Biology subjects

Xiao, Y.

Publications and source records attributed to Xiao, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Chemerin-CMKLR1 mediated OGD/R induced Mitochondrial Dysfunction, Oxidative Stress, and Autophagy differentially in Microglia and Neurons

IntroductionIschemia-reperfusion (I/R) injury exacerbates tissue damage upon reperfusion after ischemia. The impact of chemerin and its receptor, chemokine-like receptor 1 (CMKLR1) on I/R injury remains poorly understood. We hypothesized that chemerin-CMKLR1 differentially regulates signaling in microglia and neuronal cells oxygen-glucose deprivation/reoxygenation (OGD/R), influencing mitochondrial function, oxidative stress, and autophagy. MethodsUsing BV2 microglia and Neuro-2a (N2a) neuronal cells, we examined OGD/R-induced changes in autophagy associated proteins, chemerin and CMKLR1 expression. We investigated the functional consequences of CMKLR1 overexpression and chemerin treatment on oxidative stress, apoptosis, autophagy, and mitochondrial dynamics in BV2 microglia and N2a neuronal cells. ResultsOGD/R downregulated CMKLR1 while upregulating autophagy in both BV2 microglia and N2a cells; While chemerin expression decreased in BV2 microglia but increased in N2a cells following OGD/R. Treatment with chemerin dose-dependently reduced oxidative stress and apoptosis while enhancing mitochondrial fusion, suppressing fission, and promoting autophagy and mitochondrial function in both cell types under OGD/R. CMKLR1 overexpression exacerbated mitochondrial respiratory dysfunction, mitochondrial fusion, fission, and elevated autophagy (LC3II/LC3I and Pink1 levels), with cell-type-specific differences observed in Parkin and P62 regulation. ConclusionOur study demonstrates cell-type-specific regulation of chemerin-CMKLR1 signaling in I/R injury, and distinct mitophagy activation mechanisms in microglia and neurons. These findings suggest cell-type specific modulation of chemerin-CMKLR1 as a potential therapeutic target in preserving mitochondrial homeostasis, modulating autophagy, mitophagy and reducing oxidative stress, apoptosis in both microglia and neurons for mitigating I/R injury.

neuroscience↗

bioRxiv2025

Integrated small and long RNA sequencing in single oocytes reveals piRNA-mediated transposon repression during human oogenesis

The piwi-interacting RNA (piRNA) pathway plays a pivotal role in controlling transposable element (TE) activity, which is crucial for the developmental competence of gametogenesis. Although piRNAs have been studied in golden hamsters and other representative mammals, little is known about the relationship between distinct piRNA populations and their regulatory effects on TEs in human oocytes. In this study, we simultaneously profiled small and long RNA transcriptomes in individual human oocytes across four developmental stages. piRNAs, especially PIWIL3-associated short piRNAs (short-piRNAs), are the predominant small non-coding RNAs during human oogenesis. A marked increase in short-piRNAs after the primordial follicle stage coincided with a global downregulation of TE expression, particularly LINE-1 (L1) and endogenous retroviruses (ERVs). On the other hand, PIWIL1- and PIWIL2-associated long piRNAs (long-piRNAs) were correlated with the silencing of certain specific ERV subfamilies. Genomic-context analyses revealed that highly productive piRNA clusters have evolved asymmetric antisense insertion bias toward L1 and ERVs, contributing to TE families-specific regulation. Our findings highlight the global effect of piRNA-mediated TEs repression, with short-piRNAs acting as the primary and broad-spectrum suppressors, and long-piRNAs providing coordinated ERV-specific silencing. In summary, this study provides a valuable dataset of small and long RNA co-expression landscapes in developing human oocytes and offers insights into the coordinated yet distinct roles of different PIWI/piRNA classes in repressing TEs during human oogenesis.

genomics↗

bioRxiv2025

Nitrogen metabolism profiling reveals cell state-specific pyrimidine synthesis pathway choice

Conventional stable isotope tracing assays track one or several metabolites. However, cells use an array of nutrients to sustain nitrogen metabolic pathways. This incongruency hampers a system level understanding of cellular nitrogen metabolism. Therefore, we created a platform to simultaneously trace 30 nitrogen isotope-labeled metabolites. This platform revealed that while primitive cells engage both de novo and salvage pyrimidine synthesis pathways, differentiated cells nearly exclusively salvage uridine despite expressing de novo pathway enzymes. This link between cell state and pyrimidine synthesis routes persisted in physiological contexts, including primary murine and human tissues and tumor xenografts. Mechanistically, we found that Ser1900 phosphorylation of CAD, the first enzyme of the de novo pathway, was enriched in primitive cells and that mimicking this modification in differentiated cells abrogated their preference for pyrimidine salvage. Collectively, we establish a method for nitrogen metabolism profiling and define a mechanism of cell state-specific pyrimidine synthesis pathway choice.

cell biology↗

bioRxiv2025

Actin-modulated nuclear shape controls adaptive reprogramming in cancer-associated fibroblasts

Cancer-associated fibroblasts (CAFs) exhibit striking plasticity, enabling them to adapt to external cues such as therapeutic and mechanical stress in the tumor microenvironment (TME). Here, we uncover a shared mechanotransduction pathway through which both BRAF inhibition and matrix stiffness converge in nuclear remodeling to drive CAF activation. Mechanistically, BRAF inhibitors (BRAFis) accelerate RAS-dependent RAF homo and heterodimerization and ERK signaling, leading to GSK-3{beta} inactivation and Rho kinase (ROCK) activation. In parallel, stiff substrates engage integrin receptors to directly activate ROCK signaling. Activation of ROCK induces actin stress fiber assembly, generating mechanical forces that deform the nucleus. In both contexts, nuclear reshaping promotes {beta}-catenin translocation and actin polymerization through a feedback loop that continuously enforces CAF activation and promotes melanoma progression. Notably, pharmacological inhibition of ROCK activity blocks both BRAFi- and stiffness-induced nuclear remodeling and {beta}-catenin accumulation, identifying the ROCK-cytoskeleton-nucleus axis as a critical regulator of CAF adaptation and functionality. Collectively, these findings reveal a mechanically tuned nuclear signaling hub that integrates chemical and physical cues to promote stromal adaptation and suggest ROCK inhibition as a strategy to counteract therapy-induced fibroblast reprogramming and improve therapy response.

cancer biology↗

bioRxiv2025

Dysregulated nuclear Lamin B1 in DYT1 dystonia thickens the nuclear lamina and disrupts 14-3-3 proteins

Childhood-onset DYT1 dystonia is caused by a heterozygous {Delta}E mutation in the TOR1A gene, which encodes a membrane-embedded AAA+ (ATPase Associated with diverse cellular Activities) ATPase. However, the mechanism by which {Delta}E induces dystonia remains poorly understood. Previously, using patient-derived neurons, we identified dysregulation of nuclear Lamin B1, at both expression levels and subcellular distribution, as a key contributor to DYT1 pathology. In the present study, we utilized DYT1 patient fibroblast cells and induced human neurons to investigate the molecular basis and consequences of Lamin B1 dysregulation. We found that elevated nuclear Lamin B1 thickens the nuclear lamina and deforms the nucleus, impairing nucleocytoplasmic transport. Proteomic analysis of human iPSC-derived neurons revealed that mislocalized Lamin B1 disrupts essential signaling pathways involved in neuronal function. Notably, 14-3-3 proteins, abundant brain molecular chaperones critical for neuronal development and homeostasis, were the most strongly associated with mislocalized Lamin B1. Functional studies showed that downregulation of 14-3-3 proteins impairs neurodevelopment in healthy neurons, while their upregulation rescues DYT1 neuronal defects by reducing Lamin B1 mislocalization. These findings elucidate a mechanistic link between nuclear deformation and cellular dysfunction in DYT1 dystonia and highlight Lamin B1 and 14-3-3 proteins as potential therapeutic targets.

neuroscience↗

bioRxiv2025

Vector semantics of multidomain protein architectures

Multidomain proteins are mosaics of domains, protein modules that are associated with a specific structure or function and are found in diverse combinations. This modular organization facilitates the evolution of novel protein functions, but the principles that govern the relationship between the domain content of a protein and its function is poorly understood. In particular, do domains always contribute the same function, or does the functional contribution of a domain depend on the neighboring domains in the protein? To answer this question, we used vector embeddings, which account for local contextual signals, to model the protein domain content of multidomain proteins. We observe that multidomain architectures that are semantically similar share more functional attributes than multidomain architectures selected based on domain content similarity, alone, suggesting that context is important for understanding the relationship between domain content and protein function. Surprisingly, vector semantics also identified multidomain architecture pairs with significantly high functional similarity, despite having no domains in common at all, suggesting that vector semantics may be discovering domain "synonyms". Taken together, our results underscore the importance of contextual models for understanding the interplay between domain architecture evolution and functional innovation in multidomain proteins.

evolutionary biology↗

bioRxiv2025

Evolution of the Metazoan Protein Domain Toolkit Revealed by a Birth-Death-Gain Model

Domains, sequence fragments that encode protein modules with a distinct structure and function, are the basic building blocks of proteins. The set of domains encoded in the genome serves as the functional toolkit of the species. Here, we use a phylogenetic Birth-Death-Gain model to investigate the evolution of this protein toolkit in metazoa. Given a species tree and the set of protein domain families in each present-day species, this approach estimates the most likely rates of domain origination, duplication and loss. Statistical hierarchical clustering of domain family rates reveals sets of domains with similar rate profiles, consistent with groups of domains evolving in concert. Moreover, we find that domains with similar functions tend to have similar rate profiles. Interestingly, domains with functions associated with metazoan innovations, including immune response, cell adhesion, tissue repair, and signal transduction, tend to have the fastest rates. We further infer the expected ancestral domain content and the history of domain family gains, losses, expansions, and contractions on each branch of the species tree. In contrast to recent reports of widespread loss during metazoan evolution, we observe little evidence of genome streamlining. Rather, our analysis reveals an ongoing process of domain family replacement and resizing, consistent with extensive remodeling of the protein domain repertoire. The use of a powerful, probabilistic Birth-Death-Gain model reveals an unexpected level of genomic plasticity and a striking harmony between the evolution of domain usage in metazoan proteins and organismal innovation.

evolutionary biology↗

bioRxiv2025

Construction of recombinant Bacillus subtilis spores surface-displaying PRRSV ORF1b, GP5, M, and N proteins in tandem and evaluation of their immunogenicity in mice

Porcine reproductive and respiratory syndrome virus (PRRSV), a single-stranded RNA virus, is a highly contagious pathogen that causes severe reproductive and respiratory disorders in pigs, leading to significant economic losses in the swine industry worldwide. However, current commercial vaccines provide only limited protection against circulating PRRSV strains, highlighting the urgent need for novel vaccine strategies. B. Bacillus subtilis, a well-characterized probiotic, has emerged as a promising platform for mucosal vaccine delivery due to its safety profile and ability to induce robust immune responses. In this study, we screened B cell and T cell linear epitopes from PRRSV-ORF1b, GP5, M, and N proteins to construct a recombinant tandem antigen (ER), which was displayed on the surface of B. subtilis 168 spores. The resulting recombinant strain, designated B. subtilis BE, was evaluated for immunogenicity in mice via oral administration. The results showed that Oral immunization with B. subtilis BE significantly elevated antigen-specific secretory IgA levels in intestinal contents and IgG levels in serum, indicating potent mucosal and systemic humoral responses. Moreover, B. subtilis BE induced measurable neutralizing antibody titers and enhanced cellular immunity, as evidenced by increased frequencies of CD3+ and CD8+ T cells in mesenteric lymph nodes and upregulation of IFN-, TNF-, and IFN-{gamma} expression in intestinal tissues. Collectively, these findings demonstrate that B. subtilis BE elicits both humoral and cellular immune responses and may serve as a novel oral vaccine candidate against PRRSV, offering a promising alternative for controlling the ongoing epidemic.

immunology↗

bioRxiv2025

Simultaneous recording of spikes and calcium signals in odor-evoked responses of Drosophila antennal neurons

Most insects, including agricultural pests and disease vectors, rely on olfaction for key innate behaviors. Consequently, there is growing interest in studying insect olfaction to gain insights into odor-driven behavior and to support efforts in vector control. Calcium imaging using GCaMP fluorescence is widely used to identify olfactory receptor neurons (ORNs) responsive to ethologically relevant odors. However, accurate interpretation of GCaMP signals in the antenna requires understanding both response uniformity within an ORN population and how calcium signals relate to spike activity. To address this, we optimized a dual-modality recording method combining single-sensillum electrophysiology and widefield imaging for Drosophila ORNs. Calcium imaging showed that homotypic ab2A neurons exhibit similar odor sensitivity, consistent with spike recordings, indicating that a single ORNs response can reliably represent its homotypic counterparts. Furthermore, concurrent dual recordings revealed that peak calcium responses are linearly correlated with spike activity, regardless of imaging site (soma or dendrites), GCaMP variant, odorant, or fly age. These findings validate the use of somatic calcium signals as a reliable proxy for spike activity in fly ORNs and provide a foundation for future large-scale surveys of spike-calcium response relationships across diverse ORN types.

neuroscience↗

bioRxiv2025

Phase-separating enzyme-responsive condensates for inhalable delivery of biomacromolecules

Inhaled delivery of biomacromolecules shows extensive promise for treating a large variety of diseases, especially pulmonary and respiratory diseases. Although nanoparticle-based vehicles enhance intracellular uptake efficiency, it still remains challenging for biomacromolecules inhaled delivery to overcome cytotoxicity, cargo leakage and off-target effect. Here, we present an enzyme-responsive condensates based highly biocompatible and controllable platform for inhaled delivery of biomacromolecules. The condensates that can be modularly designed for rapid recruitment and enrichment of biomolecules, including Cas9 ribonucleoprotein (RNP) and mRNA, were internalized by cells via lysosomal-independent endocytosis, and subsequently released payloads triggered with endogenous physicochemical stimulus for controlled regulation of genes and proteins expression. Additionally, the micrometer sized condensates with highly structural and biological stability during lyophilization and nebulization enable inhalable delivery of biomacromolecules to lung. This condensate-based vehicle provides a promising platform for biomacromolecules inhaled delivery and controlled release, targeted cell regulation, and precise therapy.

bioengineering↗

bioRxiv2025

Fos labels a distinct excitatory neuron ensemble for memory retrieval

Experience-triggered expression of Fos has been extensively used as a marker representing memory engram. It is generally assumed that Fos-positive neurons are preferentially excited by the experience, yet this has not been directly examined. In this study, we tracked neuron activity and Fos expression in somatosensory cortex and dentate gyrus of hippocampus in mice, during electric shock-induced fear memory formation and retrieval. Contrary to the prevailing view, we found that calcium features fail to predict Fos for individual cells. Fos-positive neurons show no specific activation to stimuli during memory encoding, but their activities become stimuli-selective during retrieval. Surprisingly, inhibiting neurons that will express Fos during encoding does not affect the induction of memory-guided behavior upon their activation. Network simulation and voltage imaging further showed that connectivity to interneurons, not stimulus responsiveness, is a major factor determining Fos expression. Our results indicate that Fos labels excitatory neurons specific for memory retrieval.

neuroscience↗

bioRxiv2025

Structural Basis for Cas9-Directed Spacer Acquisition in Type II-A CRISPR-Cas Systems

CRISPR-Cas systems confer prokaryotic adaptive immunity by integrating foreign DNA (prespacers) into host arrays. Type II-A systems employ Cas9 for protospacer adjacent motif (PAM) recognition and coordinate with Csn2 and the Cas1-Cas2 integrase during spacer acquisition, yet their structural basis remains unresolved. Here, we report cryo-EM structures of the Enterococcus faecalis Cas9-Csn2-Cas1-Cas2 supercomplex in apo and DNA-bound states. The apo-state structure (Cas92-Csn28-Cas18-Cas24) adopts a resting conformation, with Cas9 locked in a nuclease-inactive state and Cas1-Cas2 sterically blocked from prespacer loading. Upon DNA engagement, Cas9 undergoes a conformational transition, forming a prespacer catching complex that threads the DNA through Csn2s central channel. This architecture enables Cas9 to interrogate the PAM sequence while sliding along the DNA, with Cas9 and Csn2 jointly define a 30-bp DNA segment which matches the prespacer length. Subsequent dissociation of Cas9 triggers a structural reconfiguration of the Csn2-Cas1-Cas2 assembly. The PAM-proximal DNA becomes accessible, and Cas1-Cas2 relocates to bind to the exposed DNA, enabling further prespacer processing and directional integration. These findings reveal how Cas9 collaborates with Csn2 and Cas1-Cas2 to couple PAM recognition with prespacer selection, resolving the dynamic structural transitions that ensure fidelity during type II-A CRISPR adaptation.

molecular biology↗

bioRxiv2025

Oblique Thick Light-Sheet Microscopy with Spatiotemporal 3D Localization for RNA Imaging in Intact 50 μm-Thick Sections

Neuron typing in intact brain sections demands 3D imaging reconciling thickness compatibility with large-area coverage--a persistent challenge for RNA imaging methods limited by either restricted fields-of-view (<1 mm2) or thin-section constraints (<20 m). Here we introduce oblique thick light-sheet microscopy integrated with spatiotemporal 3D localization, enabling multiplexed RNA imaging across 50 m-thick tissue sections and centimeter-scale regions. The 45{degrees} illumination geometry achieves optical-interference-free imaging in >100 m-thick tissues during single-plane scans, while a spatiotemporal localization algorithm recovers submicron resolution by pinpointing fluorescence in situ hybridization (FISH) spots within volumetric excitation. This strategy reveals layer-spanning neuronal distributions and region-specific expression gradients unattainable with conventional RNA imaging approaches. By resolving the historical trade-off between imaging depth and spatial coverage, our platform advances whole-brain transcriptomics, enabling 3D neuron typing capability critical for deciphering brain-wide cellular architectures.

biophysics↗

bioRxiv2025

Functional loss of CHS2 confers high levels resistance to Bacillus thuringiensis Vip3Aa, but with significant fitness costs in five lepidopteran species

Bacillus thuringiensis (Bt) crops, engineered to produce insecticidal proteins such as Vip3Aa and Cry toxins, have revolutionized pest management by providing a sustainable alternative to chemical pesticides. However, the development of resistance to these toxins has driven the investigation of underlying mechanisms to better understand how pests evade toxicity and to develop more effective resistance management strategies. Recently, a laboratory-selected Spodoptera frugiperda strain exhibited a high level of resistance to Vip3Aa (resistance ratio: 5562-fold), with the mutation of the chitin synthase gene, SfCHS2, identified as a key factor. In this study, we extend these findings to additional lepidopteran species, including Spodoptera exigua and Agrotis ipsilon. Our results show that CHS2 knockout strains lack the peritrophic matrix (PM), while the resistant Sfru_R3 strain retains its PM. Knockout of this gene resulted in high levels resistance to Vip3Aa. These findings further validate the role of the CHS2 gene in Vip3Aa resistance and highlight its potential as a target for resistance management in lepidopteran pests. This study advances our understanding of the molecular mechanisms behind resistance to Vip3Aa and supports the development of strategies to delay resistance in Bt crop management.

genetics↗

bioRxiv2025

Integrating Multimodal Data for a Comprehensive Knowledge Graph to Advance Infectious Disease Research

Infectious diseases remain a formidable threat to global public health, with their escalating morbidity and mortality rates compounded by recurrent epidemics and the alarming rise of antimicrobial resistance (AMR). These challenges have intensified the urgent demand for innovative therapeutic strategies that can accelerate drug development cycles and overcome traditional research bottlenecks. To address these critical needs, we present IDKG (Infectious Disease Knowledge Graph), a specialized large-scale biomedical knowledge network designed to bridge data fragmentation through multimodal data integration. The IDKG constructs comprehensive associations from 345 infectious diseases and 708 pathogens across heterogeneous biomedical sources systematically. The graph architecture comprises nearly 50,000 nodes (8 types, including Pathogen, Protein, etc.) and over 1.2 million edges (11 types, including treats, contains, etc.), establishing an interconnected framework that enables systematic interrogation of cross-disciplinary knowledge. The integrative approach effectively dismantles conventional data silos while preserving biological contextuality. We validated the IDKGs potential by applying graph neural network-based approaches for drug repurposing prediction in human metapneumovirus (hMPV) infection, a common acute respiratory infection for which effective specific antiviral drugs are currently absent. The successfully identification of established antiviral agents, such as ribavirin and emetine, by our M1 model demonstrated its predictive accuracy and biological relevance. IDKG unifies multimodal biomedical data into a network to accelerate drug discovery and bolster outbreak response. This establishes a data-driven, knowledge-based paradigm for infectious disease research. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/657361v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@f5dc24org.highwire.dtl.DTLVardef@147d584org.highwire.dtl.DTLVardef@113083corg.highwire.dtl.DTLVardef@81d523_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

The genomic and transcriptional landscape of the spinal cord H3K27-altered diffuse midline glioma suggests the potential therapeutic strategy

Diffuse midline glioma with H3K27-altered (DMG) is a lethal pediatric malignancy that primarily occurs in the brainstem of children. In adults, DMG arising in the spinal cord is rarely reported and remains poorly understood. The cellular architecture and clinical outcomes of DMG vary depending on the tumors location. To dissect the genomic and transcriptional architecture of a cohort of spinal cord DMG patients, we conducted whole-exome sequencing and single-cell RNA sequencing on 19 tumor samples from 7 patients. We identified previously underappreciated stem-like cells associated with hypoxia in malignant tumor cells, which were present in all samples of spinal cord DMG but absent in published intracranial DMG, corroborating cellular heterogeneity based on tumor location. We discovered that tumor-associated myeloid cells constituted the largest population of non-malignant cells in adult spinal cord DMG. Our research revealed a transition from microglia to macrophages, characterized by enhanced cell-to-cell interactions mediated through the VEGF signaling pathway network. Notably, we found that epigenetic agents can repress the expression of hypoxia-related gene programs in patient-derived spinal cord DMG cultures and inhibit cell proliferation in vitro. Collectively, our study reveals a crucial anatomical dimension that DMG exhibits a location-specific genomic and transcriptional landscape despite shared H3K27 alterations, providing the paradigm for developing precision therapeutic strategies that extend beyond DMG to other molecularly defined yet anatomically divergent malignancies.

cancer biology↗

bioRxiv2025

A key role for Canoes intrinsically disordered region in linking cell junctions to the cytoskeleton

AbstractAdherens junctions are key to tissue architecture, mediating robust yet dynamic cell-cell adhesion and, via cytoskeletal linkage, allowing cells to change shape and move. Adherens junctions contain thousands of molecules linked by multivalent interactions of folded protein domains and Intrinsically Disordered Regions (IDRs). One key challenge is defining mechanisms conferring robust linkage and mechanosensing. Drosophila Canoe and mammalian Afadin provide superb entrypoints to explore how their complex protein structures and shared IDRs enable function. We combined genetic, cell biological and biochemical tools to define how Canoes IDR functions during morphogenesis. Unlike many of Canoes folded domains, the IDR is critical for junctional localization, mechanosensing and function. We took the IDR apart, identifying two conserved stickers in the IDR that directly bind F-actin, separated by less-conserved spacers. Surprisingly, while mutants lacking the IDR die as embryos with morphogenesis defects, no sub-region of the IDR is essential for viability. Instead, IDR stickers and spacers act combinatorially to ensure localization, mechanosensing and function.

cell biology↗

bioRxiv2025

Generating 3D Models of Carbohydrates with GLYCAM-Web

The carbohydrate 3D structure-prediction tools (builders) at GLYCAM-Web (glycam.org) are widely used for generating experimentally-consistent 3D structures of oligosaccharides suitable for data interpretation, hypothesis generation, simple visualization, and subsequent molecular dynamics (MD) simulation. The graphical user interface (GUI) enables users to create carbohydrate sequences (e.g. DGalpb1-4DGlcpb1-OH) that are converted to 3D models of the carbohydrate structures in multiple formats, including PDB and OFF (AMBER software format). The resulting structures are energy minimized prior to download and online visualization. There are advanced options for selecting which shapes (rotamers) of the oligosaccharide to generate, and for creating explicitly solvated structures for subsequent MD simulation. The GLYCAM-Web builders integrate known conformational preferences of oligosaccharides, summarized here, and employ the GLYCAM forcefield for energy minimization with algorithms tailored for speed and scalability. Even for large oligosaccharides (100 residues, ~2100 atoms) a 3D structure is typically returned to the user in less than a minute.

biophysics↗