Biology subjects

Hu, Y.

Publications and source records attributed to Hu, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

ERAD Activity Distinguishes the Functional Heterogeneity of Hematopoietic Stem Cells

Hematopoietic stem cells (HSCs) rely on precisely controlled proteostasis to sustain lifelong self-renewal, yet whether intrinsic proteostatic characteristics can prospectively define functional diversity within the HSC pool remains unknown. In this study, we developed a dual-fluorescence reporter system to visualize endoplasmic reticulum-associated degradation (ERAD) activity in vivo and discovered that ERAD activity can prospectively predicts the long-term reconstitution potential of HSCs. Remarkably, ERAD states were maintained through self-renewal, revealing an inheritable "proteostatic memory" within the HSC pool. Transcriptomic and functional analyses identified SOCS2 as a key regulator of this process: SOCS2 inhibits JAK2 signaling to sustain ERAD activity, whereas hyperactive JAK2 interacts with the ERAD E3 ligase Hrd1 and suppresses VCP-mediated misfolded substrate. These findings define a SOCS2-JAK2-ERAD axis that connects cytokine signaling to intrinsic proteostasis remodeling, establishing ERAD activity as a predictive and heritable marker of HSC function and providing a conceptual framework for understanding hematopoietic stem cell heterogeneity.

cell biology↗

bioRxiv2025

Phylogenomics of Rhinogobius gobies reveal northern-southern divergence and trait evolution in China

The goby genus Rhinogobius represents a prominent radiation of freshwater fishes in East Asia, with China serving as its evolutionary hotspot harboring over 39 endemic species. Despite their ecological dominance in riverine ecosystems, phylogenetic relationships among mainland Chinese Rhinogobius species remain poorly resolved due to limited sampling and morphological conservatism, particularly in meristic traits traditionally used for classification. To address these knowledge gaps, we employed a nuclear gene enrichment approach to target 4,434 single-copy nuclear loci across 26 species spanning all major river basins in eastern and southern China. Our phylogenomic analyses based on sequence of 2,137 cleaned-up loci (477,822 bp) recovered a robust topology dividing Rhinogobius into three primary lineages: an early-diverging of R. similis sister to two major clades, the northern vs. southern clades exhibiting strong geographic structuring. Fossil-calibrated molecular dating placed the crown age of Rhinogobius at [~]9.33 million years ago (Ma) during the late Miocene, with a pivotal north-south divergence at [~]5.96 Ma coinciding with major paleo-drainage reorganizations in East Asia. Ancestral state reconstruction revealed that the southern clade uniquely evolved unstable first dorsal fin formula and near-universal presence of predorsal scales. By integrating the most extensive geographic and taxonomic sampling to date with phylogenomic data, this study establishes: (1) a revised evolutionary timeline for Rhinogobius diversification linked to East Asian geomorphological history, (2) diagnostic morphological characters for major clades, and (3) a robust phylogenetic framework to guide future taxonomic revisions and conservation efforts for this ecologically significant group. HighlightsO_LIPhylogenomics resolves north/south split in Chinese Rhinogobius gobies. C_LIO_LIFossil-dated 9.3 MYA origin of Rhinogobius and rapid divergence at 5.96 MYA. C_LIO_LISouthern lineages exhibit more predorsal scales and unstable first dorsal fin formula. C_LIO_LIFirst genomic backbone for species revision and adaptation study. C_LI

zoology↗

bioRxiv2025

BioLACE: unifying spatial geometry and marker priors for cohesive cell-type clustering in spatial transcriptomics

Spatial transcriptomics (ST) provides high-dimensional gene expression profiles together with spatial coordinates, enabling the reconstruction of tissue architecture at cellular resolution. While recent graph-based deep learning methods have advanced spatial clustering in ST, many rely on complex architectures that obscure interpretability and rarely integrate biological priors such as marker gene information. We introduce BioLACE, a scalable framework that unifies spatial structure, transcriptomic variation, and curated marker gene profiles within a shared Variational Autoencoder (VAE) latent space. BioLACEjointly optimizes three complementary objectives: (1) a VAE reconstruction loss to preserve transcriptional structure, (2) a graph Laplacian regularizer to enforce spatial smoothness, and (3) a temperature-scaled InfoNCE contrastive loss guided by marker-informed similarities. Applied to MERFISH hypothalamus, mouse spinal cord, and Slide-seq mouse cerebellum datasets, BioLACE achieves superior cell type clustering accuracy, well-defined biologically consistent boundaries, and interpretable latent representations, highlighting its generality and scalability for modern ST analysis. The source code and tutorials for BioLACE are publicly available at https://github.com/maiziezhoulab/BioLACE.

genomics↗

bioRxiv2025

Induced ubiquitination bypasses canonical ERAD to drive ER protein degradation

Heterobifunctional proteolysis-targeting chimeras (PROTACs) have emerged as a powerful strategy to degrade disease-relevant proteins, enabling targeting of previously "undruggable" proteins. Current degrader molecules primarily target cytosolic substrates, yet nearly one-third of the proteome resides in or transits the endoplasmic reticulum (ER), including receptors, secreted factors, and biosynthetic enzymes with high therapeutic relevance. Whether ER-localized proteins can be broadly targeted for induced degradation remains an open question. To address this gap, we employed a panel of fluorescent reporter cell lines and used the dTAG chemical-genetic system to recruit cytosolic E3 ligases. While lumenal substrates segregated from the cytosol were resistant to degradation, recruitment of cytosolic ligases effectively degraded ER membrane proteins across multiple topologies and with post-translational modifications. CRISPR genetic screens revealed that the induced degradation required the expected cullin RING ligase complexes but surprisingly bypassed ER-associated degradation (ERAD) machinery, with the exception of the AAA ATPase VCP. Mechanistic studies demonstrated that substrate ubiquitination was essential for VCP binding, and cleavage of ubiquitin chains released VCP, suggesting a model in which VCP directly extracts substrates independent of a dislocation apparatus. Extending this strategy to an endogenous substrate, we synthesized an HMGCR ERAD-TAC by linking atorvastatin to a cereblon E3 ligase recruiter and found that HMGCR degradation was likewise VCP-dependent. Together, these findings demonstrate that ER membrane proteins are generally susceptible to induced degradation via cytosolic ligase recruitment, uncovering a VCP-centered mechanism that operates independently of membrane-embedded ERAD machinery. This work establishes foundational principles for extending targeted protein degradation to the early secretory pathway. SIGNIFICANCE STATEMENTTargeted protein degradation has transformed drug discovery. Nearly one-third of the proteome reside in or transit the endoplasmic reticulum (ER), a compartment rich in therapeutically relevant but structurally complex targets. Whether these ER proteins can be broadly degraded using PROTACs has remained unknown. Here, we define the minimal requirements for degrading ER membrane proteins by recruiting cytosolic E3 ligases. Using chemical-genetic tools, genetic screens, and a statin-based degrader, we show that ubiquitination engages the VCP extraction machinery, enabling degradation of diverse ER membrane proteins independent of canonical ER-associated degradation components. These findings reveal a ubiquitin-driven route for membrane protein turnover, expand the landscape of druggable ER proteins, and establish principles for designing degraders operating in the early secretory pathway.

cell biology↗

bioRxiv2025

Reverse Spatiotemporal Hierarchy during Cross-modal Memory Recall and Imagery

Recalling past events is often accompanied by mental imagery of those experiences. Based on previous research, this process engages memory- and sensory-related brain areas. However, the underlying spatiotemporal dynamics remain poorly investigated. Here, we used naturalistic videos of audiovisual events and recorded fMRI data during the tasks in which human participants recalled visual contents when hearing associated sounds and recalled sounds when watching silent videos, after they had well memorized the video contents. With time-resolved fMRI multivariate pattern analyses, we observed reverse spatiotemporal hierarchy during the visual memory recall and imagery: the neural activity in primary visual cortex was delayed compared with high-order visual areas. A similar pattern was found during auditory memory recall and imagery, where the bottom-up progression from the mid-level planum temporale to the high-level superior temporal gyrus observed during auditory perception was absent. However, the primary auditory area was not involved, suggesting modality differences in the role of primary sensory areas in corresponding memory recall. We also observed the activity of the hippocampus, the parahippocampal cortex, the retrosplenial cortex, and the precuneus and examined their temporal dynamics. Overall, our study provided both spatial and temporal accounts of neural activity during the cross-modal memory recall and imagery.

neuroscience↗

bioRxiv2025

PKU tags, novel genetically encoded shape tags for cell labeling in light and electron microscopy

Distinguishing among neuronal cell types is crucial for deciphering complex neural networks and brain functions. However, the current repertoire of cell-labeling tools compatible with light microscopy (LM) and/or electron microscopy (EM) is limited compared to the vast number of cell types in the brain. Here, we introduce PKU (polymer king-size unit) tags, genetically encoded "shape tags" that leverage the polymerization of self-assembling proteins, spectrally distinct fluorescent proteins and, optionally, a nuclear targeting sequence to generate a series of multi-shaped (spherical or filamentous), multi-colored (blue, green, red, near-infrared) and multi-localized (cytosolic or nuclear) tags. By co-expressing multiple PKU tags within the same cell, a combinatorial strategy further expands the repertoire, which can theoretically yield hundreds of unique labeling patterns. Expressing PKU tags in vivo provides multi-cell-type labeling and neuronal circuit tracing, without altering the animals behavior or transcriptomic profiles. Moreover, when fused to the peroxidase APEX2, PKU tags maintain their shape-specific features, providing shape "barcoding" using EM. Thus, PKU tags represent a versatile and efficient toolkit for studying connectomics using both LM and EM.

neuroscience↗

bioRxiv2025

Delivery of collagen-encoding mRNA to the skin for cosmetic applications

Collagens, the predominant structural proteins in mammalian, maintain tissue integrity through its unique triple-helical conformation. Traditionally, cosmetic collagens have been administered as hydrolyzed peptides derived from animal sources, which exhibit poor bioavailability and functional efficacy due to limited skin penetration and disrupted tertiary/quaternary structures. To overcome these limitations, we developed a novel system for in vivo collagen expression. This system utilizes the topical application of in vitro synthesized, AI-designed mRNAs encoding types I, III, and XVII collagens to improve human skin condition. Significant upregulation of target collagen expression was observed in dermal fibroblasts, leading to improved skin condition through in situ assembly of collagens in natural conformation.

bioengineering↗

bioRxiv2025

Uncovering novel therapeutics for schizophrenia: a multitarget approach using the CANDO platform

Schizophrenia is a complex and debilitating neuropsychiatric disorder characterized by positive, negative, and cognitive symptoms, many remaining insufficiently addressed by current treatments. High rates of treatment resistance and heterogeneous pathophysiology pose significant challenges to traditional single-target drug discovery. To address this, we applied the CANDO platform to identify repurposable drugs for schizophrenia using a multitarget strategy. The platform evaluates how compounds interact with the entire human proteome, generating interaction signatures that capture a compounds effect across all targets. By comparing these signatures, CANDO computes compound similarity scores and enables consensus prediction of novel therapeutics. Across all indications and for schizophrenia in particular, CANDO outperformed controls by orders of magnitude across several benchmarking metrics, accurately recovering known drug-indication relationships. We applied our CANDO pipeline, benchmarked by its ability to recover approved drugs for their indications using similarity- and consensus-based metrics, to generate a ranked list of repurposable compounds. Our comprehensive literature review confirmed clinical or biochemical evidence supporting 25 high-corroboration drug candidates, including phenothiazine and benzamide antipsychotics, tricyclic antidepressants, benzodiazepines, and monoamine oxidase inhibitors. We identified protein targets with the highest likelihood of interaction with these top drugs and assessed prediction quality through overlap analysis with gold standards, showing significantly better concordance with established schizophrenia-related biology than controls from bottom-ranked and randomly selected drugs. Among these proteins are corroborated targets such as canonical neurotransmitter receptors of the dopamine, serotonin, and adrenergic classes, as well as monoamine transporters, tyrosine aminotransferase, and lysine-specific histone demethylase 1A. Enrichment of calcium-binding proteins among the top predicted targets for the phenothiazine antipsychotic thiethylperazine highlights a potential role for dysregulated calcium signaling, including calmodulin-CaMKK2 pathways, in schizophrenia pathology and treatment response. Another phenothiazine antipsychotic, triflupromazine, binds the serotonin transporter in addition to its canonical dopamine D2 receptor interaction, highlighting its potential relevance to depressive symptom modulation in schizophrenia. These findings demonstrate the utility and accuracy of the CANDO platform in elucidating multitarget pharmacological mechanisms and accelerating the identification of effective repurposable treatments for schizophrenia.

bioinformatics↗

bioRxiv2025

Failure of DNA repair leads to the tumorigenic transformation of a regenerating blastema in Drosophila imaginal discs

We present a Drosophila model demonstrating that repeated cycles of tissue regeneration following localized apoptosis can induce tumorigenesis in the absence of oncogene activation or tumor suppressor loss. Chronic regenerative stress leads to epithelial disorganization, loss of cell polarity, immune cell infiltration, DNA damage, centrosomal defects, and aneuploidy-- classical hallmarks of cancer. A subset of "walking dead" cells resists apoptosis and contributes to tissue overgrowth and heterogeneity. Single-cell transcriptomics identifies a distinct cell population, absent from normal tissue, emerging under both regenerative and tumorigenic conditions and characterized by enrichment in JNK pathway components. The tumorigenic signature specifically features distinctive JNK regulatory elements while excluding chaperone proteins. Notably, inhibition of JNK signaling or modulation of DNA repair suppresses neoplastic transformation. This model reveals how chronic injury and defective regeneration drive cancer initiation, establishing a mechanistic link between wound healing and tumorigenesis, and providing a powerful system to explore early tumor development and therapeutic intervention.

developmental biology↗

bioRxiv2025

AAV-mediated CSNK2B gene replacement rescues ASD-relevant phenotypes and establishes EEG biomarkers for translation in Csnk2b haploinsufficient mice

De novo CSNK2B variants are strongly associated with autism spectrum disorder (ASD) and early-onset epilepsy, yet in vivo therapeutic evidence and translatable biomarkers remain limited. We generated Csnk2b haploinsufficient (Csnk2b+/-) mice that recapitulate core clinical features--ASD-like social and cognitive deficits, heightened anxiety, spontaneous seizures, cortical and hippocampal structural compromise, and reduced PV-interneuron density with impaired cortical inhibition. Neonatal brain-wide AAV-PHP.eB-mediated CSNK2B replacement (hsyn or CAG promoters, retro-orbital P3) restored cortical/hippocampal structure, normalized neuronal numbers, prolonged survival, and ameliorated seizures and ASD-like behaviors with comparable efficacy across promoters. Critically, treatment also corrected quantitative EEG signatures that are directly deployable in human trials: theta and gamma band power were normalized, theta/gamma (and beta/gamma) ratios recovered, and inter-areal coherence and gamma-band effective connectivity were restored, indicating re-established excitation/inhibition balance and large-scale network coordination. These EEG endpoints constitute a compact, noninvasive biomarker panel of target engagement and physiological efficacy that can be harmonized with clinical EEG to support dose finding, early decision-making, and longitudinal monitoring in CSNK2B gene-therapy trials. Together, our data provide preclinical proof-of-concept that early AAV-mediated CSNK2B replacement is therapeutically effective and nominate band-limited EEG metrics as translational readouts to accelerate first-in-human studies for CSNK2B-linked neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

SELEX-HTCFQ Platform: Developing DNA Enhancers of ADAR1 to Suppress ZBP1-Dependent Immunopathology

Excessive immune activation drives pathological inflammation through dysregulated ZBP1 signaling, yet this sensor remains crucial for immune surveillance, necessitating targeted therapies that selectively inhibit pathology while preserving protective functions. Here, we developed an innovative SELEX-HTCFQ platform that combines Systematic Evolution of Ligands by Exponential Enrichment (SELEX) with high-throughput competitive fluorescence quenching (HTCFQ) to identify ADAR1-specific enhancers. Capitalizing on ADAR1s natural ability to suppress ZBP1 via competitive Z-nucleic acid binding, this platforms dual assessment of affinity and selectivity identified aptamer A4, a highly specific ADAR1 enhancers demonstrating over 40-fold selectivity over ZBP1. A4 allosterically modulates ADAR1s activity, thereby potentiating its inhibitory effect on ZBP1, which not only mitigates the excessive inflammatory response but also maintains the delicate balance of the immune system. These ADAR1 enhancers represent precision molecular tools for reprogramming Z-nucleic acid sensing, offering a promising therapeutic paradigm for cytokine storm syndromes and necroptosis-driven disorders through selective pathway modulation.

biochemistry↗

bioRxiv2025

Molecular Mechanisms Underlying Human Vγ9Vδ2 T Cell Activation by Butyrophilin-3 (BTN3) Targeted Antibodies

{gamma}{delta} T cells express T cell receptors (TCRs) composed of paired {gamma} and {delta} chains. The V{gamma}9V{delta}2 T cells are the main subpopulation of {gamma}{delta} T cells in human peripheral blood, which responds to phosphoantigens (pAgs) through butyrophilins (BTN) molecules, such as BTN3A1/2/3 and BTN2A1. Antibodies targeting BTN3As, such as ICT01, can activate V{gamma}9V{delta}2 T cells independently of pAgs, although the underlying mechanism remains poorly characterized. In this study, we reveal the molecular basis of ICT01-mediated V{gamma}9V{delta}2 T cell activation using structural, biochemical, and cellular analyses. ICT01 binds to a unique region in the extracellular domain of BTN3As, destabilizing the BTN2A1-BTN3As interface and facilitating V{gamma}9V{delta}2 TCR engagement, ultimately resulting in activation of V{gamma}9V{delta}2 T cells. Our findings provide insights into the mechanism by which agonist antibodies induce {gamma}{delta} T cell activation and provide guide strategies for developing BTN-targeted immunotherapies.

immunology↗

bioRxiv2025

A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome

AbstractProtein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-guided atlas of the human and Drosophila kinome, built by applying a new interface-aware scoring framework (iLIS) to AlphaFold-Multimer predictions. The resulting atlas recapitulates hallmark sequence preferences, confirms previously reported and functionally related protein-protein interactions, and uncovers unrecognized docking interactions. Notably, our analysis predicts a potentially widespread docking motif on homeodomain transcription factors that mediates interactions with basophilic kinases. Furthermore, we map putative allosteric interaction hotspots across the kinome and provide proof-of-concept evidence that targeting these surfaces can inhibit kinase activity. Finally, we demonstrate the physiological utility of the atlas by identifying a novel regulatory mechanism between Sgg/GSK3 and Hnf4 that controls lipid metabolism in vivo. This resource provides a blueprint for dissecting signaling networks and for the rational design of docking-site-specific kinase modulators.

bioinformatics↗

bioRxiv2025

Cell-Intrinsic Vulnerability and Immune Activation Cooperate to Drive Degeneration in a Mitochondrial Complex I Deficiency Model of Optic Neuropathy

Mitochondrial dysfunction is a central hallmark of many optic neuropathies, yet the mechanisms linking intrinsic metabolic stress to retinal ganglion cell (RGC) degeneration remain unclear. To bridge this gap, we developed conditional transgenic models targeting the mitochondrial complex I subunit Ndufs4 in the retina. Broad deletion of Ndufs4 in the retina resulted in vision loss, progressive RGC degeneration, and pronounced immune activation before overt RGC death. Strikingly, depletion of myeloid cells significantly preserved RGCs, demonstrating that inflammation is not simply a downstream consequence but a participant in the degeneration process. To further distinguish between intrinsic and extrinsic mechanisms, we generated a mosaic model in which only subsets of retinal cells lacked Ndufs4. In this paradigm, the degeneration first appeared selectively in mutant regions, suggesting that mitochondrial impairment within RGCs is necessary to initiate vulnerability. At later stages, however, the degeneration extended beyond mutant territories, highly suggestive of a propagation through non-cell autonomous processes. Together, these findings support a model in which mitochondrial dysfunction creates the conditions for neuronal vulnerability, while immune responses govern the timing and extent of cell loss. This framework explains the consistent co-occurrence of metabolic deficits and neuroinflammation in optic neuropathies and highlights the importance of their interactions in disease progression. By clarifying the intersection of intrinsic and extrinsic mechanisms, this work advances our understanding of RGC degeneration and provides a conceptual basis for deciphering pathogenic processes across diverse optic neuropathies.

neuroscience↗

bioRxiv2025

A family of lethal exotoxins defined by cell entry via the Attractin receptor

Although bacterial genomes encode numerous potential toxins, it is unclear how evolution drives the specificity of these important virulence factors. Using an insect CRISPR screen, we identified the transmembrane protein Attractin (ATRN) as the receptor for Nigritoxin (Ntx), a Vibrio toxin that causes seasonal shrimp pandemics. We found that Ntxs effector "warhead" inhibits translation via a previously uncharacterized mechanism. Moreover, we show that two related toxins require ATRN for entry but possess unrelated effector domains. One has a Rho-GTPase AMPylation function and the other an actin-targeting/proteolysis function. Our findings reveal the mechanism of Ntx entry and toxicity and show that the ATRN-targeting domain can deliver disparate effector domains, strongly indicating that this class of exotoxins can evolve as modular proteins using a common entry domain.

microbiology↗

bioRxiv2025

Hepatic ceramide synthesis links systemic inflammation to organelle dysfunction in cancer

Paraneoplastic syndromes arise when tumor-derived cytokines reprogram distant organs. Although mediators such as Interleukin-6 have been implicated, how these signals impair host organ function remains incompletely defined. Here, we identify a cytokine-lipid axis that drives hepatic autophagy dysfunction. Specifically, in Drosophila, the gut tumor-derived interleukin-like cytokine Upd3 induces the expression of the triglyceride lipase CG5SCC, which we named "cancer-associated lipid mobilizer (calm)", and the ceramide synthase schlank in the fat body. This upregulation rewires fat body lipid metabolism, resulting in an autophagic-flux blockade. Genetic reduction of either CG5SCC or schlank restores organelle homeostasis and mitigates paraneoplastic phenotypes. This mechanism is conserved in mammals: in mice, IL-6 upregulates the lipoprotein lipase Lpl and ceramide synthases which in turn trigger a hepatic autophagy-flux blockade; in humans, hepatic LPL and ceramide synthases expression correlates with poorer survival in hepatocellular carcinoma. Our findings position hepatic lipid metabolism rewiring, especially ceramide synthesis as a critical, conserved node coupling systemic inflammation to organelle dysfunction, and suggest this pathway as a possible therapeutic entry point for cancer-associated liver disorders.

genetics↗

bioRxiv2025

Mechanism of Sanliangsan Lipid-Lowering in treating hyperlipidemia: insights from network pharmacology and molecular docking

Background and ObjectiveThis study aimed to identify the active ingredients, key targets, and signaling pathways of Sanliangsan Lipid-Lowering (SLL) in the treatment of hyperlipidemia (HLP) using network pharmacology, and to further clarify the material basis and mechanism responsible for its lipid-lowering efficacy. MethodsAll active ingredients of SLL were retrieved from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), followed by the identification of target proteins corresponding to each active ingredient. Target genes associated with these target proteins were obtained from the Uniprot database, with duplicate genes excluded to generate the predicted targets of the active ingredients.Cytoscape was utilized to construct the "Herb-Active Ingredient-Predicted Target" network for SLL. Targets related to hyperlipidemia (HLP) were retrieved from the GeneCards, OMIM, and DrugBank databases using "hyperlipidemia" as the keyword. The intersection of the predicted targets of SLL active ingredients and HLP-related targets was defined as the potential therapeutic targets of SLL for HLP. Utilizing Cytoscape 3.9.1 software, the top 20 targets with the highest Degree values were selected to construct the "Herb-Active Ingredient-Target-Disease" network, (esignated as the "Herb-Active Ingredient-Target Network of SLL against HLP." The STRING database was employed to build a protein-protein interaction (PPI) network of the potential therapeutic targets, which was subsequently analyzed using the Network Analysis, CytoNCA, and CytoHubba plugins in Cytoscape to identify the top 10 key targets. The Metascape platform was used for Gene Ontology (GO) functional analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the key targets, and the Bioinformatics online tool was applied to visualize the analytical results. Furthermore, AutoDock Tools 1.5 software was utilized to perform molecular docking between the active ingredients and key targets, thereby validating the results of the network pharmacology analysis. ResultsA total of 115 active ingredients and 255 corresponding predicted targets of SLL were screened from the TCMSP database. Additionally, 2106 HLP-related targets were retrieved from the aforementioned databases, and 140 common targets (potential therapeutic targets) were identified through intersection analysis. From these common targets, the top 20 with the highest Degree values were selected for the construction of the "Active Ingredient-Potential Target-Disease" network. Network analysis revealed that kaempferol, quercetin, and formononetin were the top three active ingredients in terms of content, while tumor necrosis factor (TNF), interleukin-6 (IL6), protein kinase B1 (AKT1), interleukin-1{beta} (IL1B), prostaglandin-endoperoxide synthase 2 (PTGS2), peroxisome proliferator-activated receptor {gamma} (PPARG), caspase 3 (CASP3), and hypoxia-inducible factor 1 (HIF1A) were the targets associated with the largest number of active ingredients. The PPI network consisted of 140 nodes and 3,207 edges. By using the CytoHubba plugin for analysis, six key targets were identified: AKT1, TNF-, IL-1 {beta}, IL6, PPARG and PTGS2. The GO functional enrichment analysis revealed 30 entries, which encompassed 10 biological processes (such as positive regulation of transcription by RNA polymerase II), 10 cellular components (such as extracellular space), and 10 molecular functions (such as transcription coactivator binding). Additionally, 10 KEGG signaling pathways were identified, including Lipid and atherosclerosis, the AGE-RAGE signaling pathway in diabetic complications, and Fluid shear stress and atherosclerosis. The findings indicated that SLL exerts a therapeutic effect on HLP by regulating multiple signaling pathways. Molecular docking results demonstrated that the binding energies of the three core ingredients--kaempferol, quercetin, and formononetin--with all key targets were less than -5.0 kJ/mol, with the lowest binding energy (-10.1 kJ/mol) observed between formononetin and PTGS2, indicating a strong binding affinity between these two molecules. ConclusionThis study identified the potential active ingredients, key targets, and core signaling pathways of SLL in treating HLP, confirming that SLL exerts its lipid-lowering effect through a synergistic "multi-component, multi-target, multi-pathway" mechanism. It provides a theoretical basis for further experimental validation and clinical application of SLL in managing HLP.

molecular biology↗

bioRxiv2025

Phosphoantigen-Driven Dissociation of Butyrophilin Oligomers Activates γδ T Cells

{gamma}{delta} T cells represent a promising avenue for cancer immunotherapy. The V{gamma}9V{delta}2 T cell receptor (TCR), expressed by the predominant subset of {gamma}{delta} T cells, responds to phosphoantigen (pAg)-engaged butyrophilins (BTNs) on various cancer cells. However, the molecular mechanism underlying pAg-mediated activation of V{gamma}9V{delta}2 TCRs remains a subject of debate. Here, we employed an integrative approach to elucidate the mechanism of pAg reactivity in V{gamma}9V{delta}2 T cells. Our results demonstrate that BTNs form higher-order oligomers in the absence of pAg. Upon pAg binding, these oligomers dissociate into tetramers, enabling V{gamma}9V{delta}2 TCR engagement. This pAg-induced dissociation of higher-order BTN complexes is critical for pAg-mediated activation of {gamma}{delta} T cells. Our findings reveal a mechanism of BTN dissociation-driven pAg sensing, providing valuable insight for future immunotherapeutic strategies.

immunology↗