Biology subjects

Zhou, Q.

Publications and source records attributed to Zhou, Q..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Comparison of QuPath and HALO platforms for analysis of the tumor microenvironment in prostate cancer

QuPath, an open-source digital pathology platform, has gained widespread use for image analysis in biomedical research since its release in 2016. However, its reproducibility and reliability compared to commercial software, such as HALO, requires further validation, particularly for multiplex immunofluorescence (mIF) analysis. In this study, we performed a direct comparison of QuPath and HALO using a mIF-stained prostate cancer tissue microarray (TMA) inclusive of 192 unique cores. We evaluated performance across three key analytical modules: immune cell phenotyping, tumor infiltration with immune cells, and nearest neighbor analysis. Furthermore, we integrated QuPath with CytoMap, an open-source spatial analysis tool, to perform unsupervised clustering of immune cell infiltration--a feature not available in HALO. Our results demonstrated high concordance between two platforms, with correlation coefficients exceeding 0.89 for immune cell density, distance and pattern of cell organization in tumor microenvironment (TME). A neighborhood analysis using CytoMap was further performed and provided a more detailed spatial analysis of immune cell distribution across different prostate cancer grades. A significant increase of CD103+ T cell infiltration into TME was observed in prostate cancer, which might be associated with the expression level of its ligand (E-cadherin) in the tumor region. In conclusion, our findings validate QuPath as a robust and reproducible alternative to commercial platforms for fluorescence-based digital pathology. By demonstrating QuPaths capability to perform high-quality quantitative analysis with additional flexibility for integration with external tools, our study underscores its potential for advancing tumor microenvironment research in translational oncology.

pathology↗

bioRxiv2025

Vitamin D regulates olfactory function via dual transcriptional and mTOR-dependent translational control of synaptic proteins

Vitamin D (VitD) deficiency, affecting over 1 billion people worldwide, is associated with neurological dysfunction, but its cell-type-specific neural mechanisms remain unclear. Using a dietary mouse model, we show that VitD bidirectionally regulates olfactory acuity: deficiency impairs odor discrimination, while supplementation enhances sensitivity. Single-nucleus and spatial transcriptomics pinpoint selective vitamin D receptor (VDR) expression in olfactory bulb (OB) tufted cells, where it drives synaptic protein expression. Genetic VDR knockdown replicates deficiency-associated olfactory deficits, establishing VDR as essential for synaptic and translational regulation. Notably, we identify mTOR-mediated protein synthesis as a critical convergence point--pharmacological mTOR inhibition (rapamycin) rescues synaptic protein deficits and behavioral impairments in VitD-deficient mice. These findings delineate a noncanonical VDR-mTOR-translational axis--complementing conventional transcriptional regulation--through which VitD serves as a nutrient-sensitive neuromodulator that integrates dietary status with synaptic functions and sensory processing. Our study expands the physiological role of VitD beyond traditional endocrine signaling and reveals mechanistic insights that may inform novel therapeutic strategies for neurological and psychiatric conditions associated with VitD deficiency.

neuroscience↗

bioRxiv2025

Efficient packaging of HIV-1 genomes via recognition of its adenosine-rich content by a heterologous RNA-binding domain

The HIV-1 genome (gRNA) has an unusually biased nucleotide content and is rich in adenosines. Selective packaging of the gRNA is thought to be driven by specific binding of the nucleocapsid (NC) domain of the viral Gag protein to the packaging signal ({Psi}) in the host cell cytosol. However, deletion of regions within {Psi} reduces--but does not completely abolish--genome packaging. To probe whether another feature of the gRNA may contribute to the selective gRNA packaging process, we replaced NC with heterologous RNA-binding domains (RBDs) with distinct RNA-binding properties. Surprisingly, despite disparate RNA binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition in the cytosol is not rate limiting. Notwithstanding, many chimeras exhibiting G/C binding specificity were arrested at the assembly stage. Only the Gag-SRSF5 chimera, which multimerized efficiently on adenosine-rich sequences on the gRNA, assembled efficiently and packaged gRNA at near wild-type levels. Importantly, rationally designed mutations that altered the A/G-rich binding specificity of Gag-SRSF5 decreased genome encapsidation efficiency. Furthermore, many Gag chimeras displayed potent dominant negative activities, highlighting NC functions as a targetable step in virus replication. Together, our findings reveal an unexpected aspect of the HIV-1 gRNA, its biased nucleotide content, as a key driver of selective genome packaging. SIGNIFICANCEHow HIV-1 selectively packages its genome (gRNA) into virions is poorly understood. To probe this, we replaced the viral nucleocapsid (NC) protein with heterologous RNA-binding domains (RBDs) from cellular hnRNP and SR protein families. Remarkably, despite their distinct RNA-binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition is not rate limiting. Only the Gag-SRSF5 chimera packaged gRNA efficiently which correlated with its capacity to multimerize on adenosine-rich sequences on the gRNA. Notably, several Gag chimeras exhibited strong dominant negative effects, underscoring NC functions as a targetable step in virus replication. Together, these findings uncover that the biased nucleotide content of the HIV-1 gRNA facilitates its selective packaging into virus particles.

microbiology↗

bioRxiv2025

Dual MYC and GSPT1 Protein Degrader for MYC-Driven Cancers

Direct targeting of the oncoprotein MYC has long been attempted in cancer therapy, with limited success. We here identify a novel co-regulatory feedback loop of MYC and G1 to S phase transition protein 1 (GSPT1), where MYC promotes transcription of GSPT1, and GSPT1 senses stop codon of MYC to promote its translation. We report on the first-in-class dual MYC/GSPT1 protein degrader, GT19630. GT19630 significantly induced integrated stress response, abrogated oxidative phosphorylation through inhibition of the TCA cycle and induced cell death. Protein degradation of MYC was critical for efficacy of GT19630. GT19630 induced profound anti-proliferative effects and apoptosis agnostic to TP53 in a broad range of cancer cells, and is highly active in vivo in multiple, therapy-resistant hematologic and solid tumor models. Dual MYC/GSPT1 degradation was well tolerated in humanized CrbnI391V mice. In conclusion, we propose a novel treatment approach by directly targeting the MYC-GSPT1 axis in MYC-driven cancers. Statement of significanceMYC has been considered an undruggable protein. We found a targetable, novel positive co-regulatory feedback of MYC and GSPT1, a key translation terminator. The dual MYC/GSPT1 degrader GT19630 is highly active in MYC-driven tumors, with moderate effects on humanized Crbn mice, providing opportunities to improve treatment outcome of MYC-driven cancers.

cancer biology↗

bioRxiv2025

Disturbing immune homeostasis by neutrophil loss of Uba1 induces VEXAS-like autoinflammatory disease in mice

ObjectiveVEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is an identified haemato-rheumatoid disease caused by somatic UBA1 mutations in hematopoietic stem cells. We report Uba1 loss in various mouse hematopoietic cell types leads to diverse effects, with approximately 70% Uba1 depletion in neutrophils inducing non-lethal VEXAS-like symptoms. MethodsUsing nine different Cre/flox-mediated conditional-knockout (CKO) models, we interrogated the phenotypes caused by hematopoietic loss of Uba1. Neutrophil-specific depletion of Uba1 were validated and VEXAS-like phenotypes were examined. ResultsUba1 loss in HSCs induces extensive hematopoietic cell death while in B or T cells, or megakaryocytes induces corresponsive cell death but these mutants appear normal. Uba1 loss in monocytes and neutrophils failed to induce cell death and the mutants are viable. Among the models, only Uba1 loss in neutrophils manifests autoinflammatory symptoms including increased counts and percentage of neutrophils, increased proinflammatory cytokines, vacuoles in myeloid cells and dermatitis. Residual Uba1 is about 30% in the mutant neutrophils, which manifest disturbed cellular hemostasis. Genetic loss of Morrbid partially mitigated the VEXAS-like symptoms. ConclusionOur study reveals diverse effects of Uba1 loss in hematopoietic cells and establishes a VEXAS-like murine model, facilitating understanding and potential treatments for this syndrome prevalent in aged men. HIGHLIGHTSO_ST_ABSWHAT IS ALREADY KNOWN ON THIS TOPICC_ST_ABSVEXAS syndrome is a recently identified hematological and immunological disease prevalent in adult man but rarely in adult woman. Somatic mutations in the E1-enzyme encoding gene UBA1 in hematopoietic stem cells is the driver on the top of the genetic etiology of the disease. However, the major pathogenic cell type(s) for VEXAS syndrome has not been experimentally examined and mouse models recapitulating the disease are lacking. WHAT THIS STUDY ADDSO_LIUsing nine different conditional-knockout (CKO) murine models, we interrogated the pleiotropic phenotypes caused by loss of the ubiquitin activation enzyme Uba1 in different hematopoietic cell types; C_LIO_LIOur results demonstrated that among the nine tested CKO mutants, only neutrophil loss of Uba1 results in VEXAS-like autoinflammatory disease; C_LIO_LIThe VEXAS-like symptoms in the S100a8Cre-CKO mutant mice include: increased counts of white blood cells and neutrophils, increased percentage of neutrophils, increased serum level of proinflammatory cytokines (IL-1{beta}, IL-6 and TNF), observation of vacuoles, increased survival, and increased phagocytosis in mutant neutrophils; C_LIO_LIPharmacological treatments with IL-1 inflammatory pathway inhibitors Anakinra or Canakinumab or genetic loss of the myeloid pro-survival regulator Morrbid partially mitigated the VEXAS-like symptoms in the S100a8Cre-CKO mutants; C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYThe study reports a technical strategy of developing the murine models for VEXAS syndrome. In addition, the study dissects cellular and molecular mechanisms, especially the cell-type-dependent tolerance and pathogenicity of loss of function of Uba1, for the occurrence of the autoinflammation diseases in mice. The study provides translational implications in etiology and potential treatment choices for the newly-identified haemato-rheumatoid syndrome in clinical management.

immunology↗

bioRxiv2025

Glial betaPix is essential for blood vessel integrity in the zebrafish brain

The formation of blood-brain barrier and vascular integrity depends on the coordinative development of different cell types in the brain. Previous studies have shown that zebrafish bubblehead (bbh) mutant, which has mutation in the betaPix locus, develops spontaneous intracerebral hemorrhage during early development. However, it remains unclear in which brain cells betaPix may function. Here, we established a highly efficient conditional knockout method in zebrafish by using homology-directed repair (HDR)-mediated knockin and knockout technology, and generated betaPix conditional trap (betaPixct) allele in zebrafish. We found that betaPix in glia, but neither neurons, endothelial cells, nor pericytes, was critical for glial and vascular development and integrity, thus contributing to the formation of blood-brain barrier. Single-cell transcriptome profiling revealed that microtubule aggregation signaling stathmins and pro-angiogenic transcription factors Zfhx3/4 were down-regulated in glial and neuronal progenitors, and further genetic analysis suggested that betaPix may act upstream on the PAK1-Stathmin and Zfhx3/4-Vegfaa signaling to regulate glia migration and angiogenesis. Therefore, this work reveals that glial betaPix plays an important role in brain vascular development in zebrafish embryos and possibly human cells.

developmental biology↗

bioRxiv2025

Gene traffic mediated by transposable elements shaped the dynamic evolution of ancient sex chromosomes of varanid lizard

Lizards exhibit rapid turnovers and a much greater diversity of sex determination mechanisms compared to birds and eutherians. This makes the conserved ZW sex chromosomes of anguimorph lizards originated over 115 million years ago a seeming exception. We recently discovered in an anguimorph lizard Varanus acanthurus (Vac) that its entire W chromosome (chrW), but not chrZ is homologous to part of the chr2 by cytogenetic mapping, suggesting a complex history of its sex chromosome evolution yet to be elucidated. To address this, we assembled a chromosome-level genome, and provided evidence that the Vac sex chromosome pair had undergone at least three times of recombination suppression, forming a similar pattern of evolutionary strata to that of birds or mammals. We identified the putative sex-determining genes in the oldest evolutionary stratum that had first lost recombination. Comparison to other lizard genomes dated the stepwise propagation of specific retrotransposon subfamilies shared by chrW and chr2 to the varanid ancestor. These retrotransposons are also enriched near the duplicated genes shared by the two chromosomes and probably mediated the recruitment of many autosomal genes that rejuvenated the degenerating chrW, including members of a large vomeronasal chemosensory receptor gene family V2R. Our results challenge the canonical model of sex chromosome evolution, and suggest that the W or Y chromosome as a refugium of repetitive elements, may recurrently recruit short-lived functional genes responsible for sexual dimorphisms during its long-term course of degeneration.

evolutionary biology↗

bioRxiv2025

Cytological and preliminary genomic analysis of two Leptodactylus frog species (Anura, Leptodactylidae) with recently evolved large meiotic rings of multiple X and Y sex chromosomes

A few species have evolved multiple sex chromosome systems with more than two Xs or Ys. These involve sex chromosome-autosome translocations (sometimes called fusions as very small heterochromatic arms may be deleted), creating neo-sex chromosome systems. Among vertebrates, frogs (Anura) have the highest known number of such translocation systems. This study within the genus Leptodactylus, investigated the two species L. pentadactylus (LPE) and L. paraensis (LPA), in which large ring multivalents are seen in male meiosis, indicating translocations involving the sex chromosomes. Four other species studied do not have such rings, but they share characteristics making rearrangements less likely to be eliminated. To start understanding the formation of multivalents, we used genomic and cytogenetic methods to investigate repetitive DNA sequences, including satellite DNAs, rDNAs, and telomeric sequences, and conducted comparative genomic hybridization (CGH). The LPE genome includes a large number of satDNA families, and in situ mapping of several satDNAs individually identified eight of the ten chromosomes in its multivalent. In LPA, morphological similarities indicate that several chromosomes are shared by the multivalents of both species, and a candidate ancestral sex chromosome pair could be identified. In situ mapping in LPE suggests recent satDNA accumulation in the subtelomeric regions, which differ from those in the outgroup species, contrary to the expectation that the translocations create sex-linkage in the pericentromeric regions.

evolutionary biology↗

bioRxiv2025

SAXS reveals the molecular basis underlying pH-driven G3BP1 conformational dynamics: implications for stress granule formation

G3BP1 is the central node and molecular switch in stress granule (SG) assembly. However, structural insights into full-length G3BP1 remain elusive owing to its extensive intrinsically disordered regions (IDRs). Using size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS), we have characterized the solution architecture and conformational dynamics of full-length G3BP1. Under physiological conditions, G3BP1 adopts an elongated, head-to-head antiparallel homodimeric conformation, whereas acidification induces a pronounced conformational compaction. Subsequent biophysical studies reveal that this compact state enables robust RNA-mediated and, notably, homotypic phase separation in vitro. Deletion of the RGG region abolishes this acidity-induced compaction and markedly impairs phase separation, establishing a causal link between the RGG-dependent conformational switch and phase separation propensity. By moving beyond hypothetical models to experimental solution-state data, our work fills a longstanding void in the field and provides critical insights into the structural plasticity that underlies G3BP1 function, offering a missing structural link essential for deciphering the molecular mechanism of SG formation. We propose that stress-associated physicochemical changes, specifically localized acidification coupled with mRNA accumulation, trigger this reversible structural reconfiguration of G3BP1, thereby facilitating phase separation.

molecular biology↗

bioRxiv2025

cfMethDB: a comprehensive cfDNA methylation data resource for cancer biomarkers

Cancer is a major global health threat, and early detection of cancer is crucial for improving patient outcomes. DNA methylation in circulating cell-free DNA (cfDNA) has emerged as a promising biomarker for non-invasive cancer diagnosis. However, the integration and utilization of existing cfDNA methylation data have been limited, hindering comprehensive research efforts, especially in the discovery of cfDNA methylation biomarkers. To address this challenge, we introduce cfMethDB, a comprehensive database dedicated to cfDNA methylation in cancer that encompasses 4828 publicly available datasets. Through standardized analysis, we identified 1,048,770 differentially methylated cytosines (DMCs) as candidate biomarkers across seven cancer types. With cfMethDB, we not only identified known cfDNA methylation biomarkers, but also discovered several genes, such as ZIC4, that could be novel biomarkers. Moreover, cfMethDB offers a suite of user-friendly tools, including biomarker evaluation, pan-cancer search and end motif analysis. We hope that cfMethDB will serve as a valuable platform for the discovery of novel cancer cfDNA methylation biomarkers and will facilitate cancer research and clinical applications. cfMethDB is publicly available at: https://cfmethdb.hzau.edu.cn/home.

genomics↗

bioRxiv2025

Pangenome analyses of tea plant reveal structural variations driven gene expression alterations and agronomic trait diversification

Tea plants, one of the worlds most economically significant beverage crops, exhibit extensive genetic diversity and a rich array of secondary metabolites. While structural variations (SVs) are key drivers of phenotypic innovation, their regulatory roles in transcriptional networks and agronomic trait diversification remain underexplored in this perennial crop. We constructed a pangenome from 21 representative tea accessions and their wild relatives. Comparative analysis revealed that wild relatives harbor a greater abundance of gibberellin-related genes, whereas cultivated accessions exhibit an expansion of defense-related genes. We identified 522,428 non-redundant SVs, primarily insertions/deletions (73.56%), which were enriched in promoter regions. These SVs influenced the expression of genes governing flavor compounds, including those involved in flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions uncovered three haplotypes in the ANS3 gene promoter region, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion enhanced CtANS3 expression, increasing anthocyanin accumulation. Additionally, a 159 bp insertion in the CtLRR1 promoter reduced resistance to Colletotrichum gloeosporioides in wild relatives. Our findings underscore SVs as pivotal regulators of genomic diversity, flavor differentiation, and adaptive evolution in tea plant domestication.

genomics↗

bioRxiv2025

Structural variants contribute to the gut microbiome, blood metabolic traits and their causal relationships

Research on genetic variants affecting the gut microbiome and blood metabolites has mainly focused on single nucleotide variants (SNPs), with structural variants (SVs) remaining largely unexamined. In this study, we utilized an advanced structural variant detection pipeline on whole-genome sequencing data from 2,002 individuals with an average sequencing depth of 42 folds, identifying 138,859 high-confidence SVs, 49.57% of which were previously unreported. We performed genome-wide association studies on 22,519 common SVs with 616 gut microbial features and 121 blood metabolic traits, uncovering 30 significant links between SVs and microbial taxa/pathways and 48 connections between SVs and blood metabolites. Notable results include 19 associations reaching study-wide significance, such as an Asian-specific 6.5k deletion at the TENT2 gene, which is strongly associated with the abundance of Coprobacillus sp. 29_1 ({beta}=0.158, p=2.5x10-9), and a deletion covering HBA1/HBA2/HBM/HBQ118 linked to nine blood metabolic traits, most significantly with mean corpuscular volume (MCV; {beta}=-0.570, p=1.22x10-91). Most SVs showed a greater impact than nearby SNPs in their associations with the microbiome/metabolites. Analysis of rare SVs also identified multiple genes associated with the microbiome/metabolites. Additionally, Mendelian randomization using SVs demonstrated causal relationships, including effects from the microbiome to metabolites, such as Clostridium ramosums impact on serum uric acid and hyperuricemia, and from metabolites to the microbiome, like the influence of mean corpuscular hemoglobin concentration on MF0064: triacylglycerol degradation. This study provides a detailed SV catalog for the Chinese population and highlights the significant role of SVs in the gut microbiome, blood metabolites, and their causal relationships. HighlightsO_LIProvides a catalog of 138,859 high-confidence SVs and 49.57% of which were novel C_LIO_LIIdentify 30 genome-wide significant "SVs--microbial taxa/pathways" and 48 "SVs--blood metabolites" associations, respectively C_LIO_LIAn Asian-specific 6.5k deletion at TENT2 gene associated with the species Coprobacillus sp. 29_1 C_LIO_LIA deletion spanning HBA1/HBA2/HBM/HBQ118 associated with 9 blood metabolic traits C_LIO_LIThe majority of SVs demonstrated a more pronounced impact than neighboring SNPs in the associations with microbiome/metabolites C_LIO_LISVs help to reveal the host-microbe causal relationships such as Clostridium ramosums causal effects on serum uric acid and hyperuricemia C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/643427v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@e660d0org.highwire.dtl.DTLVardef@ddfe4dorg.highwire.dtl.DTLVardef@62a704org.highwire.dtl.DTLVardef@c31bb5_HPS_FORMAT_FIGEXP M_FIG Graphic abstract Based on a multi-omics cohort of 2,002 individuals comprising high-depth whole genome and metagenomic sequencing data, blood metabolites, and detailed questionnaires, we identified 138,859 high-confidence SVs, uncovering 36 significant associations between SVs and microbial taxa/pathways, as well as 48 associations between SVs and blood metabolites. Mendelian randomization using SVs demonstrated causal relationships, such as Clostridium ramosums causal effect on serum uric acid and hyperuricemia. This study provides a detailed SV catalog for the Chinese population and highlights the significant role of SVs in the gut microbiome, blood metabolites, and their causal relationships. C_FIG

genomics↗

bioRxiv2025

Developmental regulation of Drosophila dosage compensation in a 3D genome context

Chromosomal dosage compensation (DC) restores the expression balance of X chromosome between sexes, and is realised in Drosophila by the coordination of enriched X-linked PionX, HAS sequence elements and 1.6883F satellites, resulting in doubling the transcription of X-linked genes in males. We hypothesize that DC must be finely tuned during development and ask what are the underlying molecular mechanisms in this work. To inspect this, we collect new and published histone modification and 3D genome data of sexed samples from embryos to adults of Drosophila. We find that at least 30% of the Drosophila genes are bound by the DC complex or characteristic H4K16ac modifications specifically in only one or more tissues, and they show a higher H3K27me3 binding level than the rest DC genes constitutively compensated throughout development. The chrX harbors developmentally increasing long-range contacts (LRCs) relative to autosomes, and specifically in males. Integrative analyses with DC genes and regulatory sequences show that HAS and housekeeping genes preferentially located at the chromatin domain boundaries form stable LRCs. While PionXs and 1.6883F only form LRCs with the developmentally regulated DC genes in embryos and testes. Our results indicate that the Drosophila male chrX is characterised by two types of stable and developmentally regulated LRCs coordinating the dosage compensation to the different functional background of genes.

evolutionary biology↗

bioRxiv2025

From genetic disposition to academic achievement: The mediating role of non-cognitive skills across development

Genetic effects on academic achievement are likely to capture environmental, developmental, and psychological processes. How these processes contribute to translating genetic dispositions into observed academic achievement remains critically under-investigated. Here, we examined the role of non-cognitive skills--e.g., motivation, attitudes and self-regulation--in mediating education-associated genetic effects on academic achievement across development. Data were collected from 5,016 children enrolled in the Twins Early Development Study at ages 7, 9, 12, and 16, as well as their parents and teachers. We found that non-cognitive skills mediated polygenic score effects on academic achievement across development, and longitudinally, accounting for up to 64% of the total effects. Within-family analyses highlighted the contribution of non-cognitive skills beyond genetic, environmental and demographic factors that are shared between siblings, accounting for up to 83% of the total mediation effect, likely reflecting evocative/active gene-environment correlation. Our results underscore the role of non-cognitive skills in academic development in how children evoke and select experiences that align with their genetic propensity.

genomics↗

bioRxiv2025

Le Petit Prince (LPP) Multi-talker: Naturalistic 7T fMRI and EEG Dataset

Prior neuroimaging datasets using naturalistic listening paradigms have predominantly focused on single-talker scenarios. While these studies have been invaluable for advancing our understanding of speech and language processing in the brain, they do not capture the complexities of real-world multi-talker environments. Here, we introduce the "Le Petit Prince (LPP) Multi-talker Dataset", a high-quality, naturalistic neuroimaging dataset featuring 40 minutes of electroencephalogram (EEG) and 7T functional magnetic resonance imaging (fMRI) recordings from 26 native Mandarin Chinese speakers as they listened to both single-talker and multi-talker speech streams. Validation analyses conducted on both EEG and fMRI data demonstrate the datasets high quality and robustness. Additionally, the dataset includes detailed transcriptions and prosodic and linguistic annotations of the speech stimuli, enabling fine-grained analyses of neural responses to specific linguistic and acoustic features. The LPP Multi-talker Dataset is well-suited for addressing a wide range of research questions in cognitive neuroscience, including selective attention, auditory stream segregation, and working memory processes in naturalistic listening contexts.

neuroscience↗

bioRxiv2025

Cloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration

Zebrafish has full capacity of heart regeneration, but little is known about how blood cells, especially platelets, are involved in this regenerative process. Here we report that cloche/npas4l is a pro-regenerative platelet factor for heart regeneration. We found that haploinsufficiency of npas4l disrupted cardiomyocyte (CM) and endothelial cell (EC) proliferation and heart regeneration after injury. A single-cell transcriptomic atlas revealed that npas4l was dynamically expressed in platelets after heart injury and regulated robust interactions between platelets-CMs or -ECs. Decreasing platelets by either nitroreductase-mediated platelet depletion or platelet-deficient mutant mpl impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently induced CM and EC proliferation in uninjured hearts, as well as rescued CM and EC proliferation defects in cloche mutants. Mechanistically, Npas4l positively regulated a panel of ligands expression including bmp6 in platelets to fine-tune CM proliferation and heart regeneration. Therefore, this work unveils a novel platelet Npas4l signaling and presents mechanisms on how platelets modulate CM/EC proliferation via ligand-receptor network during zebrafish heart regeneration.

cell biology↗

bioRxiv2025

Amoebicidal Action of Licorice-Derived Compounds: Mechanisms and Effects Against Acanthamoeba castellanii

BackgroundAcanthamoeba is a widely distributed unicellular eukaryotic organism, causing Acanthamoeba keratitis, granulomatous amoebic encephalitis and chronic infectious ulcers. At present, there are no effective drugs available for treating Acanthamoeba infections, highlighting the urgent need for the development of novel anti-Acanthamoeba therapies. PurposeThis study aims to investigate the inhibitory effect of licorice on A. castellanii trophozoites growth and elucidate its molecular mechanisms. MethodsThe effect of licorice on trophozoite viability was assessed employing the CellTiter-Glo assay, while the viability of cells was evaluated via CCK-8 assay. Apoptotic cells were identified through Hoechst 33,342/PI double staining and caspase-3 detection. ROS level was measured via flow cytometry utilising DCFH-DA. Mitochondrial dysfunction was analysed with JC-1 and mtSOX Deep Red staining. RNA sequencing and RT-qPCR analysis were conducted to investigate the potential anti-Acanthamoeba mechanism. ResultsOur results showed that isoliquiritigenin (ISL) and glabridin (GLA) effectively inhibited A. castellaniitrophozoite growth in vitro dose-and time-dependently. ISL and GLA induced several apoptosis features, including Hoechst/PI-positive staining and increased caspase-3 expression. ISL and GLA increased intracellular ROS production, decreased SOD expression and mitochondrial membrane potential and enhanced mitochondrial ROS generation. ISL and GLA effectively prevent host cells from A. castellanii trophozoites invasion. RNA sequencing indicated that ISL may modulate the NAD+ metabolic process, while GLA may influence the sterol metabolic process. ISL reduced the NAD+/NADH ratio, while GLA lowered the levels of 7-dehydrocholesterol in A. castellanii trophozoites. ConclusionThese findings suggest that ISL and GLA may serve as the active components of licorice for treating A. castellanii trophozoites. Our findings suggest that ISL suppresses trophozoites by regulating NAD+ metabolism, while GLA inhibits trophozoites through the regulation of sterol metabolism. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=116 SRC="FIGDIR/small/638758v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e3ec1borg.highwire.dtl.DTLVardef@a212d2org.highwire.dtl.DTLVardef@81b710org.highwire.dtl.DTLVardef@19b003_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

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↗