Biology subjects

Kim, Y.

Publications and source records attributed to Kim, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Growth hormone is required for hippocampal engram cell maturation

Memory is thought to be stored in a sparse population of neurons or synapses 1. These neurons or synapses collectively termed the engram are necessary and sufficient for memory recall 2,3. Learning induces synaptic strengthening in engram cells at both pre- and postsynaptic sites 4,5. However, the critical time window and the molecule related to the induction of such synaptic changes are unknown. Here we show that the initial translation plays a key role in engram maturation by facilitating pre- and postsynaptic strengthening and that growth hormone (GH) is required to induce this process in the Dentate Gyrus. Using anisomycin, a protein synthesis inhibitor, we found that blocking the initial and the subsequent second wave of translation arrests the maturation of engram cells. Revisiting our hippocampal translatome during memory formation 6 proposed GH as a mediator of engram maturation. Overexpression of the dominant negative (G118R) GH blocked the maturation of the hippocampal engram cell 7. Facilitating activity-dependent GH uptake by injecting recombinant human GH (rhGH) into the animal rescued the arrestment caused by anisomycin. Together, our findings propose GH as a key mediator of hippocampal engram cell maturation.

neuroscience↗

bioRxiv2025

Social context and dopamine signaling converge in the mushroom body to drive impulsivity

Organisms adapt their behaviors flexibly in response to various internal and environmental factors. However, how and where these factors converge in the brain to alter behavior is not well understood. In this study, we examine how social context interacts with dopamine activity to influence inhibitory control in Drosophila. We found that, regardless of social context--whether isolated or in groups--wild-type flies consistently showed strong movement suppression in a go/no-go task that measures action restraint. In contrast, flies with enhanced dopamine activity suppressed their movements when tested alone or with potential mates but exhibited impulsive behaviors when exposed to same-sex peers. This social-context-dependent impulsivity was shown to rely on dopamine-D1 receptor-cAMP signaling in mushroom body (MB) neurons. Remarkably, activating the MB was sufficient to induce impulsivity, even without dopamine input or a social context. Our findings highlight MB as a critical hub where social context and dopamine signaling converge to regulate impulsive behavior in Drosophila. Signficance statementThis study demonstrates that impulsivity results from the interplay between elevated dopamine levels and social context, rather than dopamine alone, with the mushroom body (MB) serving as a key neural hub for integrating these signals in Drosophila. Social stimuli, such as the presence of same-sex peers, disrupt inhibitory control in a context-dependent manner, highlighting the importance of multimodal sensory inputs and MB activity. These findings challenge the isolation-focused approach in traditional impulsivity research and underscore the need to account for social influences when investigating cognitive processes and disorders like ADHD, autism, and substance use, where social settings often amplify symptoms. ClassificationGenetics / Neuroscience

animal behavior and cognition↗

bioRxiv2025

Cholesterol depletion activates trafficking-coupled sphingolipid synthesis

Within cellular membranes, sphingomyelin is associated with cholesterol and this complex facilitates homeostatic regulation of membrane viscosity. Acute cholesterol depletion increases the synthesis of very-long-chain (VLC) sphingomyelin, but a link between lipid sensing and sphingolipid synthesis is lacking. Using sphingolipid metabolic flux analysis, we observed that VLC-ceramide, the precursor to VLC complex sphingolipids that are produced in the Golgi apparatus, was rapidly consumed after cholesterol depletion, while synthesis of long-chain sphingolipids was unaffected. Sphingolipid trafficking assays showed that cholesterol depletion enhances VLC-Ceramide trafficking from the endoplasmic reticulum to the Golgi apparatus. Changes in the sizes of coatomer II ER exit sites were correlated with increased VLC-Ceramide trafficking and concomitant increase in sphingomyelin. Depletion of Sec16A, a component of the COPII network, abolished VLC-SM synthesis. This study reveals ER-to-Golgi trafficking of VLC-Ceramide as a key regulatory node in organelle membrane homeostasis pathways. SummaryIn cellular membranes, sphingomyelin is associated with cholesterol. Metabolic flux analysis of sphingolipid metabolism showed that synthesis rate of sphingomyelin, but not ceramide, was increased after depletion of cholesterol due increased rate of COPII-dependent ER-to-Golgi transport of ceramide.

cell biology↗

bioRxiv2025

TMEM145 is a key component in stereociliary link structures of outer hair cells

Outer hair cells (OHCs) in the cochlea contain specialized stereociliary structures essential for auditory function. These include horizontal top connectors (HTCs), linking adjacent stereocilia and tectorial membrane-attachment crowns (TM-ACs), anchoring the tallest stereocilia to the tectorial membrane. The known molecular components of these structures, such as stereocilin, otogelin, otogelin-like, and tubby, lack transmembrane domains, suggesting the existence of anchoring proteins. This study identified TMEM145, a transmembrane protein with a Golgi dynamics (GOLD) domain, as a crucial OHC stereocilia component. TMEM145 was expressed in both OHCs and spiral ganglion neurons, with specific localization to TM-ACs and HTCs in OHCs. Tmem145 knockout (KO) mice exhibited profound hearing impairment at three weeks of age, with complete loss of distortion product otoacoustic emissions, indicating OHC dysfunction. Immunostaining and scanning electron microscopy revealed the absence of TM-ACs and HTCs in Tmem145 KO mice. In heterologous cell systems, TMEM145 interacted with stereocilin and tubby, facilitating their extracellular secretion. TMEM145 was undetectable in stereocilin KO and tubby mutant mice, indicating interdependence among these proteins. These findings establish TMEM145 as an essential membrane protein for the structural integrity of OHC stereocilia, providing insights into the molecular architecture of cochlear hair cells and their role in auditory function.

neuroscience↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2025

Protein Synthesis Blockade Prevents Fear Memory Reactivation via Inhibition of Engram Synapse Strengthening

Memory relies on ensembles of engram cells in the brain. While previous studies have established the existence of these cells, the relationship between cellular and synaptic activity remains unclear. To address this, we applied the dual e-GRASP technique in mice to examine synaptic connectivity between the ventral CA1 and the basal amygdala during memory formation. We found that contextual fear conditioning increased engram-to-engram synapse (engram synapse) density and induced structural potentiation, underscoring their importance in associative memory. Additionally, we investigated the role of protein synthesis in memory formation by inducing retrograde amnesia using anisomycin, a protein synthesis inhibitor. Mice injected with anisomycin once (1xANI) showed impaired natural recall but still displayed fear responses upon optogenetic reactivation of engram cells. In contrast, mice that received four anisomycin injections over six hours (4xANI) showed significantly impaired natural recall and failed to exhibit fear responses upon optogenetic reactivation. This behavioural phenotype was correlated with synaptic changes: 1xANI mice exhibited no significant reduction in engram synapse density but had significantly smaller spine sizes, whereas 4xANI mice showed both a significant reduction in engram synapse density and spine size. Our results indicate that protein synthesis inhibition significantly reduces engram synapse density and spine size, changes that correlate with reductions in fear memory during both natural recall and artificial reactivation.

neuroscience↗

bioRxiv2025

Light-activated tetanus neurotoxin for conditional proteolysis and inducible synaptic inhibition in vivo

The light chain of tetanus neurotoxin (TeNT) is a 52 kD metalloprotease that potently inhibits synaptic transmission by cleaving the endogenous vesicle fusion protein VAMP2. To mitigate the toxicity of TeNT and harness it as a conditional tool for neuroscience, we engineered Light-Activated TeNT (LATeNT) via insertion of the light-sensitive LOV domain into an allosteric site. LATeNT was optimized by directed evolution and shown to have undetectable activity in the dark mammalian brain. Following 30 seconds of weak blue light exposure, however, LATeNT potently inhibited synaptic transmission in multiple brain regions. The effect could be reversed over 24 hours. We used LATeNT to discover an interneuron population in hippocampus that controls anxiety-like behaviors in mouse, and to control the secretion of endogenous insulin from pancreatic beta cells. Synthetic circuits incorporating LATeNT converted drug, Ca2+, or receptor activation into transgene expression or reporter protein secretion. Due to its large dynamic range, rapid kinetics, and highly specific mechanism of action, LATeNT should be a robust tool for conditional proteolysis and spatiotemporal control of synaptic transmission in vivo.

biochemistry↗

bioRxiv2025

Spatial pattern of serology against Borrelia and tick-borne encephalitis virus in roe deer (Capreolus capreolus), Northern France, 2019-2022

BackgroundLyme borreliosis and tick-borne encephalitis (TBE) are tick-borne zoonoses of public health importance, transmitted in Western Europe by the same tick vector Ixodes ricinus. Roe deer (Capreolus capreolus) is a widespread feeding host for I. ricinus stages. Here, we explored the spatial extent of both pathogens in the wild in Northern France by assessing serological status in roe deer. MethodsWe collected 3,147 blood samples (2019-2022), and searched antibodies against both pathogens using ELISA tests. We fitted logistic models to investigate exposure to both or either pathogens, and explored spatial patterns using Kulldorf clustering scan tests. ResultsThe overall ELISA IgG prevalence was 23.24% (95%CI [21.77-34.72]) for Borrelia and 8.64% (95%CI [7.45-9.86]) for TBEV. The median Borrelia seroprevalence varied from 4% to 42% between departments, with two high-risk clusters of exposure identified. TBEV seroprevalence did not show any spatial pattern, and positives by seroneutralisation tests were reported in eight departments. DiscussionOur findings suggest the presence of both pathogens over large areas. Wider spatial sampling including areas at lower risk and improved serological methods would be beneficial to further validate those estimates.

ecology↗

bioRxiv2025

Contrastive Learning for Omics-guided Whole-slide Visual Embedding Representation

While computational pathology has transformed cancer diagnosis and prognosis prediction, existing computational methods remain limited in their ability to decipher the complex molecular characteristics within tumors. We present CLOVER (Contrastive Learning for Omics-guided whole-slide Visual Embedding Representation), a novel deep learning framework that leverages self-supervised contrastive learning to integrate multi-omics data (genomics, epigenomics, and transcriptomics) with slide representations, connecting the morphological and molecular features of tumors. Using the breast cancer cohorts comprising diagnostic slides and multi-omics paired data from 610 breast cancer patients, we validated CLOVERs excellence by demonstrating its ability to generate effective slide-level representations that consider molecular states of cancer. CLOVER outperforms existing methods in few-shot learning scenarios, particularly in cancer subtype classification and clinical biomarker prediction tasks (ER, PR, and HER2 status). Through comprehensive interpretability analysis, we identified tumor microenvironment components within slides and revealed molecular features associated with breast cancer. Our results demonstrate that CLOVER enables detailed molecular characterization from single slide analysis, suggesting its potential for effective utilization in future cancer diagnosis and prognosis prediction studies.

pathology↗

bioRxiv2025

Distinct modes of dopamine modulation on striatopallidal synaptic transmission

Dopamine (DA) affects voluntary movement by modulating basal ganglia function. In the classical model, DA depletion leads to overactivity of the indirect pathway and excessively inhibits the thalamus, resulting in hypokinesia. The contribution of DA on striatopallidal synapses, an initial hub in the indirect pathway connecting the striatum to the external globus pallidus (GPe), remains poorly understood because of the sparse DA innervation. Here, we combine optogenetic projection targeting, whole cell patch clamp recordings in acute brain slices from mice, and computational modeling to overcome this limitation. We show that DA activates D2R receptors (D2Rs) and D4 receptors (D4Rs) differentially in distinct GPe subregions. In a pinwheel-like fashion, dorsolateral and ventromedial GPe expresses high levels of D2Rs, which exert presynaptic inhibition, while in dorsomedial and ventrolateral GPe D4Rs cause postsynaptic inhibition. DA depletion by 6-OHDA (6-hydroxydopamine) reverses the region- specific effect of DA, shifting it in the opposite direction and contributing to hypokinesia. These findings reveal the mechanism by which the different modality information conveyed spatially through the indirect pathway is differentially modulated by DA at striatopallidal synapses.

neuroscience↗

bioRxiv2025

Integrated Techniques for Extracellular Particle Separation and Single-Particle Multiparametric Characterization to Track Cancer Biomarkers from Tissue to Biofluids

Gastric cancer (GC) remains a formidable global health challenge, with late-stage diagnosis and high recurrence rates resulting in poor patient outcomes. This study explores the potential of advanced technologies, namely Bessel Beam Excitation Separation Technology (BEST) and multiparametric biochip assay (MBA), to track single extracellular vesicle and particle (EVP) cargo from organs of pathology into biofluids such as plasma and saliva. Using GC as a study model, we conducted high throughput, multiparametric analyses of EVPs derived from plasma, saliva, and tissue samples. Our findings demonstrate the feasibility of these techniques in isolating and characterizing EVPs, revealing consistent EVP morphology and size across biofluids. Furthermore, differential expression patterns of the developed and validated salivary GC biomarkers, miR-140-5p and miR-301a-3p, were observed in GC patient biofluids, supporting the diagnostic relevance of EVP cargo. Notably, saliva emerged as the most promising biofluid for GC diagnosis, achieving superior Receiver Operating Characteristic (ROC) curve values compared to plasma and tissue. This study highlights the role of BEST and MBA in advancing single-EVP analysis and elucidating EVP trafficking, paving the way for future diagnostic applications of EVP cargo.

cancer biology↗

bioRxiv2025

Omics-based insights into human liver reveal GTPase-driven mechanisms of MASLD progression in obesity

Metabolic dysfunction-associated steatotic liver disease (MASLD) is often asymptomatic early on but can progress to irreversible conditions like cirrhosis. Due to limited access to human liver biopsies, systematic and integrative molecular resources remain scarce. In this study, we performed transcriptomic analyses on liver and metabolomic analyses on liver and plasma samples from morbidly obese individuals without liver pathology or at early-stage MASLD. While, the plasma metabolomic profile did not fully mirror liver histological features, dual-omics integration of liver samples revealed significantly remodeled lipid and amino acid metabolism pathways. Integrative network analysis uncoupled metabolic remodeling and gene expression as independent features of hepatic steatosis and fibrosis progression, respectively. Notably, GTPases and their regulators emerged as a novel class of genes linked to early liver fibrosis. This study offers a detailed molecular landscape of early MASLD in obesity and highlights potential targets of obesity-linked liver fibrosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/632747v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1188eborg.highwire.dtl.DTLVardef@1340070org.highwire.dtl.DTLVardef@108d560org.highwire.dtl.DTLVardef@f0adda_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Pillar arrays as tunable interfacial barriers for microphysiological systems

We report on the design and fabrication of a novel circular pillar array as an interfacial barrier for microfluidic microphysiological systems (MPS). Traditional barrier interfaces, such as porous membranes and microchannel arrays, present limitations due to inconsistent pore size, complex fabrication and device assembly, and lack of tunability using a scalable design. Our pillar array overcomes these limitations by providing precise control over pore size, porosity, and hydraulic resistance through simple modifications of pillar dimensions. Serving as an interface between microfluidic compartments, it facilitates cell aggregation for tissue formation and acts as a tunable diffusion barrier that mimics diffusion in vivo. We demonstrate the utility of barrier design to engineer physiologically relevant cardiac microtissues and a heterotypic model with vasculature within the device. Its tunable properties offer significant potential for drug screening/testing and disease modeling, enabling comparisons of drug permeability and cell migration in MPS tissue with or without vasculature.

bioengineering↗

bioRxiv2025

Squid primary cell culture as a model system and experimental tool

Squid primary cells from various tissues and ages are isolated, maintained in culture, and express exogenous genes. This protocol opens up numerous opportunities in molecular biology, neuroscience, and marine biology, enabling molecular and cellular-level investigations into processes specific to squids, including their complex behaviors, rapid color change mechanisms, RNA editing capabilities, with broader implications in basic cell physiology. We also describe procedures that harness life-stage tractability in Euprymna berryi squids towards future studies of aging in this model marine organism. Highlights- Squid primary cells are isolated from optic lobes, gills, eyes, and the skin - Cells from these tissues can be dissociated from any life stage of the squid - Isolated cells can express exogenous genes through mRNA transfections and are subject to live and/or fixed cell imaging - Specific details for optimized media conditions, trypsinization, plating, and passaging are included

cell biology↗

bioRxiv2025

HeteroRepur: Efficient Modeling of Heterogeneous Disease Graph for Depression Drug Repurposing using Heterogeneous Graph Neural Networks

ObjectiveMajor Depressive Disorder (MDD) is one of the most prevalent psychiatric disorders, yet existing treatments often result in suboptimal responses and encounter high recurrence rate. Repositioning existing medications, which often significantly reduces the required time and budget, has been demonstrated to be a promising strategy for drug discovery of multiple central nervous system (CNS) disorders. However, an efficient modeling strategy of heterogeneous semantic information among biological networks has yet to be developed for drug repurposing. Material and MethodsIn this study, we proposed HeteroRepur, by integrating heterogeneous graph neural networks to learn interaction features of Depression Drug Repurposing Graph (DDRG) and then classify drugs. ResultsThe DDRG embeddings learned by HeteroRepur accurately capture graph information, including 89 types of interaction or associations among drugs, genes, pathways, and GOs, as well as disease genetic network of MDD. In drug classification task, HeteroRepur outperforms various baseline models, including existing graph neural network approaches that do not consider heterogeneous network information. Finally, HeteroRepur predicts new candidates for treating MDD, including CNS drugs that have the potential to be extended to MDD, and dietary supplements that might benefit depression patients by elevating essential nutrient levels. ConclusionHeteroRepur outperforms traditional graph-based approaches, and can be used to rank promising drugs among complex disease networks with heterogeneous topology.

bioinformatics↗

bioRxiv2024

Inhibition of Mitochondrial Fission Protein Drp1 Ameliorates Myopathy in the D2-mdx Model of Duchenne Muscular Dystrophy

Although current treatments for Duchenne Muscular Dystrophy (DMD) have proven to be effective in delaying myopathy, there remains a strong need to identify novel targets to develop additional therapies. Mitochondrial dysfunction is an early pathological feature of DMD. A fine balance of mitochondrial dynamics (fission and fusion) is crucial to maintain mitochondrial function and skeletal muscle health. Excessive activation of Dynamin-Related Protein 1 (Drp1)-mediated mitochondrial fission was reported in animal models of DMD. However, whether Drp1-mediated mitochondrial fission is a viable target for treating myopathy in DMD remains unknown. Here, we treated a D2-mdx model of DMD (9-10 weeks old) with Mdivi-1, a selective Drp1 inhibitor, every other day (i.p. injection) for 5 weeks. We demonstrated that Mdivi-1 effectively improved skeletal muscle strength and reduced serum creatine kinase concentration. Mdivi-1 treatment also effectively inhibited mitochondrial fission regulatory protein markers, Drp1(Ser616) phosphorylation and Fis1 in skeletal muscles from D2-mdx mice, which resulted in reduced content of damaged and fragmented mitochondria. Furthermore, Mdivi-1 treatment attenuated lipid peroxidation product, 4-HNE, in skeletal muscle from D2-mdx mice, which was inversely correlated with muscle grip strength. Finally, we revealed that Mdivi-1 treatment downregulated Alpha 1 Type I Collagen (Col1a1) protein expression, a marker of fibrosis, and Interleukin-6 (IL-6) mRNA expression, a marker of inflammation. In summary, these results demonstrate that inhibition of Drp1-mediated mitochondrial fission by Mdivi-1 is effective in improving muscle strength and alleviating muscle damage in D2-mdx mice. These improvements are associated with improved skeletal muscle mitochondrial integrity, leading to attenuated lipid peroxidation.

molecular biology↗

bioRxiv2024

Identification of neuron-glia signaling feedback in human schizophrenia using patient-derived, mix-and-match forebrain assembloids

Although abnormal activities across multiple cell types are believed to contribute to the development of various neurodevelopmental disorders, current brain organoid technologies fall short in accurately modeling the dynamic cellular interactions in the human brain. Recently, we developed a cellular reconstitution technology to create human forebrain assembloids with enhanced cellular diversity, representing dynamic interactions between neurons and glial cells. Here, we created patient-derived, mix-and-match forebrain assembloids, in which neurons, astrocytes, and microglia from both healthy individuals and schizophrenia patients were reconstituted in a combinatorial manner, and identified aberrant cellular interactions between neurons and glial cells in human schizophrenia. At the early stage, schizophrenia forebrain assembloids showed premature neurogenesis induced by the abnormal proliferation and differentiation of neural progenitor cells. Integrated modular analysis of gene expression in post-mortem schizophrenia brain tissue and brain assembloids found increased expression of tumor protein p53 (TP53) and nuclear factor of activated T-cells 4 (NFATC4), which functioned as master transcriptional regulators to epigenetically reprogram the transcriptome involved in the cellular dynamics of neuronal progenitor cells, leading to premature neurogenesis. At the later stage, we observed weakened structures of laminar organization of the cortical layers in forebrain assembloids and identified the neuron-dependent transcriptional plasticity of glial cells and their altered signaling feedback with neurons, in which neuronal urocortin (UCN) and protein tyrosine phosphatase receptor type F (PTPRF) elicited the expression of Wnt family member 11 (WNT11) and thrombospondin 4 (THBS4) in astrocytes and microglia, respectively. These aberrant signaling axes altered the neuronal transcriptome associated with neuronal response to various stimuli and synthetic processes of biomolecules, resulting in reduced synapse connectivity. Thus, we elucidated developmental stage-specific, multifactorial mechanisms by which dynamic cellular interplay among neural progenitor cells, neurons, and glial cells contribute to the development of the human schizophrenia brain. Our study further demonstrated the potential and applicability of patient-derived forebrain assembloid technology to advance our understanding of the pathogenesis of various neurodevelopmental disorders.

neuroscience↗

bioRxiv2024

SpaceExpress: a method for comparative spatial transcriptomics based on intrinsic coordinate systems of tissues

Spatial transcriptomics (ST) technologies have enabled new explorations into the spatial organization of tissues and their functional implications. However, one of the most fundamental analyses - comparative analysis of spatial gene expression across phenotypes - remains a formidable challenge. We introduce SpaceExpress, a novel statistical tool for detecting phenotype-associated changes in spatial expression patterns. SpaceExpress employs a neural network to embed multiple ST samples in a common latent space, enabling robust cross-sample comparisons despite structural and technical variations. It then uses spline regression to test differential spatial expression of genes between conditions, identifying specific regions of the tissue where expression patterns diverge and quantifying the magnitude of those differences, with rigorous false discovery control and handling of multiple replicates per condition. It includes visualization tools to help interpret spatial pattern differences. We demonstrate the tools effectiveness on synthetic and real ST datasets, revealing mechanistic insights into behavior- and development-related neurogenomic changes in honey bees and mice. Our work extends the highly influential paradigm of differential gene expression analysis to spatial omics.

bioinformatics↗