Biology subjects

Kim, M.-H.

Publications and source records attributed to Kim, M.-H..

13 recordsLinked to original sources

bioRxiv2025

Focused acoustic-radiation-force microscopy for live-cell selective nucleus deformation and nucleus viscoelasticity measurement

Acoustic-radiation-force (ARF) microscopy was developed for non-invasive, selective mechanical stimulation to a single live-cell nucleus and long-term measurement of its mechanical properties. High-frequency focused ultrasound wave achieved a spatially confined ARF field around target nucleus, and its cyclic deformation was induced by amplitude modulation on the ultrasound wave, which was captured by a dark-field microscopy. This method was applied to human mesenchymal stem cells, revealing their extremely high mechanical homeostasis.

biophysics↗

bioRxiv2025

Convergent Control of NREM Sleep and Anesthesia by Prefrontal Layer 5 Extratelencephalic Neurons

The cortical mechanisms that actively suppress consciousness remain poorly understood. Here, we identify a specific subset of prefrontal cortical (PFC) neurons that are activated under anesthesia while most cortical neurons are suppressed. Chemogenetic activation of these excitatory neurons enhances anesthetic potency and deepens NREM sleep, whereas their inhibition blunts anesthetic effects and disrupts sleep. We designate these cells NREM- and Anesthesia-Promoting (NAP) neurons. NAP neurons correspond to layer 5 extratelencephalic (L5 ET) neurons enriched in hyperpolarization-activated cyclic nucleotide-gated (HCN1) expression and characteristic HCN-mediated electrophysiological properties. Mechanistically distinct anesthetics act directly and specifically on PFC L5-ET neurons to increase their excitability. NAPs have sparse cortical projections and predominately innervate subcortical targets including anterior and reticular thalamic nuclei. Using a transgenic mouse line (Colgalt2-cre), we confirm that PFC L5 ET neurons are preferentially activated under anesthesia and during deep recovery NREM sleep. Finally, we show that activation of thalamic-projecting Colgalt2-expressing PFC neurons is sufficient to promote deep NREM sleep. These findings identify a novel prefrontal corticothalamic circuit that provides a shared cortical substrate for naturally occurring sleep and anesthetic-induced unconsciousness.

neuroscience↗

bioRxiv2024

HSP90 interacts with VP37 to facilitate the cell-to-cell movement of broad bean wilt virus 2

The systemic spread of viruses in plants requires successful viral cell-to-cell movement through plasmodesmata (PD). Viral movement proteins (MPs) interact with cellular proteins to modify and utilize host transport routes. Broad bean wilt virus 2 (BBWV2), a widespread plant RNA virus, moves from cell to cell as a virion through the PD gated by VP37, the MP of BBWV2. However, the host proteins that function in the cell-to-cell movement of BBWV2 remain unclear. In this study, we identified cellular heat shock protein 90 (HSP90) as an interacting partner of VP37. The interaction between HSP90 and VP37 was assessed using the yeast two-hybrid assay, co-immunoprecipitation, and bimolecular fluorescence complementation. Tobacco rattle virus-based virus-induced gene silencing analysis revealed that HSP90 silencing significantly inhibited the systemic spread of BBWV2 in N. benthamiana plants. Furthermore, in planta treatment with geldanamycin (GDA), an inhibitor of the chaperone function of HSP90, demonstrated the necessity of HSP90 in successful cell-to-cell movement and systemic infection of BBWV2. Interestingly, GDA treatment inhibited the HSP90-VP37 interaction at the PD, resulting in the inhibition of VP37-derived tubule formation through the PD. Our results suggest that the HSP90-VP37 interaction regulates VP37-derived tubule formation through the PD, thereby facilitating the cell-to-cell movement of BBWV2. IMPORTANCEThis study highlights the regulatory role of heat shock protein 90 (HSP90) in facilitating the cell-to-cell movement of broad bean wilt virus 2 (BBWV2). HSP90 interacted with VP37, the movement protein of BBWV2, specifically at plasmodesmata (PD). This study demonstrated that the HSP90-VP37 interaction is crucial for viral cell-to-cell movement and the formation of VP37-derived tubules, which are essential structures for virus transport through the PD. The ATP-dependent chaperone activity of HSP90 is integral to this interaction, as demonstrated by the inhibition of virus movement upon treatment with geldanamycin (GDA), which disrupts the function of HSP90. These findings elucidate the molecular mechanisms underlying the cell-to-cell movement of plant viruses, and highlight the role of HSP90 in viral infection. This study suggests that the chaperone activity of HSP90 may function in changing the conformational structure of VP37, thereby facilitating the assembly and function of virus-induced structures required for viral cell-to-cell movement.

microbiology↗

bioRxiv2024

Hyperactive GluN2B impairs neuroplasticity and cognition in phenylketonuria

Phenylketonuria (PKU), an inborn error of phenylalanine (Phe) metabolism, is a common cause of intellectual disability. However, the mechanism by which elevated Phe levels causes cognitive impairment remains unclear. Here, we show that submillimolar Phe perturbs synaptic plasticity through the hyperactivation of GluN2B-containing NMDARs. L-Phe exhibited dose-dependent bidirectional effects on NMDA-induced currents, without affecting synaptic NMDARs in hippocampal CA1 neurons. L-Phe-induced hyperactivation of extrasynaptic GluN2B resulted in an activity-dependent downregulation of AMPARs during burst or sustained synaptic activity. Administration of L-Phe in mice decreased neural activity and impaired memory, which were blocked by pretreatment of GluN2B inhibitors. Furthermore, pharmacological and virus-mediated suppression of GluN2B reversed impaired learning in the PahEnu2 PKU model. Collectively, these results suggest that the concentration of Phe in the cerebrospinal fluid of patients with PKU perturbs extrasynaptic NMDAR and synaptic plasticity, and that suppression of GluN2B may be a therapeutic strategy for improving cognitive function in patients with PKU.

neuroscience↗

bioRxiv2024

Digital Profiling of Tumor Extracellular Vesicle-associated RNAs Directly from Unprocessed Blood Plasma

Tumor-derived extracellular vesicle (tEV)-associated RNAs hold promise as diagnostic biomarkers, but their clinical use is hindered by the rarity of tEVs among non-tumor EVs. Here, we present EV-CLIP, a highly sensitive droplet-based digital method for profiling EV RNA. EV-CLIP utilizes the fusion of EVs with charged liposomes (CLIPs) in a microfluidic chip. Optimized CLIP surface charge enables exceptional sensitivity and selectivity for EV-derived miRNAs and mRNAs. This approach streamlines detection with minimal plasma volume (20 {micro}L) and eliminates the need for prior EV isolation or RNA preparation, preventing loss of EVs or RNA. In testing with 83 patient samples, EV-CLIP detected EGFR L858R and T790M mutations with high AUC values of 1.0000 and 0.9784, respectively. Its success in serial monitoring during chemotherapy highlights its potential for precise quantification of rare EV subpopulations, facilitating the exploration of single EV RNA content and enhancing understanding of diverse EV populations in various disease states. SUMMARYEV-CLIP: A highly sensitive digital method for tumor-derived EV RNA detection using undiluted blood plasma samples, promising for precise tumor management.

bioengineering↗

bioRxiv2021

Multi-organ analysis of low-level somatic mosaicism reveals stage- and tissue-specific mutational features in human development

Most somatic mutations arising during normal development present as low-level in single or multiple tissues depending on the developmental stage and affected organs1-4. However, it remains unclear how the human developmental stages or mutation-carrying organs affect somatic mutations features. Here, we performed a systemic and comprehensive analysis of low-level somatic mutations using deep whole-exome sequencing (WES; average read depth: [~]500x) of 498 multiple organ tissues with matched controls from 190 individuals. We found that early-stage mutations shared between multiple organs are lower in number but showed higher allele frequencies than late-stage mutations [0.54 vs. 5.83 variants per individual: 6.17% vs. 1.5% variant allele frequency (VAF)] along with less nonsynonymous mutations and lower functional impacts. Additionally, early- and late-stage mutations had unique mutational signatures distinct from tumor-originate mutations. Compared with early-stage mutations presenting a clock-like signature across all studied organs or tissues, late-stage mutations show organ, tissue, and cell-type specificity in mutation count, VAFs, and mutational signatures. In particular, analysis of brain somatic mutations shows bimodal occurrence and temporal-lobe-specific mutational signatures. These findings provide new insight into the features of somatic mosaicisms dependent on developmental stages and brain regions.

genomics↗

bioRxiv2021

Connectivity and Synaptic Physiology in the Mouse and Human Cortex

To elucidate cortical microcircuit structure and synaptic properties we present a unique, extensive, and public synaptic physiology dataset and analysis platform. Through its application, we reveal principles that relate cell type to synapse properties and intralaminar circuit organization in the mouse and human cortex. The dynamics of excitatory synapses align with the postsynaptic cell subclass, whereas inhibitory synapse dynamics partly align with presynaptic cell subclass but with considerable overlap. Despite these associations, synaptic properties are heterogeneous in most subclass to subclass connections. The two main axes of heterogeneity are strength and variability. Cell subclasses divide along the variability axis, while the strength axis accounts for significant heterogeneity within the subclass. In human cortex, excitatory to excitatory synapse dynamics are distinct from those in mouse and short-term plasticity varies with depth across layers 2 and 3. With a novel connectivity analysis that enables fair comparisons between circuit elements, we find that intralaminar connection probability among cell subclasses exhibits a strong layer dependence.These and other findings combined with the analysis platform create new opportunities for the neuroscience community to advance our understanding of cortical microcircuits.

neuroscience↗

bioRxiv2020

Molecular and genetic approaches for assaying human cell type synaptic connectivity

Rodent studies have demonstrated that synaptic dynamics from excitatory to inhibitory neuron types are often dependent on the target cell type. However, these target cell-specific properties have not been well investigated in human cortex, where there are major technical challenges in reliably identifying cell types. Here, we take advantage of newly developed methods for human neurosurgical tissue analysis with multiple patch-clamp recordings, post-hoc fluorescent in situ hybridization (FISH), and prospective GABAergic AAV-based labeling to investigate synaptic properties between pyramidal neurons and PVALB- vs. SST- positive interneurons. We find that there are robust molecular differences in synapse-associated genes between these neuron types, and that individual presynaptic pyramidal neurons evoke postsynaptic responses with heterogeneous synaptic dynamics in different postsynaptic cell types. Using molecular identification with FISH and classifiers based on transcriptomically identified PVALB neurons analyzed with Patch-seq methods, we find that PVALB neurons typically show depressing synaptic characteristics, whereas other interneuron types including SST-positive neurons show facilitating characteristics. Together, these data support the existence of target cell-specific synaptic properties in human cortex that are similar to rodent, thereby indicating evolutionary conservation of local circuit connectivity motifs from excitatory to inhibitory neurons and their synaptic dynamics.

neuroscience↗

bioRxiv2020

Hippocampal GABA-inhibitory circuitry regulates despair-like behavior in mice

Despair is a common human feeling characterized by the loss of hope and is a core symptom of depressive disorders. However, little is known regarding neural circuits mediating despair and their modulation by antidepressants. Here we show that alterations in inhibitory synaptic transmission in the hippocampus affect behavioral despair in mice. Reduced interneuron density, knockdown of GABAA receptor gamma 2 subunit gene (Gabrg2) or DREADD-mediated suppression of interneuron activity resulted in disinhibition of CA1 neurons and anti-despair-like behaviors in mice. Similarly, a low dose of pentylenetetrazol, a GABAAR antagonist, induced transient anti-despair-like behaviors, with rapid eukaryotic elongation factor 2 (eEF2) activation in the hippocampus. Conversely, pharmacological and chemogenetic potentiation of GABAergic transmission in CA1 neurons induced despair-like behaviors. The antidepressant ketamine rapidly increased c-Fos expression in CA1 neurons and induced anti-despair-like behaviors. These results suggest that the enhanced hippocampal CA1 neuron activity induces anti-despair-like behaviors and contributes to the antidepressant effects of ketamine.

neuroscience↗

bioRxiv2019

Kv4.1, a key ion channel for low frequency firing of dentate granule cells, is crucial for pattern separation

The dentate gyrus (DG) in the hippocampus may play key roles in remembering distinct episodes through pattern separation, which may be subserved by the sparse firing properties of granule cells (GCs) in the DG. Low intrinsic excitability is characteristic of mature GCs, but ion channel mechanisms are not fully understood. Here, we investigated ionic channel mechanisms for firing frequency regulation in GCs of the rat hippocampus, and identified Kv4.1 as a key player. Immunofluorescence analysis showed that Kv4.1 was preferentially expressed in the DG, and its expression level was higher at 8-week than 3-week-old mice, suggesting a developmental regulation of Kv4.1 expression. With respect to firing frequency, GCs are categorized into two distinctive groups: low frequency (LF) and high frequency (HF) firing GCs. Input resistance (Rin) of most LF-GCs is lower than 200 M{Omega}, suggesting that LF-GCs are fully mature GCs. Kv4.1 channel inhibition by intracellular perfusion of Kv4.1 antibody increased firing rates and gain of the input-output relationship selectively in LF-GCs with no significant effect on resting membrane potential and Rin, but had no effect in HF-GCs. Importantly, mature GCs from mice depleted of Kv4.1 transcripts in the DG showed increased firing frequency, and these mice showed an impairment in contextual discrimination task. Our findings suggest that Kv4.1 expression occurring at late stage of GC maturation is essential for low excitability of DG networks and thereby contributes to pattern separation.

neuroscience↗

bioRxiv2019

Temporal learning of bottom-up connections via spatially nonspecific top-down inputs

In the brain, high-order and low-order areas are connected via bottom-up connections (from low-order to high-order areas) and top-down connections (from high-order to low-order areas). While bottom-up signals are thought to be critical in generating perception, functions of top-down signals have not been clearly delineated. One popular theory is that top-down inputs modify the activity of specific cell assemblies to modulate responses to bottom-up inputs. However, a different line of studies proposes that not all top-down inputs are specifically delivered. As the leading theories cannot account for nonspecific top-down inputs, we seek potential functions of nonspecific top-down signals using network models in our study. Our simulation results suggest that top-down inputs can regulate low-order area responses by providing temporal information even without spatial specificity. Specifically, the temporal information in nonspecific top-down inputs can weaken the undesired bottom-up connections, contributing to bottom-up connections learning. Further, we found that cortical rhythms (synchronous oscillatory neural responses) are critical in the proposed learning process of bottom-up connections in our model.

neuroscience↗

bioRxiv2018

Functional selectivity and specific connectivity of inhibitory neurons in primary visual cortex

In the cerebral cortex, the interaction of excitatory and inhibitory synaptic inputs shapes the responses of neurons to sensory stimuli, stabilizes network dynamics1 and improves the efficiency and robustness of the neural code2-4. Excitatory neurons receive inhibitory inputs that track excitation5-8. However, how this co-tuning of excitation and inhibition is achieved by cortical circuits is unclear, since inhibitory interneurons are thought to pool the inputs of nearby excitatory cells and provide them with non-specific inhibition proportional to the activity of the local network9-13. Here we show that although parvalbumin-expressing (PV) inhibitory cells in mouse primary visual cortex make connections with the majority of nearby pyramidal cells, the strength of their synaptic connections is structured according to the similarity of the cells responses. Individual PV cells strongly inhibit those pyramidal cells that provide them with strong excitation and share their visual selectivity. This fine-tuning of synaptic weights supports co-tuning of inhibitory and excitatory inputs onto individual pyramidal cells despite dense connectivity between inhibitory and excitatory neurons. Our results indicate that individual PV cells are preferentially integrated into subnetworks of inter-connected, co-tuned pyramidal cells, stabilising their recurrent dynamics. Conversely, weak but dense inhibitory connectivity between subnetworks is sufficient to support competition between them, de-correlating their output. We suggest that the history and structure of correlated firing adjusts the weights of both inhibitory and excitatory connections, supporting stable amplification and selective recruitment of cortical subnetworks.

neuroscience↗

bioRxiv2017

Exclusive functional subnetworks of intracortical projection neurons in primary visual cortex

The rules by which neurons in neocortex choose their synaptic partners are not fully understood. In sensory cortex, intermingled neurons encode different attributes of sensory inputs and relay them to different long-range targets. While neurons with similar responses to sensory stimuli make connections preferentially, the relationship between synaptic connectivity within an area and long-range projection target remains unclear. We examined the local connectivity and visual responses of primary visual cortex neurons projecting to anterolateral (AL) and posteromedial (PM) higher visual areas in mice. Although the response properties of layer 2/3 neurons projecting to different targets were often similar, they avoided making connections with each other. Thus, projection target acts independently of response similarity to constrain local synaptic connectivity of cortical neurons. We propose that this segregated connectivity rule reduces the crosstalk between different populations of projection neurons, allowing top-down signal to modulate the activity of these output channels independently.

neuroscience↗