Biology subjects

Kim, S.

Publications and source records attributed to Kim, S..

At least 379 records · Page 21Linked to original sources

bioRxiv2023

Developmental Glucocorticoid exposure in zebrafish primes expression of genes linked to human psychiatric disorders

Early life stress (ELS) is one of the strongest risk factors for developing psychiatric disorders in humans. As conserved key stress hormones of vertebrates, glucocorticoids (GCs) are thought to play an important role in mediating the effects of ELS exposure in shaping adult phenotypes. In this process, early exposure to high level of GCs may induce molecular changes that alter developmental trajectory of an animal and primes differential adult responses. However, comprehensive characterization of identities of molecules that are targeted by developmental GC exposure is currently lacking. In our study, we describe lifelong molecular consequences of high level of developmental GC exposure using an optogenetic zebrafish model. First, we developed a new double-hit stress model using zebrafish by combining exposure to a high endogenous GC level during development and acute adulthood stress exposure. Our results establish that similar to ELS-exposed humans and rodents, developmental GC exposed zebrafish model shows altered behavior and stress hypersensitivity in adulthood. Second, we generated time-series gene expression profiles of the brains in larvae, in adult, and upon stress exposure to identify molecular alterations induced by high developmental GC exposure at different developmental stages. Third, we identify a set of GC-primed genes that show altered expression upon acute stress exposure only in animals exposed to a high developmental GC. Interestingly, our datasets of GC primed genes are enriched in risk factors identified for human psychiatric disorders. Lastly, we identify potential epigenetic regulatory elements and associated post-transcriptional modifications following high developmental GC exposure. Thus, we present a translationally relevant zebrafish model for studying stress hypersensitivity and alteration of behavior induced by exposure to elevated GC levels during development. Our study provides comprehensive datasets delineating potential molecular targets underlying the impact of developmental high GC exposure on adult responses.

neuroscience↗

bioRxiv2023

Lymphocyte activation gene 3 (Lag3) supports Foxp3+ Treg cell function by restraining c-Myc-dependent aerobic glycolysis

Lymphocyte activation gene 3 (Lag3) has emerged as the next-generation immune checkpoint molecule due to its ability to inhibit effector T cell activity. Foxp3+ regulatory T (Treg) cells, a master regulator of immunity and tolerance, also highly express Lag3. While Lag3 is thought to be necessary for Treg cell-mediated regulation of immunity, the precise roles and underlying mechanisms remain largely elusive. In this study, we report that Lag3 is indispensable for Treg cells to control autoimmune inflammation. Utilizing a newly generated Treg cell specific Lag3 mutant mouse model, we found that these animals are highly susceptible to autoimmune diseases, suggesting defective Treg cell function. Genome wide transcriptome analysis further uncovered that Lag3 mutant Treg cells upregulated genes involved in metabolic processes. Mechanistically, we found that Lag3 limits Treg cell expression of Myc, a key regulator of aerobic glycolysis. We further found that Lag3-dependent Myc expression determines Treg cells metabolic programming as well as the in vivo function to suppress autoimmune inflammation. Taken together, our results uncovered a novel function of Lag3 in supporting Treg cell suppressive function by regulating Myc-dependent metabolic programming.

immunology↗

bioRxiv2023

Stochastic Modeling of Tinnitus Loudness

There has been no study on the relationship between chronic tinnitus and harmonic templates. Harmonic templates are harmonically structured receptive fields in the auditory system in which all frequency components are integer multiples of a common fundamental frequency (F0). In this study, data from 19 harmonic templates from each of 196 chronic tinnitus patients were analyzed and mathematical modeling was performed to quantify the loudness of chronic tinnitus. High-resolution hearing threshold data were obtained by algorithmic pure tone audiometry (PTA) conducting automated PTA at 134 frequency bands with 1/24 octave resolution from 250 Hz to 12,000 Hz. The result showed that there is an intriguing relationship between the auditory instability of harmonic templates and simplified tinnitus severity score (STSS). This study provides several mathematical models to estimate tinnitus severity and the precise quantification of the loudness of chronic tinnitus. Our computational models and analysis of the behavioral hearing threshold fine structure suggest that the cause of severe chronic tinnitus could be a severe disparity between different temporal capacities of each neural oscillator in a certain harmonic template.

neuroscience↗

bioRxiv2023

Red2Flpe-SCON: A Versatile, Multicolor Strategy for Generating Mosaic Conditional Knockout Mice

Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a new mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We have developed the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We used the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which revealed that the stem cell gene, Sox2, is not essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.

genetics↗

bioRxiv2023

Spatial and compositional variations in fruit characteristics of papaya (Carica papaya cv. Tainung No. 2) during ripening

Papaya fruit (Carica papaya) has different degrees of ripening within a fruit, affecting its commercial market value. The fruit characteristics of Tainung No. 2 papaya was investigated at the stem-end, middle, and calyx-end parts at three ripening stages and categorized based on fruit skin coloration: unripe at ca. 16 weeks after anthesis (WAA), half-ripe at ca. 18 WAA, and full-ripe at ca. 20 WAA. The fruits maintained an elliptical shape during ripening with 2.36 of the ratios of the length to the width. The peel and pulp color changed from green to white to yellow during ripening, regardless of the fruit three parts. In the pulp, soluble solid content increased to about 320% and firmness decreased to about 99% during ripening but did not differ among fruit three parts. Individual nutrient contents, including primary and secondary metabolites, and minerals, changed dynamically between the ripening stages and fruit parts. Total carbohydrates and proteins, N, and K, were more accumulated at the stem-end during ripening, meanwhile fructose, glucose, Mg, and Mn were at the calyx-end. In the principal component analysis, ripening stages and fruit parts were distinctly determined by the first and second principal components, respectively. These results provide fundamental information for improving ripening during papaya cultivation.

plant biology↗

bioRxiv2023

Robust single membrane protein tweezers

Single-molecule tweezers, such as magnetic tweezers, are powerful mechanical manipulation tools that can probe nm-scale structural changes in a single membrane protein under force. However, the weak molecular tethers used in the tweezers limit a long time, repetitive mechanical manipulation because of their force-induced bond breakage. Here, using the metal-free click chemistry of dibenzocyclooctyne (DBCO) cycloaddition and the rapid, strong binding of traptavidin to dual biotins (2xbiotin), we developed robust single-molecule tweezers that can perform thousands of force applications on a single membrane protein. By applying up to 50 pN for each cycle, which is sufficiently high for most biological processes, we were able to observe repetitive forced unfolding for a designer membrane protein up to approximately 1000 times on average. Monte Carlo simulations showed that the average error of the unfolding kinetic values rapidly decays to 1.8% at 200-time pulling, indicating that our method can quickly produce reliable statistics. The approach established here is also applicable to highly polar DNA molecules, permitting the nanomechanical manipulation of diverse biomolecular systems.

biophysics↗

bioRxiv2023

The autism-associated loss of δ-catenin functions disrupts social behaviors

{delta}-catenin is expressed in excitatory synapses and functions as an anchor for the glutamatergic AMPA receptor (AMPAR) GluA2 subunit in the postsynaptic density. The glycine 34 to serine (G34S) mutation in the{delta} -catenin gene is found in autism spectrum disorder (ASD) patients and induces loss of {delta}-catenin functions at excitatory synapses, which is presumed to underlie ASD pathogenesis in humans. However, how the G34S mutation causes loss of {delta}-catenin functions to induce ASD remains unclear. Here, using neuroblastoma cells, we discover that the G34S mutation generates an additional phosphorylation site for glycogen synthase kinase 3{beta} (GSK3{beta}). This promotes {delta}-catenin degradation and causes the reduction of {delta}-catenin levels, which likely contributes to the loss of {delta}-catenin functions. Synaptic {delta}-catenin and GluA2 levels in the cortex are significantly decreased in mice harboring the {delta}-catenin G34S mutation. The G34S mutation increases glutamatergic activity in cortical excitatory neurons while it is decreased in inhibitory interneurons, indicating changes in cellular excitation and inhibition. {delta}-catenin G34S mutant mice also exhibit social dysfunction, a common feature of ASD. Most importantly, inhibition of GSK3{beta} activity reverses the G34S-induced loss of {delta}-catenin function effects in cells and mice. Finally, using {delta}-catenin knockout mice, we confirm that {delta}-catenin is required for GSK3{beta} inhibition-induced restoration of normal social behaviors in {delta}-catenin G34S mutant animals. Taken together, we reveal that the loss of {delta}-catenin functions arising from the ASD-associated G34S mutation induces social dysfunction via alterations in glutamatergic activity and that GSK3{beta} inhibition can reverse {delta}-catenin G34S-induced synaptic and behavioral deficits. Significance Statement{delta}-catenin is important for the localization and function of glutamatergic AMPA receptors at synapses in many brain regions. The glycine 34 to serine (G34S) mutation in the{delta} -catenin gene is found in autism patients and results in the loss of {delta}-catenin functions. {delta}-catenin expression is also closely linked to other autism-risk genes involved in synaptic structure and function, further implying that it is important for the autism pathophysiology. Importantly, social dysfunction is a key characteristic of autism. Nonetheless, the links between {delta}-catenin functions and social behaviors are largely unknown. The significance of the current research is thus predicated on filling this gap by discovering the molecular, cellular, and synaptic underpinnings of the role of {delta}-catenin in social behaviors.

neuroscience↗

bioRxiv2023

EnsDTI-kinase: Web-server for Predicting Kinase-Inhibitor Interactions with Ensemble Computational Methods and Its Applications

MotivationKinase inhibitors are a major category of drugs. Experimental panel assay protocols are routinely used as a standard procedure to evaluate the efficiency and selectivity of a drug candidate to target kinase. However, current kinase panel assays are time-consuming and expensive. In addition, the panel assay protocols neither provide insights on binding sites nor allow experiments on mutated sequences or newly-characterized kinases. Existing virtual screening or docking simulation technologies require extensive computational resources, thus it is not practical to use them for the panel of kinases. With rapid advances in machine learning and deep learning technologies, a number of DTI tools have been developed over the years. However, these methods are yet to achieve prediction accuracies at the level of practical use. In addition, the performances of current DTI tools vary significantly depending on test sets. In this case, an ensemble model can be used to improve and stabilize DTI prediction accuracies. ResultsIn this work, we propose an ensemble model, EnsDTI-kinase, that integrates eight existing machine learning and deep learning models into a unified model deployed as a web-server. Upon submission of a compound SMILES string, potential target kinases are automatically predicted and evaluated on the web-server. Importantly, EnsDTI-kinase is a computational platform where newly developed DTI tools can be easily incorporated without modifying core components so that its DTI prediction quality can improve over time. Besides, many useful functionalities are provided on our platform for users to further investigate predicted DTI: it allows confidence experiments by changing the amino acid (AA) at a specific position in a kinase sequence, named in silico mutagenesis, to investigate the effect of AA changes in binding affinity; it predicts kinase sequential regions where the query compound likely binds to by slidingly masking the sequence of selected kinases so that confidence in the predicted binding sites can be evaluated. Our model was evaluated in three experimental settings using four independent datasets, and showed accuracy of 0.82 compared to the average accuracy of 0.69 from five deep learning methods on the ChEMBL dataset. It achieved average selectivity of 0.95 within kinase families such as TK, CAMK and STE. For 8 out of 17 recent drugs, our model successfully predicted their interactions with 404 proteins at average accuracy of 0.82. Availabilityhttp://biohealth.snu.ac.kr/software/ensdti Contactsunkim.bioinfo@snu.ac.kr

bioinformatics↗

bioRxiv2022

Lipoprotein sorting to the cell surface via a crosstalk between the Lpt and Lol pathways during outer membrane biogenesis

Lipopolysaccharide (LPS) and lipoprotein, two essential components of the outer membrane (OM) in Gram-negative bacteria, play critical roles in bacterial physiology and pathogenicity. LPS translocation to the OM is mediated by LptDE, yet how lipoproteins sort to the cell surface remains elusive. Here we report the identification of an inventory of lipoproteins that are transported to the cell surface via LptDE. Notably, we determined crystal structures of LptDE from Pseudomonas aeruginosa and its complex with an endogenous Escherichia coli lipoprotein YifL. The paLptDE-YifL structure demonstrates that YifL translocates to the OM via LptDE, in a manner similar to LPS transport. The {beta}-barrel domain serves as a passage for the proteinaceous moiety while its acyl chains are transported outside. Our finding has been corroborated by results from native mass spectrometry, immunofluorescence, and photocrosslinking assays, revealing a unique mechanism through which lipoproteins are translocated across the OM in an ATP- and LPS-dependent manner. Moreover, our study expands the scope of current knowledge of lipoprotein sorting by disclosing a crosstalk between the Lpt and Lol pathways.

microbiology↗

bioRxiv2022

Intermittent Cytomegalovirus Infection Alters Neurobiological Metabolism and Induces Cognitive Deficits in Mice

Risk factors contributing to dementia are multifactorial. Pathogens as risk factors for dementia is largely correlative with few causal relationships. Here, we demonstrate that intermittent cytomegalovirus (CMV) infection in mice, mimicking human chronic infection and reactivation/reinfection events, alters blood brain barrier (BBB) metabolic pathways. An increase in basal mitochondrial function is observed in brain microvasculature endothelial cells (BMEC) at 12 months post infection but not at earlier time points and is accompanied by elevated levels of superoxide, indicative of oxidative stress. Further, these mice score lower in cognitive assays as compared to age-matched controls. Our data show that repeated systemic infection with CMV, alters BBB metabolic function and impacts cognition. These observations provide mechanistic insights through which pathogens contribute to the progression of pathologies associated with dementia. In BriefMechanistic evidence supporting an infectious etiology of dementia (e.g. Alzheimers Disease) are poorly defined. Harrison et al., show that intermittent infection with cytomegalovirus metabolically rewires the blood brain barrier and neighboring glial cells altering their function, resulting in decreased cognitive function.

neuroscience↗

bioRxiv2022

Burst firing is required for induction of Hebbian LTP at lateral perforant path to hippocampal granule cell synapses

High frequency burst firing is critical in summation of back-propagating action potentials (APs) in dendrites, which may greatly depolarize dendritic membrane potential. The physiological significance of burst firings of hippocampal dentate GCs in synaptic plasticity remains unknown. We found that GCs with low input resistance could be categorized into regular-spiking (RS) and burst-spiking (BS) cells based on their initial firing frequency (Finit) upon somatic rheobase current injection, and investigated how two types of GCs differ in long-term potentiation (LTP) induced by high-frequency lateral perforant pathway (LPP) inputs. Induction of Hebbian LTP at LPP synapses required at least three postsynaptic APs at Finit higher than 100 Hz, which was met in BS but not in RS cells. The synaptically evoked burst firing was critically dependent on persistent Na+ current, which was larger in BS than RS cells. The Ca2+ source for Hebbian LTP at LPP synapses was primarily provided by L-type calcium channels. In contrast, Hebbian LTP at medial PP synapses was mediated by T-type calcium channels, and could be induced regardless of cell types or Finit of postsynaptic APs. These results suggest that intrinsic firing properties affect synaptically driven firing patterns, and that bursting behavior differentially affects Hebbian LTP mechanisms depending on the synaptic input pathway.

neuroscience↗

bioRxiv2022

In situ quantification of osmotic pressure within living embryonic tissues

Mechanics is known to play a fundamental role in many cellular and developmental processes. Beyond active forces and material properties, osmotic pressure is believed to control essential cell and tissue characteristics. However, it remains very challenging to perform in situ and in vivo measurements of osmotic pressure. Here we introduce doubleemulsion droplet sensors that enable local measurements of osmotic pressure intra- and extra-cellularly within 3D multicellular systems, including living tissues. After generating and calibrating the sensors, we measured the osmotic pressure in blastomeres of early zebrafish embryos as well as in the interstitial fluid between the cells of the blastula by monitoring the size of droplets previously inserted in the embryo. Our results show a balance between intracellular and interstitial osmotic pressures, with values of approximately 0.7 MPa, but a large pressure imbalance between the inside and outside of the embryo. The ability to measure osmotic pressure in 3D multicellular systems (developing embryos, organoids, etc.) will help understand its role in fundamental biological processes.

biophysics↗

bioRxiv2022

Prior expectation enhances sensorimotor behavior by modulating population tuning and subspace activity in the sensory cortex

Prior knowledge facilitates our perception and goal-directed behaviors in the dynamic world, particularly when sensory input is lacking or noisy. However, the neural mechanisms underlying the improvement in sensorimotor behaviors by prior expectations remain unknown. In this study, we examine the neural activity in the middle temporal (MT) area of visual cortex while monkeys perform a smooth pursuit eye movement task with prior expectation of the visual targets motion direction. Prior expectations discriminately reduce the MT neural responses depending on their preferred directions, only when the sensory evidence is weak. This response reduction effectively sharpens neural population direction tuning. Simulations with a realistic MT population demonstrate that sharpening the tuning explains both the biases and variabilities in smooth pursuit, thus suggesting that neural computations in the sensory area alone can underpin the integration of prior knowledge and sensory evidence. State-space analysis further supports this by revealing neural signals of prior expectation in the MT population activity that correlate with behavioral changes.

neuroscience↗

bioRxiv2022

Ketamines rapid antidepressant effects are mediated by Ca2+ - permeable AMPA receptors in the hippocampus

Ketamine is shown to enhance excitatory synaptic drive in the hippocampus, which is presumed to underlie its rapid antidepressant effects. Moreover, ketamines therapeutic actions are likely mediated by enhancing neuronal Ca2+ signaling. However, ketamine is a noncompetitive NMDA receptor (NMDAR) antagonist that inhibits excitatory synaptic transmission and postsynaptic Ca2+ signaling. Thus, it is a puzzling question how ketamine enhances glutamatergic and Ca2+ activity in neurons to induce rapid antidepressant effects while blocking NMDARs in the hippocampus. Here, we find that ketamine treatment for one hour in cultured mouse hippocampal neurons significantly reduces calcineurin activity to elevate AMPA receptor (AMPAR) subunit GluA1 phosphorylation. This phosphorylation ultimately induces the expression of Ca2+- Permeable, GluA2-lacking, and GluA1-containing AMPARs (CP-AMPARs). Such ketamine-induced expression of CP-AMPARs enhances glutamatergic activity and synaptic plasticity in cultured hippocampal neurons. When a sub-anesthetic dose of ketamine is given to mice, it increases synaptic GluA1 levels, but not GluA2, and GluA1 phosphorylation in the hippocampus within one hour after treatment. These changes are likely mediated by ketamine-induced reduction of calcineurin activity in the hippocampus. Using the open field and tail suspension tests, we demonstrate that a low dose of ketamine rapidly reduces anxiety-like and depression-like behaviors in both male and female mice. However, when in vivo treatment of a CP-AMPAR antagonist abolishes the ketamines effects on animals behavior. We thus discover that ketamine at the low dose promotes the expression of CP-AMPARs via reduction of calcineurin activity in the hippocampus, which in turn enhances synaptic strength to induce rapid antidepressant actions.

neuroscience↗

bioRxiv2022

Multi-layer guilt-by-association-based drug repurposing by integrating clinical knowledge on biological heterogeneous networks

Computational drug repurposing attempts to leverage rapidly accumulating high-throughput data to discover new indications for existing drugs, often by clarifying biological mechanisms with relevant genes. Leveraging the Guilt-by-association (GBA), the principle of "similar genes share similar functions," we introduced clinical neighbors of drug and disease entities while learning their mechanisms on the biological network. To overcome the hurdle of connecting drugs and diseases through large and dense gene-gene network and simultaneously realize the concept of "semantic multi-layer GBA", we present a random walk-based algorithm with a novel clinical-knowledge guided teleport. As a result, drug-disease association prediction accuracy increased up to 8.7% compared to existing state-of-the-art models. In addition, exploration of the generated embedding space displays harmony between biological and clinical contexts. Through repurposing case studies for breast carcinoma and Alzheimers disease, we demonstrate the potential power of multi-layer GBA, a novel perspective for predicting clinical-level associations on heterogeneous biomedical networks.

bioinformatics↗

bioRxiv2022

Statistically unbiased prediction enables accurate denoising of voltage imaging data

Here we report SUPPORT (Statistically Unbiased Prediction utilizing sPatiOtempoRal information in imaging daTa), a self-supervised learning method for removing Poisson-Gaussian noise in voltage imaging data. SUPPORT is based on the insight that a pixel value in voltage imaging data is highly dependent on its spatially neighboring pixels in the same time frame, even when its temporally adjacent frames do not provide useful information for statistical prediction. Such spatiotemporal dependency is captured and utilized to accurately denoise voltage imaging data in which the existence of the action potential in a time frame cannot be inferred by the information in other frames. Through simulation and experiments, we show that SUPPORT enables precise denoising of voltage imaging data while preserving the underlying dynamics in the scene.

neuroscience↗

bioRxiv2022

Exploration of mechanisms of drug resistance by polyaneuploid cancer cells in a microfluidic device and patient tissues

Chemoresistance is a major cause of treatment failure in many cancers. However, the life cycle of cancer cells as they respond to and survive environmental and therapeutic stress is understudied. In this study, we utilized a microfluidic device to induce the development of doxorubicin-resistant (DOXR) cells from triple negative breast cancer (TNBC) cells within 11 days by generating gradients of DOX and medium. In vivo chemoresistant xenograft models, an unbiased genome-wide transcriptome analysis, and a patient data/tissue analysis all showed that chemoresistance arose from failed epigenetic control of the nuclear protein-1 (NUPR1)/histone deacetylase 11 (HDAC11) axis, and high Nupr1 expression correlated with poor clinical outcomes. These results suggest that the chip can rapidly induce resistant cells that increase tumor heterogeneity and chemoresistance, highlighting the need for further studies on the epigenetic control of the NUPR1/HDAC11 axis in TNBC.

cancer biology↗

bioRxiv2022

Epigenetic silencing by SMYD3 represses tumor intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck.

Cancers often display immune escape, but the mechanisms and potential for reversibility are incompletely understood. Epigenetic dysregulation has been implicated in the immune escape of various cancer types. We have identified the epigenetic modifier SET and MYND-domain containing protein 3 (SMYD3) as a mediator of immune escape in human papilloma virus (HPV)- negative head and neck squamous cell carcinoma (HNSCC), an aggressive disease with poor prognosis and low response to immunotherapy with pembrolizumab, a programmed-death-1 (PD-1) targeting antibody. SMYD3 loss increased the sensitivity of HNSCC cancer cells to IFN-{beta}, resulting in upregulation of type I IFN response and antigen presentation machinery genes. We found that SMYD3 regulates the transcription of Ubiquitin-Like PHD And RING Finger Domain- Containing Protein 1 (UHRF1), a key epigenetic reader of trimethylated lysine 9 on histone H3 (H3K9me3), which binds to H3K9me3-enriched promoters of key immune-related genes and silences their expression. SMYD3 further maintains the repression of immune-related genes through the deposition of H4K20me3 within the gene body regions of these genes. In an anti-PD-1 immune checkpoint resistant syngeneic mouse model of HPV-negative HNSCC, Smyd3 depletion induced influx of CD8+ T-cells, upregulated PD-L1 and MHC class I molecules, and increased sensitivity to anti-PD-1 therapy. SMYD3 overexpression was associated with decreased CD8 T-cell infiltration in tumor samples from patients with HPV-negative HNSCC, and was associated with poor response to pembrolizumab. Overall, these data highlight a previously unreported function of SMYD3 as a master epigenetic regulator of anti-tumor immune response in HPV-negative HNSCC and provide a rationale for translational approaches combining SMYD3 depletion strategies with checkpoint blockade to overcome anti-PD-1 resistance in this devastating disease.

cancer biology↗