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Yang, T.

Publications and source records attributed to Yang, T..

At least 55 records · Page 3Linked to original sources

Intermittent AP-1 activation in muscles contributes to exercise-induced health benefits

Regular physical exercise extends healthspan, yet the molecular mechanisms that translate intermittent contractile stress into lasting benefit remain incompletely understood. Using global nuclear run-on (GRO-seq) in mouse skeletal muscle after treadmill running, we profiled enhancer RNA (eRNA), a sensitive marker of enhancer activity. Activation protein-1 (AP-1), a family of pioneering factors for senescence, emerged as the top transcription factor with motif enrichment in exercise-activated enhancers. Our screen in the contracting C2C12 myotubes pinpointed cFos/JunD as the primary AP-1 factor responsible for contraction-induced transcriptional changes. Muscle-specific overexpression of A-Fos, a dominant-negative mutant of cFos, disrupted transcriptomic responses to exercise and attenuated exercise-mediated improvement in muscle functions. Interestingly, intermittent but not continuous overexpression of cFos/JunD in mouse muscles mimicked exercise-induced transcriptomic changes, increased mitochondrial volume density, enhanced muscle strength and fatigue resistance, and improved glucose tolerance. These results define a transcriptional regulatory signaling pathway linking exercise intermittency to beneficial adaptations and highlight the necessary recovery cycles in training. The paradoxical anti- and pro-aging roles of AP-1 offer insights into the timing and dynamics of stressors and stress responses in shaping senescence and healthspan.

molecular biology↗

Characterization and application of hyperthermia-evoked seizures in a mouse model of focal cortical dysplasia

Rodent models of drug-resistant epilepsy are widely used to uncover mechanisms of seizures and to test the efficacy of treatments; however, the stochastic and relatively infrequent nature of spontaneous seizures in these models makes it challenging to observe and manipulate peri-ictal activity, and to rapidly screen therapeutics. As fever has been identified as a clinical seizure trigger, we investigated the ability of induced hyperthermia to trigger seizures in a mouse model of focal cortical dysplasia (FCD), a common cause of drug-resistant epilepsy. Experimental mice were generated via in utero electroporation of a gain-of-function RHEB variant (RHEBp.P37L). In adult Rheb-FCD mice, hyperthermia elicited behavioral seizures [~]80% of the time, with a mean temperature threshold of [~]40 {degrees}C. Using this acute paradigm, as a proof-of-concept, we found that chemogenetic inhibition of a subset of excitatory neurons within the dysplasia significantly elevated the threshold for hyperthermia-evoked seizures. We then confirmed the relevance of this acute finding to spontaneous epileptiform activity, using repeated chemogenetic inhibition across chronic recordings to confirm a reduction of spontaneous seizures as well as interictal spikes. Overall, our data demonstrate that hyperthermia-evoked seizures can be readily elicited in Rheb-FCD mice, offering a tractable platform for evaluating therapeutic interventions targeting seizure susceptibility in focal epilepsy.

neuroscience↗

HINS: HLA-mediated immunogenic neoantigen score for robust prediction of immune checkpoint blockade response

Immune checkpoint blockade (ICB) therapy response prediction provides remarkable genomic and transcriptomic gains and has successfully understood the molecular mechanisms underlying various cancers. However, only a subset of patients with advanced tumors currently benefits from ICB therapies, which at times incur considerable side effects and costs. Developing predictive tools for ICB response has remained a serious challenge because of the complexity of the immune response and the shortage of large cohorts of ICB-treated patients that include both omics and response data. Here, based on a pooled genomic dataset of 919 patients across multiple solid tumors treated with anti-PD-(L)1 or anti-CTLA-4, we constructed human leukocyte antigen class I (HLA-I)-mediated immunogenic neoantigen score (HINS). HINS is a predictor of ICB response using neoantigen quality and HLA evolutionary divergence to integrate the factors associated with immune activation and evasion. It yielded an overall accuracy of AUC=0.853, outperforming existing predictors and capturing more than 75% true responders. Experimental analysis indicated that patients with higher HINS were more likely to undergo survival benefits following ICB therapy. Our results highlighted the transcriptional and genomic correlations between HINS-identified molecule features and ICB response, such as immunoresponsive gene enrich pathways, favorable and unfavorable genomic subgroups, and hotspot somatic events in driver genes. This study presented an interpretable, accurate deep-learning method using meaningful predictive features to predict the response to ICB, providing biological insights into the complexity of the determinants underlying immunotherapy.

bioinformatics↗

Bcl-2 protein Noxa is required for metabolic reprogramming to glutamine dependence and for apoptosis in stimulated human CD8+ T cells

Naive or memory T cells reprogram their metabolism upon antigenic stimulation. They increase their glucose uptake, relying on aerobic glycolysis for generating biomass while switching to glutamine to fuel energy production. Here we have identified a requirement for human Bcl-2 family, Noxa, in the metabolic switch to glutamine dependence in activated CD8+ T cells, that is independent of its canonical role in apoptosis at the end of the immune response. Using an in vitro co-stimulation model, we demonstrate that Noxa is induced in CD8+ T cells and remains elevated during the proliferative and differentiation phases of the response and through the onset of apoptosis. Noxa protein induction requires glutamine, is mediated via mTOR, and is independent of glutaminolysis. Glutamine, in turn, requires Noxa to facilitate its conversion to glutamate. CD8+ T cells lacking Noxa showed reduced levels of intracellular glutamate but no impairment of mitochondrial or effector function, and decreased dependence on glutamine for both respiration and growth during the proliferative phase. NOXA knockout CD8 T cells also displayed significantly higher viability in the apoptotic phase of the immune response. CD8+ T cells from a human NOXA gene-replacement mouse responded normally to in vitro stimulation and in vivo acute infection. However, human Noxa-expressing murine CD8+ T cells displayed a distinctly proliferative gene signature in their transcriptome following activation, supporting an early growth-promoting role for this BH3-only protein. Our studies suggest that knocking out NOXA in human CD8+ T cells to increase their lifespan as well as their ability to survive and function in glutamine-poor microenvironments could be a promising immunotherapeutic strategy.

immunology↗

gffutilsAI: An AI-Agent for Interactive Genomic Feature Exploration in GFF files

AO_SCPLOWBSTRACTC_SCPLOWThe General Feature Format (GFF) is widely used to represent genomic annotations, but its hierarchical, multi-attribute structure makes manual querying and analysis challenging. Existing libraries such as gffutils provide programmatic interfaces, yet they require coding proficiency. gffutilsAI is a novel AI-powered command-line agent that enables researchers to perform interactive, natural-language-driven exploration of GFF files. Built on top of the gffutils library and the Strands AI agent framework, gffutilsAI integrates local and cloud-based large language models (LLMs) such as Llama 3.1, GPT-5, and Claude 3.5 to translate human queries into executable actions. The tool supports coordinate-based queries, attribute and GO searches, hierarchical traversal, statistical summaries, and CSV export, offering a new paradigm for accessible conversational genomics.

bioinformatics↗

Cell-Based Immunization Combined with Single-Round Cell Panning Enables Discovery of PSMA-Targeting Nanobodies from Phage Display Libraries

There is a strong need for nanobodies targeting novel cancer-associated antigens to advance radioligand imaging and antibody-based therapeutics. In this study, we investigated whether non-targeted Llama immunization using tumor cells, combined with non-targeted phage display panning on human cell lines, could yield nanobodies specific to Prostate Specific Membrane Antigen (PSMA). Nanobody selection using both classical three round PSMA negative-positive panning and single round panning of cell lines positive or negative for PSMA showed clear enrichment for PSMA binders in both strategies. Using shRNA knockdown, flow cytometry, cell-ELISA, immunohistochemistry and structural modeling and docking, we confirmed the PSMA targeting of selected nanobodies. Two distinct epitopes were predicted to be bound by nanobodies PSMANb9 and A7 (JVZ-007), corroborated by epitope competition assays. These findings support the feasibility of non-targeted immunization and panning strategies for isolating clinically relevant cancer nanobodies.

cancer biology↗

The Dishevelled C-terminus interacts with the centrosomal protein Kizuna to regulate microtubule organization during ciliogenesis.

Microtubules (MTs) serve as dynamic scaffolds that support diverse cellular processes, including cell division, intracellular transport, and epithelial morphogenesis. In ciliated cells, MTs not only form the axonemal backbone of cilia but also work in tandem with actin to build an apical meshwork that anchors and orients basal bodies. However, the mechanisms regulating apical MT organization during ciliogenesis remain poorly understood. Here, we identify the centrosomal protein Kizuna (Kiz) as a critical regulator of apical MT architecture. Kiz interacts with the C-terminus of Dishevelled 2 (Dvl-C), inducing an open conformation and enabling the recruitment of Protein Kinase C delta (PKC{delta}) to stabilize the apical MT meshwork. This Dvl2-Kiz-PKC{delta} signaling axis is essential for ciliogenesis across multiple contexts, including the formation of primary cilia in the eye, multicilia in the mucociliary epidermis (MCE), and mono-motile cilia in the left-right organizer, the gastrocoel roof plate (GRP). These findings reveal a conserved molecular mechanism linking Dvl2 conformational dynamics to MT organization and highlight Kizuna as a key mediator coupling non-canonical Wnt signaling to ciliogenesis, left-right patterning, and the organization of the apical actin microtubule meshwork in ciliated cells of embryos.

developmental biology↗

An EEG-based Multi-Scale Hybrid Attention and Squeeze Network for objective taste assessment

Taste perception is central to flavor experiences. Electroencephalography (EEG) signals carry rich information about taste perception. Because these neural data are independent of verbal reports and bypassing conscious filtering, EEG holds promise as a neural-sensing platform for objective taste representation. However, taste-evoked EEG signals exhibit complex spatiotemporal and spectral dynamics that require advanced computational approaches to decode effectively. This study developed an EEG-based Multi-Scale Hybrid Attention and Squeeze Network (MHASNet) for taste evaluation. EEG signals evoked by distinct taste stimuli were recorded, a dedicated taste-EEG dataset was compiled, and a novel deep learning architecture, MHASNet, was designed to classify these signals. MHASNet synergistically integrates multi-scale convolutions to capture temporal dynamics across different time scales, dual-attention mechanisms to localize discriminative brain regions and electrode positions, and a squeeze-and-excitation module to optimize frequency-band contributions-collectively enabling precise extraction of taste-specific neural signatures. Results showed that the proposed model achieved superior performance across five taste categories (sweet, sour, salty, bitter, and tasteless), with 94.33% accuracy, 91.37% F1-score, 91.89% precision, and 92.07% recall. These results surpass benchmark models while maintaining millisecond-level inference latency suitable for real-time applications. By complementing subjective evaluations and instrumental analyses, the model offers an objective, neurophysiology-based solution for taste evaluation.

neuroscience↗

Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires

Scalable identification of antigen-specific antibodies from whole immune repertoire V(D)J sequences is a central challenge in biomedical engineering. We show that protein language models (PLMs) fine-tuned on antibody heavy-chain sequences can directly predict antigen specificity from unselected immune repertoires. We assessed our model, Antigen Specificity Predictor (ASPred), against SARS-CoV-2, influenza, and HIV-AIDS antigens, observing comparable predictive performance. In the whole immune repertoire V(D)J sequences of mice immunized with the SARS-CoV-2 spike proteins receptor-binding domain (RBD), ASPred identified antibody sequences specific to RBD. Several candidate sequences were validated, including one as a heavy chain-only nanobody with 20.7 nM dissociation constant. Molecular dynamics simulations supported the predicted interactions at coarse-grained and atomic levels. Benchmarking against Barcode-Enabled Antigen Mapping (BEAM) of B cell receptor sequence data had highly significant overlaps with ASPred predictions, suggesting scalability. The predicted SARS-CoV-2 binders differed substantially from training sequences, demonstrating generalization beyond sequence memorization. Together, we establish that heavy chain antibody sequences encode sufficient information for PLMs to infer specificity, offering a scalable framework for antibody discovery with broad applications.

bioinformatics↗

Lysine-R2HGylation identified as a post-translational modification in R2HG-elevated cancers

R-2-Hydroxyglutarate (R2HG), an oncometabolite predominantly produced by mutated isocitrate dehydrogenase 1/2 (IDH1/2) in various cancers, is known to drive cancer progression through noncovalent inhibition of -ketoglutarate (KG)-dependent enzymes. In this work, we propose an alternative mechanism wherein R2HG contributes to cancer development via covalent modification of biologically critical lysines, a process termed lysine-R2HGylation (KR2HG). We designed and synthesized R2HG-mimicking probes, demonstrating their effectiveness in facilitating KR2HG target profiling and site mapping. We identified KR2HG as a previously unrecognized post-translational modification, confirmed its C5-linkage on GSTP1(K209), and demonstrated that SIRT5 functions as a deacylase for GSTP1-KR2HG in vitro. Furthermore, we found that R2HG slightly but significantly inhibits the enzymatic activity of GSTP1 through KR2HG and dramatically suppresses monocyte differentiation via this catalytically important lysine modification. Our findings provide an alternative perspective on the role of R2HG in leukemia progression and offer a practical tool for the clinical investigation of R2HG-elevated cancers.

molecular biology↗

Multi-omics profiling reveals microenvironmental remodeling as a key driver of house dust mite-induced lung cancer progression

Chronic exposure to the common aeroallergen house dust mite (HDM) induces lung inflammation and DNA damage, but its impact on lung cancer development remains largely unexplored. Using whole-genome sequencing, RNA-seq, and DNA methylation profiling, we assessed HDM effects in lung epithelial cell lines and a mouse orthotopic lung cancer model. HDM accelerated tumor growth without altering mutational burden. Transcriptomic and epigenetic analyses revealed tissue-specific effects: in normal lung, HDM enhanced pro-inflammatory and immune activation programs, whereas in tumors it suppressed T cell responses, antigen presentation, and chemokine signaling. Immune deconvolution showed a shift toward myeloid enrichment and lymphoid suppression, with reduced cytotoxic T and NK signatures. Notably, HDM-driven tumor promotion was abolished in Il17a-/- but not Il1b-/-mice, identifying IL-17A as a critical mediator. These findings demonstrate that chronic aeroallergen exposure reshapes the lung microenvironment to promote immune suppression and accelerate lung cancer progression. HighlightsChronic house dust mite (HDM) exposure accelerates lung tumor growth through non-mutagenic, immune-mediated mechanisms. HDM activates pro-inflammatory and immune programs in normal lung tissue but suppresses antitumor T cell responses in tumors. Multi-omics profiling reveals epigenetic silencing of immune genes and a myeloid-enriched, lymphoid-deficient tumor microenvironment. HDM-driven tumor promotion depends on IL-17A but not IL-1{beta}, establishing IL-17A as a central driver of lung tumor promotion.

cancer biology↗

Interaction of Carbamoyl-Phosphate Synthase 1 with Agmatinase in the Liver of Torpid Bats

Mammalian torpor imposes unique metabolic constraints, yet the mechanisms of nitrogen metabolism during this state remain unclear. In this study, we show that the urea cycle is selectively regulated rather than broadly suppressed in torpid bats. A significantly increased abundance of carbamoyl-phosphate synthase 1 (CPS1) maintained its functional capacity during torpor and arousal in Myotis ricketti. Proteomic analyses and confocal microscopy identified a specific association and co-localization between CPS1 and agmatinase (AGMAT), an ATP-independent enzyme involved in nitrogen metabolism. Co-localization of CPS1 and AGMAT was also observed in torpid Rhinolophus ferrumequinum, a phylogenetically distant species. Fluorescence resonance energy transfer (FRET) further supported an indirect CPS1-AGMAT interaction. Most urea cycle enzymes exhibited stable or only moderately reduced expression during bat torpor, and metabolic profiling demonstrated sustained nitrogen flux. Together, these findings reveal a conserved adaptive mechanism that maintains urea cycle function, potentially enhancing osmotic stability and energy efficiency during prolonged fasting and water scarcity.

zoology↗

Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits

A high-quality horse genome assembly is crucial for genetic analysis of equine. Benefiting from long-read sequencing techniques and trio-binning strategy, we assembled a complete telomere-to-telomere horse genome (T2T-horse 1.0) with a size of 2.80 Gb and a base accuracy of more than 99.9999%, comprising a 34.11-Mb entire Y chromosome. T2T-horse 1.0 filled the gaps and corrected errors in previous assemblies, and added 180.30 Mb of previously unresolved regions and 77 new genes compared with the previous reference genome TB-T2T. We identified five types of centromeric satellites and revealed the features of the horse centromeric regions. We characterized the structure of the Y chromosome, and determined the borders of PAR transposed region, and annotated 59 novel genes on Y chromosome of T2T-horse 1.0. Using SNPs in the X-degenerate region of the Y chromosome of T2T-horse 1.0, we performed selection signatures analysis between indigenous horses and horses from intensively selected breeds, and detected the selected genes ARSF and NLGN4Y, which are closely associated with reproduction and temperamental traits, respectively.

genomics↗

A neuroendocrine principle: Pancreatic islets actively shape sympathetic innervation

Survival critically depends on maintaining blood glucose levels to provide essential energy, especially during emergencies such as the fight-or-flight response, when timely glucose control via neural integration is vital. However, pancreatic islets constitute only a small fraction of the pancreas and are dispersed throughout the organ, raising the fundamental question of how the nervous system coordinates synchronized control of multiple islets. Using whole-organ clearing and 3D imaging, we mapped pancreatic sympathetic innervation, revealing specialized anatomical integration between sympathetic nerves and islets. Transplanted islets intrinsically attracted sympathetic nerves independent of their native environment. Chronic islet injury disrupted sympathetic innervation and markedly impaired nerve regeneration after denervation. Sympathetic denervation markedly elevated islet-derived Reg2 and Reg3{beta}; administration of these proteins accelerated sympathetic regeneration and improved islet graft function. Our findings identify an islet-sympathetic architecture actively maintained by islets, uncovering an endocrine-driven mechanism for neural regulation, highlighting Reg2 and Reg3{beta} as therapeutic candidates for diabetes management.

neuroscience↗

EHMT2 Controls Neural Crest-Derived Craniofacial Development but is Dispensable in Limb Development

Post-translational modifications of histones, such as methylation of histone H3 at lysine 9 (H3K9), play critical roles in regulating chromatin structure and gene expression. EHMT2 (also called G9A), a histone methyltransferase, mediates H3K9 mono- and dimethylation and has been implicated in both transcriptional repression and context-specific gene activation. Although global knockout of the mouse Ehmt2 gene results in early embryonic lethality, tissue-specific knockouts have uncovered diverse roles in organ development. However, how EHMT2 contributes to skeletal development in a lineage-specific manner remains to be fully elucidated. Here, we investigated the role of EHMT2 in skeletal development by conditionally inactivating Ehmt2 in neural crest-derived and mesoderm-derived progenitors using Wnt1-Cre and Prx1-Cre mouse lines, respectively. Loss of Ehmt2 function in neural crest cells led to postnatal growth failure and craniofacial defects, including delayed intramembranous ossification and malformations of the jaw and cranial base. Transcriptomic analysis of neural crest cells revealed disrupted chromatin regulatory networks, reduced expression of proliferation-associated genes, and upregulation of inflammatory pathways. In contrast, inactivation of Ehmt2 in Prx1-expressing mesodermal progenitors had minimal impact on limb and cranial bone development, with no significant alterations in bone mass or osteoblast function. Together, these results reveal a lineage-specific requirement for EHMT2 in neural crest-derived skeletal tissues, suggesting that distinct progenitor populations exhibit differential dependency for bone development.

cell biology↗

Post-inhibitory rebound firing drives hypothalamic activation for male mating

Many behaviorally relevant limbic circuits are dominated by inhibitory connections, raising the question of how neuronal activation arises in such contexts. In male mating, both activation of mPOA and its inhibitory inputs are essential--a paradox previously ascribed to disinhibition. Here, we show that the mPOA largely lacks local inhibitory circuits, arguing against disinhibition. Instead, in vivo recordings reveal that mount-active mPOA neurons are suppressed prior to behavioral onset, and this inhibition negatively correlates with subsequent activation, consistent with post- inhibitory rebound firing (PIR). A biologically plausible conductance-based model demonstrates that synaptic inhibition interacts with T-type Ca{superscript 2} currents -- the ionic basis of PIR -- to promote mPOA neuron firing. Experimentally, bidirectional manipulations of mPOA T-type Ca{superscript 2} channels confirm this mechanism: knockdown reduces PIR and impairs male mating, while overexpression enhances mating. Together, these results identify PIR as a critical mechanism by which inhibition promotes activation in limbic circuits to drive male mating.

neuroscience↗

Intrarenal Generation of Aldosterone Contributes to Ischemia-Induced Hypertension and Nephropathy in Mice

BackgroundThe past few years have witnessed a significant advancement in aldosterone (Aldo)-targeted therapies for the management of treatment-resistant hypertension and chronic kidney disease, which often exist in tandem. While Aldo is believed to predominantly originate from the adrenal glands, this study provides evidence to support the involvement of intrarenal Aldo biosynthesis in the pathogenesis of ischemic nephropathy and hypertension in a two-kidney, one-clip (2K1C) model. MethodsWe generated inducible renal tubule-specific deletion of C11B2 (RT C11B2 KO) and characterized the phenotype during the 2K1C procedure. We investigated the underlying mechanisms involving the use of mice with collecting duct-specific (pro)renin receptor (CD PRR KO) or renin (CD renin KO). ResultsRT C11B2 KO induced a partial blockade of the hypertensive response but a much greater improvement in renal fibrosis and inflammation four weeks post-2K1C. This phenotype was associated with an effective blockade of intrarenal generation of Aldo contrasting to unchanged circulating Aldo concentrations. Furthermore, clipping-induced acute kidney injury was also attenuated 24 hours post-2K1C, at which point blood pressure (BP) did not increase. Similarly, sodium nitroprusside effectively lowered BP in C57BL/6j/2K1C mice but failed to improve renal injury. Additionally, we identified CD) PRR and renin as key upstream regulators of intrarenal Aldo biosynthesis following the 2K1C procedure. ConclusionsTogether, these results support the idea that CD PRR/renin-dependent generation of intrarenal Aldo may play a primary role in the pathogenesis of ischemic nephropathy and a secondary role in hypertension development during renovascular constriction. Therefore, targeting intrarenal Aldo biosynthesis may represent a more effective and safer intervention than existing Aldo-targeted therapy to manage ischemic nephropathy as well as hypertension.

physiology↗

HerbComb: an integrated database for the discovery of novel combinational therapies from herbal medicines

Drug combinations have gained increasing interest due to their potential for optimal efficacy and the ability to overcome drug resistance. Herbal medicine is a complex system with multiple ingredients and has illustrated apparent therapeutic effects through thousands of years of clinical experience, offering a rich resource for combinational therapies. However, the underlying mechanism of their synergistic therapeutic effects for disease treatment remains obscure for most herbal medicines. To fill this gap, we developed an integrated database named HerbComb (https://herbcomb.com/) to discover combinatorial therapies in herbal medicine, featuring three unique functions: drug prepositioning, customized combinatorial analysis, and biological and pharmacological features. Additionally, transcriptional gene signatures and ADMET properties were also interrogated as interactive functionalities to facilitate combinational analysis. Using Tongxinluo for Stroke as a case study, we identified and validated Oleanolic acid and Ferulic acid as synergistic ingredients. In summary, HerbComb is a versatile data exploration platform designed to characterize synergistic interactions among herbal medicines, enhancing the understanding of synergistic mechanisms and facilitating the discovery of effective drug combinations.

pharmacology and toxicology↗