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Yu, J.

Publications and source records attributed to Yu, J..

At least 145 records · Page 8Linked to original sources

SOX2 is a dispensable modulator of NUT carcinoma oncogenesis in mouse

NUT carcinoma (NC) is a highly aggressive malignancy driven by BRD4::NUTM1 and other NUTM1 fusion oncogenes. BRD4::NUTM1 aberrantly activates transcription factors (TFs) linked to basal progenitor identity, producing poorly differentiated squamous phenotypes. Among these TFs, SOX2 has been proposed as a critical oncogenic driver, but its functional requirement in NC has not been tested in vivo. Using a genetically engineered mouse model that faithfully recapitulates human NC, we performed lineage-specific conditional deletion of Sox2 in both squamous and non-squamous tissues. We found that Sox2 is dispensable for NC initiation and progression, with tumors retaining characteristic histology and expression of key drivers including BRD4::NUTM1, MYC, and TP63. Transcriptomic profiling revealed only modest changes in Sox2-deficient tumors, mainly affecting metabolic and biosynthetic pathways, without disrupting core oncogenic programs. These findings challenge the assumption that SOX2 is universally required in NC and suggest that SOX2-targeted therapies may have limited utility, refining the framework for therapeutic prioritization. Summary blurbThis study shows that SOX2 is not required for NUT carcinoma initiation or maintenance in vivo, challenging its assumed oncogenic role and refining therapeutic target prioritization.

cancer biology↗

CloneCoordinate: Open-source software for collaborative DNA construction

Custom DNA constructs have never been more common or important in the life sciences. Many researchers therefore devote substantial time and effort to molecular cloning, aided by abundant computer-aided design tools. However, support for managing and documenting the construction process, and for effectively handling and reducing the frequency of setbacks, is lacking. To address this need, we developed CloneCoordinate, a free, open-source electronic laboratory notebook specifically designed for cloning and fully implemented in Google Sheets. By maintaining a real-time, automatically prioritized task list, a uniform physical sample inventory, and standardized data structures, CloneCoordinate enables productive, collaborative cloning for individuals or teams. We demonstrate how the information captured by CloneCoordinate can be leveraged to troubleshoot assembly problems and provide data-driven insights into cloning efficiency. CloneCoordinate offers a new and uniquely accessible model for how to carry out, and iteratively improve on, real-world DNA assembly.

synthetic biology↗

Med14 phosphorylation shapes genomic response to GLP-1 Agonist

Under feeding conditions, release of glucagon-like peptide (GLP-1) from intestinal L cells promotes insulin secretion and pancreatic beta cell viability. Binding of GLP-1 to its cognate receptor on the beta cell surface results in induction of the cAMP signaling pathway, leading to the protein kinase A (PKA) mediated phosphorylation of CREB and induction of CREB target genes. By contrast with the acute effects of this pathway on immediate early CREB target genes, which attenuate the cAMP-CREB response, sustained exposure of beta cells to the stable GLP-1 receptor agonist Exendin-4 stimulates the expression of beta cell specific CREB target genes with delayed kinetics. In a proteomic screen for transcriptional co-regulators that mediate the long-term effects of GLP-1 analogs, we identified Med14, a backbone subunit of the Mediator complex. Exposure to Exendin-4 stimulates Med14 phosphorylation at Ser983, corresponding to a conserved PKA recognition site (RRXS) that is located within an intrinsically disordered region of Med14. Phosphorylation of Med14 by PKA is essential for maintenance of enhancers that drive induction of beta cell-specific and diabetes-linked genes. Mutation of Med14 at Ser983 to alanine decreased beta cell numbers and repressed Exendin-4 induced gene regulation in primary mouse beta cells. Our work reveals how phosphorylation of a general transcription factor in response to GLP-1 analogs triggers a broad genomic response with salutary effects on beta cell function.

genomics↗

Human CXCL17 Activates and Binds to Fish GPR25 Orthologs

C-X-C motif chemokine ligand 17 (CXCL17) functions as a chemoattractant, though its receptor has been controversial. Recent independent studies, including our own, identified CXCL17 as an agonist for the orphan G protein-coupled receptor 25 (GPR25). While GPR25 orthologs are found across fishes to mammals, CXCL17 orthologs appear to be mammalian-specific, leaving the endogenous ligand for non-mammalian GPR25 orthologs unknown. This study unexpectedly found that human CXCL17 exhibits high activity towards GPR25 orthologs from the zebrafish (Danio rerio) and coelacanth (Latimeria chalumnae). Recombinant human CXCL17 efficiently activated both fish GPR25 orthologs in a NanoLuc Binary Technology (NanoBiT)-based {beta}-arrestin recruitment assay, and induced chemotactic movement in transfected human embryonic kidney (HEK) 293T cells expressing fish GPR25. A human CXCL17 mutant lacking three C-terminal residues showed no such effect. A NanoBiT-based binding assay revealed that a SmBiT-tagged human CXCL17 C-terminal fragment specifically bound to secretory large NanoLuc fragment (sLgBiT)-fused fish GPR25 orthologs. Fish GPR25 orthologs had significantly higher cell surface expression in transfected HEK293T cells compared to human GPR25, improving {beta}-arrestin recruitment assay data quality. Despite approximately 400 million years of divergence between humans and fishes, the high activity of human CXCL17 on fish GPR25 orthologs suggests that the CXCL17-GPR25 pair may be conserved across all vertebrates, even though non-mammalian CXCL17 orthologs remain unidentified.

biochemistry↗

Advancing Ligand Binding Affinity Prediction with Cartesian Tensor-Based Deep Learning

0.We present PBCNet2.0, a cartesian tensor-based Siamese Neural Network for protein-ligand relative binding affinity prediction. Trained on 8.6 million protein-ligand complex structure pairs, PBCNet2.0 achieves zero-shot performance comparable to computationally intensive physics-based simulations. Our prioritization experiments show that PBCNet2.0 speeds up binding affinity optimization by 718% while reducing resource use by 41%. Through extensive retrospective experiments, we demonstrate that PBCNet2.0 intrinsically comprehends protein-ligand interactions, showing high sensitivity to intermolecular interactions and exceptional perception of spatial geometric information. Strikingly, PBCNet2.0 exhibits an emergent capability to predict affinity changes induced by binding residue variations, highlighting its potential for identifying resistance mutation. We prospectively validated these capabilities on two targets ENPP1 and ALDH1B1, where PBCNet2.0 successfully identified affinity shifts arising from subtle molecular interactions and conformational differences, and pinpointed critical binding residues with an 83% hit rate. This combination of computational efficiency, spatial geometric perception of binding site, and generalizable affinity prediction establishes PBCNet2.0 as a transformative tool for developing pharmacological probes for all human proteins.

molecular biology↗

Expression of Lysyl Oxidase Family Enzymes During Human Endometrial Decidualization

Lysyl oxidases (LOXs), comprising lysyl oxidase (LOX) and lysyl oxidase like 1-4 (LOXL1-4), constitute a highly conserved enzyme family. Their primary function is the crosslinking of collagen and elastic fibers, thereby modulating the structure and function of the extracellular matrix. Our primary objective was to elucidate the localization of LOXs within human endometrial tissues and to investigate the expression profile of LOXs during in vitro human endometrial stromal cell decidualization. Immunohistochemical localization revealed that all LOXs were expressed in human endometrium during both the proliferative and secretory phases of menstrual cycle. All five LOXs were expressed in human endometrial stromal cells cultured in vitro. Gene expression levels of LOX, LOXL1, and LOXL2 significantly decreased during endometrial stromal cell decidualization in vitro. In contrast, LOXL3 and LOXL4 gene expression remained unaffected. Protein levels of LOX, LOXL1, and LOXL3 also showed a significant reduction. Additionally, conditioned media analysis revealed abundant secretion and release of LOX and LOXL1-3 into the extracellular space at all time points examined, with their levels remaining constant. The primary targets of LOXs, collagen and elastic fibers, undergo significant synthesis and processing during endometrial stromal cell decidualization in vitro. This observation was supported by the differential gene expression levels of factors involved in their processing and assembly. Collectively, this study demonstrates the expression of LOXs in the human endometrium and their potential role in extracellular matrix reorganization during decidualization.

cell biology↗

Source tracking of larval bacterial community of Pacific white shrimp across the developmental cycle: ecological insights for microbial management and pathogen prevention in larviculture

Health of postlarvae (as products of larviculture) of Pacific white shrimp (Penaeus vannamei) is critical to subsequent culture. Larval microbiota establishment has potential long-term impact on host health, but bacterial sources of larval shrimps remain largely unexplored. We investigated the larviculture cycles of two shrimp strains by utilizing 16S rRNA gene sequencing alongside mainstream microbial source-tracking tools. Our goal was to evaluate the contributions of environmental elements, feeds, and internal succession to larval bacterial community. Regardless of shrimp strains or tools, the mouth opening marked a pivotal shift in bacterial source composition of larvae, with a notable contribution from the rearing water at the beginning of mouth opening, followed by enhanced internal succession, emphasizing the critical role of early microbiota establishment. Notably, the dominance of external sources at zoea II highlights the necessity for ensuring microbial safety due to the prevalence of zoea-II syndrome at this vital stage. Source tracking of specific bacterial groups suggests regulatory timing and routes of Roseobacteraceae (with potential probiotics) and frozen Artemia as a major source of vibrios (with opportunistic pathogens). The determinism-dominated assembly of bacteria, sourced either internally or externally, highlights strong host selection. This process exhibits overall similarities in taxonomic preferences for internal succession, while differences in taxonomic preferences from external sources reflect the influence of the genetic backgrounds of shrimp strains. Our work presents the first systematic assessment on bacterial sources of P. vannamei larvae across the complete developmental cycle, providing new insights that facilitate microbial management and pathogen prevention in larviculture.

microbiology↗

Human chronic inflammation is orchestrated by spatially restricted inflammation-activated Dendritic cells

Dendritic cells (DCs) form coordinated networks that orchestrate inflammatory responses across tissues. Upon activation, conventional dendritic cells (DCs) undergo changes in their transcriptome, phenotype, and function, depending on the tissue microenvironment. The role of DC activation during human chronic inflammation has yet to be explored. To address this, we aimed to investigate activated DCs across a range of chronically inflamed human tissues, with a focus on cervical lymph nodes (LNs). We performed scRNAseq and flow cytometry on healthy, acutely, chronically inflamed, and cancer-associated human cervical (LNs) and identified a novel inflammation-associated DC (iaDC) cell state, found only within chronically inflamed LNs. iaDCs were defined by a unique cytokine expression profile (CXCL9, CXCL10, IL1B) and could be phenotypically distinguished from other activated DCs by their elevated expression of CD1C, CD206, CD319, and CD274. Functionally, we found that IFN{gamma} signaling induces DC2s to enter the iaDC cell state and that this process can be abrogated by inhibition of JAK-STAT signaling. Using spatial transcriptomics, we observed LN iaDC residing within a specific chronic inflammatory niche, which was enriched for inflammatory monocytes, NK cells, and effector memory CD4+ and CD8+ T cells. Extrapolating our findings to other chronic inflammation-associated diseases, we similarly observed the emergence of iaDCs within the intestines of treatment-resistant Crohns Disease patients, synovial membranes and lymph nodes of rheumatoid arthritis patients and lungs of sarcoidosis patients. Similarly to the lymph node, iaDCs were found to reside in conserved chronic inflammation-associated spatial niches within the small intestine of affected individuals and displayed equivalent transcriptional characteristics and surrounding cellular neighborhoods. Collectively, these data highlight a previously unexplored role of iaDCs in human chronic inflammatory diseases and propose a conserved spatially restricted iaDC-populated chronic inflammatory niche associated with resistance to therapy. These findings highlight novel avenues to shape inflammatory trajectories by targeting iaDCs and their spatial niches, for example, by inhibiting JAK-STAT signaling.

immunology↗

Disturbed engram network caused by NPTXs downregulation underlies aging-related memory deficits

Engram cells storing specific memories are allocated to separate neuronal ensembles, which preferentially recruit either excitatory or inhibitory inputs to drive precise memory expression. However, how these formed neuronal ensembles maintain their stability, and whether the disturbed stability contributes to aging-related memory deficits remain elusive. Here, we show that neuronal pentraxin1 (NPTX1) facilitates Kv7.2-mediated inhibition of Fos+ensemble hyperexcitability, thereby restricting its response to excitatory inputs from medial entorhinal cortex (MEC) and promoting memory expression in the fear context. Meanwhile, NPTX2 facilitates the perisomatic inhibition of the Npas4+ ensemble by parvalbumin+ (PV+) interneurons, thus preventing fear memory overgeneralization. Pharmacological activation of Kv7.2 or chemogenetic activation of PV+ interneurons repaired memory deficits caused by engram specific NPTXs depletion. Contextual fear memory precision and NPTXs expression in dentate gyrus (DG) engram cells are decreased in aged mice. Overexpression of NPTX1 in Fos+ensemble or AMPAR binding domain of NPTX2 in Npas4+ ensemble rescued memory imprecision. These findings elucidate that the coordination of NPTXs prevents engram ensembles from becoming hyperactive and provide a causal link between engram network destabilization and aging-associated memory deficits.

neuroscience↗

CXCL17 activates three MAS-related G protein-coupled receptors independently of its conserved C-terminal fragment

C-X-C motif chemokine ligand 17 (CXCL17) is a chemoattractant whose receptor remains controversial. While recent studies identified CXCL17 as an agonist of G protein-coupled receptor 25 (GPR25), it was also reported to activate MAS-related GPR family member X2 (MRGPRX2), a member of MAS-related G protein-coupled receptors (MRGPRs), though this finding has not yet been reproduced by other laboratories. In this study, we confirmed that micromolar concentrations of human CXCL17 activate human MRGPRX2 in transfected human embryonic kidney (HEK) 293T cells using a NanoLuc Binary Technology (NanoBiT)-based {beta}-arrestin recruitment assay. We further demonstrated that human CXCL17 also activates MRGPRX1 and MAS1 among 10 human MRGPRs in the same assay. CXCL17 could also induce chemotactic movement of transfected HEK293T cells expressing MRGPRX2, MRGPRX1, or MAS1. However, removal of C-terminal residues from CXCL17 did not affect its activation of these three MRGPRs, even though this region is essential for GPR25 activation. These results suggest that CXCL17 activates MRGPRX2, MRGPRX1, and MAS1 through a mechanism distinct from GPR25 activation. Further investigation is needed to determine whether these MRGPRs mediate the in vivo functions of CXCL17.

biochemistry↗

Probing relaxed myosin states in hypertrophic cardiomyopathy by second harmonic-generation microscopy

This study explores the use of polarized second-harmonic generation (pSHG) to investigate myosin conformation in the relaxed state, differentiating between the actin-available, disordered (ON) state and the energy-conserving, ordered (OFF) state. By shifting the ON/OFF equilibrium using both physical and chemical manipulations, we demonstrate the sensitivity of pSHG in quantifying the ON/OFF ratio in skeletal and cardiac tissues. Comparisons with X-ray diffraction measurements further validate our findings. Applying this approach to a sarcomeric mutation associated with hypertrophic cardiomyopathy, we show that R403Q/MYH7-mutated minipig ventricle tissue exhibits a higher ON fraction compared to controls. This difference is abolished under high concentrations of a myosin activator (2-deoxyATP) and an inhibitor (Mavacamten), indicating structural similarity between R403Q and controls in these two states. ATPase assays reveal increased resting ATPase activity in R403Q samples, which persists even in the presence of 2-deoxyATP, suggesting that the elevated energy consumption in the R403Q mutation is driven by both a population shift toward the ON state and enhanced myosin ATPase activity per motor head.

physiology↗

The Establishment of Prostate-specific, SKP2 Humanized Mice by CRISPR Knock-in Method Reveals Neoplastic Initiation and Microenvironmental Reprogramming

A recent study has shown that SKP2 inactivation can prevent cancer initiation by extension of total cell cycle duration without perturbing normal division, which suggests a new strategy for cancer prevention. However, direct in vivo evidence for human SKP2 on cancer initiation and prostatic microenvironment is still lacking and a prostate-specific SKP2 humanized mouse model is critical for developing prostate cancer immunoprevention approaches through targeting human SKP2. We therefore have established a prostate-specific human SKP2 (hSKP2) knock-in mouse model by a CRISPR knock-in approach. Overexpression of hSKP2, which is driven by an endogenous mouse probasin promoter, induces prostatic lesions including hyperplasia, mouse prostate intraepithelial neoplasia (mPIN), and low-grade carcinoma and increases prostate weights. Transcriptional profiling by RNA-sequencing analysis revealed significant gene expression alterations in epithelial to mesenchymal transition (EMT), extracellular matrix, and interferon signaling in the prostate of hSKP2 knock-in mice compared to wild-type mice. Single cell deconvolution showed an increase of fibroblasts population and a decrease of CD8+ T cell and B cell populations in the prostate of hSKP2-knock-in mice. Consistently with these results from the SKP2 humanized mouse, overexpression of hSKP2 in human prostate cancer PC3 cells markedly increased cell migration and invasion and induced the gene expression of EMT and interferon pathways, including FMOD, THY1, PFKP, USP18, IL15, etc. In addition, paired prostate organoids were derived from SKP2 humanized and wild-type mice for drug screening and validated by known SKP2 inhibitors, Flavokawain A and C1. Both of which selectively decrease the viability and alter the morphologies of organoids of hSKP2 knock-in rather than wild-type mice. Our studies provide a well-characterized prostate-specific hSKP2 knock-in mouse model and offer new mechanistic insights for understanding the oncogenic role of SKP2 in shaping the prostatic microenvironment during early carcinogenesis.

cancer biology↗

PhysDock: A Physics-Guided All-Atom Diffusion Model for Protein-Ligand Complex Prediction

Accurate prediction of protein-ligand complexes remains a central challenge in structural biology. Traditional methods are computationally inefficient and prone to local minima, whereas deep learning approaches struggle to capture structural flexibility and physical plausibility. We introduce PhysDock, a physics-guided diffusion model that uniquely integrates (i) all-atom diffusion to model ligand flexibility and protein precision-flexibility (i.e., subtle conformational adjustments); (ii) physical priors as diffusion conditioning, alongside two-phase physics guidance during the denoising diffusion to ensure physical plausibility. PhysDock demonstrates state-of-the-art performance in redocking benchmarks and excels in the more challenging cross-docking assessments. For practical utility, PhysDock (i) resolves cannabinoid receptor selectivity across diverse molecules, achieving accuracy comparable to experiments; (ii) distinguishes most drug candidates from weak binders in virtual screening of NTRK3 kinase, while uncovering novel candidates with structural insights. PhysDock serves as a versatile tool for protein-ligand complex prediction, with substantial potential to accelerate structure-based drug discovery.

bioinformatics↗

Systematic discovery of single-cell protein networks in cancer with Shusi

Context-specific protein-protein interaction (PPI) drive heterogeneity of primary tumor, forming a formidable challenge to effective cancer therapy. However, systematically mapping and modeling these interactions at single-cell resolution across diverse cancer types remains an unmet need. Here, we present Shusi, a large language model-enhanced variational graph auto-encoder model trained on over single cells across 23 cancer types, to predict context-specific PPIs. Shusi outperforms existing state-of-the-art methods, as validated through orthogonal experimental evidence. Cancer-specific mutations are significantly enriched in Shusi-predicted networks, offering complementary insights to conventional marker gene-based approaches. Through systematic evaluations, we demonstrate strong associations between Shusi-predicted network topologies, genetic vulnerabilities, and therapeutic sensitivity. Finally, in acute myeloid leukemia (AML), a blood cancer where cell-state heterogeneity drives clinical resistance, Shusi pinpointed potential targets as actionable vulnerabilities of resistant leukemia subpopulations, as validated experimentally in primary AML. Shusi offers a deep-learning tool for implementing precision medicine based on context-specific protein network architecture.

bioinformatics↗

Shiny-Calorie: A context-aware application for indirect calorimetry data analysis and visualization using R

Indirect calorimetry is a cornerstone technique for metabolic phenotyping of animal models in preclinical research, with well-established experimental protocols and platforms. However, a flexible, extensible, and user-friendly software suite that enables standardized integration of data and metadata from diverse metabolic phenotyping platforms--followed by unified statistical analysis and visualization--remains absent. We present Shiny-Calorie, an open-source interactive web application for transparent data and metadata integration, comprehensive statistical data analysis, and visualization of indirect calorimetry datasets. Shiny-Calorie is compatible with data formats from widely used commercial metabolic phenotyping platforms, such as TSE and Sable Systems, and includes functionality for exporting processed data in these formats. Built using GNU R and a Shiny-based reactive interface, Shiny-Calorie enables intuitive exploration of complex, multi-modal longitudinal datasets comprising categorical, continuous, ordinal, and count variables. The platform incorporates state-of-the-art statistical methods for robust hypothesis testing, thereby facilitating biologically meaningful interpretation of energy metabolism phenotypes, including resting metabolic rate and energy expenditure. Overall, Shiny-Calorie streamlines routine analysis workflows and enhances reproducibility and transparency in metabolic phenotyping studies.

bioinformatics↗

Imputation Disparities Driven by Recent Selectionand Their Impact on Disease Risk Estimation in East and Southeast Asian Populations

Using genotype data consisting of 8,316 individuals, we systematically evaluated imputation performance across six state-of-the-art reference panels for Chinese and Thai populations. A substantial proportion of variants identified through whole-genome sequencing, especially low-frequency variants, remained undetected by existing reference panels. In the Chinese population, the TOPMed panel required an R2 threshold of 0.60-0.70 to achieve comparable imputation accuracy of the ChinaMAP panel without R2 filtering, challenging the standard practice of applying a fixed R2 threshold for downstream analyses. Regional analysis highlighted the role of recent selection in imputation discrepancies and revealed an enrichment of immune-related genes in poorly imputed regions. In addition, we showed that the selection of reference panels and R2 thresholds could significantly influence estimation of polygenic risk score for disease prediction. These findings underscore the importance of developing ancestrally diverse reference panels and provide valuable guidelines for improving genotype imputation in East and Southeast Asian populations.

genomics↗

THA_1941 from Thermosipho africanus: A Thermostable β-1,3-Glucan Phosphorylase for Efficient β-1,3-Glucan Synthesis

{beta}-1,3-Glucan phosphorylases capable of utilizing glucose as a priming substrate are key biocatalysts for the synthesis of functional {beta}-1,3-glucan. In this study, we identified THA_1941 from Thermosipho africanus (Ta{beta}GP) as a GH161 {beta}-1,3-glucan phosphorylase exhibiting robust synthetic activity towards glucose, as confirmed by 13C nuclear magnetic resonance, liquid chromatography-mass spectrometry, and sequence and structural analyses. Ta{beta}GP displayed exceptional thermostability, retaining 93% of its activity at 60 {degrees}C for 180 h, and showed broad pH tolerance ranging from pH 5.0 to 10.0, surpassing the performance of previously reported homologs. In addition, Ta{beta}GP exhibited broad substrate flexibility, accepting both - and {beta}-linked disaccharides, and demonstrated strong resistance to metal ions and lignocellulose-derived inhibitors. In the presence of 150 mM glucose 1-phosphate as the donor substrate, Ta{beta}GP synthesized {beta}-1,3-glucan with a tunable average degree of polymerization (10-32), depending on the concentration of glucose used as the primer. The combination of thermostability, inhibitor resistance, and substrate versatility makes Ta{beta}GP a promising biocatalyst for the economically viable and environmentally sustainable synthesis of {beta}-1,3-glucan from non-food biomass sources.

biochemistry↗

Boosting Antitumour Efficacy and Immunity by Boron Neutron Capture Therapy with Size-Controlled Nanoparticles

Boron neutron capture therapy (BNCT) is emerging cancer radiotherapy requiring 10B sensitizer. Although boronophenylalanine (BPA)-BNCT is approved clinically in Japan, the low tumour selectivity and retentivity result in the long-time infusion of high doses. Based on our finding of the size-controllable mechanochemical synthesis of boron-10 carbide nanoparticles (10B4C NPs), the 50 nm size NPs grafted with poly(glycerol), {superscript 1}BC(50)-PG, is found to show superior tumour selectivity and retentivity to enhance the eradication efficacy at much lower dosage (5 mg [10B] / kg (mouse)). The dosage is further reduced by twice neutron irradiation or combination with an immune checkpoint inhibitor (ICI). Antitumour immunity is found to be boosted by {superscript 1}BC(50)-PG-BNCT to induce abscopal effect to treat remote or metastatic tumours and long-term memory to prevent cancer recurrence. Additionally, minimal side effects and gradual NP excretion are observed for one year. The 10B4C(50)-PG is concluded to be a promising 10B carrier for clinical application of BNCT due to the prominent antitumour efficacy and immune-activation with minimal toxicity.

cancer biology↗