Biology subjects

Xu, W.

Publications and source records attributed to Xu, W..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Excessive zinc reduces histone acetylation in mouse cardiomyocytes by downregulating acetyltransferases

Zinc plays a critical role in cellular functions, but its excess may lead to detrimental effects, including cardiac abnormalities. The impact of zinc overload on cardiomyocytes is investigated in this study. For the first time, we report the regulatory relationship between zinc and histone acetylation. Excessive zinc downregulates the transcription of Bmp4 in HL-1 cell line and primary cardiomyocytes. This downregulation is linked to reduced histone acetylation (H3K9ac), mediated by the suppression of histone acetyltransferases (HATs), rather than changes in histone deacetylases (HDACs). When zinc is introduced directly into the nucleus, Bmp4 expression is upregulated, suggesting that the reduction of histone acetylation by zinc is in an indirect way. This study underscores the importance of zinc homeostasis in maintaining cardiac health and provides insights into the molecular basis of zinc-induced cardiac dysfunction.

cell biology↗

bioRxiv2025

Inheritance of the genome-less apicoplast in the 'apicoplast-minus' Plasmodium falciparum

Most apicomplexan parasites contain a plastid-derived organelle called the apicoplast, which originated through secondary endosymbiosis. As a result of this evolutionary trajectory, the non-photosynthetic apicoplast is surrounded by four membranes and contains many bacterial-like, druggable targets. It is widely accepted that asexual malaria parasites (Plasmodium falciparum) can thrive under antibiotic treatment if supplemented with high concentrations of isopentenyl pyrophosphate (IPP, 200 {micro}M) and these IPP-rescued parasites are thought to lack the apicoplast and its 35 kb genome but possess many vesicles. However, our findings challenge this apicoplast-minus concept. In late-stage schizonts, we observed that the apicoplast-derived vesicles nearly colocalize with mitochondria and are properly distributed into merozoites during schizogony, suggesting that they are inherited rather than newly synthesized in each asexual cycle. Further, immuno-electron microscopy (immuno-EM) revealed that the "apicoplast-minus" parasites possess structures surrounded by four membranes, in addition to single-membrane-surrounded entities. The presence of four-membrane-bound structures suggests that the apicoplast has not truly disappeared in the "apicoplast-minus" P. falciparum but remains in a distinct, diminished form. We termed this genome-less apicoplast derivative the apicosome, drawing an analogy to the genome-less mitochondrial derivative known as the mitosome. We propose that apicosomes retain essential biochemical and/or structural functions, which act as barriers to the complete loss of apicoplast when the parasites face antibiotic stress and IPP rescue.

microbiology↗

bioRxiv2025

Mechanism of biomimetic virus-like nanoparticles in triggering immune response elucidated by proteomics

The use of biomimetic nanoparticles (NPs) with virus-like morphology have recently attracted research interest as novel delivery platforms and immune adjuvants. However, the exact interactions between the nanoparticles and immune cells as well as the mechanism involved are not known in detail. This motivated us to develop virus-like mesoporous silica nanoparticles (VLP) to characterize their physicochemical properties, and to determine the immune pathways induced by the particles in mouse macrophages. The results showed inclusion of spikes mimicking virion structures on the surface increased cellular uptake and enhanced immune response as compared to spherical NPs. Proteomic analysis revealed that the RIG-I-like receptor signaling pathway, Chemokine signaling pathway, MAPK signaling pathway, NF-{kappa}B signaling pathway, Toll-like receptor signaling pathway, B cell receptor signaling pathway and Th1 and Th2 cell differentiation pathways were involved in regulating the immune response when macrophages interacted with VLP. When the spikes increased from 5 to 30 nm, the expression levels of immune-related proteins including TRAF6 and PIAS4 proteins enhanced. This study revealed the interaction pathways and key proteins in the activation of immune response with VLP, which may provide insights to develop novel immunotherapy for enhanced efficacy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=177 SRC="FIGDIR/small/640536v3_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@395d6forg.highwire.dtl.DTLVardef@25238dorg.highwire.dtl.DTLVardef@41001borg.highwire.dtl.DTLVardef@16dfe2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Specificities of Chemosensory Receptors in the Human Gut Microbiota

The human gut is rich in metabolites and harbors a complex microbial community, yet the sensory repertoire of its commensal bacteria remains largely uncharacterized. Here we systematically mapped ligand specificities of extracytoplasmic sensory domains from twenty members of the human gut microbiota, with a primary focus on the abundant and physiologically important class of Clostridia. We identified diverse metabolites as specific stimuli for three major functional classes of transmembrane receptors. We further characterized novel subsets of sensors belonging to the Cache superfamily, specific for lactate, dicarboxylic acids, and for uracil and short-chain fatty acids (SCFAs), respectively, and investigated the evolution of their ligand specificity. Structural and biochemical analysis of the newly described dCache_1UR domain revealed an independent binding of uracil and SCFA at distinct modules. Altogether, we could identify or predict specificities for over a half of the Cache-type chemotactic sensors in the selected gut commensals, with the carboxylic acids representing the largest class of ligands. Among those, the most commonly found specificities were for lactate and formate, indicating particular importance of these metabolites in the human gut microbiome and consistent with their observed beneficial impact on the growth of selected bacterial species.

microbiology↗

bioRxiv2024

Pan-cancer N-glycoproteomic atlas of patient derived xenografts uncovers FAT2 as a therapeutic target for head and neck cancers

Cell surface proteins offer significant cancer therapeutic potential attributable to their accessible membrane localization and central role in cellular signaling. Despite this, their promise remains largely untapped due to the technical challenges inherent to profiling cell surface proteins. Here, we employed N-glycoproteomics to analyze 85 patient-derived xenografts (PDX), constructing Glyco PDXplorer - an in vivo pan-cancer atlas of cancer-derived cell surface proteins. We developed a target discovery pipeline to prioritize proteins with favorable expression profiles for immunotherapeutic targeting and validated FAT2 as a head and neck squamous cancer (HNSC) enriched surface protein with limited expression in normal tissue. Functional studies revealed that FAT2 is essential for HNSC growth and adhesion through regulation of surface architecture and integrin-PI3K signaling. Chimeric antigen receptor (CAR) T cells targeting FAT2 demonstrated potent anti-tumor activity in HNSC models. This work lays the foundation for developing FAT2-targeted therapies and represents a pivotal resource to inform therapeutic target discovery for multiple cancers. HIGHLIGHTSO_LIPan-cancer landscape of cancer-derived cell surface proteins detected in vivo C_LIO_LIDevelopment of a multi-omic discovery pipeline to prioritize proteins with optimal expression profiles as immunotherapy targets C_LIO_LIIdentification and validation of FAT2 as a head and neck squamous cancer enriched surface protein with minimal expression in normal tissues C_LIO_LIFAT2 coordinates cell surface organization, adhesion, growth and survival through the integrin-PI3K-AKT pathway C_LIO_LIFAT2 CAR T cells demonstrate anti-tumour activity in pre-clinical models C_LI

cancer biology↗

bioRxiv2024

NCPepFold: Accurate Prediction of Non-canonical Cyclic Peptide Structures via Cyclization Optimization with Multigranular Representation

Artificial intelligence-based peptide structure prediction methods have revolutionized biomolecular science. However, restricting predictions to peptides composed solely of 20 natural amino acids significantly limits their practical application, as such peptides often demonstrate poor stability under physiological conditions. Here, we present NCPepFold, a computational approach that can utilize a specific cyclic position matrix to directly predict the structure of cyclic peptides with non-canonical amino acids. By integrating multi-granularity information at the residue- and atomic-level, along with fine-tuning techniques, NCPepFold significantly improves prediction accuracy, with the average peptide RMSD for cyclic peptides being 1.640 [A]. In summary, this is a novel deep learning model designed specifically for cyclic peptides with non-canonical amino acids without length restrictions, offering great potential for peptide drug design and advancing biomedical research.

bioinformatics↗

bioRxiv2024

Retrotransposon LINE1 trans-regulatory differentiation process maintain embryonic stem cell identity

Long Interspersed Nuclear Elements-1s (LINE1s) are one of the >17% most abundant Retrotransposons in mammalian genomes. LINE1 RNA is high expression during early embryonic development, meanwhile is under tight epigenetic control. Some studies have confirmed LINE1 play a critical role in early embryo development and ESC identity. Previous studies focused on the role of LINE1 in cis-regulation, however, the function of L1 RNA in tans-regulation remains largely unknown. In this study, we performed a high-throughput proximity MARGI (pxMARGI) experiment found transposon LINE1 RNA trans-regulated prefer to young LINE1 subfamily, and in hybrid and non-hybrid two different manner repress ESC to dual progress of 2C-like cells and differentiation. In differentiation process, LINE1 RNA as a scaffold recruit polycomb core subunits combine three core pluripotent factors maintain ESC identity. In 2C process, LINE1 RNA in a sequence-specific manner recruit Kap1 to old L1 subfamily, and recruit ELL3 to RE 5 UTR maintain ESC self-renewal. Our data point to LINE1 transcriptions more detail trans-regulation mechanism to orchestrate developmental progression for the self-renewal of embryonic stem cells (ESCs). LINE1 RNA may be potential biomarker for noninvasive embryo selection.

genomics↗

bioRxiv2024

PlantRing: A high-throughput wearable sensor system for decoding plant growth, water relations and innovating irrigation

The combination of flexible electronics and plant science has generated various plant-wearable sensors, yet challenges persist in their applications in real-world agriculture, particularly in high-throughput settings. Overcoming the trade-off between sensing sensitivity and range, adapting them to a wide range of crop types, and bridging the gap between sensor measurements and biological understandings remain the primary obstacles. Here we introduce PlantRing, an innovative, nano-flexible sensing system designed to address the aforementioned challenges. PlantRing employs bio-sourced carbonized silk georgette as the strain sensing material, offering exceptional resolution (tensile deformation: < 100 m), stretchability (tensile strain up to 100 %), and remarkable durability (season long), exceeding existing plant strain sensors. PlantRing effectively monitors plant growth and water status, by measuring organ circumference dynamics, performing reliably under harsh conditions and being adaptable to a wide range of plants. Applying PlantRing to study fruit cracking in tomato and watermelon reveals novel hydraulic mechanism, characterized by genotype-specific excess sap flow within the plant to fruiting branches. Its high-throughput application enabled large-scale quantification of stomatal sensitivity to soil drought, a traditionally difficult-to-phenotype trait, facilitating drought tolerant germplasm selection. Combing PlantRing with soybean mutant led to the discovery of a potential novel function of the GmLNK2 circadian clock gene in stomatal regulation. More practically, integrating PlantRing into feedback irrigation achieves simultaneous water conservation and quality improvement, signifying a paradigm shift from experience- or environment-based to plant-based feedback control. Collectively, PlantRing represents a groundbreaking tool ready to revolutionize botanical studies, agriculture, and forestry.

plant biology↗

bioRxiv2024

Cycledesigner Leveraging RFdiffusion and HighFold to Design Cyclic Peptide Binders for Specific Targets

Cyclic peptides are potentially therapeutic in clinical applications, due to their great stability and activity. Yet, designing and identifying potential cyclic peptide binders targeting specific targets remains a formidable challenge, entailing significant time and resources. In this study, we modified the powerful RFdiffusion model to allow the cyclic peptide structure identification and integrated it with ProteinMPNN and HighFold to design binders for specific targets. This innovative approach, termed cycledesigner, was followed by a series of scoring functions that efficiently screen. With the combination of effective cyclic peptide design and screening, our study aims to further broaden the scope of cyclic peptide binder design.

bioinformatics↗

bioRxiv2024

Hypocretin Receptor 1 Blockade Early in Abstinence Prevents Incubation of Cocaine Seeking and Normalizes Dopamine Transmission

Abstinence from cocaine use has been shown to elicit a progressive intensification or incubation of cocaine craving/seeking that is posited to contribute to propensity for relapse. While the mechanisms underlying incubation of cocaine seeking remain elusive, considerable evidence suggests that abstinence from cocaine promotes mesolimbic dopamine adaptations that contribute to exaggerated cocaine seeking. Consequently, preventing these dopamine adaptations may reduce incubation of cocaine seeking and thereby reduce the likelihood of relapse. In the present studies, we first examined if incubation of cocaine seeking was associated with aberrant dopamine transmission in the nucleus accumbens after seven days of abstinence from intermittent access to cocaine. Given the extensive evidence that hypocretins/orexins regulate motivation for cocaine, we then examined to what extent hypocretin receptor 1 antagonism on the first day of abstinence prevented incubation of cocaine seeking and dopamine adaptations later in abstinence. Results indicated that abstinence from intermittent access to cocaine engendered robust incubation of cocaine seeking in both female and male rats. We also observed aberrant dopamine transmission, but only in rats that displayed incubation of cocaine seeking. Further, we showed that a single injection of the hypocretin receptor 1 antagonist, RTIOX-276, on the first day of abstinence prevented incubation of cocaine seeking and aberrant dopamine transmission. These findings suggest that hypocretin receptor 1 antagonism may serve as a viable therapeutic for reducing cocaine craving/seeking, thus reducing the likelihood of relapse.

neuroscience↗

bioRxiv2024

Biomimetic porous silicon for rationally engineered combination therapy to induce immunogenic cell death

Combined chemo-photothermal therapy (CHT-PTT) is a promising treatment for metastatic cancers. It enables the synergistic induction of immunogenic cell death (ICD), while sensitising suppressive tumour microenvironment to immunotherapy. To induce ICD, the rational design of a combined CHT-PTT regimen remains unclear. In the present study, black porous silicon nanoparticles (BPSi NPs) were utilized as both drug carriers and photothermal conversion agents. To enhance their colloidal stability and homotypic targeting, BPSi NP surfaces were modified with polyethylene glycol and further coated with cancer cell membranes (CMs). Six chemotherapeutic drugs with different cell growth inhibition mechanisms were tested against metastatic MDA-MB-231 breast cancer cells to evaluate their ICD induction potentials. Finally, in the combined CHT-PTT, the effect of temperature was evaluated. Based on the analysis of ICD markers, high-mobility group box 1 and calreticulin proteins, we found that bromodomain-containing protein 4 inhibitor, (+)-JQ-1 (JQ1) was the optimal drug, and the mild-hyperthermia temperature of 45 {degrees}C was the best temperature setting in the combined CHT-PTT to induce ICD. Thus, our study provides rationally designed CHT-PTT regimen for efficient cancer treatment with high efficacy and low side effects.

bioengineering↗

bioRxiv2024

A Full Window Data Independent Acquisition Method for DeeperTop-down Proteomics

Top-down proteomics (TDP) is emerging as a vital tool for the comprehensive characterization of proteoforms. However, as its core technology, top-down mass spectrometry (TDMS) still faces significant analytical challenges. While data-independent acquisition (DIA) has revolutionized bottom-up proteomics and metabolomics, they are rarely employed in TDP. The unique feature of protein ions in an electrospray mass spectrum, as well as the data complexity require the development of new DIA strategies. This study introduces a machine learning assisted Full Window DIA (FW-DIA) method that eliminates precursor ion isolation, making it compatible with a wide range of commercial mass spectrometers. Moreover, FW-DIA leverages all precursor protein ions to generate high-quality tandem mass spectra, enhancing signal intensities by [~]50-fold and protein sequence coverage by threefold in a modular protein analysis. The method was successfully applied to the analysis of a five-protein mixture under native conditions and Escherichia coli ribosomal proteoform characterization.

bioinformatics↗

bioRxiv2024

AI Assisted Native Proteomics: Delineating Ribosomal Protein Conformations Pre- and Post-Assembly

The simultaneous identification of proteins as well as their conformations in a biological system would greatly enhance our understanding of cellular mechanisms and disease. As an emerging technique, native proteomics analyzes proteins in their native states, facilitating the acquisition of protein stoichiometry, post-translational modifications (PTMs), and interactions with ligands. However, revealing protein conformations at the proteome scale remains a significant challenge. In this study, we propose an AI-assisted native proteomics method that integrates a protein structure prediction (PSP) module with top-down proteomics (TDP) and native mass spectrometry (nMS) to acquire both proteome identity and conformations. First, protein sequences and PTMs are obtained using the TDP method, while protein solvent-accessible surface area (SASA) is measured in parallel by nMS. These data are then input into the PSP module to acquire the most probable conformation of the protein under nMS experimental conditions. We validate the feasibility and accuracy of this method through the analysis of both a globular protein and an intrinsically disordered protein. Additionally, we apply this approach to delineate the conformations of ribosomal proteins pre- and post-assembly. Interactions of ribosomal proteins with drug molecules are also explored. By enabling proteome identification and conformation characterization from relatively small amounts of endogenous proteins, this method would bridge the gap between structural biology and conventional proteomics technologies.

molecular biology↗

bioRxiv2024

A Genetic Toggle Switch in Plants

In synthetic biology, genetic components are assembled to make transcriptional units, and transcriptional units are assembled into circuits to perform specific and predictable functions of a genetic device. Genetic devices have been described in bacteria, mammalian cell cultures and small organoids, yet development of programmable genetic circuits for devices in plants has lagged. Programmable genetic devices require defining the components quantitative functions. Because plants have long life spans, studies often use transient analysis to define quantitative functions while verification in stably engineered plants is often neglected and largely unknown. This raises a question if unique attributes of plants such as environmental sensitivity, developmental plasticity, or alternation of generations, adversely impacts predictability of plant genetic circuits and devices. Alternatively, it is also possible that genetic elements to produce predictable genetic devices for plants require rigorous characterization with detailed mathematical modeling. Here we use plant genetic elements with quantitatively characterized transfer functions and developed in silico models to guide their assembly into a genetic device: a toggle switch or a mutually inhibitory gene-regulatory device. Our approach allows computational selection of plant genetic components and iterative refinement of the circuit if the desired genetic functions are not initially achieved. We show that our computationally selected genetic circuit functions as predicted in stably engineered plants including through tissue and organ differentiation. Developing abilities to produce predictable and programmable plant genetic devices opens the prospect of predictably engineering plants unique abilities in sustainable human and environmental systems.

synthetic biology↗

bioRxiv2024

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

DNA synthesis serves as the fundamental enabling technology of engineering biology, aiming to provide DNA molecules of designed composition, length, and complexity at scale and low cost. Current high-throughput DNA synthesis technologies rely on intricate chip manufacturing and microfluidic systems to provide large-scale synthetic oligonucleotides, at the expense of low concentration and limited compatibility in the processing of longer DNA constructs assembly. Here, we report a microchip-based massive in parallel synthesis (mMPS), pioneering an "identification-sorting-synthesis-recycling" iteration mechanism to microchips for high throughput DNA synthesis. In comparison to microarray-based methods, we demonstrate that our method can increase the DNA product concentration by 4 magnitudes (to picomole-scale per sequence) and greatly simplifies the downstream processes for large-scale gene synthesis construction. By the construction of 1.97 million-diversity variant libraries that cover 1,254 human protein domains, we demonstrated the uniformity of the constructed variant libraries using mMPS-derived oligos is greatly improved, with amino acid distribution highly consistent as designed. In addition, by synthesizing 285 1kb-to-3kb genes with varying degrees of sequence complexity from previously reported strains A501 and 3DAC, potential ancestor of early archaea and bacteria, our result shows that the overall gene assembly success rate using mMPS-derived oligos is increased by 10-fold in comparison to other methods. Our mMPS technology holds the potential to close the gap between the quality and cost of writing DNA in increasing demand across many sectors of research and industrial activities.

synthetic biology↗

bioRxiv2024

Probing Biomass Precursor Synthesis as a Key Factor in Microbial Adaptation to Unadapted Carbon Sources

Industrial microorganisms often face challenges in utilizing renewable substrates such as methanol, formate, and xylose. We present findings that the proportion of biomass precursors that must be synthesized from unadapted carbon sources is a critical determinant of the evolutionary driving force and minimal substrate requirements, using a new computational framework, AdaptUC. We predict metabolic engineering strategies for Adaptive Laboratory Evolution (ALE). These strategies enable microorganisms to co-utilize an adapted co-substrate and an unadapted carbon source or, in some cases, rely exclusively on the unadapted source. AdaptUC was validated through experimental records and literature, confirming its effectiveness in identifying gene knockout strategies. Case studies in Escherichia coli and Corynebacterium glutamicum highlight superior strategies with higher driving forces and reduced substrate requirements. This method has the potential to transform industrial biosynthesis by enabling more efficient use of renewable carbon sources. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/619944v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@36fe02org.highwire.dtl.DTLVardef@5e73fdorg.highwire.dtl.DTLVardef@110ffdaorg.highwire.dtl.DTLVardef@10d45dc_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Development of novel flavonoid senolytics through phenotypic drug screening and drug design

Accumulation of senescent cells drives aging and age-related diseases. Senolytics, which selectively kill senescent cells, offer a promising approach for treating many age-related diseases. Using a senescent cell-based phenotypic drug discovery approach that combines drug screening and drug design, we developed two novel flavonoid senolytics, SR29384 and SR31133, derived from the senolytic fisetin. These compounds demonstrated enhanced senolytic activities, effectively eliminating multiple senescent cell types, reducing tissue senescence in vivo, and extending healthspan in a mouse model of accelerated aging. Mechanistic studies utilizing RNA-Seq, machine learning, network pharmacology, and computational simulation suggest that these novel flavonoid senolytics target PARP1, BCL-xL, and CDK2 to induce selective senescent cell death. This phenotype-based discovery of novel flavonoid senolytics, coupled with mechanistic insights, represents a key advancement in developing next-generation senolyticss with potential clinical applications in treating aging and age-related diseases.

cell biology↗

bioRxiv2024

Identification of lipid senolytics targeting senescent cells through ferroptosis induction

Cellular senescence is a key driver of the aging process and contributes to tissue dysfunction and age-related pathologies. Senolytics have emerged as a promising therapeutic intervention to extend healthspan and treat age-related diseases. Through a senescent cell-based phenotypic drug screen, we identified a class of conjugated polyunsaturated fatty acids, specifically -eleostearic acid and its methyl ester derivative, as novel senolytics that effectively killed a broad range of senescent cells, reduced tissue senescence, and extended healthspan in mice. Importantly, these novel lipids induced senolysis through ferroptosis, rather than apoptosis or necrosis, by exploiting elevated iron, cytosolic PUFAs and ROS levels in senescent cells. Mechanistic studies and computational analyses further revealed their key targets in the ferroptosis pathway, ACSL4, LPCAT3, and ALOX15, important for lipid-induced senolysis. This new class of ferroptosis-inducing lipid senolytics provides a novel approach to slow aging and treat age-related disease, targeting senescent cells that are primed for ferroptosis.

cell biology↗