional transcriptome-wide association studies

Transcriptome-wide association studies (TWASs) have been developed to nominate candidate genes associated with complex traits by integrating genome-wide association studies (GWASs) with expression quantitative trait loci (eQTL) data. However, most existing TWAS methods evaluate the marginal association between a single gene and the trait of interest without accounting for other genes within the same genomic region or the same gene from different tissues. Additionally, false-positive gene-trait pairs can arise due to correlations with the direct effects of genetic variants. In this study, we introduce TWASKnockoff, a new knockoff-based framework for detecting causal gene-tissue pairs using GWAS summary statistics and eQTL data. Unlike marginal testing in traditional TWAS methods, TWASKnockoff examines the conditional independence for each gene-trait pair, considering both correlations in cis-predicted expression across genes and correlations between gene expression levels and genetic variants. TWASKnockoff estimates the theoretical correlation matrix for all genetic elements (cis-predicted expression across genes and genotypes for genetic variants) by averaging estimations from parametric boot-strap samples and then performs knockoff-based inference to detect causal gene-trait pairs while controlling the false discovery rate (FDR). Through empirical simulations and an application to type 2 diabetes (T2D) data, we demonstrate that TWASKnockoff achieves superior FDR control and improves the average power in detecting causal gene-trait pairs at a fixed FDR level.

genetics↗

bioRxiv2025

Cortical astrocyte activation triggers meningeal nociception and migraine-like pain

Migraine attacks are believed to originate in the brain, but the exact mechanisms by which the brain generates peripheral nociceptive signals that drive migraine pain remain unclear. Sensory cortex hyperexcitability has been observed consistently across different migraine subtypes. Astrocytes detect aberrant increases in cortical activity via their Gq-coupled receptors and respond by releasing gliotransmitters and other factors with proinflammatory and nociceptive properties. In the present study, we used a rat model to investigate whether heightened cortical astrocyte Gq-coupled signaling is sufficient to drive peripheral trigeminal meningeal nociceptive responses linked to the generation of migraine headaches. We used an AAV-based chemogenetic approach that allows selective activation of cortical astrocyte Gq-GPCR signaling. We targeted astrocytes in the visual cortex as hyperexcitability in this region has been implicated in migraine. Furthermore, the meninges overlying the visual cortex are densely innervated by nociceptive fibers. We combined this chemogenetic approach with in vivo single-unit recording of meningeal nociceptors to assess changes in their ongoing activity and mechanosensitivity, along with testing of migraine-like behaviors. We further targeted calcitonin gene-related peptide (CGRP), using a monoclonal antibody (anti-CGRP mAb), to assess the relevance of cortical astrocyte activation to migraine. We discovered that heightened activation of Gq-coupled signaling in visual cortex astrocytes drives persistent discharge and increased mechanosensitivity of meningeal nociceptors. Cortical astrocytic activation also generated cephalic mechanical pain hypersensitivity, reduced exploratory behavior, and anxiety-like behaviors linked to migraine headaches. Blocking calcitonin gene-related peptide signaling suppressed astrocyte-mediated increases in meningeal nociceptor discharge and alleviated associated migraine-related behaviors. Our findings reveal a previously unappreciated role for augmented visual cortex astrocyte signaling as a triggering factor sufficient to generate meningeal nociception and migraine pain and greatly expand our understanding of migraine pathophysiology.

neuroscience↗

bioRxiv2025

DAZAP2 functions as a pan-coronavirus restriction factor by inhibiting viral entry and genomic replication

The SARS-CoV-2 pandemic and the emergence of novel variants underscore the need to understand host-virus interactions and identify host factors that restrict viral infection. Here, we perform a genome-wide CRISPR knockout screen to identify host restriction factors for SARS-CoV-2, revealing DAZAP2 as a potent antiviral gene. DAZAP2, previously implicated in SARS-CoV-2 restriction, is found to inhibit viral entry by blocking virion fusion with both endolysosomal and plasma membranes. Additionally, DAZAP2 suppresses genomic RNA replication without affecting the primary translation of viral replicases. We demonstrate that DAZAP2 functions as a pan-coronavirus restriction factor across four genera of coronaviruses. Importantly, knockout of DAZAP2 enhances SARS-CoV-2 infection in mouse models and in human primary airway epithelial cells, confirming its physiological relevance. Mechanistically, antiviral activity of DAZAP2 appears to be indirect, potentially through the regulation of host gene expression, as it primarily localizes to the nucleus. Our findings provide new insights into the host defense system against coronaviruses and highlight DAZAP2 as a potential target for host-directed antiviral therapies. IMPORTANCEDuring viral infection, the host defense response is mediated by a variety of host factors through distinct mechanisms that have yet to be fully elucidated. Although DAZAP2 was previously implicated in SARS-CoV-2 restriction, its mechanisms of action and in vivo relevance remain unclear. In this study, we identify the DAZAP2 as a potent pan-coronavirus restriction factor that inhibits viral infection through dual mechanisms: blocking virion fusion with both endolysosomal and plasma membranes, and suppressing genomic RNA replication. We confirm its physiological relevance in host defense using mouse models and primary cell cultures. This study advances our understanding of host-pathogen interactions. Targeting DAZAP2 or its regulatory pathways could provide a new approach to enhance host defense against current and future coronavirus threats.

microbiology↗

bioRxiv2025

Novel Pipelines to Extract Differences in Proteome Dynamics Based on Health Status

Understanding dynamics and co-regulatory patterns in the human proteome is a promising path for unraveling the molecular basis of health and disease. Nevertheless, there remains an open challenge in extracting concise information from high-throughput proteomic data that can effectively characterize and predict health. We develop novel statistical and computational pipelines to tackle this problem in a longitudinal saliva proteomics data set collected throughout the awakening response in six healthy controls and six subjects with severe mitochondrial disease (MitoD), a clinical condition caused by genetic mitochondrial defects that affects cellular energy transformation and alters multiple dimensions of health. We undertook three independent unsupervised approaches to characterize proteome dynamics and assessed their ability to separate MitoD individuals from controls. First, we designed a permutation test to detect the global difference in the proteomic co-regulation structure between healthy and unhealthy subjects. Second, we performed non-linear embedding and cluster analysis on elasticity to capture a more complicated relationship between health and the proteome. Third, we developed a machine learning algorithm to extract low-dimensional representations of the proteome dynamic and use them to cluster subjects into healthy and unhealthy groups without any knowledge of their true status. All three methods showed clear differences between MitoD individuals and controls. Our results revealed a significant and consistent association between MitoD status and the saliva proteome at multiple levels during the awakening response, including its dynamic change, co-regulation structure, and elasticity. This connection is not restricted to a few MitoD-specific proteins but spreads over a wide range of proteins from many body functions and pathways. Pipelines such as those shown here are the first step toward establishing interpretable and accurate prediction rules for health based on proteome dynamics.

bioinformatics↗

bioRxiv2025

Endothelial Slit2 guides the Robo1-positive sympathetic innervation during heart development

Axon guidance cues direct nerves in the heart during development, disease and regeneration. These cues determine cardiac innervation patterning by regulating the balance between chemo-attraction and chemo-repulsion. However, the role of one of the most crucial ligand-receptor combinations among axon guidance molecules, the Slit chemo-active ligands and their Roundabout (Robo) transmembrane receptors, remains unknown during cardiac innervation patterning. To test if Slit-Robo signalling is important for cardiac innervation guidance, we analysed Slit and Robo mouse knock-outs. Constitutive Slit2-/- ventricles showed significantly reduced innervation, while Slit3-/- hearts showed temporary increased levels of innervation compared to wild-type littermate controls. Whereas innervation was not affected in Robo2-/- mice, the phenotype seen in Slit2-/- ventricles was recapitulated in Robo1-/- mice. Detailed expression analysis identified expression of Slit2 ligand in the endothelium of the coronary vessels, while Slit3 was highly present in the coronary smooth muscle wall and in the innervation. Both the Robo1 and Robo2 receptors were present in the nerves and at low levels in the vessels. Knocking out Slit2 specifically in the endothelium recapitulated the defects seen in the constitutive Slit2-/- hearts. Ex vivo axon guidance cultures showed that attraction of axons extending from the ganglia was strongly reduced in ventricles with absence of endothelial Slit2 compared to wild-type controls. In absence of endothelial Slit2, adult mice showed reduced response to challenging the sympathetic innervation. In conclusion, we have identified an important new chemo-active Slit2-Robo1 pathway required for correct cardiac innervation development.

developmental biology↗

bioRxiv2025

Extracellular stiffness regulates site-specific lung development

Extracellular matrix (ECM) stiffness plays a crucial role in regulating cell fate and maturation, but its influence on lung development is limited known. Here we utilized stiffness-tunable gelatin methacryloyl (GelMA) hydrogels to investigate how ECM stiffness influences site-specific lung development in a stem cell-derived lung organoid model. We found increased stiffness promoted NKX2-1+ lung progenitor cells (LPCs) generation. In airway organoids (hAWOs), stiff hydrogels directed proximal airway differentiation enriched with goblet, ciliated, and basal cells; whereas the decreased stiffness favored emergence of secretory cells in the proximal-distal transition zone and distal airway. In alveolar organoids (hALOs), increased stiffness enhanced AT2 and AT1 cells transition. Moreover, infection assays with Omicron BA.1.1 and Delta variants recapitulated the proximal-to-distal tropism of SARS-CoV-2 in the lung. Transcriptomic sequencing revealed ECM stiffness regulates lung development via Hippo, TGF-{beta}, HIF and Wnt pathways. These findings advance mechanism understanding of ECM stiffness on lung development and provide a novel mechanical regulation for generating site-specific lung organoids.

cell biology↗

bioRxiv2025

Flaviviruses Hijack HuR to Suppress CNPY3: A Novel Pathway for Immune Evasion and Therapeutic Intervention

Flaviviruses represent a serious global health threat, infecting millions annually with high rates of cross-infection among different flaviviruses, yet no broad-spectrum antiviral therapy currently targets these pathogens. Through biological big data analysis, we observed a significant downregulation of Canopy FGF Signaling Regulator 3 (CNPY3), a positive regulator of defense responses, in flavivirus-infected patients, with the level of downregulation correlating with infection severity. This observation was validated in cellular and animal models. Mechanistically, we demonstrate that flaviviruses hijack the RNA-binding protein Human antigen R (HuR) to destabilize CNPY3 mRNA via adenine-uridine-rich elements (AREs), thus downregulating CNPY3 expression and promoting viral replication. Our findings identify CNPY3 as a novel antiviral mediator essential for the TLR-mediated type I interferon (IFN-I) pathway in defense against flaviviruses. In vitro, CNPY3 overexpression reduced DENV and ZIKV replication, confirming its antiviral role. To explore therapeutic potential, we developed lipid nanoparticles (LNPs) encapsulating CNPY3 mRNA (LNP-CNPY3), and early administration in flavivirus-infected mice improved survival, reduced viral loads, and attenuated neuroinflammation by enhancing antiviral and interferon responses. Together, these findings establish CNPY3 as a critical antiviral target and support LNP-CNPY3 as a promising therapeutic approach against flavivirus infections.

microbiology↗

bioRxiv2024

Single-cell RNA sequencing analysis reveals new insights for intersex gonad initiation and early sex differentiation of goats

Polled intersex syndrome in goats severely impacts productivity and economic benefits, serving as a potential model for human reproductive defects. However, its specific molecular and cellular regulatory mechanisms remain unclear. This study combined single-cell RNA-sequencing (scRNA-seq) with tissue morphology and immunofluorescence detection to investigate the cellular heterogeneity, pseudo-time differentiation trajectory, differentially expressed genes, and regulatory networks of female, intersex, and male gonads during the 55-65 days embryonic stage of goats. The results indicated significant heterogeneity and cell fate transition in the somatic and germ cells of female, intersex, and male gonads at different developmental stages. Stromal cells may initiate female and intersexual gonad development, and epithelial cells may be the source of gonad cells in male fetuses. The abnormal expression of FOXL2, SOX9, AMH, DMRT1, RSPO1, INSL3, TCF21 and CSF1R may cause female-to-male sex reversal. The new candidate genes like PHLDB2, ZNRF3 and TEAD1 may contribute to the gender differentiation. Additionally, TREM2+ macrophages analogous to those in humans were identified in male gonads, while genes such as CSF1R and TYROBP potentially regulate macrophage immune privilege mechanisms. Early gonadal development in goats may also be regulated by circadian rhythm mechanisms similar to humans, with genes such as NR1D1, LGR4, and ATG5 involved in granulosa cell development, while genes such as ATG5, NRIP1, and FBXW11 may affect intersex trait development. In general, this study provided an important reference for exploring molecular and cellular mechanisms of intersex initiation during early embryonic development in goats and also for modelling human reproductive defects. Author summaryIn this study, we investigated the cell fate trajectory and key gene expression profile of goat fetus gonads using scRNA-seq. The analysis revealed cellular heterogeneity among normal male, normal female, and intersex gonadal somatic and germ cells, alongside their dynamic fate transitions across various developmental states. Pseudo-time trajectory analysis suggested that stromal cells might act as the initiation signal for female and intersexual gonad development, while epithelial cells could serve as the primary source of gonadal cells in male fetal goats. GO functional enrichment and KEGG analyses confirmed that abnormal expression of FOXL2, SOX9, AMH, DMRT1 and RSPO1 was linked to the emergence of intersexual gonads. Newly identified candidate genes including LRP2, PITX2, ARX, LHX9, PHLDB2, ZNRF3 and TEAD1 may contribute to sex-specific differences, while INSL3 and TCF21 could be linked to intersexual gonads. We identified TREM2+ macrophages analogous to those in humans, which could regulate immune privilege mechanisms. Circadian rhythmic changes were observed during early goat gonadal development.

developmental biology↗

bioRxiv2024

KAT8 facilitates the proliferation of cancer cells through enhancing E7 function in HPV-associated cervical cancer

Persistent human papillomavirus (HPV) infection serves as the principal etiological factor in cervical cancer, with the oncoprotein E7, encoded by the virus, playing a key role in tumorigenesis. Despite this, targeted therapeutic strategies against E7 remain underexplored. KAT8, a lysine acetyltransferase, significantly contributes to oncogenesis through the regulation of transcription. However, its involvement in cervical cancer remains inadequately characterized. This study employs HPV18-positive HeLa and HPV16-positive SiHa cell lines to investigate how KAT8 modulates E7 expression and function in cervical cancer cells. Upon KAT8 knockdown, a marked reduction in cell viability is observed, alongside a downregulation of E7 expression. This is associated with elevated levels of retinoblastoma protein (pRb) and decreased E2F1 expression, indicating that KAT8 depletion inhibits E7 expression, resulting in E2F1 inactivation and cell cycle arrest. Furthermore, KAT8 is found to directly bind to the promoter regions of the HPV18 LCR, enhancing transcription of the HPV18 E7 gene. This study also demonstrates that KAT8 is essential for the acetylation of E7, and plays a critical role in facilitating the interaction between pRb/E2F1 and E7 in cervical cancer cells. In conclusion, these results highlight KAT8 as a key driver of cervical cancer progression, promoting HPV E7 expression and its associated oncogenic signaling pathways.

cancer biology↗