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Chen, C.

Publications and source records attributed to Chen, C..

At least 109 records · Page 6Linked to original sources

Hypothalamic Orexin Input to the Medial Amygdala Links Vigilance to Arousal

Arousal circuits govern anesthetic state transitions, but emergence is often complicated by agitation, and the neural circuits linking anesthetic arousal to vigilance remain unclear. Here, we identify a lateral hypothalamic orexin-to-medial amygdala pathway (LHAOx[->]MeA) that links anesthetic state transitions to vigilance-like behavioral bias. Synaptic labeling and slice recordings revealed dense LHAOx innervation in the MeA, and RNAscope showed predominant Ox2R expression in MeA GABAergic (MeAvGAT) neurons. LHAOx[->]MeA terminal activation increased local orexin release, promoted arousal from isoflurane anesthesia, delayed loss of righting reflex during induction, and accelerated recovery during emergence. In vigilance assays, stimulation acutely suppressed open-field exploration and produced real-time place preference without conditioned reinforcement. Fiber photometry demonstrated preferential recruitment of MeAvGAT neurons across anesthetic states. Direct MeAvGAT activation recapitulated cortical engagement, arousal, and vigilance phenotypes, whereas TeLC-mediated silencing of MeAvGAT output abolished induction delay and reversed vigilance-like bias while sparing light-anesthesia arousal and emergence acceleration.

neuroscience↗

STING agonist-mediated endothelial cell activation drives NK cells and neutrophils-dependent pulmonary inflammation

Stimulator of interferon genes (STING) agonists and derivative molecules have been extensively developed for tumor immunotherapy. However, systemic exposure toxicity risks have constrained clinical trial progression and even threatened patient lives. Currently, systematic toxicity assessments for STING agonists remain lacking, with the mode of action for major organ injury yet to be elucidated. Here, we focused on STING agonist-induced lung injury, revealing that systemic administration of STING agonists caused pulmonary hemorrhage, inflammatory alterations, and respiratory dysfunction. Through single-cell RNA sequencing and immune deletion studies, we found that lung endothelial cells could be stimulated by STING agonists and then secreted chemokines and IL-15 to recruit and activate NK cells. NK cells could induce endothelial cell apoptosis via IFN-{gamma}. Tbx21+ NK subpopulations, which activated by endothelial cells, could produce chemokines to recruit neutrophils. Neutrophils secreted IL-1{beta} through positive feedback pathways and form neutrophil extracellular traps during lung injury. This study elucidates the critical role of the endothelial cell-NK cell-neutrophil axis in mediating STING agonist-associated pneumonia, offering insights for developing intervention strategies for STING agonist toxicity.

pharmacology and toxicology↗

A Genetic Tool for Specific Tracking of Mature Neutrophils

Tracking mature neutrophils remains challenging due to the lack of reliable cell surface markers. Although CD101 is a promising candidate for mature neutrophils, its stability under pathological conditions is unclear. Using a CD101-tdTomato reporter mouse model, we confirmed that the reporting system does not alter CD101 expression, and tdTomato fluorescence is predominantly expressed in mature neutrophils across peripheral tissues. Further analysis revealed that CD101+ and tdTomato+ neutrophils display identical characteristics of mature neutrophil, including poly-segmented nuclei, cell size, and key functions under homeostasis. By comparing tdTomato fluorescence with CD101 protein levels, we demonstrate that reduced CD101 expression under pathological states was not attributed to shedding or degradation. Our finding enhances CD101 as a robust and reliable marker of neutrophil maturity, providing a foundation for future applications in spatial transcriptomics and lineage tracing studies to dissect neutrophil heterogeneity and function. Highlights of the studyO_LIIn CD101-tdTomato homozygous mice, tdTomato is predominantly expressed in neutrophils and labels nearly 100% of mature neutrophils, aligning with the phenotype of CD101+ mature neutrophils; C_LIO_LIThe CD101-tdTomato reporting system does not interrupt CD101 expression or neutrophil functions; C_LIO_LICD101 remains a stable and reliable cell surface marker for labeling mature neutrophils, even under pathological conditions. C_LI

immunology↗

Single-molecule spatial genomics reveals the multi-scale organization and plasticity of extrachromosomal DNA in glioblastoma

Extrachromosomal DNA (ecDNA) is a major driver of intratumoral heterogeneity and is associated with poor clinical outcomes across cancers, yet how individual ecDNA molecules are organized and regulated within intact tumors remains unknown. Here, we leveraged single-molecule, multi-modal spatial genomics to resolve the three-dimensional chromatin organization and transcriptional activity of individual EGFR-containing ecDNA molecules in glioblastoma (GBM) cells in vitro, in orthotopic xenografts, and in patient-derived GBM tissue. At the larger scale, we find that distinct GBM molecular and functional states emerge depending on the local cellular environment. EGFR expression was markedly different between GBM subpopulations, and perturbations of EGFR dosage shifted GBM cellular states. ecDNA expression was modulated by multiple mechanisms, including variation in copy number, chromatin organization, DNA sequence, and chromosomal reintegration, which were simultaneously measured within the same cells. At the single-molecule scale, ecDNA adopts a physically expanded chromatin configuration with larger ecDNA molecules having higher transcriptional activity and interaction with active transcriptional machinery. ecDNA regulation was coordinated within cells and across GBM states, and ecDNA copy number, structure, and transcription were spatially organized across the tumor architecture. Co-culturing GBM cells with neurons recapitulated key features of infiltrative regions, including lower EGFR expression, reduced ecDNA copy number, and increased chromosomal reintegration, suggesting a causal role for the microenvironment in shaping ecDNA regulation. Collectively, these findings support a model in which GBM states and ecDNA are linked, plastic, and influenced by microenvironmental contexts, revealing a previously inaccessible layer of genome organization underlying tumor heterogeneity and malignant cell behavior.

genomics↗

Parkinson's disease linked LRRK2 G2019S drives oxidative nuclear DNA damage and PARP1 hyperactive signaling

LRRK2 mutations are the most common cause of autosomal-dominant Parkinsons disease (PD), with G2019S linked to both familial and sporadic PD. Although LRRK2-mediated mitochondrial DNA damage is implicated in PD, the contribution of nuclear DNA damage is less understood. Using CRISPR/Cas9-generated LRRK2G2019S/G2019S knock-in cells, we discovered increased sensitivity to oxidative and alkylating DNA-damaging agents compared to wild-type, consistent with compromised tolerance/repair of lesions processed by base excision repair (BER). The oxRADD assay revealed elevated endogenous oxidative nuclear base damage in LRRK2 mutant cells. Concomitantly, PARP1-dependent poly(ADP-ribose) (PAR) levels were markedly increased, with chromatin enrichment of PARP1 and BER factors (XRCC1, DNA ligase III) only in LRRK2G2019S/G2019S cells, indicating BER initiation, without successful resolution. LRRK2G2019S/G2019S cells displayed synthetic lethality with PARP-trapping inhibitors (olaparib) but tolerated PARP1 knockdown, suggesting cytotoxicity from stabilized PARP-DNA complexes rather than loss of catalytic activity. The SOD/catalase mimetic EUK-134 abrogated LRRK2 G2019S-dependent PAR accumulation, whereas the mitochondrial complex I inhibitor rotenone exacerbated PAR levels, linking reactive oxygen species (ROS) to BER dysfunction and PARP1 hyperactivation. Overall, we have identified a ROS-dependent PARP1 hyperactivation pathway that underlies LRRK2 G2019S-associated cellular vulnerability.

cell biology↗

Vampire bats target their social grooming to hard-to-reach body parts

Many group-living mammals and birds groom the fur (or preen the feathers) of their close associates to build and maintain affiliative relationships. Several lines of evidence suggest that social grooming in female common vampire bats (Desmodus rotundus) is a low-cost form of helping, but it has yet to be shown that vampire bats preferentially groom others in locations that are difficult to self-groom, as has been found in multiple primate species. In this short note, we show that vampire bat social grooming (n = 1586 events) occurs most often on parts of the recipient's body where self-grooming (n = 1515 events) is least likely, and often in locations where the recipient could not lick itself, like the back of the head. The finding that vampire bats preferentially groom each other in hard-to-reach locations provides further support for the hypothesis that social grooming is both a social signal and a low-cost form of helping.

animal behavior and cognition↗

Widespread symbiosis of ciliate epibionts colonizing gills of shrimps inhabiting vents and seeps across the Pacific Ocean

Although bacterial symbiosis is well-documented in chemosynthetic-based ecosystems, associations with microeukaryotes remain overlooked. In this study, using scanning electron microscopy and 18S rDNA barcoding, we investigate the presence, diversity, and biogeographic patterns of ciliate epibionts associated with two deep-sea caridean shrimp families: Alvinocarididae, and Thoridae. We identified a widespread lineage of ciliates colonizing the gills of different alvinocaridid species, extending their previously known distribution in freshwater and coastal habitats to deep-sea areas down to 3388 m. These ciliates form a distinct clade related to coastal Chonotrichia, but showing clear genetic divergence from the previously-described species. Geographic divergence of these ciliate populations was observed across the Pacific Ocean, with no evident structure related to their host species. These chonotrichian ciliates exhibited variation occurrence across host species, individuals, and regions, indicating a facultative association with their hosts. In contrast, the thorid shrimps harbored rare and phylogenetically diverse ciliates. More rarely, we found ciliates related to known parasitic lineages hosted by both shrimp families, with signs of immune response - black gills - in some individuals colonized by these ciliates. Our results reveal previously overlooked protist-crustacean associations in chemosynthetic ecosystems and highlight the ecological and biogeographic importance of this group in the deep ocean.

microbiology↗

rRNA Expansion Segments Mediate Ribosome Dimerization as a Conserved Stress Response

Inhibition of mRNA translation is a common feature in proteostatic stress cellular responses. Puromycin, a widely used compound for studying translation, disrupts protein synthesis by mimicking the 3 end of aminoacyl-tRNAs. Despite its extensive use as a research tool to probe the connection between translation activity and various physiological and pathological states, the cellular response associated with puromycin-induced translation stress remains incompletely understood. Utilizing in situ cellular electron tomography and topology analysis, we visualized the translation machinery at high resolution. Our analysis revealed that puromycin-treated neuronal cells exhibit an accumulation of "idle ribosomes" characterized by the binding of eIF5A, indicating a close association of this factor with translationally inactive ribosome states under stress. Additionally, the idle ribosomes formed dimeric complexes mediated by ribosomal RNA expansion segments, suggesting an evolved mechanism involving these regions in translation hibernating and protecting idle ribosomes. We show that the hibernating disome formation is not unique to puromycin administration but represents a conserved mechanism as a response to different cellular stressors including those associated with endoplasmic reticulum (ER) stress and amino acid depletion. Altogether, our findings shed light on previously unexplored aspects regarding unique states of mammalian ribosome hibernation, and collectively offers new avenues for understanding the correlation of cellular stress response and the regulation of protein synthesis.

molecular biology↗

Discovery and dynamic pharmacology of μ-opioid receptor positive allosteric modulators

Opioid agonists such as morphine and fentanyl exert analgesic effects by binding and activating the {micro}-opioid receptor ({micro}OR), yet agonism of the {micro}OR causes a slate of serious side effects. {micro}OR-mediated addiction and respiratory depression are the major causes of the current opioid overdose crisis, largely driven by the explosion in illicit use of fentanyl, a potent opioid receptor full agonist. Given these serious side effects (and high resulting societal cost), molecules that act as analgesics with distinct mechanisms of action are of great interest. Positive allosteric modulators (PAMs) of the {micro}OR have the potential to avoid many off-target side effects of conventional opioid orthosteric agonists by enhancing the signaling properties of natural opioid peptide systems. We used a DNA-encoded chemical library screening approach to selectively discover active-state-specific {micro}OR PAMs. Two out of 3 selected prospective PAMs displayed the anticipated enhancement in agonist activity. The most effective of these compounds enhanced the activity of all orthosteric opioid agonists tested, including the native opioid peptide met-enkephalin. Little is known about the underlying dynamic basis of allosteric modulation of Family A GPCRs like the {micro}OR. To that end, we used single-molecule fluorescence resonance energy transfer experiments to detail the impact that our novel {micro}OR PAM has on the dynamic activation behavior of a key region on the intracellular face of the receptor. Our results here provide both a new chemical scaffold that acts as a {micro}OR PAM and detailed pharmacological and dynamic insights into its mechanism of action.

biophysics↗

Representations of semantic relations in the human cerebral cortex

An essential aspect of human cognition is the ability to explicitly think about semantic relations between concepts. Neuroimaging studies have found that individual concepts are encoded by distributed patterns of cortical activity, but relatively little is known about how semantic relations between concepts are encoded in the brain. Some theoretical models suggest that relation representations are embedded within concept representations, while others suggest that relation representations are independent of any specific concept pair. We designed a study to compare how semantic relations and concepts are encoded across the cerebral cortex. To characterize how relations are encoded across cortex, fMRI was used to record brain activity while six participants each answered over one thousand questions about different semantic relations. We find that relations are encoded independently of the specific concepts that are connected in any particular instance of the relation. Our results further suggest that relations and concepts are represented in the same set of cortical regions, and that, within these regions, each location is preferentially selective for specific relations. Overall, these results suggest that in the human cerebral cortex, relations and concepts may have the same type of functional representation.

neuroscience↗

Mechanisms of HIV Latency in Hematopoietic Progenitors: GFI1 as a Key Regulator

Durable control of HIV infection is challenged by persistent latent reservoirs, including hematopoietic stem and progenitor cells (HSPCs), which provide a unique niche for proviral silencing. Mechanisms of HIV latency in HSPCs remain poorly studied. Here, we utilized a dual-reporter HIV (89.6 VT1) and single-cell RNA sequencing to identify host factors governing latency in HSPCs. Transcriptomic profiling revealed elevated expression of several genes in latently infected cells, among them the transcriptional repressor GFI1. Functional studies showed that GFI1 suppresses HIV gene expression by binding a conserved sequence near the primer binding site within the long terminal repeat (LTR). Disruption of GFI1 DNA-binding or corepressor recruitment domains diminished its silencing effect. GFI1 also antagonized Tat and NF-{kappa}B-mediated activation, and reversal of GFI1-mediated suppression was most robust with combined HDAC inhibition and NF-{kappa}B activation. These findings position GFI1 as an important regulator of HIV latency in HSPCs.

microbiology↗

Improving Growth Predictions in Aquaculture through an Improved Bioenergetics Model Incorporating Feed Composition and Nutrient Digestibility for Largemouth Bass (Micropterus salmoides)

Bioenergetics models serve as mechanistic tools to predict growth by linking energy intake, metabolic expenditure, and nutrient partitioning. However, traditional models rely primarily on gross energy (GE) intake, thereby oversimplifying the effects of feed composition and nutrient availability on fish growth. This work therefore proposed a refined bioenergetics model incorporating nutrient-specific digestibility coefficients (ADCs) and feed composition and tested using a compiled dataset (n=235; 165 for calibration and 70 for independent validation) and a field experimental dataset of largemouth bass (Micropterus salmoides). We first optimized parameters of a gross energy intake-based bioenergetics model, increasing R2 from 0.62 to 0.96 and thereby providing a calibrated foundation for subsequent refined model. The refined model demonstrated superior predictive performance on the compiled dataset (R2 = 0.97) with RMSE = 19.86 g and MAE = 10.31 g), representing reductions of 4.13% in RMSE and 19.98% in MAE and a 1.03% increase in R2 compared with the optimized GE-based model. In the field experiment, the refined model achieved high predictive accuracy (R2 = 0.98 and 0.97), whereas the optimized GE-based model showed poor performance (R2 = 0.33 and 0.06 respectively). This study is, to our knowledge, the first bioenergetics framework for largemouth bass that decomposes feed composition and nutrient-specific ADCs to compute macronutrient-resolved digestible energy, enabling formulation-aware growth prediction and nutrient-oriented optimization.

bioengineering↗

Brainwide dopamine dynamics across sleep-wake transitions

Dopaminergic signaling plays a critical role in regulating arousal and transitions between sleep states, yet brainwide dynamics underlying these transitions remain incompletely characterized. Here, we employed multi-site fiber photometry with the dopamine sensor GRAB-DA2m, combined with electroencephalogram (EEG)/electromyogram (EMG) recordings, to systematically assess regional dopamine (DA) dynamics across sleep-wake states in the medial prefrontal cortex (mPFC), striatal subregions, central amygdala (CeA), and midbrain nuclei in mice. We found that DA levels prominently increased in the mPFC, dorsolateral striatum (DLS), ventral tegmental area (VTA), substantia nigra pars compacta (SNc), and dorsal raphe nucleus (DRN) during transitions from non-rapid eye movement (NREM) sleep to wakefulness (WAKE), supporting their role in arousal. Conversely, DA decreased in the CeA and nucleus accumbens lateral parts (NAc-L) during these transitions. During transitions from NREM to rapid eye movement sleep (REM), DA elevations were observed in the CeA and middle accumbens subregion (NAc-M), rather than NAc-L, while other regions exhibited decreases. Cross-regional DA correlations revealed synchronized network activity across sleep-wake transitions. Optogenetic activation of VTA and DRN dopamine neurons induced robust DA release in cortical and subcortical regions, and chemogenetic activation promoted wakefulness selectively via VTA and DRN, but not SNc DA neurons. These results elucidate distinct brainwide DA dynamics across state transitions and highlight differential roles for DA signaling in modulating sleep-wake states.

neuroscience↗

A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

The basal ganglia (BG) underlie motor control, reward processing, and many neurological and psychiatric disorders, but a comprehensive epigenomic and 3D-genome atlas of the human BG is lacking. Here we present a multimodal single-cell atlas profiling DNA methylation and 3D chromatin conformation in 261,331 nuclei (snm3C-seq) across eight subregions, resolving 12 classes, 31 subclasses, and 59 groups. Harmonized under the HMBA basal-ganglia consensus taxonomy, this atlas integrates with matched RNA, ATAC-seq, and histone-modification data across five regulatory layers. We identify millions of cell-type- and region-specific differentially methylated regions enriched for distinct transcription factor motifs and link them to disease-associated heritability. Neuron-specific loops dominate cell-type-specific 3D contact remodeling, while most non-neuron-specific loops are constitutive. Among spiny projection neurons (SPNs), chromatin loops, rather than TAD boundaries, distinguish D1, D2, and eccentric SPN subclasses, with eccentric SPNs showing the most loop-level reorganization among the three. We characterize STR D2 SMYD2-HTR7 SPN, a newly recognized POU6F2 D2-SPN subtype, and reveal region-specific methylation and contact gradients of disease-associated genes, including CADM1 and PDE8B. Integrative gene-regulatory networks reconstruct cell-type-resolved enhancer-promoter links to interpret Parkinsons disease risk variants at SNCA. Finally, MERFISH spatial profiling combined with cross-species Patch-seq identifies non-SPN neuronal subtypes, including a MOXD1 striosomal STR FS PTHLH-PVALB GABA subtype with distinct electrophysiology, partitioning across the striatal matrix-striosome boundary. HighlightsO_LIA multimodal single-cell atlas maps DNA methylation and 3D genome architecture across human basal ganglia cell types and subregions. C_LIO_LINeuron-specific loops dominate cell-type-specific 3D contact remodeling in the human BG, whereas most non-neuron-specific loops are constitutive. C_LIO_LISpiny Projection Neuron (SPN) subtypes exhibit regionally organized epigenomic and 3D genome signatures that align with dorsal-ventral identities. C_LIO_LIChromatin loops are the primary distinguishing feature among D1, D2, and eccentric SPN subclasses, with eccentric SPNs being the most 3D-reorganized. C_LIO_LIIntegrated regulatory maps link cell-type-specific enhancers to disease-associated genetic risk in the human basal ganglia. C_LIO_LINon-SPN interneurons differ in distribution and in transcriptional and epigenetic identity across the matrix-striosome boundary. C_LI

neuroscience↗

Fully Automated and Noise-Robust SEEG Electrode Localization under Practical Clinical Conditions

Stereoelectroencephalography (SEEG) provides direct intracranial recordings of epileptic activity with high spatial and temporal resolution and is widely regarded as the gold standard for presurgical evaluation of drug-resistant epilepsy. Accurate localization of SEEG contacts is essential for seizure onset analysis and surgical planning. However, existing localization approaches are often semi-automated, sensitive to imaging quality, and require manual intervention, limiting scalability and routine clinical deployment. We present a fully automated and noise-robust SEEG contact localization pipeline that integrates adaptive artifact suppression, data-driven thresholding, and flexible geometry-based reconstruction. The method was evaluated on six patients from two centers, including diverse resolution CT acquisitions, comprising 57 electrodes and 652 contacts in total. The proposed framework successfully reconstructed all electrodes and achieved an overall recall of 98.3% and precision of 97.1% for contact localization compared with expert labeling, with a mean deviation of 0.248 {+/-} 0.066 mm. Processing time was approximately two minutes per subject on standard hardware. These results demonstrate reliable performance across heterogeneous imaging conditions. By reducing processing time from hours of manual effort to approximately two minutes per subject, the proposed fully automated workflow facilitates routine clinical deployment and scalable multi-center studies.

bioinformatics↗

Genetic variation shapes human mRNA translation and disease risk

Genetic variation can influence protein abundance through translation, yet this regulatory layer remains poorly defined. We developed a deep learning approach to systematically map the effects of single-nucleotide variant (SNV) on translation efficiency (TE) across the human genome. In lymphoblastoid cells, >90,000 variants substantially altered TE, with strong positional and sequence-context biases. Importantly, the missense variants, traditionally considered only for their effect on protein recoding, were also found to reshape translation efficiency, with proline substitutions consistently reducing TE in a length-dependent manner. Extending our analysis to eight additional cell types revealed a two-layer architecture of translational regulation: 5UTR variants produced highly concordant effects across cell types, whereas synonymous and missense variants in coding region exhibited cell type-specific outcomes, suggesting context-dependent translation regulation. TE-altering variants were enriched among GWAS loci and linked to cancer, immune, cardiometabolic, and neurological traits, positioning translation as a key mediator of genetic effects on disease.

genetics↗

What and where manifolds emerge and align with perception in deep neural network models of sound localization

Whether the auditory cortex has parallel pathways for sound identification ("what") and localization ("where"), and whether it contains a map of auditory space, is debated. Here, we examined the low-dimensional structure (manifold) of "what" and "where" representations in deep neural network models of sound localization. Unexpectedly, models trained for "where" learned untangled "what" manifolds, including voice type, reverberation, and spectral detail. The distribution of "what" manifolds was not random, but geometrically organized by spectral similarity. The separability and distance of both "what" and "where" manifolds were aligned with human behavior. "What" also determined whether "where" manifolds organized into a map: maps emerged when "what" contained localization cues that were topographically organized. However, forming a spatial map reduced localization accuracy in both models and human listeners. Together, object manifolds reveal learned task-irrelevant attributes of object that are ignored when measuring task performance alone, and task-optimized neural networks can provide insights into brain and behavior, not just replicate them.

neuroscience↗

PlantMDCS: A code-free, modular toolkit for rapid deployment of plant multi-omics databases

With the rapid accumulation of diverse omics datasets, achieving efficient management and integrative analysis of plant multi-omics data remains a major challenge. Conventional solutions rely on constructing web-based databases, which often demand substantial programming expertise and long-term financial support. To address these limitations, we developed the Plant Multi-omics Database Construction System (PlantMDCS)-a locally deployable, user-friendly, and collaborative platform that unifies database construction and downstream multi-omics analysis within a graphical environment. PlantMDCS adopts a decoupled front-end/back-end architecture. The back end serves as the core engine for data management and computation, and is responsible for the storage, preprocessing, integration, and hierarchical association of multi-omics data. Once initialized, the front end supports the complete research workflow, including data import, querying, integrative analysis and visualization. All operations can be performed without programming, while local resource usage is dominated by disk storage required for user-provided datasets rather than sustained computational overhead. Benchmarking across plant species ranging from Arabidopsis to hexaploid wheat demonstrated that database construction can be completed within minutes, independent of genome size or data complexity. PlantMDCS is designed for local deployment to ensure data security, while allowing multi-user collaboration within local networks and supporting controlled remote access for teams distributed across different regions. Overall, PlantMDCS offers a secure and sustainable framework that integrates data management and analysis within a unified system. This design shifts multi-omics research away from fragmented file-based processing toward persistent, database-driven exploration, thereby enhancing analytical efficiency and reproducibility.

bioinformatics↗