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Wang, C.

Publications and source records attributed to Wang, C..

At least 289 records · Page 16Linked to original sources

Degradation of biopesticidal triterpenoid saponins by the soil bacterium Arthrobacter sp. α-11c

BackgroundSaponins, a diverse group of glycosylated triterpenoid and steroid compounds produced by plants, exhibit potent insecticidal activity and are promising candidates for sustainable pest management. However, their potential persistence in soil raises concerns about ecological impacts, highlighting the need to understand microbial degradation rates and pathways. ResultsThis study reports the isolation of Arthrobacter sp. 11c, and its ability of fully degrading two hederagenin-based pentacyclic triterpenoid saponins: -hederin, hederacoside C, and the corresponding sapogenin hederagenin. All three compounds were fully metabolized within six hours when provided as carbon source. Fractionation experiments confirmed intracellular uptake and degradation of the saponins. Genome analysis of 11c revealed diverse and multiple glycosidase genes, yet basal glucosidase activity remained unchanged when cultured with these saponins. Comparative genomics with Arthrobacter sp. 12b, a closely related strain unable to degrade saponins, revealed two unique glycosidase gene clusters in 11c, suggesting a role in adaptation to saponin metabolism. ConclusionThese findings enhance our understanding of bacterial degradation of plant triterpenoid saponins and provide a foundation for evaluating their environmental fate. This knowledge supports the safe and sustainable use of saponin-based biopesticides in agriculture by identifying microbial partners that contribute to their breakdown in soil ecosystems.

microbiology↗

Differential transcriptomics and metabolomics analyses of the skin of coarse and fine Liaoning cashmere goats

Secondary follicles in cashmere goats determine cashmere yield and quality. The present study investigated the relationship between the regulatory factors and cashmere fiber diameter through transcriptomics and metabolomics methods. Diameters of the fibers of 400 (18 months old) female Liaoning cashmere goats were measured and categorized into coarse and fine hair types (200 goats per category). Six goats were selected as representatives of each group for further analysis. Fiber diameters were significantly different between groups (P < 0.05). Transcriptomic analysis revealed 211 differentially expressed genes between groups, including FGF18, KRT36, KRT79, AWAT2, and MOGAT1, which were enriched in the PPAR and glycerol-lipid metabolism signaling pathways that regulate hair follicle growth and sebum secretion. Metabolomics analysis revealed 50 differentially expressed metabolites in the skin, which regulate cellular ion channels and participate in neurological channels by enriching ABC transporter protein pathways, amino acid biosynthesis and metabolism, and arachidonic acid metabolism. The findings of the present study could facilitate improvement of cashmere quality in cashmere goats.

genetics↗

MORC2 Mediates Transcriptional Regulation Through Liquid-Liquid Phase Separation and DNA Binding

MORC2 is a chromatin-associated ATPase essential for transcriptional silencing and genome stability, yet the biophysical principles governing its regulatory activity remain elusive. Here, we demonstrate that full-length MORC2 undergoes biomolecular condensation to form dynamic nuclear assemblies, a process fundamentally required for its repressor function. Endogenous MORC2 forms discrete, dynamic condensates in neurons from EGFP-MORC2 knock-in mice, supporting the physiological relevance of these assemblies in vivo. Mechanistically, a 3.1 [A] crystal structure of coiled-coil 3 (CC3) identifies a dimeric scaffold that serves as a structural hub, while multivalent sticker interactions between an intrinsically disordered region (IDR) and a newly defined IDR-binding domain (IBD) drive condensation. We show that DNA acts as a molecular scaffold that triggers MORC2 condensation, which in turn allosterically stimulates its ATPase activity. Critically, by employing a "killswitch" strategy to decouple assembly from internal fluidity, we reveal that only dynamic MORC2 condensates--not static aggregates or condensation-deficient mutants--can restore transcriptional repression in MORC2-knockout cells. Furthermore, pathogenic variants linked to CMT2Z and SMA differentially perturb these material properties and enzymatic turnover, providing a mechanistic link between condensate dysregulation and human neuropathies. Together, our findings establish a DNA-templated condensation mechanism for MORC2 and provide a molecular framework for understanding how the material state of chromatin-associated machinery dictates gene regulation and disease pathogenesis

cell biology↗

EpiPred: A gene-specific machine learning model for classifying missense variants in the epilepsy-related gene STXBP1

Missense variants in the STXBP1 gene are a frequent cause of early-onset developmental and epileptic encephalopathies and related neurodevelopmental disorders, but the clinical interpretation of these variants remains a major challenge. Most reported STXBP1 missense variants are classified as variants of uncertain significance (VUS), complicating diagnosis, counseling, and patient eligibility for precision therapies. Here, we developed EpiPred, a gene-specific machine learning classifier that predicts the pathogenicity of STXBP1 missense variants by integrating computational features with empirical evidence from cellular assays. Trained on a curated set of pathogenic and benign variants, EpiPred outperformed leading global prediction tools in accuracy, sensitivity, and specificity. We validated the models predictions using functional assays that measure protein abundance, solubility, stability, and interaction with the SNARE complex partner syntaxin 1. These biochemical readouts aligned closely with model outputs and enabled reclassification of several likely misdiagnosed variants. We deployed EpiPred in an interactive web application that allows clinicians, researchers, and patients to explore predictions for all possible missense variants in STXBP1. Our approach illustrates the power of gene-specific predictive modeling combined with experimental validation to improve variant interpretation and diagnostic resolution. By identifying likely pathogenic STXBP1 variants, including those that may respond to emerging therapies such as molecular chaperones, EpiPred supports more precise genetic diagnoses and offers a generalizable framework for other clinically relevant genes in neurological disease. ONE SENTENCE SUMMARYEpiPred improves STXBP1 variant interpretation, enabling precision genetic diagnoses and promoting access to targeted precision therapies

genetics↗

Sequence-Dependent Conformational Landscapes of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) exhibit highly dynamic and heterogeneous conformational ensembles that are strongly influenced by sequence features. While global properties such as chain compaction and scaling behavior have been widely studied, they often fail to resolve the fine-grained, sequence-specific structural variation that underlies IDP function. Here, we perform long-timescale atomistic simulations of 47 representative IDP sequences from the yeast proteome to systematically investigate the relationship between sequence composition and conformational ensemble. To analyze the high-dimensional structural data, we apply uniform manifold approximation and projection (UMAP), a nonlinear dimensionality reduction technique that preserves local structural relationships. The resulting low-dimensional embeddings effectively differentiate IDP ensembles and reveal a novel descriptor--local compactness asymmetry--that quantifies directional differences in chain organization. This metric, denoted{gamma} Rg , captures conformational features orthogonal to traditional global measures such as radius of gyration and end-to-end distance. We show that{gamma} Rg correlates with sequence-level asymmetries in charge and hydropathy, and that conformational dynamics preferentially occur in the more extended region of the chain. The simulation dataset generated in this work also provides a valuable resource for training machine learning models and developing improved coarse-grained force fields for disordered proteins.

biophysics↗

Sequestration of the phagocyte metabolite itaconate by P. aeruginosa RpoN promotes successful pulmonary infection

AbstractThe phagocyte immunometabolite itaconate, normally toxic to bacteria, functions as a signal to stimulate the adaptation of the pulmonary pathogen Pseudomonas aeruginosa to the lung. Itaconate is actively transported into P. aeruginosa where it induces {sigma}54 rpoN expression and co-valently binds cysteine residues on RpoN. RpoN not only functions as a sink to limit itaconate toxicity but S- itaconated RpoN promotes increased utilization of the Entner Doudoroff pathway, optimizing bacterial metabolism in the setting of inflammation. S-itaconation of RpoN directs a global metabolic response that fuels pulmonary infection.

microbiology↗

Production of unreduced microspores in Arabidopsis flowers cultivated in culture medium suggests a role of sucrose in facilitating meiotic cytokinesis

Live-imaging microscopy technology has been increasingly applied for meiosis study in plants, which largely relies on the set up of a healthy ex vivo culture system for inflorescences ensuring that the captured chromosomes dynamics approaches the natural features of meiosis. Here, we report that Arabidopsis thaliana flowers cultivated in a culture medium (CCM) composed of the half-strength Murashige and Skoog basal salt, MES, Myo-inositol, sucrose and agar produce diploid microspores due to occurrence of meiotic restitution. Cytological studies revealed adjacent nuclei distribution and incomplete cytokinesis at late meiosis II in meiocytes within the CCM flowers. Immunolocalization of -tubulin and the microtubule-associated protein MAP65-3 showed that the orientation of spindles at metaphase II and the organization of radial microtubule arrays at the tetrad stage are interfered, which explains the production of meiotically-restituted microspores. Moreover, the CCM flowers showed a gradually impaired expression of Aborted Microspores (AMS), a key transcription factor regulating tapetum development and meiotic cytokinesis. Interestingly, an increased supply of sucrose in culture medium promoted the expression of AMS and partially rescued haploid microspore formation in the CCM flowers. Taken together, this study suggests a role of sucrose in facilitating meiotic cytokinesis and gametophytic ploidy stability in plants. One-sentence summaryArabidopsis flowers cultivated in culture medium produce unreduced microspores due to interfered meiotic cytokinesis, which is partially rescued by increased sucrose supply.

plant biology↗

Clathrin-mediated endocytosis of ERECTA family receptors is essential for proper stomatal development in Arabidopsis

Stomata, specialized structures of plant epidermis, are crucial for gas (e.g. CO2, O2 and H2O) exchange between plants and the environment. Stomatal density and pattern are governed by ERECTA Family (ERf) receptor-like kinases (RLKs)-controlled signaling. Clathrin-mediated endocytosis (CME) is a new mechanism for the internalization of receptor to activate the downstream signaling in animals. Here, we found that mutation of CME components resulted in formation of stomatal clusters and thus increased stomatal index. The adaptor protein 2 {sigma} (AP2{sigma}) subunit of CME interacted with ERf. ERf receptor internalization required CME. Furthermore, the ERf receptor motifs were identified to be recognized by AP2{sigma}. Genetic analysis showed that CME components CHC2, CLC2, and CLC3 acted downstream of EPIDERMAL PATTERNING FACTOR 1/2 (EPF1/2) while upstream of YODA, and worked together with ERf to regulate stomatal development. Consistently, EPF2-induced MAPK activation was significantly reduced in chc2-2 clc2 clc3 and ap2 clc2 clc3 mutants or when the ERf endocytic motifs were mutated, leading to stabilized SPEECHLESS protein and misregulated stomatal lineage progression. Overall, our findings demonstrate that activation of the ERf receptors via internalization is essential for stomatal development, establishing a novel mechanism of CME-mediated receptor internalization activation in plants. Significance StatementStomatal development in Arabidopsis is well characterized, but how EPF-ERf signals activate the MAPK cascade remains unclear. While animals employ clathrin-mediated endocytosis (CME) for receptor internalization and signaling, this mechanism was unknown in plants. We identified CME as a novel regulator of stomatal development. The ERf receptors represent the first identified cargo proteins for AP2{sigma} in plants, undergoing internalization through CME. Clathrin acts downstream of EPF but upstream of YODA, and blocking ERf internalization impairs MAPK activation. Thus, ERf internalization is essential for downstream signaling, revealing a novel CME-dependent activation mechanism in plants.

cell biology↗

NLRP3 inflammasome is regulated in osteoclasts through a Tmem178-dependent mechanism that restricts calcium influx

Osteoclasts (OCs) differentiate from macrophages in response to RANKL. Here, we investigated the role of the NLRP3 inflammasome in mouse macrophages, with or without exposure to RANKL. Unexpectedly, we found that NLRP3 expression gradually declined during osteoclastogenesis but could be restored with LPS treatment. LPS and nigericin robustly activated this inflammasome in macrophages, as expected, but not in OCs. Mechanistically, we identified Tmem178, a protein that restrains Ca2+ release from the endoplasmic reticulum (ER) and highly expressed in OCs, as an inhibitor of this inflammasome. Notably, NLRP3 inflammasome activation was robust in OCs lacking Tmem178 or wild-type (WT) OCs exposed to high calcium concentrations. In vivo studies demonstrated that under the conditions where OCs efficiently release Ca2+ from bone, inflammasome formation was enhanced. Furthermore, deletion of Nlrp3 rescued osteopenia in Tmem178-/- mice. Thus, we found that Tmem178 uniquely restricts Ca2+ release from ER in OCs, thereby suppressing NLRP3 inflammasome activation. One Sentence SummaryThe NLRP3 inflammasome is silenced in the OC lineage by Tmem178 to prevent pathological bone loss.

immunology↗

The ten dollar proteome: low-cost, deep and quantitative proteome profiling of limited sample amounts using the Orbitrap Astral and timsTOF Ultra 2 mass spectrometers

Mass spectrometry (MS)-based proteomics remains technically demanding and prohibitively expensive for many large-scale or routine applications, with per-sample costs of hundreds of dollars or more. To democratize access to proteomics and facilitate its integration into more high-throughput multi-omic studies, we present a robust analytical framework for achieving in-depth, quantitative proteome profiling at a cost of approximately $10 per sample, termed the "$10 proteome." Using the Thermo Fisher Orbitrap Astral and Bruker timsTOF Ultra 2 mass spectrometers, we evaluated performance across sample inputs ranging from 200 pg to 100 ng and active gradient lengths from 5 to 60 minutes. Proteome coverage saturated within the low-nanogram input range, with [~]8000 protein groups quantified from as little as 10 ng of input and nearly 6000 protein groups from 200 pg. With already demonstrated low-cost one-pot sample preparation workflows that are appropriate for this sample input range, standardized MS acquisition settings, and high-throughput nanoLC operated at [~]10 min per sample, the $10 proteome becomes feasible. This study establishes a practical, scalable, and cost-effective foundation for global proteome profiling, paving the way for routine, large-scale applications in systems biology, clinical research and beyond.

systems biology↗

A structure-informed evolutionary model for predicting viral immune escape and evolution

Persistent emergence of viral variants capable of evading host immunity constitutes a significant threat to public health. This antigenic evolution frequently outpaces the development of vaccines and therapeutics, highlighting the necessity of predictive models surveilling the immune escape potential of emerging variants. However, existing models suffer from two key limitations: they inadequately incorporate protein structural information and neglect the importance of distinguishing large-impact mutations from neutral ones given multiple mutations. To address these gaps, we presented KEScape, a deep learning model designed to predict viral immune escape and evolution. KEScape integrates evolutionary context with protein structural information, introduces a novel top-K L2-differential pooling mechanism to prioritize mutations with large functional effects, and incorporates a supervised L2 margin loss to facilitate the L2-distance-based ranking of high-impact mutations. We demonstrated that KEScape significantly outperformed state-of-the-art models on the most comprehensive benchmark to date, comprising eleven deep mutational scanning experiments spanning diverse viruses. Furthermore, KEScape exhibited outstanding performance in the practical applications of identifying immune escape hotspots and variants in emerging lineages and real-time surveillance of lineages associated with WHO-designated variants of SARS-CoV-2. These results show that KEScape is an effective model to predict viral immune escape and evolution. Its capacity for early warning can directly inform public health interventions and guide the development of countermeasures, thereby mitigating the threat of future viral pandemics.

microbiology↗

Targeting RUNX1 in Macrophages Facilitates Cardiac Recovery

Despite advances in disease treatment, our understanding of how damaged organs recover and the mechanisms governing this process remain poorly defined. Here, we mapped the transcriptional and regulatory landscape of human cardiac recovery using single cell multiomics. Macrophages emerged as the most reprogrammed cell type. Deep learning identified the transcription factor RUNX1 as a key regulator of this process. Macrophage-specific Runx1 deletion recapitulated the human cardiac recovery phenotype in a chronic heart failure model. Runx1 deletion reprogrammed macrophages to a reparative phenotype, reduced fibrosis, and promoted cardiomyocyte adaptation. RUNX1 chromatin profiling revealed a conserved regulon that diminished during recovery. Mechanistically, the epigenetic reader BRD4 controlled Runx1 expression in macrophages. Chromatin activity mapping, combined with CRISPR perturbations, identified the precise regulatory element governing Runx1 expression. Therapeutically, small molecule Runx1 inhibition was sufficient to promote cardiac recovery. Our findings uncover a druggable RUNX1 epigenetic mechanism that orchestrates recovery of heart function.

immunology↗

The Dayhoff Atlas: scaling sequence diversity for improved protein generation

Organized information powers modern biology, a framework pioneered by Margaret Dayhoffs Atlas of Protein Sequence and Structure and advanced by todays databases and computational methods. Here, we extend this paradigm for the AI era, presenting the Dayhoff Atlas of protein sequence data and generative models to accelerate protein biology and design. The Atlas introduces GigaRef, the largest open dataset of natural proteins, spanning 3.34B genomic and metagenomic sequences across 1.70B clusters, and BackboneRef, which distills structural information from 240,811 synthetic backbones into 46M synthetic sequences. Leveraging these datasets, we trained the Dayhoff protein language models, which can predict mutation effects, scaffold structural motifs, and generate novel proteins within families. Training on metagenomic and structure-based synthetic sequences increased the expression rates of generated proteins, demonstrating the value of data diversity and scale. We release the Dayhoff Atlas code, datasets, and models under a permissive license to empower computation in protein design.

bioengineering↗

Functional screening of TCR-like antibodies for targeted cancer immunotherapy

Although hybridomas and display technologies have long been used in antibody discovery, identifying TCR-like antibodies that recognize major histocompatibility (MHC)-presented neoantigens remains an inefficient process. Here, we present a functional screening approach for antibody discovery based on T cell-specific functionality. By constructing Synthetic T cell receptor and Antigen Receptor (STAR)-T cells expressing antibody libraries and co-culturing them with target cells, we observed distinct antigen-specific STAR endocytosis and T cell activation. These two indicators are combined into an E-A functional index, which we demonstrate as an effective screening strategy for identifying antibodies with strict antigen sensitivity and specificity. Using this E-A functional screening method, we successfully discovered antibodies or nanobodies targeting cell-surface tumor antigens and neoantigens presented by human leukocyte antigen (HLA). These antibodies exhibited potent anti-tumor efficacy both in vitro and in vivo. Moreover, converting these antibodies into chimeric antigen receptors (CARs) and bispecific antibodies also induced T cell activation and tumor killing. In summary, our study establishes a robust functional screening strategy for identifying antibodies or TCR-like nanobodies targeting tumor-specific neoantigens, offering significant potential for advancing targeted cancer therapies.

immunology↗

CMG2 interaction with actin is required for growth factor-induced chemotaxis in endothelial cells.

Capillary morphogenesis gene 2 (CMG2/ANTXR2) is a cell surface receptor that contributes to corneal angiogenesis and is essential for orienting endothelial cell chemotaxis in growth factor gradients. However, the mechanism by which CMG2 transmits signals to orient endothelial cells is unknown. Here, we use affinity proteomics to identify proteins that interact with CMG2. This led us to investigate CMG2 interaction with F-actin in the context of serum and individual growth factors (bFGF/PDGF/VEGF) in both primary and immortalized endothelial cells. We also measured different matrix-protein-mediated changes in chemotaxis. We find that CMG2 function is matrix dependent, and that CMG2-actin interaction is required for serum- and growth-factor-induced chemotaxis. Inhibiting chemotaxis with CMG2 antagonists (collagen 6, penta-galloyl-glucose, or anthrax toxin protective antigen; PA) leads to the release of actin cytoskeleton from CMG2. Furthermore, CMG2 co-localizes with actin at the leading edge during live migration. This colocalization is disrupted by PA, which also disrupts directional movement. Finally, we demonstrate that the conserved actin binding domain of CMG2 directly binds to F-actin in vitro where it bundles F-actin, suggesting a mechanism by which it enables directional migration.

molecular biology↗

Procrastination partly reflects an evolutionary byproduct of non-planning impulsivity

Procrastination has immediately visible repercussions on health and survival resilience, yet shows stably heritable and remains increasingly pervasive across human societies. Despite a paradox, this behavior is theoretically explained to represent a byproduct of evolutionary advantages underlying impulsivity, yet not deciphered well by scientific evidences. After adjusting psychometric endogeneity, we demonstrate the unique predictive roles of non-planning impulsivity (NPI) during late adolescence and early adulthood uniquely predicts procrastination in later adulthood in a twin cohort (N = 154). This association was further replicated in two independent cohorts (N = 327, N = 1,543). Using AE models, in conjunction of single-paper meta-analytic synthesis (N = 3,656 twin pairs), we observed significant shared genetic contributions underlying this NPI-procrastination association (rg = 0.51, 95% CI: 0.18 - 0.84). Beyond to the phenotypic heritability, employing a Genome-Wide-Association Study (GWAS), six NPI-procrastination overlapping SNPs are identified, functionally accounting for neural dysregulation. Thus, leveraging neurodevelopmental normative modelling (N = 37,407), online meta-analytic estimations (k = 198, loci = 5,855) and seed-based d mapping estimates (N = 893), cortical deviations in the left dorsolateral prefrontal cortex (DLPFC) - the brain region showing highest probabilistic overlap mapping NPI to procrastination, partly explains their shared genetic variants, but are substantially independent in genetic contribution. Mendelian Randomization analysis finally indicates causal roles of NPI and procrastination both, to DLPFC deviations. Our findings empirically clarified this theory that procrastination partly derives from NPI as an evolutionary byproduct indeed, but is still unique in neurogenetic entities. Brief summaryProcrastination is a puzzling human behavior that compromises survival-relevant outcomes yet remains both widespread and heritable. Although theorized as a byproduct of impulsivitys evolutionary advantages, empirical support for this account has been limited. Here, we provide converging evidence across psychometric, genetic, and neuroimaging modalities to show that non-planning impulsivity during late adolescence and early adulthood uniquely predicts later procrastination, and that the two traits share significant genetic overlap. We further identify specific genetic variants and morphological deviations in the DLPFC that link, but also partially dissociate, their biological pathways. These findings clarify the evolutionary and neurogenetic architecture of procrastination and underscore its partial derivation from impulsivity alongside distinct developmental origins.

neuroscience↗

Genome-Wide Investigation of Transcription Factor Occupancy and Dynamics Using cFOOT-seq

Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences. Notably, cFOOT-seq, combined with FootTrack analysis, predicts TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.

molecular biology↗

mTORC1-Dependent Regulation of the CCL24-CCR3 Axis Controls Granuloma Formation and Maintenance in Sarcoidosis

Sarcoidosis is a chronic granulomatous disease marked by persistent inflammation and immune cell aggregation, yet its molecular underpinnings remain incompletely understood, hindering the development of effective targeted therapies. Here, we report that deletion of TSC1 or TSC2 in mice using a Fsp1-Cre leads to spontaneous formation of sarcoid-like granulomas, driven by hyperactivation of the mTORC1 pathway in fibroblasts and interstitial macrophages. Through inflammatory cytokine/chemokine array, we identified CCL24, a chemokine ligand for CCR3, as a key immunoregulatory molecule downregulated in both our murine model and sarcoid cohort plasma. Mechanistically, mTORC1 suppresses CCL24 expression via aberrant STAT3 signaling in fibroblasts and promotes CCR3 expression in interstitial macrophages, uncovering a novel regulatory axis in granuloma formation and maintenance. Pharmacological inhibition using rapamycin and azithromycin markedly attenuated granuloma burden and normalized CCL24-CCR3 signaling, underscoring the therapeutic relevance of this axis. Together, our study establishes a mechanistic link between mTORC1 activation, CCL24-CCR3 dysregulation, and granuloma persistence, offering not only a new insight into molecular mechanisms in sarcoidosis but also identifying promising targets for clinical intervention.

immunology↗